几类重要蛋白的结构及其催化机理的理论研究
|
摘要
本文采用分子力学、分子动力学和量子力学的方法,对四种蛋白体系进行了深入的理论模拟研究,主要结果如下:
1.通过同源模建和分子动力学模拟方法,构建了人类酸性哺乳动物壳多糖水解酶(hAMCase)的三维结构,预测其活性区域,并在此基础上进行了与内源性和外源性抑制剂的分子对接研究。从理论上确认了对复合物形成起到重要作用的氨基酸残基,对进一步揭示hAMCase的生物学功能以及以hAMCase为靶点的抑制剂设计具有重要的意义。
2.通过同源模建和分子动力学模拟的方法,给出了人类丝氨酸消旋酶(hSR)的三维结构模型及其与多肽类抑制剂结合的复合物模型,揭示了在多肽类抑制剂的R位点上引入体积较大的苯甲基更适合作为hSR的抑制剂,同时明确了hSR与此类抑制剂结合时起重要作用的氨基酸残基,为基于人类丝氨酸消旋酶三维结构的药物设计提供了重要的参考信息。
3.通过同源模建和分子动力学的模拟方法,构建了人类脂肪酰胺水解酶的(hFAAH)三维结构。通过对活性位点的分析,预测了与抑制剂的结合部位,并进行了与药物二异丙酚及其结构类似物的分子对接研究。研究结果表明,hFAAH在与抑制剂的相互作用主要是范德华相互作用。另外,氨基酸残基Phe192, Ile238, Thr377, Leu380, Phe381, Phe388和Leu404与抑制剂对接过程中起主要作用。
4.通过分子力学和量子力学方法,研究了Sirtuins家族蛋白酶的催化机理。计算结果表明,该家族蛋白酶的第一步催化反应为SN2反应,第二步反应为协同反应。此外,我们还研究了Sirtuins蛋白酶家族中的保守残基Phe33在催化中所起的作用,从计算结果来看,Phe33在催化过程中起到了非常重要的作用。
In recently years, along with the rapid development of computer technology and computational chemistry, molecule mechanics, molecular dynamics and quantum mechanics theories play an important role in life sciences. The molecular simulations of proteins have already become a very important and active research field. By the theoretical simulation, the three dimension (3D) structure, the interactions between receptor and lingand, and protein biochemistry mechanism can be obtained. In our thesis, molecular mechanics, molecular dynamics and quantum mechanics were used to theoretically study the 3D models of four proteins and investigate their structure properties in detail. The main results are summarized as follows:
1. Homology modeling and docking studies of human acid mammalian chitinase
Chitinases are endo-β-1,4-N-acetylglucosaminidases that can fragment chitin and have been identified in several organisms varying from bacteria to humans. Human chitinase (hAMCase) is a functional chitinase and the experiment showed that hAMCase contributes to Th2-mediated inflammation through IL-13-dependent mechanism, and inhibition of AMCase decreases airway inflammation and airway hyper-responsiveness. Thus, hAMCase is a potential therapeutic target for anti-inflammatory therapy in Th2-mediated diseases such as asthma.
By means of the homology modeling and molecular dynamics methods, the 3D structure of hAMCase is created and refined. With this model, a flexible docking study is performed and the results indicate that allosamidin is a more preferred inhibitor than NAG2, which is in good agree with the experimental facts by Yi-Te et al. From the docking studies, the important residues for binding were identified.Glu49 and Glu276 may be the key amino acids residues interacting with the substrates, and Asp192 and Trp10 may help allosamidin steadily interact with hAMCase. These results will offer further experimental studies of structure-function relationships.
2. Theoretical study of human serine racemase
D-Serine occurs at high levels in the mammalian brain, higher than even some common amino acids, and it has been shown to be an endogenous ligand for the“glycine site”of N-methyl-D-aspartate (NMDA) receptors. These receptors play central roles in excitatory neurotransmission, neuronal plasticity, and learning and memory. Over activation of the NMDA receptor is proposed to be responsible for the cell death that occurs in strokes. Other studies suggest that D-serine and NMDA receptor dysfunction play a role in the pathophysiology of Alzheimer’s disease. The enzyme serine racemase has been shown to be responsible for the physiological conversion of L-serine to D-serine. The involvement of D-serine in this breadth of pathophysiological processes makes serine racemase an excellent drug target.
The three dimensional structure of human serine racemase (hSR) was modeled and refined using homology modeling and molecular dynamics simulation. The binding pattern predicted by docking studies revealed that important residues interacted with the peptide inhibitors, which are Asn148, His76, Glu130 and Lys235. The module provided further refinement of the hSR/inhibitor binding interaction that may be used as a basis for new structure based design efforts.
3. Homology modeling and inhibitors binding study of human fatty acid amide hydrodase
Fatty acid amide hydrolase (FAAH) is responsible for the hydrolysis of the fatty acid amide class of lipid transmitters which include the endogenous cannabinoid N-arachidonoyl ethanolamine, sleep-inducing agent oleamide, anorexigenic agent N-oleoyl ethanolamide and anti-inflammatory agent N-palmitoyl ethanolamide. Studies of FAAH inactivation suggest that this enzyme could be an attractive target for the treatment of pain, inflammatory, or sleep disorders.
With the aid of homology modeling and molecular dynamics methods, the 3D model of hFAAH is constructed. The docking study is performed on the basis of propofol and its structural analogs. The results indicate the residues Phe192, Ile238, Thr377, Leu380, Phe381, Phe388 and Leu404 in hFAAH are seven important determinant residues in binding as they have strong van der Waals interactions with the inhibitors.
4. Theoretical studies on the reaction mechanism catalyzed by Sirtuins
Sirtuins comprise a broadly conserved family of NAD+-dependent protein deacetylases and mono ADP-ribosyltransferases whose functionis crucial to the apoptosis and cell survival, transcriptional silencing, neurodegeneration and calorie restriction. As a key player in a broad variety of biological processes, sirtuins may be attractive targets for treatment of cardiovascular disease, diabetes, cancers and the aging. A thorough understanding of the catalytic mechanism of these enzymes will facilitate the development specific, mechanism-based regulators of sirtuins activity in order to treat the diseases related with these enzymes.
Using molecular mechanism and quantum mechanism methods, the reaction mechanism catalyzed by Sirtuins were theoretically studied. The calculated results indicate that the fist step take places in a concerted SN2 step. The second step of the catalytic mechanism was further explored and confirmed that subsequent proton is abstracted from 2' hydroxyl of N-ribose to His116 coupled with proton transferred from 2' hydroxyl to 3' hydroxyl, which is concerted reaction. In addition, we also examine the role of Phe33 in the protein structure, and the results of the calculations confirm that the Phe33 plays an important role in the first step of catalytic mechanism, which positions above the ribose oxygen adjacent to the ribose C1' position to prevent nicotinamide exchange reaction.
1.通过同源模建和分子动力学模拟方法,构建了人类酸性哺乳动物壳多糖水解酶(hAMCase)的三维结构,预测其活性区域,并在此基础上进行了与内源性和外源性抑制剂的分子对接研究。从理论上确认了对复合物形成起到重要作用的氨基酸残基,对进一步揭示hAMCase的生物学功能以及以hAMCase为靶点的抑制剂设计具有重要的意义。
2.通过同源模建和分子动力学模拟的方法,给出了人类丝氨酸消旋酶(hSR)的三维结构模型及其与多肽类抑制剂结合的复合物模型,揭示了在多肽类抑制剂的R位点上引入体积较大的苯甲基更适合作为hSR的抑制剂,同时明确了hSR与此类抑制剂结合时起重要作用的氨基酸残基,为基于人类丝氨酸消旋酶三维结构的药物设计提供了重要的参考信息。
3.通过同源模建和分子动力学的模拟方法,构建了人类脂肪酰胺水解酶的(hFAAH)三维结构。通过对活性位点的分析,预测了与抑制剂的结合部位,并进行了与药物二异丙酚及其结构类似物的分子对接研究。研究结果表明,hFAAH在与抑制剂的相互作用主要是范德华相互作用。另外,氨基酸残基Phe192, Ile238, Thr377, Leu380, Phe381, Phe388和Leu404与抑制剂对接过程中起主要作用。
4.通过分子力学和量子力学方法,研究了Sirtuins家族蛋白酶的催化机理。计算结果表明,该家族蛋白酶的第一步催化反应为SN2反应,第二步反应为协同反应。此外,我们还研究了Sirtuins蛋白酶家族中的保守残基Phe33在催化中所起的作用,从计算结果来看,Phe33在催化过程中起到了非常重要的作用。
In recently years, along with the rapid development of computer technology and computational chemistry, molecule mechanics, molecular dynamics and quantum mechanics theories play an important role in life sciences. The molecular simulations of proteins have already become a very important and active research field. By the theoretical simulation, the three dimension (3D) structure, the interactions between receptor and lingand, and protein biochemistry mechanism can be obtained. In our thesis, molecular mechanics, molecular dynamics and quantum mechanics were used to theoretically study the 3D models of four proteins and investigate their structure properties in detail. The main results are summarized as follows:
1. Homology modeling and docking studies of human acid mammalian chitinase
Chitinases are endo-β-1,4-N-acetylglucosaminidases that can fragment chitin and have been identified in several organisms varying from bacteria to humans. Human chitinase (hAMCase) is a functional chitinase and the experiment showed that hAMCase contributes to Th2-mediated inflammation through IL-13-dependent mechanism, and inhibition of AMCase decreases airway inflammation and airway hyper-responsiveness. Thus, hAMCase is a potential therapeutic target for anti-inflammatory therapy in Th2-mediated diseases such as asthma.
By means of the homology modeling and molecular dynamics methods, the 3D structure of hAMCase is created and refined. With this model, a flexible docking study is performed and the results indicate that allosamidin is a more preferred inhibitor than NAG2, which is in good agree with the experimental facts by Yi-Te et al. From the docking studies, the important residues for binding were identified.Glu49 and Glu276 may be the key amino acids residues interacting with the substrates, and Asp192 and Trp10 may help allosamidin steadily interact with hAMCase. These results will offer further experimental studies of structure-function relationships.
2. Theoretical study of human serine racemase
D-Serine occurs at high levels in the mammalian brain, higher than even some common amino acids, and it has been shown to be an endogenous ligand for the“glycine site”of N-methyl-D-aspartate (NMDA) receptors. These receptors play central roles in excitatory neurotransmission, neuronal plasticity, and learning and memory. Over activation of the NMDA receptor is proposed to be responsible for the cell death that occurs in strokes. Other studies suggest that D-serine and NMDA receptor dysfunction play a role in the pathophysiology of Alzheimer’s disease. The enzyme serine racemase has been shown to be responsible for the physiological conversion of L-serine to D-serine. The involvement of D-serine in this breadth of pathophysiological processes makes serine racemase an excellent drug target.
The three dimensional structure of human serine racemase (hSR) was modeled and refined using homology modeling and molecular dynamics simulation. The binding pattern predicted by docking studies revealed that important residues interacted with the peptide inhibitors, which are Asn148, His76, Glu130 and Lys235. The module provided further refinement of the hSR/inhibitor binding interaction that may be used as a basis for new structure based design efforts.
3. Homology modeling and inhibitors binding study of human fatty acid amide hydrodase
Fatty acid amide hydrolase (FAAH) is responsible for the hydrolysis of the fatty acid amide class of lipid transmitters which include the endogenous cannabinoid N-arachidonoyl ethanolamine, sleep-inducing agent oleamide, anorexigenic agent N-oleoyl ethanolamide and anti-inflammatory agent N-palmitoyl ethanolamide. Studies of FAAH inactivation suggest that this enzyme could be an attractive target for the treatment of pain, inflammatory, or sleep disorders.
With the aid of homology modeling and molecular dynamics methods, the 3D model of hFAAH is constructed. The docking study is performed on the basis of propofol and its structural analogs. The results indicate the residues Phe192, Ile238, Thr377, Leu380, Phe381, Phe388 and Leu404 in hFAAH are seven important determinant residues in binding as they have strong van der Waals interactions with the inhibitors.
4. Theoretical studies on the reaction mechanism catalyzed by Sirtuins
Sirtuins comprise a broadly conserved family of NAD+-dependent protein deacetylases and mono ADP-ribosyltransferases whose functionis crucial to the apoptosis and cell survival, transcriptional silencing, neurodegeneration and calorie restriction. As a key player in a broad variety of biological processes, sirtuins may be attractive targets for treatment of cardiovascular disease, diabetes, cancers and the aging. A thorough understanding of the catalytic mechanism of these enzymes will facilitate the development specific, mechanism-based regulators of sirtuins activity in order to treat the diseases related with these enzymes.
Using molecular mechanism and quantum mechanism methods, the reaction mechanism catalyzed by Sirtuins were theoretically studied. The calculated results indicate that the fist step take places in a concerted SN2 step. The second step of the catalytic mechanism was further explored and confirmed that subsequent proton is abstracted from 2' hydroxyl of N-ribose to His116 coupled with proton transferred from 2' hydroxyl to 3' hydroxyl, which is concerted reaction. In addition, we also examine the role of Phe33 in the protein structure, and the results of the calculations confirm that the Phe33 plays an important role in the first step of catalytic mechanism, which positions above the ribose oxygen adjacent to the ribose C1' position to prevent nicotinamide exchange reaction.
引文
[1]骆建新.人类基因组计划与后基因组时代[J].中国生物工程杂志, 2003, 23(11): 87-94.
[2]陈铭.后基因组时代的生物信息学[J].生物信息学, 2004, 2(2): 29-34.
[3]张春霆.生物信息学的现状与展望[J].世界科技研究与发展, 2000, 22(6): 17-20.
[4] BENTON D. Bioinformatics principles and potential of a new multidisciplinary tool [J]. Trends in Biotechnology, 1996, 14: 261-272.
[5] NIH and DOE, The U. S. Human Genome Project: The First Five Years FY 1991-1995.
[6]唐旭清.后基因组时代生物信息学的发展趋势[J].生物信息学, 2008, 3(6): 142-146.
[7]赵国屏等.生物信息学[M].北京:科学出版社,2002.
[8] LEE F S, SHAPIRO R, VALLEE B L. Tight-binding inhibition of angiogenin and ribonuclease A by placental ribonuclease inhibitor [J]. Biochemistry, 1989, 28: 225-230.
[9] BAIROCH A. The ENZYME database in 2000 [J]. Nucleic Acids Research, 2000, 28: 304-305.
[10] RADZICKA A, WOLFENDEN R. A proficient enzyme [J]. Science, 1995, 6: 90-931.
[11] MARDEN M C, GRIFFON N, POYART C. Oxygen delivery and autoxidation of hemoglobin [J]. Transfusion Clinique et Biologique, 1995, 2: 473-480.
[12] SHI N, YE S, ALAM A, et al. Atomic structure of a Na+- and K+-conducting channel [J]. Nature, 2006, 440: 570-574.
[13] HIROKAWA N, NODA Y, OKADA Y. Kinesin and dynein superfamily proteins in organelle transport and cell division [J]. Current Opinion in Cell Biology, 1998, 10: 60-73.
[14] GIBBONS I R. The role of dynein in microtubule-based motility [J]. Cell Struct Funct. 1996, 21: 331-342.
[15] CURTIN N A, WOLEDGE R C. Energy changes and muscular contraction [J]. Physiological Reviews, 1978, 58: 690-761.
[16] SAUNDERS S A, GRACY R W, SCHNACKERZ K D, et al. Are honeybees deficient in phosphomannose isomerase? [J]. Science, 1969, 164: 858-859.
[17] GRACY R W, NOLTMANN E A. Studies on phosphomannose isomerase. 3. A mechanism for catalysis and for the role of zinc in the enzymatic and the nonenzymatic isomerization [J]. Journal of Biological Chemistry,1968, 243: 5410-5419.
[18] GRACY R W, NOLTMANN E A. Studies on phosphomannose isomerase. II. Characterization as a zinc metalloenzyme [J]. Journal of Biological Chemistry, 1968, 243: 4109-4116.
[19] GRACY R W, NOLTMANN E A. Studies on phosphomannose isomerase. I. Isolation, homogeneity measurements, and determination of some physical properties [J]. Journal of Biological Chemistry, 1968, 243: 3161-3168.
[20] MARKOVITZ A, LIEBERMAN M M, ROSENBAUM N. Derepression of phosphomannose isomerase by regulator gene mutations involved in capsular polysaccharide synthesis in Escherichia coli K-12 [J]. Journal of Bacteriology, 1967, 94: 1497-1501.
[21] MARKOVITZ A, SYDISKIS R J, LIEBERMAN M M. Genetic and biochemical studies on mannose-negative mutants that are deficient in phosphomannose isomerase in Escherichia coli K-12 [J]. Journal of Bacteriology, 1967, 94: 1492-1496.
[22] KIRK J E. The phosphoglucomutase, phosphoglyceric acid mutase, and phosphomannose isomerase activities of arterial tissue in individuals of various ages [J]. Journal of Gerontology, 1966, 21: 420-425.
[23] Rosen S M, Zeleznick L D, Fraenkel D, et al. Characterization of the cell wall lipopolysaccharide of a mutant of Salmonella typhimurium lacking phosphomannose isomerase [J]. Biochemische Zeitschrift, 1965, 342: 375-386.
[24] KIZER D.E, MCCOY T A. Phosphomannose isomerase activity in a spectrum of normal and malignant rat tissues [J]. Proceedings of the Society for Experimental Biology and Medicine, 1960, 103: 772-774.
[25] NOLTMANN E, BRUNS F H. Phosphomannose isomerase. II. Purification of the enzyme from yeast and separation of phosphomannose isomerase by column chromatography on hydroxyapatite [J]. Biochemische Zeitschrift, 1958, 330: 514-520.
[26] BRUNS F H, NOLTMANN E, WILLEMSEN A. Phosphomannose isomerase. I. Activity measurement and dependence of enzyme action on sulfhydryl groups and metals in some animal tissues [J]. Biochemische Zeitschrift, 1958, 330: 411-420.
[27] ALVARADO F, SOLS A. Borate and phosphoglucose isomerase in the assay of phosphomannose isomerase [J]. Biochimica et biophysica acta, 1957, 25: 75-77.
[28] TOPPER Y J. On the mechanism of action of phosphoglucose isomerase and phosphomannose isomerase [J]. Journal of Biological Chemistry, 1957, 225: 419-425。
[29] CHUNG V, WAKEFIELD A E, KINSMAN O S, et al. DNA amplification of a portion of the phosphomannose isomerase (PMI) gene in Pneumocystis carinii-enriched extracts [J]. Journal of Eukaryotic Microbiology, 1994, 41: 82S-83S.
[30] WELLS T N, PAYTON M A, PROUDFOOT A E. Inhibition of phosphomannose isomerase by mercury ions [J]. Biochemistry, 1994, 33: 7641-7646.
[31] WELLS T N, SCULLY P, MAGNENAT E. Arginine 304 is an active site residue in phosphomannose isomerase from Candida albicans [J]. Biochemistry, 1994, 33, 5777-5782.
[32] BRANDEN C, TOOZE J. Introduction to Protein Structure 2nd ed. 1999, Garland Publishing: New York, NY
[33] GONEN T, CHENG Y, SLIZ P, et al. Lipid-protein interactions in double-layered two-dimensional AQP0 crystals [J]. Nature, 2005, 438: 633-638.
[34]唐焕文.蛋白质结构预测的优化模型与方法[J],工程数学学报, 2002, 19(2): 13-22.
[35] ANFINSEN, C B. Principles that goven the folding of protein chains [J]. Science, 1973, 181: 223-230.
[36]赵南明.生物物理学[M],北京:高等教育出版社,2000.
[37] FRAUENFELDER H, PETSKO G A, TSERNOGLOU D. Temperature-dependent X-ray diffraction as a probe of protein structural dynamics [J]. Nature, 1979, 280: 558–563.
[38] ARTYMIUK P J, BLAKE C C, GRACE D E, et al. Crystallographic studies of the dynamic properties of lysozyme [J]. Nature, 1979, 280: 563–568.
[39] ICHIYE T, KARPLUS M. Fluorescence depolarization of tryptophan residues in proteins: a molecular dynamics study [J]. Biochemistry, 1983, 22: 2884–2893.
[40] DOBSON C M, KARPLUS M. Internal motion of proteins: Nuclear magneticresonance measurements and dynamic simulations [J]. Methods in Enzymology, 1986, 131: 362–389.
[41] SMITH J, CUSACK S, PEZZECA U, et al. Inelastic neutron scattering analysis of low frequency motion in proteins: A normal mode study of the bovine pancreatic trypsin inhibitor [J]. Journal of Chemical Physics, 1986, 85: 3636–3654.
[42] BRüNGER A T, BROOKS C L III, KARPLUS M. Active site dynamics of ribonuclease [J]. The Proceeding of the National Academy of Sciences USA, 1985, 82: 8458–8462.
[43] FRAUENFELDER H, HARTMANN H, KARPLUS M, et al. Thermal expansion of a protein [J]. Biochemistry, 1987, 26: 254–261.
[44] BRüNGER A T, KURIYAN J, KARPLUS M. Crystallographic R factor refinement by molecular dynamics [J]. Science, 1987, 235: 458–460.
[45] DE VLIEG J, SCHEEK R M, VAN GUNSTEREN W F, et al. Combined procedure of distance geometry and restrained molecular dynamics techniques for protein structure determination from nuclear magnetic resonance data: application to the DNA binding domain of lac repressor from Escherichia coli [J].Proteins-structrue function and genetics, 1988, 3:209-218.
[46] FRY D C, MADISON V S, BOLIN D R, et al. Solution structure of an analogue of vasoactive intestinal peptide as determined by two-dimensional NMR and circular dichroism spectroscopies and constrained molecular dynamics [J]. Biochemistry, 1989, 28:2399-2409.
[47] DE LOOF H, NILSSON L, RIGLER R. Molecular dynamics simulation of galanin in aqueous and nonaqueous solution [J]. Journal of the American Chemical Society, 1992, 114:4028-4035.
[48] BLACKLEDGE M J, MEDVEDEVA S, PONCIN M, et al. Structure and dynamics of ferrocytochrome c553 from Desulfovibrio vulgaris studied by NMR spectroscopy and restrained molecular dynamics [J]. Journal of Molecular Biology, 1995, 245: 661-681.
[49] HAYWARD S KITAO, A. BERENDSEN H J C. Model-free methods of analyzing domain motions in proteins from simulation: A comparison of normal mode analysis and molecular dynamics simulation of lysozyme [J]. Proteins-Structure Function and Genetics, 1997, 27: 425-437
[50] LI L, DARDEN T A, FREEDMAN S J, et al. Refinement of the NMR solution structure of the gamma-carboxyglutamic acid domain of coagulation factor IX using molecular dynamics simulation with initial Ca2+ positions determined by a genetic algorithm [J]. Biochemistry, 1997, 36:2132-2138
[51] CREGUT D, SERRANO L. Molecular dynamics as a tool to detect protein foldability. A mutant of domain B1 of protein G with non-native secondary structure propensities [J]. Protein Science, 1999, 8:271-282.
[52] CHOWDHURY S, BANSAL M. G-quadruplex structure can be stable with only some coordination sites being occupied by cations: A six-nanosecond molecular dynamics study [J]. Journal of Physical Chemistry B, 2001, 105: 7572-7578.
[53] GERVASIO F L, CHELLI R, MARCHI M, et al. Determination of the potential of mean force of aromatic amino acid complexes in various solvents using molecular dynamics simulations: The case of the tryptophan-histidine pair [J]. Journal of Physical Chemistry B, 2001, 105: 7835-7846.
[54] FEIG M, MACKERELL A D, BROOKS C L. Force field influence on the observation of pi-helical protein structures in molecular dynamics simulations [J]. Journal of Physical Chemistry B, 2003, 107: 2831-2836.
[55] REDDY S Y, BRUICE T C. Determination of enzyme mechanisms by molecular dynamics: Studies on quinoproteins, methanol dehydrogenase, and soluble glucose dehydrogenase [J]. Protein Science, 2004, 13: 1965-1978.
[56] BONNET P, BRYCE R A. Scoring binding affinity of multiple ligands using implicit solvent and a single molecular dynamics trajectory: Application to Influenza neuraminidase [J]. Journal of Molecular Graphics & Modelling, 2005, 24: 147-156.
[57] PETER C, HUMMER G. Ion transport through membrane-spanning nanopores studied by molecular dynamics simulations and continuum electrostatics calculations [J]. Biophysical Journal, 2005, 89: 2222-2234.
[58] SEEBER M, FANELLI F, PACI E, et al. Sequential unfolding of individual helices of bacterioopsin observed in molecular dynamics simulations of extraction from the purple membrane [J]. Biophysical Journal. 2006, 91: 3276-3284.
[59] SHARMA S, GONG P, TEMPLE B, et al. Molecular dynamic simulations of cisplatin- and oxaliplatin-d(GG) intrastand cross-links reveal differences in their conformational dynamics [J]. Journal of Molecular Biology, 2007, 373: 1123-1140.
[60] BISMUTO E, DI MAGGIO E, PLEUS S, et al. Molecular dynamics simulation of the acidic compact state of apomyoglobin from yellowfin tuna [J]. Proteins-Structure Function and Bioinformatics 2009, 74: 273-290.
[61] ROY S, SEN S. Homology Modeling Based Solution Structure of Hoxc8-DNA Complex: Role of Context Bases Outside TAAT Stretch [J]. Journal of Biomolecular Structure & Dynamics, 2005, 22: 707-718.
[62] MOEGLICH A, WEINFURTNER D, MAURER T, et al. A Restraint Molecular Dynamics and Simulated Annealing Approach for Protein Homology Modeling Utilizing Mean Angles [J].BMC Bioinformatics, 2005, 8: 91.
[63] SIVOZHELEZOV V, NICOLINI C, KARPINSKI S, et al. Toward a blueprint forUDP-glucose pyrophosphorylase structure/function properties: homology-modeling analyses [J]. Plant Molecular Biology, 2004, 56:783-794.
[64] MALHERBE P, KRATOCHWIL N, ZENNER M T, et al. Mutational analysis and molecular modeling of the binding pocket of the metabotropic glutamate 5 receptor negative modulator 2-methyl-6- (phenylethynyl)-pyridine [J]. Molecular Pharmacology, 2003, 64: 823-832.
[65] YASAR F, CELIK S, KOKSEL H. Molecular modeling of various peptide sequences of gliadins and low-molecular-weight glutenin subunits [J]. Die Nahrung, 2003, 47:238-242.
[66] TAKEDA-SHITAKA M, TAKAYA, D, CHIBA, C, et al. Protein structure prediction in structure based drug design [J]. Current Medicine in Chemistry, 2004, 11: 551-558.
[67] BAKHRAT A, JURICA M S, STODDARD B L, et al. Homology modeling and mutational analysis of Ho endonuclease of yeast [J]. Genetics, 2004, 166:721-728.
[68] ANDREINI C, BANCI L, BERTINI I, et al. Bioinformatic comparison of structures and homology-models of matrix metalloproteinases [J]. J. Proteome. Res., 2004, 3:21-31.
[69] LEE K W, BRIGGS J M. Molecular modeling study of the editing active site of Escherichia coli leucyl-tRNA synthetase: two amino acid binding sites in the editing domain [J]. Proteins, 2004, 54:693-704.
[70] KUBALA M, OBSIL T, OBSILOVA V, et al. Protein modeling combined with spectroscopic techniques: an attractive quick alternative to obtain structural information [J]. Physiological Research, 2004, 53 Suppl 1: S187-S197.
[71] ROHL C A, STRAUSS C E, CHIVIAN D, et al. Modeling structurally variable regions in homologous proteins with rosetta [J]. Proteins, 2004, 55: 656-677.
[72] LEE S C, RUSSELL A F, LAIDIG W D. Three-dimensional structure of bradykinin in SDS micelles. Study using nuclear magnetic resonance, distance geometry, and restrained molecular mechanics and dynamics [J]. Intentional Journal of Peptide Protein Research, 1990, 35: 367-377.
[73] PELLEGRINI M, MIERKE D F. Threonine6-bradykinin: molecular dynamicssimulations in a biphasic membrane mimetic [J]. Journal of Medicinal Chemistry, 1997, 40: 99-104.
[74] BEN-TAL N, SITKOFF D, BRANSBURG-ZABARY S, et al. Theoretical calculations of the permeability of monensin-cation complexes in model bio-membranes [J]. Biochimica et biophysica acta, 2000, 1466: 221-233.
[75] BADER R, BETTIO A, BECK-SICKINGER A G, et al. Structure and dynamics of micelle-bound neuropeptide Y: comparison with unligated NPY and implications for receptor selection [J]. Journal of Molecular Biology, 2001, 305: 307-329.
[76] CHIVIAN D, BAKER D. Homology modeling using parametric alignment ensemble generation with consensus and energy-based model selection [J]. Nucleic Acids Research, 2006, 34: e112-e130.
[77] FANO A, RITCHIE D W, CARRIERI A. Modeling the structural basis of human CCR5 chemokine receptor function: From homology model building and molecular dynamics validation to agonist and antagonist docking [J]. Journal of Chemical Information and Modeling, 2006, 46: 1223-1235.
[78] HARIHARAN R, PILLAI M R. Homology modeling of the DNA-binding domain of human Smad5: A molecular model for inhibitor design [J]. Journal of Molecular Graphics & Modeling 2006, 24:271-277.
[79] MASUDA S, PROSSER D E, GUO Y D, et al. Generation of a homology model for the human cytochrome P450, CYP24A1, and the testing of putative substrate binding residues by site-directed mutagenesis and enzyme activity studies [J]. Archives of Biochemistry and Biophysics, 2007, 460: 177-191.
[80] SCHLEGEL B, LAGGNER C, MEIER R, et al. Generation of a homology model of the human histamine H-3 receptor for ligand docking and pharmacophore-based screening [J]. Journal of Computer-Aided Molecular Design, 2007, 21: 437-453.
[81] RICHARTZ A, HOLTJE M, BRANDT B, et al. Targeting human DNA polymerase alpha for the inhibition of keratinocyte proliferation. Part 1. Homology model, active site architecture and ligand binding [J]. Journal ofEnzyme Inhibition and Medicinal Chemistry, 2008, 23: 94-100.
[82] LISUREK M, SIMGEN B, ANTES I, et al. Theoretical and experimental evaluation of a CYP106A2 low homology model and production of mutants with changed activity and selectivity of hydroxylation [J]. Chembiochem, 2008, 9: 1439-1449.
[83] FLETCHER S, CUMMINGS C G, RIVAS K, et al. Potent, plasmodium-selective farnesyltransferase inhibitors that arrest the growth of malaria parasites: Structure-activity relationships of ethylenediamine-analogue scaffolds and homology model validation [J]. 2008, 51: 5176-5197.
[84] PIETRA F. Binding of ciguatera toxins to the voltage-gated Kv1.5 potassium channel in the open state. Docking of gambierol and molecular dynamics simulations of a homology model [J]. Journal of Physical Organic Chemistry, 2008, 21: 997-1001.
[85] JONES D T, TAYLOR W R, THORNTON J M. A new approach to protein fold recognition [J]. Nature, 1992, 358:86-89.
[86]倪红春.遗传算法在蛋白质结构预测中的应用[J].上海大学学报自然科学版, 2001,7(3):225-230.
[87]靳利霞.模拟退火算法的一种改进及其在蛋白质结构预测中的应用[J].系统工程理论与实际, 2002, 9,92-96.
[88]贾孟文.蛋白质结构预测的研究[J].内蒙古大学学报自然科学版,2002, 33(3):276-279.
[89]卢本卓.用于真实蛋白质结构预测的一种新的优化方法[J].化学物理学报, 2003,16(2):117-121.
[90] KNELLER G R, HINSEN K. Fractional Brownian dynamics in proteins [J]. Journal of Chemical Physics, 2004, 121:10278-83.
[91] MANAS E S, UNWALLA R J, XU Z B, et al. Structure-based design of estrogen receptor-beta selective ligands [J]. Journal of American Chemical Society, 2004, 126:15106-19.
[92] KAZLAUSKAS R. Modeling-A tool for experimentalists [J]. Science, 2001, 293, 2277-2278.
[93] BJELIC S, AQVIST J. Computational prediction of structure, substrate binding mode, mechanism, and rate for a malaria protease with a novel type of active site [J]. Biochemistry, 2004, 43: 14521-14528.
[94] TSUCHIYA H, KUWATA K, NAGAYAMA S, et al. Pharmacokinetic modeling of species-dependent enhanced bioavailability of trifluorothymidine by thymidine phosphorylase inhibitor. Drug Metabolism Pharmacokinetics, 2004, 19:206-215.
[95] PATNAIK S S, TROHALAKI S, PACHTER R. Molecular modeling of green luorescent protein: structural effects of chromophore deprotonation [J]. Biopolymers, 2004, 75:441-52.
[96] MAJUMDER S, ROY A, MANDAL C. Prediction of 3-D structures of fucose-binding proteins and structural analysis of their interaction with ligands [J]. Glycoconjugate Journal, 2004, 20:545-50.
[97] CHEATHAM TE 3RD. Simulation and modeling of nucleic acid structure, dynamics and interactions. Current Opinion in Structure Biology, 2004, 14:360-367.
[98] Goodfellow J M, Moss D S, Computer Modeling of Biomolecular Process. New York: Ellis Horwood, 1992.
[99] Warshel A, Computer Modeling of Chemical Reactions in Enzymes and Solutions. New York: Jonh Wiley & Sons, 1991.
[100]陈正隆.分子模拟的理论与时间[M].北京:化学工业出版社,2007.
[101] WEINER P W, KOLLMAN P A. AMBER: assisted model building with energy refinement. A general program for modelling molecules and their interactions [J]. Journal of Computational Chemistry, 1981, 2: 287–303.
[102] SCOTT W R P, HUNENBERGER P H, TIRONI H G, et al. The GROMOS biomolecular simulation program package [J]. Journal of Physical Chemistry A, 1999, 103: 3596–3607.
[103] TUCKERMAN M E, MARTYNA G J. Understanding modern molecular dynamics: techniques and applications. Journal of Physical Chemistry, 2000, 104:159–178.
[104] van Gunsteren W F, Weiner P K, Wilkinson A J. Computational Simulationof Biomolecular Systems: Theoretical and Experimental Applications Vol. 2 (ESCOM, Leiden; 1993).
[105] Becker O M, MacKerell A D, Jr Roux B, et al. Computational Biochemistry and Biophysics (Marcel Dekker, New York; 2001).
[106] HAYWARD S, KITAO A, GO N. Harmonicity and anharmonicity in protein dynamics [J]. Proteins: Structure, Function and Genetics. 1995, 23:177–186.
[107] ZALOJ V, ELBER R. Parallel computations of molecular dynamics trajectories usingthe stochastic path approach [J]. Computer Physics Communication, 2000, 128:118–127.
[108] LAMB M L, JORGENSON W. Computational approaches to molecular recognition [J]. Current Opinion in Structure Biology, 1997, 1: 449–457.
[109] KOLLMAN P. Free energy calculations: Application to chemical and biological phenomena. Chemical Reviews, 1993, 93: 2395–2421.
[110] van Gunsteren W F, Mark A E. Validation of molecular dynamics simulations [J]. Journal of Chemical Physics, 1998, 108: 6109–6116 .
[111] GAO J, TRUHLAR D G. Quantum mechanical methods for enzyme kinetics [J]. Annual Review of Physical Chemistry, 2002, 53: 467–505.
[112]李廷风.生物信息学在药物研究中的应用
[113]陈凯先.蒋华良.计算机辅助药物设计[M].上海:上海科技出版社,2000.
[114]郑珩.药物生物信息学[M].北京:化学工业出版社,2004.
[115]孙之荣.后基因组信息学[M].北京:清华大学出版社,2002.
[116] ROOS D S. Bioinformatics-Trying to swim in a sea of data [J]. Science, 2001, 291, 1260-1261.
[117] SPENGLER S J. Bioinformatics in the information age [J]. Science, 2000, 287, 1221-1223.
[118]陈竺.基因组科学与人类疾病[M].北京:科学出版社,2001.
[119]欧阳曙光.生物实验数据和计算技术结合的新领域[J].科学通报,1999, 44: 1457-1469.
[120]马大龙.从人类基因组中发掘药物宝藏[J].生物学通报,2000, 35: 5-9.
[121]李违章.生物信息学与新药研究[J].科学,1999, 51: 17-19.
[122]郭利.基因组学在寻找新型抗生素中的应用[J].国外医学药学分册,2001, 28: 34-38.
[123] TERSTAPPEN G C, REQQIANI A. Insilico research in drug discovery [J]. Trends in Pharmacological Sciences, 2001, 22: 23-26.
[124] DAVID B S. Using bioinformatics in gene and drug disconvery, Drug Discovery Today, 2000, 5: 135-143.
[125] SUZANNE B. Drug discovery in the wake of genomics [J]. Trends in biotechnology. 2001, 19: 239-240.
[126] DAVID A C. Making drug discovery a SN(i)P [J] Drug Discovery Today, 2000.5(9): 338-347.
[127] PFOST D R, BOYCE-JACINO M T, GRANT D M. A SNPshot: pharmacogenetics and the future of drug therapy [J]. Trends in biotechnology, 2000, 18: 334-338.
[128] OSBORNE R P. Panel session at Allicense 99: pharmacogenomics efforts pay off, despite roadblocks. BioWord Today, 1999(29):p1
[129] ADAM G I. The development of pharmacogenomic models to predict drug response [J]. Current Opinion in Drug Disconvery and Development, 2001, 4:296-300.
[1] STERNBERG M J E. Protein structure prediction-a piratical approach Oxford: Oxford Press, 1996.
[2] SALI A, SANCHEZ R. Comparative protein structure modeling in genomics [J]. 1999, 151: 388-401.
[3] DODGE, C. The HSSP database of protein structure sequence alignments and family profiles [J]. Nucleic Acid Research, 1998, 26: 313-315.
[4] BLUNDELL T L, SIBANDA B L, STERNBERG M J E, et al. Knowledge-based prediction of protein structures and the design of novel molecules [J]. Nature, 1987, 326: 347-352.
[5] BLUNDELL T L, CARNEY D, GARDNER S, et al. Knowledge-based protein modelling and design [J]. European Journal of Biochemistry, 1988, 172:513-520.
[6] JIANG T, XU Y, ZHANG M Q. Current Topic in Computational Molecular Biology [M], Bei Jing: Tinghua University Press, 2002.
[7] SALI A, OVERINGTON J P, JOHNSON M S, et al. From comparisons of protein sequences and structures to protein modeling and design [J]. Trends in Biochemical Sciences, 1990, 15(6): 235-240.
[8] PEARSON W R. Rapid and sensitive sequence comparison with FASTP and FASTA [J]. Methods in Enzymology, 1990, 183: 63-98.
[9] BACON D J, ANDERSON W F. Multiple sequence alignment [J]. Journal of Molecular Biology, 1986, 191: 153-161.
[10] SCHULER G. D, ALTSCHUL S F., LIPMAN D J. A workbench for multiple alignment construction and analysis [J]. Proteins: Structure Function and Genetics, 1991, 9: 180-190.
[11] BERGER M P, MUNSON P J. A novel randomized iterative strategy for aligning multiple protein sequences [J]. Computer Applications in the Biosciences, 1991, 7: 479-484.
[12] WESSON L, EISENBERG D. Atomic solvation parameters applied to molecular-dynamics of proteins in solution [J]. Protein Science, 1992, 1: 227-235.
[13] PASCARELLA S, ARGOS P. Analysis of insertions deletions in protein structures [J]. Journal of Molecular Biology, 1992, 224:461-471.
[14] ALLEN F H, KENNARD O. The Cambridge Crystallographic Data Centre: computer-based search, retrieval, analysis and display of information [J]. Chemical Design Automation News, 1993, 8: 31-37.
[15] FREYBERG B V, RICHMOND T J, BRAUN W. Surface-area included in energy refinement of proteins-a comparative-study on atomic solvation parameters [J]. Journal of Molecular Biology, 1993, 233: 275-292.
[16] MACARTHUR M W, THORNTON J M. Conformational analysis of protein structures derived from NMR data [J]. Proteins, 1993, 17: 232-251.
[17]王禄山.生物信息学应用技术[M].北京:化学工业出版社,2008.
[18] BAXEVANIS A D, OUELLETTE B F F. A Practical Guide to the Analysis of Genes and Proteins. In Bioinformatics, Wiley-Liss. Inc., 1998.
[19] NEEDLEMAN S B, WUNSCH C D. A general method applicable to the search for similarities in the amino acid sequence of two proteins [J]. Journal of Molecular Biology, 1970, 48: 443-453.
[20] BOWIE J U, LUTHY R, EISENBERG D. A method to identify protein sequences that fold into a known 3-dimensional structure [J]. Science, 1991, 253: 164-170.
[21] LUTHY R, BOWIE J U, EISENBERG D. Assessment of protein models with three-dimensional profiles [J]. Nature, 1992, 356: 83-85.
[22] RICHMOND T J, RICHARDS F M. Packing ofα-helices: Geometrical constraints and contact areas [J]. Journal of Molecular Biology, 1978, 119: 537-555.
[23]蒋华良.顾健德.配体一受体相互作用的计算机模拟及其在药物设计中的应用[J].化学进展,1998, 10 (4): 427-441.
[24] KENNETH M, MERZ JR. Computer simulation of enzymatic reactions [J]. Current Opinion in Structural Biology, 1993, 3: 234-240
[25]阎隆飞.蛋白质分子结构[M].北京:清华大学出版社, 1999.
[26]王志中.现代量子化学计算方法[M].长春:吉林大学出版社,1998
[27]唐敖庆.量子化学[M].北京:科学出版社, 1982
[28]唐敖庆,杨忠志.大分子体系的量子化学[M].长春:吉林大学出版社,2000.
[29]田安民.量子化学[M].四川:四川大学出版社,1989.
[30]廖沐真.量子化学从头计算方法[M].北京:清华大学出版社,1989.
[31]江逢霖.量子化学原理[M].上海:复旦大学出版社,1990.
[32] SLATER J C. Quantum Theory of Molecular and Solids. Vol. 4: The Self-Consistent Field for Molecular and Solids McGraw-Hill: New York, 1974.
[33] SALAHUB D R, ZERNER M C. The Challenge of d and f Electrons ACS: Washington, D.C. 1989
[34] Parr R G, Yang W. Density-functional theory of atoms and molecules Oxford Univ. Press: Oxford, 1989
[35] Andrew R L. Molecular Modeling: Principles and Applications, 1996, Addison Wesley Longman Limited, London
[36]陈凯先.计算机辅助药物设计─原理、方法及应用[M].上海:上海科学技术出版社,2006.
[37] KAO J, ALLINGER N L. Conformational analysis. 122. Heats of formation of conjugated hydrocarbons by the force field method [J]. Journal of the American Chemical Society, 1977, 99: 975-986.
[38] WEINER S J, KOLLMAN P A, NGUYEN D T, et al. An all atom force field for simulations of proteins and nucleic acids [J]. Journal of Computational Chemistry, 1986, 7: 230-252.
[39] MOMANY F A, RONE R. Validation of the general purpose QUANTA ?3.2/CHARMm? force field [J]. Journal of Computational Chemisty, 1992, 13: 888-900.
[40] HAGLER A T, HULER E, LIFSON S. Energy functions for peptides and proteins. I. Derivation of a consistent force field including the hydrogen bond from amide crystals [J]. Journal of the American Chemical Society, 1974, 96: 5319-5327.
[41] MAYO S L, OLAFSON B D, GODDARD W A. DREIDING: A Generic Force Field for Molecular Simulations [J]. Journal of Physical Chemistry, 1990, 94: 8897-8909.
[42] PAPPE A K, CASEWIT C J, COLWELL K S, et al. UFF, a full periodic table force field for molecular mechanics and molecular dynamics simulations [J]. Journal of the American Chemical Society, 1992, 114 : 10024-10035.
[43] BUNTE S W. Molecular Modeling of Energetic Materials: The Parameterization and Validation of Nitrate Esters in the COMPASS Force Field [J]. Journal of Physical Chemistry B, 2001, 104, 2477-2489.
[44] Casewit C J, Colwell K S, Rappe A K. Application of a universal force field to organic molecules [J]. Journal of the American Chemical Society, 1992, 114, 10035-10046.
[45] Rosenthal A B, Garofalini S H. Molecular dynamics of amorphous titanium silicate [J]. Journal of Non-Crystalline Solids, 1988, 107, 65-72.
[46] Weiner S J, Kollman P A, Case D A. et al. A new force field for molecular mechanical simulation of nucleic acids and proteins [J]. Journal of the American Chemical Society, 1984, 106, 765-784.
[47] Kohler A E, Garofalini S H. Effect of Composition on the Penetration of Inert Gases Adsorbed onto Silicate Glass Surfaces [J]. Langmuir, 1994, 10, 4664-4669.
[48] Levitt M, Lifson S. Refinement of protein conformations using a macromolecular energy minimization procedure [J]. Journal of Molecular Biology, 1969, 46, 269-279.
[49] Flecher R, Reeves C M. Function minimization by conjugate gradients [J]. The Computer Journal, 1964, 7, 149-154.
[50] FLECHER R. Practical Methods of Optimization, Vol. 1, Unconstrained Optimization, 1980, John Wiley & Sons, New York
[51] POWELL M J D. Restart procedures for the conjugate gradient method [J]. Mathematical Programming, 1977, 12, 241-254.
[52] GUNSTEREN W F, KARPLUS M. A method for constrained energy minimization of macromolecules [J]. Journal of Computationl Chemistry, 1980, 1, 266-274.
[53] Broyden C G. The Convergence of a Class of Double-rank Minimization Algorithms [J]. Journal of International Mathematical. Application, 1970, 6,222-231
[54] FLECHER R. A new approach to variable metric algorithms [J]. The Computer Journal, 1970, 13, 317-322.
[55] Goldfarb, D. A Family of Variable Metric Updates Derived by Variational Means [J]. Mathematics of Computing, 1970, 24, 23-26.
[56] Shanno, D. F. Conditioning of Quasi-Newton Methods for Function Minimization [J]. Mathematics of Computing, 1970, 24, 647-656.
[57] FERMI E, PASTA J, ULAM S. Collected Papers of Enrico Fermi. Edited by Segre E. Chicago: University of Chicago Press, 1965.
[58] ALDER B J, Wainwright T E. Studies in Molecular Dynamics. I. General Method [J]. Journal of Chemical Physics, 1959, 31, 459-467.
[59] RAHMAN A. Correlations in the Motion of Atoms in Liquid Argon [J]. Physical Review, 1964, 136: A405-A411.
[60] VERLET L. Computer "Experiments" on Classical Fluids. I. Thermodynamical Properties of Lennard-Jones Molecules [J]. Physcal Review, 1967, 159: 98-103.
[61] DUAN Y, KOLLMAN P A. Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution [J]. Science, 1998, 282: 740-744.
[62] ZHONG Q, JIANG Q, MOORE P B, et al. Molecular dynamics simulation of a synthetic ion channel [J]. Biophysical Journal, 1998, 74: 3-10.
[63] Zhong Q, Moore P B, Newns D M, et al. Molecular dynamics study of the LS3 voltage-gated ion channel [J]. FEBS Letter, 1998, 427: 267-270.
[64] Mi H, Tuckerman M E, Schuster D I, et al. A molecular dynamics study of HIV-1 protease complexes with C60 and fullerene-based anti-viral agents [J]. Proceedings of the Electrochemical Society, 1999, 99, 256-269.
[65] TUCHERMAN M E, MARTYNA G. J. Understanding Modern Molecular Dynamics: Techniques and Applications [J]. Journal of Physics Chemistry B, 2000, 104: 159-178.
[66] VERLET L. Computer "Experiments" on Classical Fluids. I. Thermodynamical Properties of Lennard-Jones Molecules [J]. Physical Review, 1963, 159: 98-103.
[67] BEEMAN D. Some Multistep Methods for Use in Molecular Dynamics Calculations [J]. Journal of Computational Chemistry, 1976, 20, 130-139.
[68] NOSE S. A molecular dynamics method for simulations in the canonical ensemble [J]. Molecular Physics, 1984, 53: 255-268.
[69] NOSE S, KLEIN M L. Constant pressure molecular dynamics for molecular systems [J]. Molecular Physics, 1983, 50: 1055-1076.
[70] HOOVER W G. Canonical dynamics: Equilibrium phase-space distributions [J]. Physical Review A, 1985, 31: 1695-1697.
[71] NOSE S, YONEZAWA F. Isothermal–isobaric computer simulations of melting and crystallization of a Lennard-Jones system [J]. Journal of Chemical Physics, 1986, 84: 1803-1815.
[72] HAILE J M, GRABEN H W. Molecular dynamics simulations extended to various ensembles. I. Equilibrium properties in the isoenthalpic–isobaric ensemble [J]. Journal of Chemical Physics, 1980, 73: 2412-2420.
[73]徐筱杰.计算机辅助药物分子设计[M].北京:化学工业出版社,2004.
[74] KUNTZ I D. Structure-based strategies for drug design and discovery [J]. Science, 257, 1992: 1078-1082.
[75] KUNTZ I D, AGARD D A. Assessment of the role of computations in structural biology [J]. Advance in Protein Chemistry, 2003, 66: 1-25.
[76] MENG E C, GSCHWEND D A, BLANEY J M, et al. Orientational sampling and rigid-body minimization in molecular docking [J]. Proteins, 1993, 17: 266-278.
[77] MORRIS G. M, GOODSELL D S, HUEY R, et al. Distributed automated docking of flexible ligands to proteins: parallel applications of AutoDock 2.4 [J]. Journal of Computational Aided Molecular Design, 1996, 10: 293-304.
[78] GOODSELL D S, OLSON A J. Automated docking of substrates to proteins by simulated annealing [J]. Proteins, 1990, 8: 195-202.
[79] OSTERBERG F, MORRIS G. M, SANNER M F, et al. Automated docking to multiple target structures: incorporation of protein mobility and structural water heterogeneity in AutoDock [J]. Proteins, 2002, 46: 34-40.
[80] KION A E, GLICK M, THOMA M, et al. Finding more needles in the haystack:A simple and efficient method for improving high-throughput docking results [J]. Journal of Medicinal Chemistry, 2004, 47: 2743-2749.
[81] LUTY B A, WASSERMAN Z R, STOUTEN P F W, et al. A molecular mechanics/grid method for evaluation of ligand-receptor interactions [J]. Journal of Computational Chemistry, 1995, 16, 454-464.
[1] KURANDA M J, ROBBINS P W. Chitinase is required for cell separation during growth of Saccharomyces cerevisiae [J]. Journal of Biological Chemistry, 1991, 266: 19758-19767.
[2] WU Y, EGERTON G, UNDERWOOD A P, et al. Expression and secretion of a larval-specific chitinase (family 18 glycosyl hydrolase) by the infective stages of the parasitic nematode, Onchocerca volvulus [J]. Journal of Biological Chemistry 2001, 276: 42557-42564.
[3] VINETZ J M, DAVE S K, SPECHT C A, et al. The chitinase PfCHT1 from the human malaria parasite Plasmodium falciparum lacks proenzyme and chitin-binding domains and displays unique substrate preferences [J]. Proceedings of Natlonal Academy of Sciences USA, 1999, 96: 14061-14066.
[4] CHOHEN E. Chitin synthesis and degradation as targets for pesticide action [J]. Archives of Insect Biochemistry and Physiolgy, 1993, 22: 245-261.
[5] FLACH J, PILET P E, JOLLES P. What's new in chitinase research [J]. Experientia 1992, 48: 701-716
[6] BOOT R G, RENKEMA G H, STRIJLAND A, et al. Cloning of a cDNA encoding chitotriosidase, a human chitinase produced by macrophages [J]. Journal of Biological Chemistry 1995, 270: 26252-26256.
[7] SAKUDA S, ISOGAI A, MATSUMOTO S, et al. Search for microbial insect growth regulators [J]. Journal of Antibiotics 1987, 40: 296-300.
[8] SANDOR E, PUSZTAHELYI T, KARAFFA L, et al. Allosamidin inhibits the fragmentation of Acremonium chrysogenum but does not influence the cephalosporin-C production of the fungus [J]. FEMS Microbiology Letters, 1998, 164: 231-236.
[9] VINETZ J M, VALENZUELA J G, SPECHT C A, et al. Structural insights into the catalytic mechanism of a family 18 exo-chitinase [J]. Current Opinion in Structural Biology, 1997, 7: 637-644.
[10] RENKEMA G H, BOOT R G, STRIJLAND A, et al. Synthesis, sorting, andprocessing into distinct isoforms of human macrophage chitotriosidase. Koopman [J]. European Jouranl of Biochemistry, 1997, 244: 279-285.
[11] BOOT R G, BLOMMAART EF C, SWART E, et al. Structure of Human Chitotriosidase implications for specific inhibitor design and function of mammalian chitinase-like lectins [J]. Journal of Biological Chemistry, 2001, 276: 6770-6778.
[12] ZHU Z, ZHENG T, HOMER R J, et al.Acidic Mammalian Chitinase in Asthmatic Th2 Inflammation and IL-13 Pathway Activation [J]. Science, 2004, 304: 1678-82.
[13] ELIAS J A, HOMER R J, HAMID Q, et al. Chitinases and chitinase-like proteins in TH2 inflammation and asthma [J]. Journal of Allergy and Clinical Immunology, 2005, 116: 497-500.
[14] ZHENG Q C, LI Z S, SUN M, et al. Homology modeling and substrate binding study of Nudix hydrolase Ndx1 from Thermos thermophilus HB8 [J]. Biochemical and Biophysical Research Communications, 2005, 333(3):881-887
[15] XU W, CAI P, YAN M, et al. Molecular Docking of Xylitol and Xylose Isomerase from Thermus thermophilus and Model Analysis [J]. Chemical Journal of Chinese Universities, 2007, 28: 971-973.
[16] HE Y P, HU H R, XU L S. Structure-activity Relationship Studies on 6-Naphthylmethyl Substituted HEPT Derivatives as Non-nucleoside Reverse Transcriptase Inhibitors Based on Molecular Docking [J]. Chemical Journal of Chinese Universities, 2005, 26: 254-258
[17] RAO F V, HOUSTON D R, BOOT R G., et al. Crystal Structures of Allosamidin Derivatives in Complex with Human Macrophage Chitinase [J]. Journal of Biological Chemistry, 2003, 278: 20110-20116
[18] InsightII, User Guid, San Diego: Biosym/MSI (2000)
[19] InsightII, Homology User Guide, San Diego: Accelrys Inc (2000)
[20] ALTSCHUL S F, MADDEN T L, SCHFER A A, et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs [J]. Nucleic Acids Research, 1997, 25:3389-3402
[21] SALI A, OVERINGTON J P. Derivation of rules for comparative proteinmodeling from a database of protein structure alignments [J]. Protein Science, 1994, 3 (9): 1582–1596.
[22] Sali A, Potterton L, Yuan F, et al. Evaluation of comparative protein modeling by MODELLER [J]. Proteins: Structure, Function, and Genetics. 1995, 23 (3): 318–326.
[23] SALI A. Modelling mutations and homologous proteins [J]. Current Opinion in Biotechnology, 1995, 6 (4): 437–451
[24] InsightII Discover3 User Guide, San Diego: Biosym/MSI (2000)
[25] InsightII Profile-3D User Guide, San Diego: Biosym/MSI (2000)
[26] LASKOWSKI RA, MACARTHUR M W, MOSS D S, et al. PROCHECK: a program to check the stereochemical quality of protein structures [J]. (1993) Journal of Applied Crystallography, 1993, 26: 283-291
[27] Binding Site Analysis User Guide, Accelrys Inc., San Dieg, USA 2000.
[28] InsightII Affinity User Guide San Diego: Biosym/MSI (2000)
[29] FRISCH M J, TRUCKS G W, SCHLEGEL H B, et al.Gaussian 03 (Revision A.1) Gaussian Pittsburgh (2003)
[30] InsightII Ludi User Guide San Diego: Biosym/MSI (2000)
[31] JANNICK D B, HENRIK N, GUNNAR V H, et al. Improved prediction of signal peptides: SignalP 3.0. [J]. Journal of Molecular Biology, 2004, 340: 783-795
[32] VAN AALTEN D M, SYNSTAD B, BRUBERG M B, et al. Structure of a two-domain chitotriosidase from Serratia marcescens at 1.9-? resolution [J]. Proceedings of Natlonal Academy of Sciences USA, 2000, 97: 5842-5847.
[33] SAKUDA S. Studies on the chitinase inhibitors,allosamidins [J]. (1996) Chitin Enzymology, 1996, 2: 203-212
[34] BERECIBAR A, GRANDJEAN C, SIRIWARDENA, et al. Synthesis and Biological Activity of Natural Aminocyclopentitol Glycosidase Inhibitors: Mannostatins, Trehazolin, Allosamidins, and Their Analogues [J]. Chemical Reviews, 1999, 99: 779-844
[35] CHOU Y-T, YAO S, CZERWINSKI R, et al. Kinetic Characterization of4444-4454。
Recombinant Human Acidic Mammalian Chitinase [J]. Biochemistry, 2006, 45:
[1] CORRIGAN J J. D-Amino acids in animals [J]. Science, 1969, 164: 142-149.
[2] Corrigan J J, Srinivasan N G. The Occurrence of Certain D-Amino Acids in Insects [J]. Biochemistry,1966,5: 1185-1190.
[3] PANIZZUTTI R. DE MIRANDA J. RIBEIRO C S, et al. A new strategy to decrease N-methyl-d-aspartate (NMDA) receptor coactivation: Inhibition of d-serine synthesis by converting serine racemase into an eliminase [J]. Proceeding of the National Academy of Sciences USA, 2001, 98: 5294-5299.
[4] DE MIRANDA J, SANTORO A, ENGELENDER S, Human serine racemase: moleular cloning, genomic organization and functional analysis [J]. Gene 2000, 256: 183-188.
[5] NAGATA Y, KONNO R, YASUMURA Y, et al. Involvement of D-amino acid oxidase in elimination of free D-amino acids in mice [J]. Biochemical Journal, 1989, 257: 291-292.
[6] HASHIMOTO A, NISHIKAWA T, HAYASHI T, et al. The presence of free D-serine in rat brain [J]. FEBS Letter, 1992, 296: 33-36.
[7] HASHIMOTO A, NISHIKAWA T, OKA T, et al. Endogenous D-serine in rat brain: N-methyl-D-aspartate receptor-related distribution and aging [J]. Journal Neurochemistry, 1993, 60: 783-786.
[8] NAGATA Y, HORIIKE K, MAEDA T. Distribution of free D-serine in vertebrate brains [J]. Brain Research, 1994, 634: 291.
[9] Matsui T, Sekiguchi M, Hashimoto A, Tomita U, Nishikawa T, Wada K. J. Neurochem. 1995, 65: 454.
[10] IVANOVIC A, REILANDER H, LAUBE B, et al. Expression and initial characterization of a soluble glycine binding domain of the N-methyl-D-aspartate receptor NR1 subunit [J]. Journal of Biology Chemistry, 1998, 273: 19933-19937.
[11] MIYAZAKI J, NAKANISHI S, JINGAMI H. Expression and characterization of a glycine-binding fragment of the N-methyl-D-aspartate receptor subunit NR1 [J]. The Biochemical Journal, 1999, 340: 687-692.
[12] CHOI D W, ROTHMAN S M. The role of glutamate neurotoxicity in hypoxic-ischemic neuronal death [J]. Annual Review of Neuroscience, 1990, 13: 171-182.
[13] WOLOSKER H, BLACKSHAW S, SNYDER S H. Serine racemase: a glial enzyme synthesizing D-serine to regulate glutamate-N-methyl-D-aspartate neurotransmission [J]. Proceeding of the National Academy of Sciences USA, 1999 ,96: 13409-13414.
[14] De Miranda J, Santoro A, Engelender S, et al. Human serine racemase: moleular cloning, genomic organization and functional analysis [J]. Gene, 2000, 256: 183-188.
[15] MENGHANG X, YUAN L, DAVID J F, et al. Characterization and localization of a human serine racemase [J]. Molecular Brain Research. 2004, 125: 96-104.
[16] Dixon S M, Li P, Liu R, Slow-binding human serine racemase inhibitors from high-throughput screening of combinatorial libraries [J]. Journal of Medicinal Chemistry, 2006 49: 2388-2397.
[17] Zheng X L, Zhang H X, Sun J Z, et al. Molecular docking study of HIV-1 in/inhibitor in the presence of double metal conditions [J]. Chemical Journal of Chinese University, 2006 27(7): 1298-1302
[18] HU J P, KE G T, CHANG S, et al. Conformational Change of HIV-1 Viral DNAafter Binding with Integrase [J]. Acta Physico-Chimica Sinica, 2008 24(10): 1803-1810.
[19] Insight II user Guide. San Diego: Molecular Simulation Inc. 2000
[20] MORRIS A L, MACARTHUR M W, HUTCHINSON E G., et al. Stereochemical quality of protein structure coordinates [J]. Proteins, 1992, 12: 345-364.
[21] LIANG J, EDELSBRUNNER H, WOODWARD C. Anatomy of protein pockets and cavities: measurement of binding site geometry and implications for ligand design [J]. Protein Science, 1998, 7: 1884-1897.
[22] DAMBORSKY J, PET?EK M, BANá? P, et al. Identification of tunnels in proteins, nucleic acids, inorganic materials and molecular ensembles [J]. Biotechnology Journal, 2007, 2: 62-67.
[23] BECKE A D. Density-functional thermochemistry. III. The role of exact exchange [J] Journal of Chemistry Physics, 1993, 98: 5648-5652.
[24] BECKE A D. Density-functional thermochemistry. I. The effect of the exchange-only gradient correction [J]. Journal of Chemistry Physics, 1992 96: 2155-2160.
[25] BARONE V, COSSI M. Quantum Calculation of Molecular Energies and Energy Gradients in Solution by a Conductor Solvent Model [J]. Journal of Physical Chemistry A, 1998 102: 1995-2001.
[26] FRISCH M. J, TRUCKS G W, SCHLEGEL H B, et al. Gaussian 03 Revision D.01. Pittsburgh PA: Gaussian Inc. 2003
[27] YOSHIMURA T, ESAKI N. Amino acid racemases: functions and mechanisms [J]. Journal of Bioscience Bioengineering, 2003 96:103-109.
[1] CRAVATT B F, GIANG, D K, MAYFIELD S P, et al. Molecular characterization of an enzyme that degrades neuromodulatory fatty-acid amides [J]. Nature, 1996, 384: 83–87.
[2] GIANG D K, CRAVATT, B F. Molecular characterization of human and mouse fatty ccid amide hydrolases [J]. Proceedings of Natlonal Academy of Sciences USA, 1997, 4: 2238–2242.
[3] CHEBROU H, BIGEY F, ARNAUD A, et al. Study of the amidase signature group [J]. Biochimical Biophysica Acta 1996, 1298: 285–293.
[4] DEVANE W A, HANUS L, BREUER A, et al. Isolation and Structure of a Brain Constituent that Binds to the Cannabinoid Receptor [J]. Science, 1992, 258: 1946–1949.
[5] MARTIN B R, MECHOULAM R, RAZDAN, R K. Discovery and Characterization of Endogenous Cannabinoids [J]. Life Science, 1999, 65: 573–595.
[6] DI MARZO V, BISOGNO T, DE PETROCELLIS L, et al. Cannabimimetic Fatty Acid Derivatives: The Anandamide Family and Other“Endocannabinoids”[J]. Current Medicinal Chemistry, 1999, 6: 721–744.
[7] SCHMID H H, SCHMID P C, NATARAJAN V. N-Acylated Glycerophospholipids and Their Derivatives [J]. Progress in Lipid Reseach, 1990, 29: 1–43.
[8] BOGER D L, HENRIKSEN S J, CRAVATT B F. Oleamide: An EndogenousSleep-Inducing Lipid and Prototypical Member of a New Class of Lipid Signaling Molecules [J]. Current Pharmaceutical Design, 1998, 4: 303–314.
[9] CRAVATT B F, LERNER R A, BOGER D L. Structure Determination of an Endogenous Sleep-Inducing Lipid cis-9-Octadecenamide (Oleamide): A Synthetic Approach to the Chemical Analysis of Trace Quantitites of a Natural Product [J]. Journal of American Chemistry Society, 1996, 118: 580–590.
[10] CRAVATT B F, PROSPERO-GARCIA O, SUIZDAK G, et al. A ChemicalCharacterization of a Family of Brain Lipids that Induce Sleep [J]. Science, 1995, 268: 1506–1509.
[11] LAMBERT D M, VANDEVOORDE S, JONSSON K O, et al. The palmitoylethanolamide family: A new class of antiinflammatory agents? [J]. Current Medicinal Chemistry, 2002, 9: 663–674.
[12] RODRIGUEZ DE FONSECA F, NAVARRO M, GOMEZ R, et al (2001) An anorexic lipid mediator regulated by feeding [J]. Nature, 2001, 414: 209–212.
[13] CRAVATT B F, DEMAREST K, PATRICELLI M P, et al. Supersensitivity to Anandamide and Enhanced Endogenous Cannabinoid Signaling in Mice Lacking Fatty Acid Amide Hydrolase [J]. Proceedings of Natlonal Academy of Sciences USA, 2001, 98: 9371–9376.
[14] LICHTMAN A H, SHELTON C C, ADVANI T, et al. Mice Lacking Fatty Acid Amide Hydrolase Exhibit a Cannabinoid Receptor-Mediated Phenotypic Hypoalgesia [J]. Pain, 2004, 109: 319–327.
[15] CRAVATT B F, SAGHATELIAN A, HAWKINS E G, et al. Functional Disassociation of the Central and Peripheral Fatty Acid Amide Signaling Systems [J]. Proceedings of National Academy of Sciences USA, 2004, 101: 10821–10826.
[16] KARSAK M, GAFFAL E, DATE R, et al. Attenuation of Allergic Contact Dermatitis Through the Endocannabinoid System [J]. Science, 2007, 316: 1494–1497.
[17] (a) HUITRO′N-RESE′NDIZ S, GOMBART L, CRAVATT B F, et al. Effect of Oleamide on Sleep and Its Relationship to Blood Pressure, Body Temperature, and Locomotor Activity in Rats [J]. Exprimental Neurology, 2001, 172: 235–243. (b) HUITRO′N-RESE′NDIZ S, SANCHEZ-ALAVEZ M, WILLS D N, et al. Characterization of the Sleep-Wake Patterns in Mice Lacking Fatty Acid Amide Hydrolase [J]. Sleep, 2004, 27: 857–865.
[18] LEUNG D, HARDOUIN C, BOGER D L, et al. Discovering potent and selective reversible inhibitors of enzymes in complex proteomes [J]. Nature Biotechnology, 2003, 21: 687–691.
[19] BOGER D L, SATO H, LERNER A E, et al. Exceptionally potent inhibitors of fatty acid amide hydrolase: The enzyme responsible for degradation of endogenous oleamide and anandamide [J]. Proceedings of National Academy of Sciences USA, 2000, 97: 5044–5049.
[20] AHN K, JOHNSON D S, FITZGERALD L R, et al Novel mechanistic class of fatty acid amide hydrolase inhibitors with remarkable selectivity [J]. Biochemistry, 2007, 46: 13019–13030.
[21] ZHENG Q C, LI Z S, SUN M, et al. Homology modeling and substrate binding study of Nudix hydrolase Ndx1 from Thermos thermophilus HB8 [J]. Biochemical and Biophysical Research Communications, 2005, 333(3):881-887.
[22] XU W, CAI P, YAN M, et al. Molecular Docking of Xylitol and Xylose Isomerase from Thermus thermophilus and Model Analysis [J]. Chemical Journal of Chinese Universities, 2007, 28: 971-973.
[23] HE Y P, HU H R, XU L S. Structure-activity Relationship Studies on 6-Naphthylmethyl Substituted HEPT Derivatives as Non-nucleoside Reverse Transcriptase Inhibitors Based on Molecular Docking [J]. Chemical Journal of Chinese Universities, 2005, 26: 254-258.
[24] RAO F V, HOUSTON D R, BOOT R G., et al. Crystal Structures of Allosamidin Derivatives in Complex with Human Macrophage Chitinase [J]. Journal of Biological Chemistry, 2003, 278: 20110-20116.
[25] BAIROCH A, APWEILER R. The SWISS-PORT protein sequence data bank and its supplement TrEMBL [J]. Nucleic Acids Research, 1997, 25 (1): 31-36.
[26] ALTSCHUL S F, MADDEN T L, SCHFER A A, et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs [J]. Nucleic Acids Research, 1997, 25:3389-3402.
[27] SALI A, OVERINGTON J P. Derivation of rules for comparative protein modeling from a database of protein structure alignments [J]. Protein Science, 1994, 3 (9): 1582–1596.
[28] SALI A, BLUNDELL T L. Comparative protein modeling by satisfaction of spatial restraints [J]. Journal of Molecular Biology, 1993:234: 779-815.
[29] Sali A, Potterton L, Yuan F, et al. Evaluation of comparative protein modeling by MODELLER [J]. Proteins: Structure, Function, and Genetics. 1995, 23 (3): 318–326.
[30] SALI A. Modelling mutations and homologous proteins [J]. Current Opinion in Biotechnology, 1995, 6 (4): 437–451.
[31] CASE D A, CHEATHAM T E, III, DARDEN T, et al. The Amber bimolecular simulation programs [J]. Journal of Computational Chemistry, 2005, 26: 1668-1688.
[32] DUAN Y, WU C, CHOWDHURY S, et al. A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations [J]. J Computational Chemistry, 2003, 24: 1999–2012.
[33] JORGENSEN W L, CHANDRASKHAR J, MADURA J, et al. Comparison of simple potential functions for simulating liquid water [J]. Journal of Chemistry Physics, 1983, 79: 926-935.
[34] RYCHAERT J P, CICCOTTI G, BERENDSEN H J C. Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes [J]. Journal of Computational Physics, 1977, 23: 327–341.
[35] InsightII Profile-3D User Guide, San Diego: Biosym/MSI (2000)
[36] LASKOWSKI RA, MACARTHUR M W, MOSS D S, et al. PROCHECK: a program to check the stereochemical quality of protein structures [J]. (1993) Journal of Applied Crystallography, 1993, 26: 283-291.
[37] SIPPL M J. Recognition of errors in three-dimensional structures of proteins [J]. Proteins, 1993, 17: 355–362.
[38] Binding Site Analysis User Guide, Accelrys Inc, San Dieg, USA 2000
[39] InsightII Affinity User Guide San Diego: Biosym/MSI (2000)
[40] FRISCH M J, TRUCKS G W, SCHLEGEL H B, et al.Gaussian 03 (Revision A.1) Gaussian Pittsburgh (2003)
[41] InsightII Ludi User Guide San Diego: Biosym/MSI (2000)
[42] BRACEY M H, HANSON M A, MASUDA K R, et al. Structural adaptations in a membrane enzyme that terminates endocannabinoid signaling [J]. Science, 2002,298, 1793–1796.
[43] DEUTCH D G, LIN S, HILL W A, et al. A Fatty acid sulfonyl fluorides inhibit anandamide metabolism and bind to the cannabinoid Receptor [J]. Biochemical and Biophysical Research Communications, 1997, 231: 217–221.
[44] SEGALL Y, QUISTAD G B, NOMURA D K, et al. Arachidonylsulfonyl derivatives as cannabinoid CB1 receptor and fatty Acid amide hydrolase inhibitors [J]. Bioorganic and Medicinal Chemistry Letters, 2003, 13: 3301–3303.
[45] DEUTCH D G, OMEIR R, ARREAZA G, et al. Methyl arachidonyl fluorophosphonate: a potent irreversible inhibitor of anandamide amidase [J]. Biochemical Pharmacology, 1997, 53: 255–260.
[46] KOUTEK B, PRESTWICH G D, HOWLETT A C, et al. Inhibitors of arachidonoyl ethanolamide hydrolysis [J]. Journal of Biological Chemistry, 1994, 269: 22937–22940.
[47] De Petrocellis L, Melck D, Ueda N, et al. Novel inhibitors of brain, neuronal, and basophilic anandamide amidohydrolase [J]. Biochemical and Biophysical Research Communications, 1997, 231: 82–88.
[48] LICHTMAN A H, LEUNG D, SHELTON C, et al. Reversible inhibitors of fatty acid amide hydrolase that promote analgesia: evidence for an unprecented combination of potency and selectivity [J]. Journal of Pharmacology and Experimental Therapeutics, 2004, 311: 441–448.
[49] MYLLYMA¨KI M J, SAARIO S M, KATAJA A, et al. Design, synthesis, and in vitro evaluation of carbamate derivatives of 2-benzoxazolyl- and 2-benzothiazolyl-(3-hydroxyphenyl)-methanones as novel fatty acid amide hydrolase inhibitors [J]. Journal of Medicinal Chemistry, 2007, 50: 4236–4242.
[50] SIT, S-Y XIE, K WO Patent 087569, 2002
[51] PATEL S, WOHLFEIL E R, RADEMACHER D J, et al. The general anesthetic propofol increases brain N-arachidonylethanolamine (anandamide) content and inhibits fatty acid amide hydrolase [J]. British Journal of Pharmacology, 2003, 139: 1005–1013.
[52] SEIERSTAD M, BREITENBUCHER J G. Discovery and Development of FattyAcid Amide Hydrolase (FAAH) inhibitors [J]. Journal of Medicinal Chemistry, 2008, 51: 7327-7343.
[1] SAUVE A A, WOLBERGER C, SCHRAMM V L, et al. The Biochemistry of Sirtuins [J]. Annual Review of Biochemistry, 2006, 75: 435-465.
[2] TANNY J C, DOWD, G J, HUANG J, et al. An Enzymatic Activity in the Yeast Sir2 Protein that Is Essential for Gene Silencing [J]. Cell, 1999, 99: 735-745.
[3] LONGO V D, KENNEDY B K. Sirtuins in Aging and Age-Related Disease [J]. Cell, 2006, 126: 257-268.
[4] LI W, ZHANG B, TANG J, et al. Sirtuin 2, a Mammalian Homolog of Yeast Silent Information Regulator-2 Longevity Regulator, Is an Oligodendroglial Protein That Decelerates Cell Differentiation through Deacetylating -Tubulin [J]. Journal of Neuroscience, 2007, 27: 2606-2616.
[5] CHEN D, GUARENTE L. SIR2: a potential target for calorie restriction mimetics [J]. Trends in Molecular Medicine, 2007, 13: 64-71.
[6] MICHAN S, SINCLAIR A Sirtuins in mammals: insights into their biological function [J]. Biochemical Journal, 2007, 404: 1-13.
[7] JOHN M D. The Sir2 family of protein deacetylases [J]. Current Opinion in Chemical Biology, 2005, 9: 431-440.
[8] YAMAMOTO H, SCHOONJANS K, AUWERX J. Sirtuin Functions in Health and Disease [J]. Molecular Endocrinology, 2007, 21, 1745-1755.
[9] ZHAO K, CHAI X, CLEMENTS A, et al. Structure and autoregulation of the yeast Hst2 homolog of Sir2 [J]. Natural Structural Biology, 2003a, 10: 864-871.
[10] MICHAEL D J, JOHN M D. Structural Identification of 2'- and 3'-O-Acetyl-ADP-ribose as Novel Metabolites Derived from the Sir2 Family of -NAD+-dependent Histone/Protein Deacetylases [J]. Journal of Biological Chemistry, 2002, 277: 18535-18544.
[11] AVALOS J L, CELIC I, MUHAMMAD S, et al. Structure of a Sir2 Enzyme Bound to an Acetylated p53 Peptide [J]. Molecular Cell, 2002, 10: 523-535.
[12] AVALOS J L, BOEKE J D, WOLBERGER, C. Structural Basis for the Mechanism and Regulation of Sir2 Enzymes [J]. Molecular Cell, 2004, 13:639-648.
[13] CHANG J H, KIM H C, HWANG K Y, et al. Structural Basis for the NAD-dependent Deacetylase Mechanism of Sir2 [J]. Journal of Biological Chemistry, 2002, 277: 34489-34498.
[14] MIN J, LANDRY J, STERNGLANZ R, et al. Crystal Structure of a SIR2 Homolog–NAD Complex [J]. Cell, 2001, 105: 269-279.
[15] ZHAO K, CHAI X, CLEMENTS A, et al. Structure of the Yeast Hst2 Protein Deacetylase in Ternary Complex with 2′-O-Acetyl ADP Ribose and Histone Peptide [J]. Structure 2003b, 11: 1403-1411.
[16] FINNIN M S, DONIGIAN J R, PAVLETICH N P. Structure of the histone deacetylase SIRT2 [J]. Nature Structural Biology, 2001, 8: 621-623.
[17] TANNER K G, LANDRY J, STERNGLANZ R, et al. The Sir2 protein family: A novel deacetylase for gene silencing and more [J]. The Proceeding of the National Academy of Science USA, 2000, 97: 14178-14182.
[18] HOFF K G, AVALOS J L, SENS K, et al. Insights into the Sirtuin Mechanism from Ternary Complexes Containing NAD+ and Acetylated Peptide [J]. Structure, 2006, 14: 1231-1240.
[19] SAUVE A A, CELIC I, AVALOS J, et al. Chemistry of gene silencing: the mechanism of NAD+-dependent deacetylation reactions [J]. Biochemistry, 2001, 40: 15456-15463.
[20] BECKE A D. Density-functional thermochemistry III The role of exact exchange [J]. Journal of Chemical Physics, 1993, 98: 5648-5652.
[21] BECKE A D. Density-functional thermochemistry I The effect of the exchange-only gradient correction [J]. Journal of Chemical Physics, 1992, 96: 2155-2160.
[22] BECKE A D. Density-functional thermochemistry II The effect of the Perdew–Wang generalized-gradient correlation correction [J]. Journal of Chemical Physics, 1992, 97: 9173-9177.
[23] LEE C, YANG W, PARR R G. Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density [J]. PhysicalReview B, 1988, 37: 785-789.
[24] (a) Siegbahn P E M, Blomberg M R A. A Quantum Chemical Approach to the Study of Reaction Mechanisms of Redox-Active Metalloenzymes [J]. Journal of Physical Chemistry B, 2001, 105: 9375-9386. (b) Siegbahn P E M. Mechanisms of metalloenzymes studied by quantum chemical methods [J]. Quarterly Reviews of Biophysics, 2003, 36: 91-145. (c) Himo F, Siegbahn P E M. Quantum chemical studies of radical-containing enzymes [J]. Chemical Reviews. 2003, 103: 2421-2456.
[25] Biopolymer User Guide, Accelrys Inc., San Diego, USA 1999.
[26] AVALOS J L, BEVER K M, WOLBERGER C. Mechanism of sirtuin inhibition by nicotinamide: altering the NAD(+) cosubstrate specificity of a Sir2 enzyme [J]. Molecular Cell, 2005, 17: 855-868.
[27] SMITH B C, DENU J M. Sir2 Deacetylases Exhibit Nucleophilic Participation of Acetyl-Lysine in NAD+ Cleavage [J]. Journal of American Chemical Society, 2007, 129: 5802-5803.
[28] InsightII, version 98.0.San Diego: Accelrys Inc. 1998.
[29] Discover3 User Guide, Accelrys Inc., San Diego, USA 1999.
[30] FRISCH M J, TRUCKS G W, SCHLEGEL H B, et al.Gaussian 03 (Revision A.1) Gaussian Pittsburgh (2003)
[31] (a) CAMMI R, MENNUCCI B, TOMASI J. Second-Order M ller-Plesset Analytical Derivatives for the Polarizable Continuum Model Using the Relaxed Density Approach [J]. Journal of Physical Chemistry A, 1999, 103: 9100-9108; (b) CAMMI R, MENNUCCI B, TOMASI, J. Evaluation of Geometries and Properties of Excited Molecules in Solution: A Tamm-Dancoff Model with Application to 4-Dimethylaminobenzonitrile, Journal of Physical Chemistry A, 2000, 104: 5631-5637; (c) COSSI M, REGA N, SCALMANI G, et al. Polarizable dielectric model of solvation with inclusion of charge penetration effects, Journal of Chemical Physics, 2001, 114: 5691-5701; (d) COSSI M, SCALMANI G, REGA N, et al. New developments in the polarizable continuum model for quantum mechanical and classical calculations on molecules in solution [J]. Journal ofChemical Physics, 2002, 117: 43-54.
[32] HOPMANN K H, HALLBERG B M, HIMO F. Catalytic Mechanism of Limonene Epoxide Hydrolase: a Theoretical Study [J]. Journal of American Chemical Society, 2005, 127: 14339-14347.
[33] HIMO F, SIEGBAHN P E M. Catalytic Mechanism of Glyoxalase I: A Theoretical Study [J]. Journal of American Chemical Society, 2001, 123: 10280-10289.
[34] HIMO F. Quantum chemical modeling of enzyme active sites and reaction mechanisms [J]. Theoretical Chemistry Accounts:Theory, Computation, and Modeling, 2006, 116: 232-240.
[35] CURTISS L A, KRISHNAN R, REDFERN P C, et al. Assessment of Gaussian-2 and density functional theories for the computation of enthalpies of formation [J]. Journal of Chemical Physics, 1997, 106: 1063-1080.
[36] SLAMA J T, SIMMONS A M. Carbanicotinamide Adenine Dinucleotide: Enzymological Properties Synthesis and of a Carbocyclic Analogue of Oxidized Nicotinamide Adenine Dinucleotide [J]. Biochemistry, 1988, 27: 183-193.
[37] ZHAO K, HARSHAW R, CHAI X, et al. Structural basis for nicotinamide cleavage and ADP-ribose transfer by NAD+-dependent Sir2 histone/protein deacetylases [J]. The Proceeding of the National Academy of Science USA, 2004, 101: 8563-8568.
[38] SMITH B C, DENU J M. Sir2 Protein Deacetylases: Evidence for Chemical Intermediates and Functions of a Conserved Histidine [J]. Biochemistry, 2006, 45: 272-282.
[39] HAWSE W F, HOFF K G, FATKINS D G, et al. Structural insights into intermediate steps in the Sir2 deacetylation reaction [J]. Structure, 2008, 16: 1368-1377.
[40] ARMSTRONG C M, KAEBERLEIN M, IMAI S I, et al. Mutations in Saccharomyces cerevisiae Gene SIR2 Can Have Differential Effects on In Vivo Silencing Phenotypes and In Vitro Histone Deacetylation Activity [J]. Molecular Biological Cell, 2002, 13: 1427-1438.
[41] ZHU X, HEINE A, MONNAT F, et al. Structural Basis for Antibody Catalysis of a Cationic Cyclization Reaction [J]. Journal of Molecular Biology, 2003, 329: 69-83.
[42] SANDERS B D, ZHAO K H, SLAMA J T, et al. Structural Basis for Nicotinamide Inhibition and Base Exchange in Sir2 Enzymes [J]. Molecular Cell, 2007, 25: 463-472.
[2]陈铭.后基因组时代的生物信息学[J].生物信息学, 2004, 2(2): 29-34.
[3]张春霆.生物信息学的现状与展望[J].世界科技研究与发展, 2000, 22(6): 17-20.
[4] BENTON D. Bioinformatics principles and potential of a new multidisciplinary tool [J]. Trends in Biotechnology, 1996, 14: 261-272.
[5] NIH and DOE, The U. S. Human Genome Project: The First Five Years FY 1991-1995.
[6]唐旭清.后基因组时代生物信息学的发展趋势[J].生物信息学, 2008, 3(6): 142-146.
[7]赵国屏等.生物信息学[M].北京:科学出版社,2002.
[8] LEE F S, SHAPIRO R, VALLEE B L. Tight-binding inhibition of angiogenin and ribonuclease A by placental ribonuclease inhibitor [J]. Biochemistry, 1989, 28: 225-230.
[9] BAIROCH A. The ENZYME database in 2000 [J]. Nucleic Acids Research, 2000, 28: 304-305.
[10] RADZICKA A, WOLFENDEN R. A proficient enzyme [J]. Science, 1995, 6: 90-931.
[11] MARDEN M C, GRIFFON N, POYART C. Oxygen delivery and autoxidation of hemoglobin [J]. Transfusion Clinique et Biologique, 1995, 2: 473-480.
[12] SHI N, YE S, ALAM A, et al. Atomic structure of a Na+- and K+-conducting channel [J]. Nature, 2006, 440: 570-574.
[13] HIROKAWA N, NODA Y, OKADA Y. Kinesin and dynein superfamily proteins in organelle transport and cell division [J]. Current Opinion in Cell Biology, 1998, 10: 60-73.
[14] GIBBONS I R. The role of dynein in microtubule-based motility [J]. Cell Struct Funct. 1996, 21: 331-342.
[15] CURTIN N A, WOLEDGE R C. Energy changes and muscular contraction [J]. Physiological Reviews, 1978, 58: 690-761.
[16] SAUNDERS S A, GRACY R W, SCHNACKERZ K D, et al. Are honeybees deficient in phosphomannose isomerase? [J]. Science, 1969, 164: 858-859.
[17] GRACY R W, NOLTMANN E A. Studies on phosphomannose isomerase. 3. A mechanism for catalysis and for the role of zinc in the enzymatic and the nonenzymatic isomerization [J]. Journal of Biological Chemistry,1968, 243: 5410-5419.
[18] GRACY R W, NOLTMANN E A. Studies on phosphomannose isomerase. II. Characterization as a zinc metalloenzyme [J]. Journal of Biological Chemistry, 1968, 243: 4109-4116.
[19] GRACY R W, NOLTMANN E A. Studies on phosphomannose isomerase. I. Isolation, homogeneity measurements, and determination of some physical properties [J]. Journal of Biological Chemistry, 1968, 243: 3161-3168.
[20] MARKOVITZ A, LIEBERMAN M M, ROSENBAUM N. Derepression of phosphomannose isomerase by regulator gene mutations involved in capsular polysaccharide synthesis in Escherichia coli K-12 [J]. Journal of Bacteriology, 1967, 94: 1497-1501.
[21] MARKOVITZ A, SYDISKIS R J, LIEBERMAN M M. Genetic and biochemical studies on mannose-negative mutants that are deficient in phosphomannose isomerase in Escherichia coli K-12 [J]. Journal of Bacteriology, 1967, 94: 1492-1496.
[22] KIRK J E. The phosphoglucomutase, phosphoglyceric acid mutase, and phosphomannose isomerase activities of arterial tissue in individuals of various ages [J]. Journal of Gerontology, 1966, 21: 420-425.
[23] Rosen S M, Zeleznick L D, Fraenkel D, et al. Characterization of the cell wall lipopolysaccharide of a mutant of Salmonella typhimurium lacking phosphomannose isomerase [J]. Biochemische Zeitschrift, 1965, 342: 375-386.
[24] KIZER D.E, MCCOY T A. Phosphomannose isomerase activity in a spectrum of normal and malignant rat tissues [J]. Proceedings of the Society for Experimental Biology and Medicine, 1960, 103: 772-774.
[25] NOLTMANN E, BRUNS F H. Phosphomannose isomerase. II. Purification of the enzyme from yeast and separation of phosphomannose isomerase by column chromatography on hydroxyapatite [J]. Biochemische Zeitschrift, 1958, 330: 514-520.
[26] BRUNS F H, NOLTMANN E, WILLEMSEN A. Phosphomannose isomerase. I. Activity measurement and dependence of enzyme action on sulfhydryl groups and metals in some animal tissues [J]. Biochemische Zeitschrift, 1958, 330: 411-420.
[27] ALVARADO F, SOLS A. Borate and phosphoglucose isomerase in the assay of phosphomannose isomerase [J]. Biochimica et biophysica acta, 1957, 25: 75-77.
[28] TOPPER Y J. On the mechanism of action of phosphoglucose isomerase and phosphomannose isomerase [J]. Journal of Biological Chemistry, 1957, 225: 419-425。
[29] CHUNG V, WAKEFIELD A E, KINSMAN O S, et al. DNA amplification of a portion of the phosphomannose isomerase (PMI) gene in Pneumocystis carinii-enriched extracts [J]. Journal of Eukaryotic Microbiology, 1994, 41: 82S-83S.
[30] WELLS T N, PAYTON M A, PROUDFOOT A E. Inhibition of phosphomannose isomerase by mercury ions [J]. Biochemistry, 1994, 33: 7641-7646.
[31] WELLS T N, SCULLY P, MAGNENAT E. Arginine 304 is an active site residue in phosphomannose isomerase from Candida albicans [J]. Biochemistry, 1994, 33, 5777-5782.
[32] BRANDEN C, TOOZE J. Introduction to Protein Structure 2nd ed. 1999, Garland Publishing: New York, NY
[33] GONEN T, CHENG Y, SLIZ P, et al. Lipid-protein interactions in double-layered two-dimensional AQP0 crystals [J]. Nature, 2005, 438: 633-638.
[34]唐焕文.蛋白质结构预测的优化模型与方法[J],工程数学学报, 2002, 19(2): 13-22.
[35] ANFINSEN, C B. Principles that goven the folding of protein chains [J]. Science, 1973, 181: 223-230.
[36]赵南明.生物物理学[M],北京:高等教育出版社,2000.
[37] FRAUENFELDER H, PETSKO G A, TSERNOGLOU D. Temperature-dependent X-ray diffraction as a probe of protein structural dynamics [J]. Nature, 1979, 280: 558–563.
[38] ARTYMIUK P J, BLAKE C C, GRACE D E, et al. Crystallographic studies of the dynamic properties of lysozyme [J]. Nature, 1979, 280: 563–568.
[39] ICHIYE T, KARPLUS M. Fluorescence depolarization of tryptophan residues in proteins: a molecular dynamics study [J]. Biochemistry, 1983, 22: 2884–2893.
[40] DOBSON C M, KARPLUS M. Internal motion of proteins: Nuclear magneticresonance measurements and dynamic simulations [J]. Methods in Enzymology, 1986, 131: 362–389.
[41] SMITH J, CUSACK S, PEZZECA U, et al. Inelastic neutron scattering analysis of low frequency motion in proteins: A normal mode study of the bovine pancreatic trypsin inhibitor [J]. Journal of Chemical Physics, 1986, 85: 3636–3654.
[42] BRüNGER A T, BROOKS C L III, KARPLUS M. Active site dynamics of ribonuclease [J]. The Proceeding of the National Academy of Sciences USA, 1985, 82: 8458–8462.
[43] FRAUENFELDER H, HARTMANN H, KARPLUS M, et al. Thermal expansion of a protein [J]. Biochemistry, 1987, 26: 254–261.
[44] BRüNGER A T, KURIYAN J, KARPLUS M. Crystallographic R factor refinement by molecular dynamics [J]. Science, 1987, 235: 458–460.
[45] DE VLIEG J, SCHEEK R M, VAN GUNSTEREN W F, et al. Combined procedure of distance geometry and restrained molecular dynamics techniques for protein structure determination from nuclear magnetic resonance data: application to the DNA binding domain of lac repressor from Escherichia coli [J].Proteins-structrue function and genetics, 1988, 3:209-218.
[46] FRY D C, MADISON V S, BOLIN D R, et al. Solution structure of an analogue of vasoactive intestinal peptide as determined by two-dimensional NMR and circular dichroism spectroscopies and constrained molecular dynamics [J]. Biochemistry, 1989, 28:2399-2409.
[47] DE LOOF H, NILSSON L, RIGLER R. Molecular dynamics simulation of galanin in aqueous and nonaqueous solution [J]. Journal of the American Chemical Society, 1992, 114:4028-4035.
[48] BLACKLEDGE M J, MEDVEDEVA S, PONCIN M, et al. Structure and dynamics of ferrocytochrome c553 from Desulfovibrio vulgaris studied by NMR spectroscopy and restrained molecular dynamics [J]. Journal of Molecular Biology, 1995, 245: 661-681.
[49] HAYWARD S KITAO, A. BERENDSEN H J C. Model-free methods of analyzing domain motions in proteins from simulation: A comparison of normal mode analysis and molecular dynamics simulation of lysozyme [J]. Proteins-Structure Function and Genetics, 1997, 27: 425-437
[50] LI L, DARDEN T A, FREEDMAN S J, et al. Refinement of the NMR solution structure of the gamma-carboxyglutamic acid domain of coagulation factor IX using molecular dynamics simulation with initial Ca2+ positions determined by a genetic algorithm [J]. Biochemistry, 1997, 36:2132-2138
[51] CREGUT D, SERRANO L. Molecular dynamics as a tool to detect protein foldability. A mutant of domain B1 of protein G with non-native secondary structure propensities [J]. Protein Science, 1999, 8:271-282.
[52] CHOWDHURY S, BANSAL M. G-quadruplex structure can be stable with only some coordination sites being occupied by cations: A six-nanosecond molecular dynamics study [J]. Journal of Physical Chemistry B, 2001, 105: 7572-7578.
[53] GERVASIO F L, CHELLI R, MARCHI M, et al. Determination of the potential of mean force of aromatic amino acid complexes in various solvents using molecular dynamics simulations: The case of the tryptophan-histidine pair [J]. Journal of Physical Chemistry B, 2001, 105: 7835-7846.
[54] FEIG M, MACKERELL A D, BROOKS C L. Force field influence on the observation of pi-helical protein structures in molecular dynamics simulations [J]. Journal of Physical Chemistry B, 2003, 107: 2831-2836.
[55] REDDY S Y, BRUICE T C. Determination of enzyme mechanisms by molecular dynamics: Studies on quinoproteins, methanol dehydrogenase, and soluble glucose dehydrogenase [J]. Protein Science, 2004, 13: 1965-1978.
[56] BONNET P, BRYCE R A. Scoring binding affinity of multiple ligands using implicit solvent and a single molecular dynamics trajectory: Application to Influenza neuraminidase [J]. Journal of Molecular Graphics & Modelling, 2005, 24: 147-156.
[57] PETER C, HUMMER G. Ion transport through membrane-spanning nanopores studied by molecular dynamics simulations and continuum electrostatics calculations [J]. Biophysical Journal, 2005, 89: 2222-2234.
[58] SEEBER M, FANELLI F, PACI E, et al. Sequential unfolding of individual helices of bacterioopsin observed in molecular dynamics simulations of extraction from the purple membrane [J]. Biophysical Journal. 2006, 91: 3276-3284.
[59] SHARMA S, GONG P, TEMPLE B, et al. Molecular dynamic simulations of cisplatin- and oxaliplatin-d(GG) intrastand cross-links reveal differences in their conformational dynamics [J]. Journal of Molecular Biology, 2007, 373: 1123-1140.
[60] BISMUTO E, DI MAGGIO E, PLEUS S, et al. Molecular dynamics simulation of the acidic compact state of apomyoglobin from yellowfin tuna [J]. Proteins-Structure Function and Bioinformatics 2009, 74: 273-290.
[61] ROY S, SEN S. Homology Modeling Based Solution Structure of Hoxc8-DNA Complex: Role of Context Bases Outside TAAT Stretch [J]. Journal of Biomolecular Structure & Dynamics, 2005, 22: 707-718.
[62] MOEGLICH A, WEINFURTNER D, MAURER T, et al. A Restraint Molecular Dynamics and Simulated Annealing Approach for Protein Homology Modeling Utilizing Mean Angles [J].BMC Bioinformatics, 2005, 8: 91.
[63] SIVOZHELEZOV V, NICOLINI C, KARPINSKI S, et al. Toward a blueprint forUDP-glucose pyrophosphorylase structure/function properties: homology-modeling analyses [J]. Plant Molecular Biology, 2004, 56:783-794.
[64] MALHERBE P, KRATOCHWIL N, ZENNER M T, et al. Mutational analysis and molecular modeling of the binding pocket of the metabotropic glutamate 5 receptor negative modulator 2-methyl-6- (phenylethynyl)-pyridine [J]. Molecular Pharmacology, 2003, 64: 823-832.
[65] YASAR F, CELIK S, KOKSEL H. Molecular modeling of various peptide sequences of gliadins and low-molecular-weight glutenin subunits [J]. Die Nahrung, 2003, 47:238-242.
[66] TAKEDA-SHITAKA M, TAKAYA, D, CHIBA, C, et al. Protein structure prediction in structure based drug design [J]. Current Medicine in Chemistry, 2004, 11: 551-558.
[67] BAKHRAT A, JURICA M S, STODDARD B L, et al. Homology modeling and mutational analysis of Ho endonuclease of yeast [J]. Genetics, 2004, 166:721-728.
[68] ANDREINI C, BANCI L, BERTINI I, et al. Bioinformatic comparison of structures and homology-models of matrix metalloproteinases [J]. J. Proteome. Res., 2004, 3:21-31.
[69] LEE K W, BRIGGS J M. Molecular modeling study of the editing active site of Escherichia coli leucyl-tRNA synthetase: two amino acid binding sites in the editing domain [J]. Proteins, 2004, 54:693-704.
[70] KUBALA M, OBSIL T, OBSILOVA V, et al. Protein modeling combined with spectroscopic techniques: an attractive quick alternative to obtain structural information [J]. Physiological Research, 2004, 53 Suppl 1: S187-S197.
[71] ROHL C A, STRAUSS C E, CHIVIAN D, et al. Modeling structurally variable regions in homologous proteins with rosetta [J]. Proteins, 2004, 55: 656-677.
[72] LEE S C, RUSSELL A F, LAIDIG W D. Three-dimensional structure of bradykinin in SDS micelles. Study using nuclear magnetic resonance, distance geometry, and restrained molecular mechanics and dynamics [J]. Intentional Journal of Peptide Protein Research, 1990, 35: 367-377.
[73] PELLEGRINI M, MIERKE D F. Threonine6-bradykinin: molecular dynamicssimulations in a biphasic membrane mimetic [J]. Journal of Medicinal Chemistry, 1997, 40: 99-104.
[74] BEN-TAL N, SITKOFF D, BRANSBURG-ZABARY S, et al. Theoretical calculations of the permeability of monensin-cation complexes in model bio-membranes [J]. Biochimica et biophysica acta, 2000, 1466: 221-233.
[75] BADER R, BETTIO A, BECK-SICKINGER A G, et al. Structure and dynamics of micelle-bound neuropeptide Y: comparison with unligated NPY and implications for receptor selection [J]. Journal of Molecular Biology, 2001, 305: 307-329.
[76] CHIVIAN D, BAKER D. Homology modeling using parametric alignment ensemble generation with consensus and energy-based model selection [J]. Nucleic Acids Research, 2006, 34: e112-e130.
[77] FANO A, RITCHIE D W, CARRIERI A. Modeling the structural basis of human CCR5 chemokine receptor function: From homology model building and molecular dynamics validation to agonist and antagonist docking [J]. Journal of Chemical Information and Modeling, 2006, 46: 1223-1235.
[78] HARIHARAN R, PILLAI M R. Homology modeling of the DNA-binding domain of human Smad5: A molecular model for inhibitor design [J]. Journal of Molecular Graphics & Modeling 2006, 24:271-277.
[79] MASUDA S, PROSSER D E, GUO Y D, et al. Generation of a homology model for the human cytochrome P450, CYP24A1, and the testing of putative substrate binding residues by site-directed mutagenesis and enzyme activity studies [J]. Archives of Biochemistry and Biophysics, 2007, 460: 177-191.
[80] SCHLEGEL B, LAGGNER C, MEIER R, et al. Generation of a homology model of the human histamine H-3 receptor for ligand docking and pharmacophore-based screening [J]. Journal of Computer-Aided Molecular Design, 2007, 21: 437-453.
[81] RICHARTZ A, HOLTJE M, BRANDT B, et al. Targeting human DNA polymerase alpha for the inhibition of keratinocyte proliferation. Part 1. Homology model, active site architecture and ligand binding [J]. Journal ofEnzyme Inhibition and Medicinal Chemistry, 2008, 23: 94-100.
[82] LISUREK M, SIMGEN B, ANTES I, et al. Theoretical and experimental evaluation of a CYP106A2 low homology model and production of mutants with changed activity and selectivity of hydroxylation [J]. Chembiochem, 2008, 9: 1439-1449.
[83] FLETCHER S, CUMMINGS C G, RIVAS K, et al. Potent, plasmodium-selective farnesyltransferase inhibitors that arrest the growth of malaria parasites: Structure-activity relationships of ethylenediamine-analogue scaffolds and homology model validation [J]. 2008, 51: 5176-5197.
[84] PIETRA F. Binding of ciguatera toxins to the voltage-gated Kv1.5 potassium channel in the open state. Docking of gambierol and molecular dynamics simulations of a homology model [J]. Journal of Physical Organic Chemistry, 2008, 21: 997-1001.
[85] JONES D T, TAYLOR W R, THORNTON J M. A new approach to protein fold recognition [J]. Nature, 1992, 358:86-89.
[86]倪红春.遗传算法在蛋白质结构预测中的应用[J].上海大学学报自然科学版, 2001,7(3):225-230.
[87]靳利霞.模拟退火算法的一种改进及其在蛋白质结构预测中的应用[J].系统工程理论与实际, 2002, 9,92-96.
[88]贾孟文.蛋白质结构预测的研究[J].内蒙古大学学报自然科学版,2002, 33(3):276-279.
[89]卢本卓.用于真实蛋白质结构预测的一种新的优化方法[J].化学物理学报, 2003,16(2):117-121.
[90] KNELLER G R, HINSEN K. Fractional Brownian dynamics in proteins [J]. Journal of Chemical Physics, 2004, 121:10278-83.
[91] MANAS E S, UNWALLA R J, XU Z B, et al. Structure-based design of estrogen receptor-beta selective ligands [J]. Journal of American Chemical Society, 2004, 126:15106-19.
[92] KAZLAUSKAS R. Modeling-A tool for experimentalists [J]. Science, 2001, 293, 2277-2278.
[93] BJELIC S, AQVIST J. Computational prediction of structure, substrate binding mode, mechanism, and rate for a malaria protease with a novel type of active site [J]. Biochemistry, 2004, 43: 14521-14528.
[94] TSUCHIYA H, KUWATA K, NAGAYAMA S, et al. Pharmacokinetic modeling of species-dependent enhanced bioavailability of trifluorothymidine by thymidine phosphorylase inhibitor. Drug Metabolism Pharmacokinetics, 2004, 19:206-215.
[95] PATNAIK S S, TROHALAKI S, PACHTER R. Molecular modeling of green luorescent protein: structural effects of chromophore deprotonation [J]. Biopolymers, 2004, 75:441-52.
[96] MAJUMDER S, ROY A, MANDAL C. Prediction of 3-D structures of fucose-binding proteins and structural analysis of their interaction with ligands [J]. Glycoconjugate Journal, 2004, 20:545-50.
[97] CHEATHAM TE 3RD. Simulation and modeling of nucleic acid structure, dynamics and interactions. Current Opinion in Structure Biology, 2004, 14:360-367.
[98] Goodfellow J M, Moss D S, Computer Modeling of Biomolecular Process. New York: Ellis Horwood, 1992.
[99] Warshel A, Computer Modeling of Chemical Reactions in Enzymes and Solutions. New York: Jonh Wiley & Sons, 1991.
[100]陈正隆.分子模拟的理论与时间[M].北京:化学工业出版社,2007.
[101] WEINER P W, KOLLMAN P A. AMBER: assisted model building with energy refinement. A general program for modelling molecules and their interactions [J]. Journal of Computational Chemistry, 1981, 2: 287–303.
[102] SCOTT W R P, HUNENBERGER P H, TIRONI H G, et al. The GROMOS biomolecular simulation program package [J]. Journal of Physical Chemistry A, 1999, 103: 3596–3607.
[103] TUCKERMAN M E, MARTYNA G J. Understanding modern molecular dynamics: techniques and applications. Journal of Physical Chemistry, 2000, 104:159–178.
[104] van Gunsteren W F, Weiner P K, Wilkinson A J. Computational Simulationof Biomolecular Systems: Theoretical and Experimental Applications Vol. 2 (ESCOM, Leiden; 1993).
[105] Becker O M, MacKerell A D, Jr Roux B, et al. Computational Biochemistry and Biophysics (Marcel Dekker, New York; 2001).
[106] HAYWARD S, KITAO A, GO N. Harmonicity and anharmonicity in protein dynamics [J]. Proteins: Structure, Function and Genetics. 1995, 23:177–186.
[107] ZALOJ V, ELBER R. Parallel computations of molecular dynamics trajectories usingthe stochastic path approach [J]. Computer Physics Communication, 2000, 128:118–127.
[108] LAMB M L, JORGENSON W. Computational approaches to molecular recognition [J]. Current Opinion in Structure Biology, 1997, 1: 449–457.
[109] KOLLMAN P. Free energy calculations: Application to chemical and biological phenomena. Chemical Reviews, 1993, 93: 2395–2421.
[110] van Gunsteren W F, Mark A E. Validation of molecular dynamics simulations [J]. Journal of Chemical Physics, 1998, 108: 6109–6116 .
[111] GAO J, TRUHLAR D G. Quantum mechanical methods for enzyme kinetics [J]. Annual Review of Physical Chemistry, 2002, 53: 467–505.
[112]李廷风.生物信息学在药物研究中的应用
[113]陈凯先.蒋华良.计算机辅助药物设计[M].上海:上海科技出版社,2000.
[114]郑珩.药物生物信息学[M].北京:化学工业出版社,2004.
[115]孙之荣.后基因组信息学[M].北京:清华大学出版社,2002.
[116] ROOS D S. Bioinformatics-Trying to swim in a sea of data [J]. Science, 2001, 291, 1260-1261.
[117] SPENGLER S J. Bioinformatics in the information age [J]. Science, 2000, 287, 1221-1223.
[118]陈竺.基因组科学与人类疾病[M].北京:科学出版社,2001.
[119]欧阳曙光.生物实验数据和计算技术结合的新领域[J].科学通报,1999, 44: 1457-1469.
[120]马大龙.从人类基因组中发掘药物宝藏[J].生物学通报,2000, 35: 5-9.
[121]李违章.生物信息学与新药研究[J].科学,1999, 51: 17-19.
[122]郭利.基因组学在寻找新型抗生素中的应用[J].国外医学药学分册,2001, 28: 34-38.
[123] TERSTAPPEN G C, REQQIANI A. Insilico research in drug discovery [J]. Trends in Pharmacological Sciences, 2001, 22: 23-26.
[124] DAVID B S. Using bioinformatics in gene and drug disconvery, Drug Discovery Today, 2000, 5: 135-143.
[125] SUZANNE B. Drug discovery in the wake of genomics [J]. Trends in biotechnology. 2001, 19: 239-240.
[126] DAVID A C. Making drug discovery a SN(i)P [J] Drug Discovery Today, 2000.5(9): 338-347.
[127] PFOST D R, BOYCE-JACINO M T, GRANT D M. A SNPshot: pharmacogenetics and the future of drug therapy [J]. Trends in biotechnology, 2000, 18: 334-338.
[128] OSBORNE R P. Panel session at Allicense 99: pharmacogenomics efforts pay off, despite roadblocks. BioWord Today, 1999(29):p1
[129] ADAM G I. The development of pharmacogenomic models to predict drug response [J]. Current Opinion in Drug Disconvery and Development, 2001, 4:296-300.
[1] STERNBERG M J E. Protein structure prediction-a piratical approach Oxford: Oxford Press, 1996.
[2] SALI A, SANCHEZ R. Comparative protein structure modeling in genomics [J]. 1999, 151: 388-401.
[3] DODGE, C. The HSSP database of protein structure sequence alignments and family profiles [J]. Nucleic Acid Research, 1998, 26: 313-315.
[4] BLUNDELL T L, SIBANDA B L, STERNBERG M J E, et al. Knowledge-based prediction of protein structures and the design of novel molecules [J]. Nature, 1987, 326: 347-352.
[5] BLUNDELL T L, CARNEY D, GARDNER S, et al. Knowledge-based protein modelling and design [J]. European Journal of Biochemistry, 1988, 172:513-520.
[6] JIANG T, XU Y, ZHANG M Q. Current Topic in Computational Molecular Biology [M], Bei Jing: Tinghua University Press, 2002.
[7] SALI A, OVERINGTON J P, JOHNSON M S, et al. From comparisons of protein sequences and structures to protein modeling and design [J]. Trends in Biochemical Sciences, 1990, 15(6): 235-240.
[8] PEARSON W R. Rapid and sensitive sequence comparison with FASTP and FASTA [J]. Methods in Enzymology, 1990, 183: 63-98.
[9] BACON D J, ANDERSON W F. Multiple sequence alignment [J]. Journal of Molecular Biology, 1986, 191: 153-161.
[10] SCHULER G. D, ALTSCHUL S F., LIPMAN D J. A workbench for multiple alignment construction and analysis [J]. Proteins: Structure Function and Genetics, 1991, 9: 180-190.
[11] BERGER M P, MUNSON P J. A novel randomized iterative strategy for aligning multiple protein sequences [J]. Computer Applications in the Biosciences, 1991, 7: 479-484.
[12] WESSON L, EISENBERG D. Atomic solvation parameters applied to molecular-dynamics of proteins in solution [J]. Protein Science, 1992, 1: 227-235.
[13] PASCARELLA S, ARGOS P. Analysis of insertions deletions in protein structures [J]. Journal of Molecular Biology, 1992, 224:461-471.
[14] ALLEN F H, KENNARD O. The Cambridge Crystallographic Data Centre: computer-based search, retrieval, analysis and display of information [J]. Chemical Design Automation News, 1993, 8: 31-37.
[15] FREYBERG B V, RICHMOND T J, BRAUN W. Surface-area included in energy refinement of proteins-a comparative-study on atomic solvation parameters [J]. Journal of Molecular Biology, 1993, 233: 275-292.
[16] MACARTHUR M W, THORNTON J M. Conformational analysis of protein structures derived from NMR data [J]. Proteins, 1993, 17: 232-251.
[17]王禄山.生物信息学应用技术[M].北京:化学工业出版社,2008.
[18] BAXEVANIS A D, OUELLETTE B F F. A Practical Guide to the Analysis of Genes and Proteins. In Bioinformatics, Wiley-Liss. Inc., 1998.
[19] NEEDLEMAN S B, WUNSCH C D. A general method applicable to the search for similarities in the amino acid sequence of two proteins [J]. Journal of Molecular Biology, 1970, 48: 443-453.
[20] BOWIE J U, LUTHY R, EISENBERG D. A method to identify protein sequences that fold into a known 3-dimensional structure [J]. Science, 1991, 253: 164-170.
[21] LUTHY R, BOWIE J U, EISENBERG D. Assessment of protein models with three-dimensional profiles [J]. Nature, 1992, 356: 83-85.
[22] RICHMOND T J, RICHARDS F M. Packing ofα-helices: Geometrical constraints and contact areas [J]. Journal of Molecular Biology, 1978, 119: 537-555.
[23]蒋华良.顾健德.配体一受体相互作用的计算机模拟及其在药物设计中的应用[J].化学进展,1998, 10 (4): 427-441.
[24] KENNETH M, MERZ JR. Computer simulation of enzymatic reactions [J]. Current Opinion in Structural Biology, 1993, 3: 234-240
[25]阎隆飞.蛋白质分子结构[M].北京:清华大学出版社, 1999.
[26]王志中.现代量子化学计算方法[M].长春:吉林大学出版社,1998
[27]唐敖庆.量子化学[M].北京:科学出版社, 1982
[28]唐敖庆,杨忠志.大分子体系的量子化学[M].长春:吉林大学出版社,2000.
[29]田安民.量子化学[M].四川:四川大学出版社,1989.
[30]廖沐真.量子化学从头计算方法[M].北京:清华大学出版社,1989.
[31]江逢霖.量子化学原理[M].上海:复旦大学出版社,1990.
[32] SLATER J C. Quantum Theory of Molecular and Solids. Vol. 4: The Self-Consistent Field for Molecular and Solids McGraw-Hill: New York, 1974.
[33] SALAHUB D R, ZERNER M C. The Challenge of d and f Electrons ACS: Washington, D.C. 1989
[34] Parr R G, Yang W. Density-functional theory of atoms and molecules Oxford Univ. Press: Oxford, 1989
[35] Andrew R L. Molecular Modeling: Principles and Applications, 1996, Addison Wesley Longman Limited, London
[36]陈凯先.计算机辅助药物设计─原理、方法及应用[M].上海:上海科学技术出版社,2006.
[37] KAO J, ALLINGER N L. Conformational analysis. 122. Heats of formation of conjugated hydrocarbons by the force field method [J]. Journal of the American Chemical Society, 1977, 99: 975-986.
[38] WEINER S J, KOLLMAN P A, NGUYEN D T, et al. An all atom force field for simulations of proteins and nucleic acids [J]. Journal of Computational Chemistry, 1986, 7: 230-252.
[39] MOMANY F A, RONE R. Validation of the general purpose QUANTA ?3.2/CHARMm? force field [J]. Journal of Computational Chemisty, 1992, 13: 888-900.
[40] HAGLER A T, HULER E, LIFSON S. Energy functions for peptides and proteins. I. Derivation of a consistent force field including the hydrogen bond from amide crystals [J]. Journal of the American Chemical Society, 1974, 96: 5319-5327.
[41] MAYO S L, OLAFSON B D, GODDARD W A. DREIDING: A Generic Force Field for Molecular Simulations [J]. Journal of Physical Chemistry, 1990, 94: 8897-8909.
[42] PAPPE A K, CASEWIT C J, COLWELL K S, et al. UFF, a full periodic table force field for molecular mechanics and molecular dynamics simulations [J]. Journal of the American Chemical Society, 1992, 114 : 10024-10035.
[43] BUNTE S W. Molecular Modeling of Energetic Materials: The Parameterization and Validation of Nitrate Esters in the COMPASS Force Field [J]. Journal of Physical Chemistry B, 2001, 104, 2477-2489.
[44] Casewit C J, Colwell K S, Rappe A K. Application of a universal force field to organic molecules [J]. Journal of the American Chemical Society, 1992, 114, 10035-10046.
[45] Rosenthal A B, Garofalini S H. Molecular dynamics of amorphous titanium silicate [J]. Journal of Non-Crystalline Solids, 1988, 107, 65-72.
[46] Weiner S J, Kollman P A, Case D A. et al. A new force field for molecular mechanical simulation of nucleic acids and proteins [J]. Journal of the American Chemical Society, 1984, 106, 765-784.
[47] Kohler A E, Garofalini S H. Effect of Composition on the Penetration of Inert Gases Adsorbed onto Silicate Glass Surfaces [J]. Langmuir, 1994, 10, 4664-4669.
[48] Levitt M, Lifson S. Refinement of protein conformations using a macromolecular energy minimization procedure [J]. Journal of Molecular Biology, 1969, 46, 269-279.
[49] Flecher R, Reeves C M. Function minimization by conjugate gradients [J]. The Computer Journal, 1964, 7, 149-154.
[50] FLECHER R. Practical Methods of Optimization, Vol. 1, Unconstrained Optimization, 1980, John Wiley & Sons, New York
[51] POWELL M J D. Restart procedures for the conjugate gradient method [J]. Mathematical Programming, 1977, 12, 241-254.
[52] GUNSTEREN W F, KARPLUS M. A method for constrained energy minimization of macromolecules [J]. Journal of Computationl Chemistry, 1980, 1, 266-274.
[53] Broyden C G. The Convergence of a Class of Double-rank Minimization Algorithms [J]. Journal of International Mathematical. Application, 1970, 6,222-231
[54] FLECHER R. A new approach to variable metric algorithms [J]. The Computer Journal, 1970, 13, 317-322.
[55] Goldfarb, D. A Family of Variable Metric Updates Derived by Variational Means [J]. Mathematics of Computing, 1970, 24, 23-26.
[56] Shanno, D. F. Conditioning of Quasi-Newton Methods for Function Minimization [J]. Mathematics of Computing, 1970, 24, 647-656.
[57] FERMI E, PASTA J, ULAM S. Collected Papers of Enrico Fermi. Edited by Segre E. Chicago: University of Chicago Press, 1965.
[58] ALDER B J, Wainwright T E. Studies in Molecular Dynamics. I. General Method [J]. Journal of Chemical Physics, 1959, 31, 459-467.
[59] RAHMAN A. Correlations in the Motion of Atoms in Liquid Argon [J]. Physical Review, 1964, 136: A405-A411.
[60] VERLET L. Computer "Experiments" on Classical Fluids. I. Thermodynamical Properties of Lennard-Jones Molecules [J]. Physcal Review, 1967, 159: 98-103.
[61] DUAN Y, KOLLMAN P A. Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution [J]. Science, 1998, 282: 740-744.
[62] ZHONG Q, JIANG Q, MOORE P B, et al. Molecular dynamics simulation of a synthetic ion channel [J]. Biophysical Journal, 1998, 74: 3-10.
[63] Zhong Q, Moore P B, Newns D M, et al. Molecular dynamics study of the LS3 voltage-gated ion channel [J]. FEBS Letter, 1998, 427: 267-270.
[64] Mi H, Tuckerman M E, Schuster D I, et al. A molecular dynamics study of HIV-1 protease complexes with C60 and fullerene-based anti-viral agents [J]. Proceedings of the Electrochemical Society, 1999, 99, 256-269.
[65] TUCHERMAN M E, MARTYNA G. J. Understanding Modern Molecular Dynamics: Techniques and Applications [J]. Journal of Physics Chemistry B, 2000, 104: 159-178.
[66] VERLET L. Computer "Experiments" on Classical Fluids. I. Thermodynamical Properties of Lennard-Jones Molecules [J]. Physical Review, 1963, 159: 98-103.
[67] BEEMAN D. Some Multistep Methods for Use in Molecular Dynamics Calculations [J]. Journal of Computational Chemistry, 1976, 20, 130-139.
[68] NOSE S. A molecular dynamics method for simulations in the canonical ensemble [J]. Molecular Physics, 1984, 53: 255-268.
[69] NOSE S, KLEIN M L. Constant pressure molecular dynamics for molecular systems [J]. Molecular Physics, 1983, 50: 1055-1076.
[70] HOOVER W G. Canonical dynamics: Equilibrium phase-space distributions [J]. Physical Review A, 1985, 31: 1695-1697.
[71] NOSE S, YONEZAWA F. Isothermal–isobaric computer simulations of melting and crystallization of a Lennard-Jones system [J]. Journal of Chemical Physics, 1986, 84: 1803-1815.
[72] HAILE J M, GRABEN H W. Molecular dynamics simulations extended to various ensembles. I. Equilibrium properties in the isoenthalpic–isobaric ensemble [J]. Journal of Chemical Physics, 1980, 73: 2412-2420.
[73]徐筱杰.计算机辅助药物分子设计[M].北京:化学工业出版社,2004.
[74] KUNTZ I D. Structure-based strategies for drug design and discovery [J]. Science, 257, 1992: 1078-1082.
[75] KUNTZ I D, AGARD D A. Assessment of the role of computations in structural biology [J]. Advance in Protein Chemistry, 2003, 66: 1-25.
[76] MENG E C, GSCHWEND D A, BLANEY J M, et al. Orientational sampling and rigid-body minimization in molecular docking [J]. Proteins, 1993, 17: 266-278.
[77] MORRIS G. M, GOODSELL D S, HUEY R, et al. Distributed automated docking of flexible ligands to proteins: parallel applications of AutoDock 2.4 [J]. Journal of Computational Aided Molecular Design, 1996, 10: 293-304.
[78] GOODSELL D S, OLSON A J. Automated docking of substrates to proteins by simulated annealing [J]. Proteins, 1990, 8: 195-202.
[79] OSTERBERG F, MORRIS G. M, SANNER M F, et al. Automated docking to multiple target structures: incorporation of protein mobility and structural water heterogeneity in AutoDock [J]. Proteins, 2002, 46: 34-40.
[80] KION A E, GLICK M, THOMA M, et al. Finding more needles in the haystack:A simple and efficient method for improving high-throughput docking results [J]. Journal of Medicinal Chemistry, 2004, 47: 2743-2749.
[81] LUTY B A, WASSERMAN Z R, STOUTEN P F W, et al. A molecular mechanics/grid method for evaluation of ligand-receptor interactions [J]. Journal of Computational Chemistry, 1995, 16, 454-464.
[1] KURANDA M J, ROBBINS P W. Chitinase is required for cell separation during growth of Saccharomyces cerevisiae [J]. Journal of Biological Chemistry, 1991, 266: 19758-19767.
[2] WU Y, EGERTON G, UNDERWOOD A P, et al. Expression and secretion of a larval-specific chitinase (family 18 glycosyl hydrolase) by the infective stages of the parasitic nematode, Onchocerca volvulus [J]. Journal of Biological Chemistry 2001, 276: 42557-42564.
[3] VINETZ J M, DAVE S K, SPECHT C A, et al. The chitinase PfCHT1 from the human malaria parasite Plasmodium falciparum lacks proenzyme and chitin-binding domains and displays unique substrate preferences [J]. Proceedings of Natlonal Academy of Sciences USA, 1999, 96: 14061-14066.
[4] CHOHEN E. Chitin synthesis and degradation as targets for pesticide action [J]. Archives of Insect Biochemistry and Physiolgy, 1993, 22: 245-261.
[5] FLACH J, PILET P E, JOLLES P. What's new in chitinase research [J]. Experientia 1992, 48: 701-716
[6] BOOT R G, RENKEMA G H, STRIJLAND A, et al. Cloning of a cDNA encoding chitotriosidase, a human chitinase produced by macrophages [J]. Journal of Biological Chemistry 1995, 270: 26252-26256.
[7] SAKUDA S, ISOGAI A, MATSUMOTO S, et al. Search for microbial insect growth regulators [J]. Journal of Antibiotics 1987, 40: 296-300.
[8] SANDOR E, PUSZTAHELYI T, KARAFFA L, et al. Allosamidin inhibits the fragmentation of Acremonium chrysogenum but does not influence the cephalosporin-C production of the fungus [J]. FEMS Microbiology Letters, 1998, 164: 231-236.
[9] VINETZ J M, VALENZUELA J G, SPECHT C A, et al. Structural insights into the catalytic mechanism of a family 18 exo-chitinase [J]. Current Opinion in Structural Biology, 1997, 7: 637-644.
[10] RENKEMA G H, BOOT R G, STRIJLAND A, et al. Synthesis, sorting, andprocessing into distinct isoforms of human macrophage chitotriosidase. Koopman [J]. European Jouranl of Biochemistry, 1997, 244: 279-285.
[11] BOOT R G, BLOMMAART EF C, SWART E, et al. Structure of Human Chitotriosidase implications for specific inhibitor design and function of mammalian chitinase-like lectins [J]. Journal of Biological Chemistry, 2001, 276: 6770-6778.
[12] ZHU Z, ZHENG T, HOMER R J, et al.Acidic Mammalian Chitinase in Asthmatic Th2 Inflammation and IL-13 Pathway Activation [J]. Science, 2004, 304: 1678-82.
[13] ELIAS J A, HOMER R J, HAMID Q, et al. Chitinases and chitinase-like proteins in TH2 inflammation and asthma [J]. Journal of Allergy and Clinical Immunology, 2005, 116: 497-500.
[14] ZHENG Q C, LI Z S, SUN M, et al. Homology modeling and substrate binding study of Nudix hydrolase Ndx1 from Thermos thermophilus HB8 [J]. Biochemical and Biophysical Research Communications, 2005, 333(3):881-887
[15] XU W, CAI P, YAN M, et al. Molecular Docking of Xylitol and Xylose Isomerase from Thermus thermophilus and Model Analysis [J]. Chemical Journal of Chinese Universities, 2007, 28: 971-973.
[16] HE Y P, HU H R, XU L S. Structure-activity Relationship Studies on 6-Naphthylmethyl Substituted HEPT Derivatives as Non-nucleoside Reverse Transcriptase Inhibitors Based on Molecular Docking [J]. Chemical Journal of Chinese Universities, 2005, 26: 254-258
[17] RAO F V, HOUSTON D R, BOOT R G., et al. Crystal Structures of Allosamidin Derivatives in Complex with Human Macrophage Chitinase [J]. Journal of Biological Chemistry, 2003, 278: 20110-20116
[18] InsightII, User Guid, San Diego: Biosym/MSI (2000)
[19] InsightII, Homology User Guide, San Diego: Accelrys Inc (2000)
[20] ALTSCHUL S F, MADDEN T L, SCHFER A A, et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs [J]. Nucleic Acids Research, 1997, 25:3389-3402
[21] SALI A, OVERINGTON J P. Derivation of rules for comparative proteinmodeling from a database of protein structure alignments [J]. Protein Science, 1994, 3 (9): 1582–1596.
[22] Sali A, Potterton L, Yuan F, et al. Evaluation of comparative protein modeling by MODELLER [J]. Proteins: Structure, Function, and Genetics. 1995, 23 (3): 318–326.
[23] SALI A. Modelling mutations and homologous proteins [J]. Current Opinion in Biotechnology, 1995, 6 (4): 437–451
[24] InsightII Discover3 User Guide, San Diego: Biosym/MSI (2000)
[25] InsightII Profile-3D User Guide, San Diego: Biosym/MSI (2000)
[26] LASKOWSKI RA, MACARTHUR M W, MOSS D S, et al. PROCHECK: a program to check the stereochemical quality of protein structures [J]. (1993) Journal of Applied Crystallography, 1993, 26: 283-291
[27] Binding Site Analysis User Guide, Accelrys Inc., San Dieg, USA 2000.
[28] InsightII Affinity User Guide San Diego: Biosym/MSI (2000)
[29] FRISCH M J, TRUCKS G W, SCHLEGEL H B, et al.Gaussian 03 (Revision A.1) Gaussian Pittsburgh (2003)
[30] InsightII Ludi User Guide San Diego: Biosym/MSI (2000)
[31] JANNICK D B, HENRIK N, GUNNAR V H, et al. Improved prediction of signal peptides: SignalP 3.0. [J]. Journal of Molecular Biology, 2004, 340: 783-795
[32] VAN AALTEN D M, SYNSTAD B, BRUBERG M B, et al. Structure of a two-domain chitotriosidase from Serratia marcescens at 1.9-? resolution [J]. Proceedings of Natlonal Academy of Sciences USA, 2000, 97: 5842-5847.
[33] SAKUDA S. Studies on the chitinase inhibitors,allosamidins [J]. (1996) Chitin Enzymology, 1996, 2: 203-212
[34] BERECIBAR A, GRANDJEAN C, SIRIWARDENA, et al. Synthesis and Biological Activity of Natural Aminocyclopentitol Glycosidase Inhibitors: Mannostatins, Trehazolin, Allosamidins, and Their Analogues [J]. Chemical Reviews, 1999, 99: 779-844
[35] CHOU Y-T, YAO S, CZERWINSKI R, et al. Kinetic Characterization of4444-4454。
Recombinant Human Acidic Mammalian Chitinase [J]. Biochemistry, 2006, 45:
[1] CORRIGAN J J. D-Amino acids in animals [J]. Science, 1969, 164: 142-149.
[2] Corrigan J J, Srinivasan N G. The Occurrence of Certain D-Amino Acids in Insects [J]. Biochemistry,1966,5: 1185-1190.
[3] PANIZZUTTI R. DE MIRANDA J. RIBEIRO C S, et al. A new strategy to decrease N-methyl-d-aspartate (NMDA) receptor coactivation: Inhibition of d-serine synthesis by converting serine racemase into an eliminase [J]. Proceeding of the National Academy of Sciences USA, 2001, 98: 5294-5299.
[4] DE MIRANDA J, SANTORO A, ENGELENDER S, Human serine racemase: moleular cloning, genomic organization and functional analysis [J]. Gene 2000, 256: 183-188.
[5] NAGATA Y, KONNO R, YASUMURA Y, et al. Involvement of D-amino acid oxidase in elimination of free D-amino acids in mice [J]. Biochemical Journal, 1989, 257: 291-292.
[6] HASHIMOTO A, NISHIKAWA T, HAYASHI T, et al. The presence of free D-serine in rat brain [J]. FEBS Letter, 1992, 296: 33-36.
[7] HASHIMOTO A, NISHIKAWA T, OKA T, et al. Endogenous D-serine in rat brain: N-methyl-D-aspartate receptor-related distribution and aging [J]. Journal Neurochemistry, 1993, 60: 783-786.
[8] NAGATA Y, HORIIKE K, MAEDA T. Distribution of free D-serine in vertebrate brains [J]. Brain Research, 1994, 634: 291.
[9] Matsui T, Sekiguchi M, Hashimoto A, Tomita U, Nishikawa T, Wada K. J. Neurochem. 1995, 65: 454.
[10] IVANOVIC A, REILANDER H, LAUBE B, et al. Expression and initial characterization of a soluble glycine binding domain of the N-methyl-D-aspartate receptor NR1 subunit [J]. Journal of Biology Chemistry, 1998, 273: 19933-19937.
[11] MIYAZAKI J, NAKANISHI S, JINGAMI H. Expression and characterization of a glycine-binding fragment of the N-methyl-D-aspartate receptor subunit NR1 [J]. The Biochemical Journal, 1999, 340: 687-692.
[12] CHOI D W, ROTHMAN S M. The role of glutamate neurotoxicity in hypoxic-ischemic neuronal death [J]. Annual Review of Neuroscience, 1990, 13: 171-182.
[13] WOLOSKER H, BLACKSHAW S, SNYDER S H. Serine racemase: a glial enzyme synthesizing D-serine to regulate glutamate-N-methyl-D-aspartate neurotransmission [J]. Proceeding of the National Academy of Sciences USA, 1999 ,96: 13409-13414.
[14] De Miranda J, Santoro A, Engelender S, et al. Human serine racemase: moleular cloning, genomic organization and functional analysis [J]. Gene, 2000, 256: 183-188.
[15] MENGHANG X, YUAN L, DAVID J F, et al. Characterization and localization of a human serine racemase [J]. Molecular Brain Research. 2004, 125: 96-104.
[16] Dixon S M, Li P, Liu R, Slow-binding human serine racemase inhibitors from high-throughput screening of combinatorial libraries [J]. Journal of Medicinal Chemistry, 2006 49: 2388-2397.
[17] Zheng X L, Zhang H X, Sun J Z, et al. Molecular docking study of HIV-1 in/inhibitor in the presence of double metal conditions [J]. Chemical Journal of Chinese University, 2006 27(7): 1298-1302
[18] HU J P, KE G T, CHANG S, et al. Conformational Change of HIV-1 Viral DNAafter Binding with Integrase [J]. Acta Physico-Chimica Sinica, 2008 24(10): 1803-1810.
[19] Insight II user Guide. San Diego: Molecular Simulation Inc. 2000
[20] MORRIS A L, MACARTHUR M W, HUTCHINSON E G., et al. Stereochemical quality of protein structure coordinates [J]. Proteins, 1992, 12: 345-364.
[21] LIANG J, EDELSBRUNNER H, WOODWARD C. Anatomy of protein pockets and cavities: measurement of binding site geometry and implications for ligand design [J]. Protein Science, 1998, 7: 1884-1897.
[22] DAMBORSKY J, PET?EK M, BANá? P, et al. Identification of tunnels in proteins, nucleic acids, inorganic materials and molecular ensembles [J]. Biotechnology Journal, 2007, 2: 62-67.
[23] BECKE A D. Density-functional thermochemistry. III. The role of exact exchange [J] Journal of Chemistry Physics, 1993, 98: 5648-5652.
[24] BECKE A D. Density-functional thermochemistry. I. The effect of the exchange-only gradient correction [J]. Journal of Chemistry Physics, 1992 96: 2155-2160.
[25] BARONE V, COSSI M. Quantum Calculation of Molecular Energies and Energy Gradients in Solution by a Conductor Solvent Model [J]. Journal of Physical Chemistry A, 1998 102: 1995-2001.
[26] FRISCH M. J, TRUCKS G W, SCHLEGEL H B, et al. Gaussian 03 Revision D.01. Pittsburgh PA: Gaussian Inc. 2003
[27] YOSHIMURA T, ESAKI N. Amino acid racemases: functions and mechanisms [J]. Journal of Bioscience Bioengineering, 2003 96:103-109.
[1] CRAVATT B F, GIANG, D K, MAYFIELD S P, et al. Molecular characterization of an enzyme that degrades neuromodulatory fatty-acid amides [J]. Nature, 1996, 384: 83–87.
[2] GIANG D K, CRAVATT, B F. Molecular characterization of human and mouse fatty ccid amide hydrolases [J]. Proceedings of Natlonal Academy of Sciences USA, 1997, 4: 2238–2242.
[3] CHEBROU H, BIGEY F, ARNAUD A, et al. Study of the amidase signature group [J]. Biochimical Biophysica Acta 1996, 1298: 285–293.
[4] DEVANE W A, HANUS L, BREUER A, et al. Isolation and Structure of a Brain Constituent that Binds to the Cannabinoid Receptor [J]. Science, 1992, 258: 1946–1949.
[5] MARTIN B R, MECHOULAM R, RAZDAN, R K. Discovery and Characterization of Endogenous Cannabinoids [J]. Life Science, 1999, 65: 573–595.
[6] DI MARZO V, BISOGNO T, DE PETROCELLIS L, et al. Cannabimimetic Fatty Acid Derivatives: The Anandamide Family and Other“Endocannabinoids”[J]. Current Medicinal Chemistry, 1999, 6: 721–744.
[7] SCHMID H H, SCHMID P C, NATARAJAN V. N-Acylated Glycerophospholipids and Their Derivatives [J]. Progress in Lipid Reseach, 1990, 29: 1–43.
[8] BOGER D L, HENRIKSEN S J, CRAVATT B F. Oleamide: An EndogenousSleep-Inducing Lipid and Prototypical Member of a New Class of Lipid Signaling Molecules [J]. Current Pharmaceutical Design, 1998, 4: 303–314.
[9] CRAVATT B F, LERNER R A, BOGER D L. Structure Determination of an Endogenous Sleep-Inducing Lipid cis-9-Octadecenamide (Oleamide): A Synthetic Approach to the Chemical Analysis of Trace Quantitites of a Natural Product [J]. Journal of American Chemistry Society, 1996, 118: 580–590.
[10] CRAVATT B F, PROSPERO-GARCIA O, SUIZDAK G, et al. A ChemicalCharacterization of a Family of Brain Lipids that Induce Sleep [J]. Science, 1995, 268: 1506–1509.
[11] LAMBERT D M, VANDEVOORDE S, JONSSON K O, et al. The palmitoylethanolamide family: A new class of antiinflammatory agents? [J]. Current Medicinal Chemistry, 2002, 9: 663–674.
[12] RODRIGUEZ DE FONSECA F, NAVARRO M, GOMEZ R, et al (2001) An anorexic lipid mediator regulated by feeding [J]. Nature, 2001, 414: 209–212.
[13] CRAVATT B F, DEMAREST K, PATRICELLI M P, et al. Supersensitivity to Anandamide and Enhanced Endogenous Cannabinoid Signaling in Mice Lacking Fatty Acid Amide Hydrolase [J]. Proceedings of Natlonal Academy of Sciences USA, 2001, 98: 9371–9376.
[14] LICHTMAN A H, SHELTON C C, ADVANI T, et al. Mice Lacking Fatty Acid Amide Hydrolase Exhibit a Cannabinoid Receptor-Mediated Phenotypic Hypoalgesia [J]. Pain, 2004, 109: 319–327.
[15] CRAVATT B F, SAGHATELIAN A, HAWKINS E G, et al. Functional Disassociation of the Central and Peripheral Fatty Acid Amide Signaling Systems [J]. Proceedings of National Academy of Sciences USA, 2004, 101: 10821–10826.
[16] KARSAK M, GAFFAL E, DATE R, et al. Attenuation of Allergic Contact Dermatitis Through the Endocannabinoid System [J]. Science, 2007, 316: 1494–1497.
[17] (a) HUITRO′N-RESE′NDIZ S, GOMBART L, CRAVATT B F, et al. Effect of Oleamide on Sleep and Its Relationship to Blood Pressure, Body Temperature, and Locomotor Activity in Rats [J]. Exprimental Neurology, 2001, 172: 235–243. (b) HUITRO′N-RESE′NDIZ S, SANCHEZ-ALAVEZ M, WILLS D N, et al. Characterization of the Sleep-Wake Patterns in Mice Lacking Fatty Acid Amide Hydrolase [J]. Sleep, 2004, 27: 857–865.
[18] LEUNG D, HARDOUIN C, BOGER D L, et al. Discovering potent and selective reversible inhibitors of enzymes in complex proteomes [J]. Nature Biotechnology, 2003, 21: 687–691.
[19] BOGER D L, SATO H, LERNER A E, et al. Exceptionally potent inhibitors of fatty acid amide hydrolase: The enzyme responsible for degradation of endogenous oleamide and anandamide [J]. Proceedings of National Academy of Sciences USA, 2000, 97: 5044–5049.
[20] AHN K, JOHNSON D S, FITZGERALD L R, et al Novel mechanistic class of fatty acid amide hydrolase inhibitors with remarkable selectivity [J]. Biochemistry, 2007, 46: 13019–13030.
[21] ZHENG Q C, LI Z S, SUN M, et al. Homology modeling and substrate binding study of Nudix hydrolase Ndx1 from Thermos thermophilus HB8 [J]. Biochemical and Biophysical Research Communications, 2005, 333(3):881-887.
[22] XU W, CAI P, YAN M, et al. Molecular Docking of Xylitol and Xylose Isomerase from Thermus thermophilus and Model Analysis [J]. Chemical Journal of Chinese Universities, 2007, 28: 971-973.
[23] HE Y P, HU H R, XU L S. Structure-activity Relationship Studies on 6-Naphthylmethyl Substituted HEPT Derivatives as Non-nucleoside Reverse Transcriptase Inhibitors Based on Molecular Docking [J]. Chemical Journal of Chinese Universities, 2005, 26: 254-258.
[24] RAO F V, HOUSTON D R, BOOT R G., et al. Crystal Structures of Allosamidin Derivatives in Complex with Human Macrophage Chitinase [J]. Journal of Biological Chemistry, 2003, 278: 20110-20116.
[25] BAIROCH A, APWEILER R. The SWISS-PORT protein sequence data bank and its supplement TrEMBL [J]. Nucleic Acids Research, 1997, 25 (1): 31-36.
[26] ALTSCHUL S F, MADDEN T L, SCHFER A A, et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs [J]. Nucleic Acids Research, 1997, 25:3389-3402.
[27] SALI A, OVERINGTON J P. Derivation of rules for comparative protein modeling from a database of protein structure alignments [J]. Protein Science, 1994, 3 (9): 1582–1596.
[28] SALI A, BLUNDELL T L. Comparative protein modeling by satisfaction of spatial restraints [J]. Journal of Molecular Biology, 1993:234: 779-815.
[29] Sali A, Potterton L, Yuan F, et al. Evaluation of comparative protein modeling by MODELLER [J]. Proteins: Structure, Function, and Genetics. 1995, 23 (3): 318–326.
[30] SALI A. Modelling mutations and homologous proteins [J]. Current Opinion in Biotechnology, 1995, 6 (4): 437–451.
[31] CASE D A, CHEATHAM T E, III, DARDEN T, et al. The Amber bimolecular simulation programs [J]. Journal of Computational Chemistry, 2005, 26: 1668-1688.
[32] DUAN Y, WU C, CHOWDHURY S, et al. A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations [J]. J Computational Chemistry, 2003, 24: 1999–2012.
[33] JORGENSEN W L, CHANDRASKHAR J, MADURA J, et al. Comparison of simple potential functions for simulating liquid water [J]. Journal of Chemistry Physics, 1983, 79: 926-935.
[34] RYCHAERT J P, CICCOTTI G, BERENDSEN H J C. Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes [J]. Journal of Computational Physics, 1977, 23: 327–341.
[35] InsightII Profile-3D User Guide, San Diego: Biosym/MSI (2000)
[36] LASKOWSKI RA, MACARTHUR M W, MOSS D S, et al. PROCHECK: a program to check the stereochemical quality of protein structures [J]. (1993) Journal of Applied Crystallography, 1993, 26: 283-291.
[37] SIPPL M J. Recognition of errors in three-dimensional structures of proteins [J]. Proteins, 1993, 17: 355–362.
[38] Binding Site Analysis User Guide, Accelrys Inc, San Dieg, USA 2000
[39] InsightII Affinity User Guide San Diego: Biosym/MSI (2000)
[40] FRISCH M J, TRUCKS G W, SCHLEGEL H B, et al.Gaussian 03 (Revision A.1) Gaussian Pittsburgh (2003)
[41] InsightII Ludi User Guide San Diego: Biosym/MSI (2000)
[42] BRACEY M H, HANSON M A, MASUDA K R, et al. Structural adaptations in a membrane enzyme that terminates endocannabinoid signaling [J]. Science, 2002,298, 1793–1796.
[43] DEUTCH D G, LIN S, HILL W A, et al. A Fatty acid sulfonyl fluorides inhibit anandamide metabolism and bind to the cannabinoid Receptor [J]. Biochemical and Biophysical Research Communications, 1997, 231: 217–221.
[44] SEGALL Y, QUISTAD G B, NOMURA D K, et al. Arachidonylsulfonyl derivatives as cannabinoid CB1 receptor and fatty Acid amide hydrolase inhibitors [J]. Bioorganic and Medicinal Chemistry Letters, 2003, 13: 3301–3303.
[45] DEUTCH D G, OMEIR R, ARREAZA G, et al. Methyl arachidonyl fluorophosphonate: a potent irreversible inhibitor of anandamide amidase [J]. Biochemical Pharmacology, 1997, 53: 255–260.
[46] KOUTEK B, PRESTWICH G D, HOWLETT A C, et al. Inhibitors of arachidonoyl ethanolamide hydrolysis [J]. Journal of Biological Chemistry, 1994, 269: 22937–22940.
[47] De Petrocellis L, Melck D, Ueda N, et al. Novel inhibitors of brain, neuronal, and basophilic anandamide amidohydrolase [J]. Biochemical and Biophysical Research Communications, 1997, 231: 82–88.
[48] LICHTMAN A H, LEUNG D, SHELTON C, et al. Reversible inhibitors of fatty acid amide hydrolase that promote analgesia: evidence for an unprecented combination of potency and selectivity [J]. Journal of Pharmacology and Experimental Therapeutics, 2004, 311: 441–448.
[49] MYLLYMA¨KI M J, SAARIO S M, KATAJA A, et al. Design, synthesis, and in vitro evaluation of carbamate derivatives of 2-benzoxazolyl- and 2-benzothiazolyl-(3-hydroxyphenyl)-methanones as novel fatty acid amide hydrolase inhibitors [J]. Journal of Medicinal Chemistry, 2007, 50: 4236–4242.
[50] SIT, S-Y XIE, K WO Patent 087569, 2002
[51] PATEL S, WOHLFEIL E R, RADEMACHER D J, et al. The general anesthetic propofol increases brain N-arachidonylethanolamine (anandamide) content and inhibits fatty acid amide hydrolase [J]. British Journal of Pharmacology, 2003, 139: 1005–1013.
[52] SEIERSTAD M, BREITENBUCHER J G. Discovery and Development of FattyAcid Amide Hydrolase (FAAH) inhibitors [J]. Journal of Medicinal Chemistry, 2008, 51: 7327-7343.
[1] SAUVE A A, WOLBERGER C, SCHRAMM V L, et al. The Biochemistry of Sirtuins [J]. Annual Review of Biochemistry, 2006, 75: 435-465.
[2] TANNY J C, DOWD, G J, HUANG J, et al. An Enzymatic Activity in the Yeast Sir2 Protein that Is Essential for Gene Silencing [J]. Cell, 1999, 99: 735-745.
[3] LONGO V D, KENNEDY B K. Sirtuins in Aging and Age-Related Disease [J]. Cell, 2006, 126: 257-268.
[4] LI W, ZHANG B, TANG J, et al. Sirtuin 2, a Mammalian Homolog of Yeast Silent Information Regulator-2 Longevity Regulator, Is an Oligodendroglial Protein That Decelerates Cell Differentiation through Deacetylating -Tubulin [J]. Journal of Neuroscience, 2007, 27: 2606-2616.
[5] CHEN D, GUARENTE L. SIR2: a potential target for calorie restriction mimetics [J]. Trends in Molecular Medicine, 2007, 13: 64-71.
[6] MICHAN S, SINCLAIR A Sirtuins in mammals: insights into their biological function [J]. Biochemical Journal, 2007, 404: 1-13.
[7] JOHN M D. The Sir2 family of protein deacetylases [J]. Current Opinion in Chemical Biology, 2005, 9: 431-440.
[8] YAMAMOTO H, SCHOONJANS K, AUWERX J. Sirtuin Functions in Health and Disease [J]. Molecular Endocrinology, 2007, 21, 1745-1755.
[9] ZHAO K, CHAI X, CLEMENTS A, et al. Structure and autoregulation of the yeast Hst2 homolog of Sir2 [J]. Natural Structural Biology, 2003a, 10: 864-871.
[10] MICHAEL D J, JOHN M D. Structural Identification of 2'- and 3'-O-Acetyl-ADP-ribose as Novel Metabolites Derived from the Sir2 Family of -NAD+-dependent Histone/Protein Deacetylases [J]. Journal of Biological Chemistry, 2002, 277: 18535-18544.
[11] AVALOS J L, CELIC I, MUHAMMAD S, et al. Structure of a Sir2 Enzyme Bound to an Acetylated p53 Peptide [J]. Molecular Cell, 2002, 10: 523-535.
[12] AVALOS J L, BOEKE J D, WOLBERGER, C. Structural Basis for the Mechanism and Regulation of Sir2 Enzymes [J]. Molecular Cell, 2004, 13:639-648.
[13] CHANG J H, KIM H C, HWANG K Y, et al. Structural Basis for the NAD-dependent Deacetylase Mechanism of Sir2 [J]. Journal of Biological Chemistry, 2002, 277: 34489-34498.
[14] MIN J, LANDRY J, STERNGLANZ R, et al. Crystal Structure of a SIR2 Homolog–NAD Complex [J]. Cell, 2001, 105: 269-279.
[15] ZHAO K, CHAI X, CLEMENTS A, et al. Structure of the Yeast Hst2 Protein Deacetylase in Ternary Complex with 2′-O-Acetyl ADP Ribose and Histone Peptide [J]. Structure 2003b, 11: 1403-1411.
[16] FINNIN M S, DONIGIAN J R, PAVLETICH N P. Structure of the histone deacetylase SIRT2 [J]. Nature Structural Biology, 2001, 8: 621-623.
[17] TANNER K G, LANDRY J, STERNGLANZ R, et al. The Sir2 protein family: A novel deacetylase for gene silencing and more [J]. The Proceeding of the National Academy of Science USA, 2000, 97: 14178-14182.
[18] HOFF K G, AVALOS J L, SENS K, et al. Insights into the Sirtuin Mechanism from Ternary Complexes Containing NAD+ and Acetylated Peptide [J]. Structure, 2006, 14: 1231-1240.
[19] SAUVE A A, CELIC I, AVALOS J, et al. Chemistry of gene silencing: the mechanism of NAD+-dependent deacetylation reactions [J]. Biochemistry, 2001, 40: 15456-15463.
[20] BECKE A D. Density-functional thermochemistry III The role of exact exchange [J]. Journal of Chemical Physics, 1993, 98: 5648-5652.
[21] BECKE A D. Density-functional thermochemistry I The effect of the exchange-only gradient correction [J]. Journal of Chemical Physics, 1992, 96: 2155-2160.
[22] BECKE A D. Density-functional thermochemistry II The effect of the Perdew–Wang generalized-gradient correlation correction [J]. Journal of Chemical Physics, 1992, 97: 9173-9177.
[23] LEE C, YANG W, PARR R G. Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density [J]. PhysicalReview B, 1988, 37: 785-789.
[24] (a) Siegbahn P E M, Blomberg M R A. A Quantum Chemical Approach to the Study of Reaction Mechanisms of Redox-Active Metalloenzymes [J]. Journal of Physical Chemistry B, 2001, 105: 9375-9386. (b) Siegbahn P E M. Mechanisms of metalloenzymes studied by quantum chemical methods [J]. Quarterly Reviews of Biophysics, 2003, 36: 91-145. (c) Himo F, Siegbahn P E M. Quantum chemical studies of radical-containing enzymes [J]. Chemical Reviews. 2003, 103: 2421-2456.
[25] Biopolymer User Guide, Accelrys Inc., San Diego, USA 1999.
[26] AVALOS J L, BEVER K M, WOLBERGER C. Mechanism of sirtuin inhibition by nicotinamide: altering the NAD(+) cosubstrate specificity of a Sir2 enzyme [J]. Molecular Cell, 2005, 17: 855-868.
[27] SMITH B C, DENU J M. Sir2 Deacetylases Exhibit Nucleophilic Participation of Acetyl-Lysine in NAD+ Cleavage [J]. Journal of American Chemical Society, 2007, 129: 5802-5803.
[28] InsightII, version 98.0.San Diego: Accelrys Inc. 1998.
[29] Discover3 User Guide, Accelrys Inc., San Diego, USA 1999.
[30] FRISCH M J, TRUCKS G W, SCHLEGEL H B, et al.Gaussian 03 (Revision A.1) Gaussian Pittsburgh (2003)
[31] (a) CAMMI R, MENNUCCI B, TOMASI J. Second-Order M ller-Plesset Analytical Derivatives for the Polarizable Continuum Model Using the Relaxed Density Approach [J]. Journal of Physical Chemistry A, 1999, 103: 9100-9108; (b) CAMMI R, MENNUCCI B, TOMASI, J. Evaluation of Geometries and Properties of Excited Molecules in Solution: A Tamm-Dancoff Model with Application to 4-Dimethylaminobenzonitrile, Journal of Physical Chemistry A, 2000, 104: 5631-5637; (c) COSSI M, REGA N, SCALMANI G, et al. Polarizable dielectric model of solvation with inclusion of charge penetration effects, Journal of Chemical Physics, 2001, 114: 5691-5701; (d) COSSI M, SCALMANI G, REGA N, et al. New developments in the polarizable continuum model for quantum mechanical and classical calculations on molecules in solution [J]. Journal ofChemical Physics, 2002, 117: 43-54.
[32] HOPMANN K H, HALLBERG B M, HIMO F. Catalytic Mechanism of Limonene Epoxide Hydrolase: a Theoretical Study [J]. Journal of American Chemical Society, 2005, 127: 14339-14347.
[33] HIMO F, SIEGBAHN P E M. Catalytic Mechanism of Glyoxalase I: A Theoretical Study [J]. Journal of American Chemical Society, 2001, 123: 10280-10289.
[34] HIMO F. Quantum chemical modeling of enzyme active sites and reaction mechanisms [J]. Theoretical Chemistry Accounts:Theory, Computation, and Modeling, 2006, 116: 232-240.
[35] CURTISS L A, KRISHNAN R, REDFERN P C, et al. Assessment of Gaussian-2 and density functional theories for the computation of enthalpies of formation [J]. Journal of Chemical Physics, 1997, 106: 1063-1080.
[36] SLAMA J T, SIMMONS A M. Carbanicotinamide Adenine Dinucleotide: Enzymological Properties Synthesis and of a Carbocyclic Analogue of Oxidized Nicotinamide Adenine Dinucleotide [J]. Biochemistry, 1988, 27: 183-193.
[37] ZHAO K, HARSHAW R, CHAI X, et al. Structural basis for nicotinamide cleavage and ADP-ribose transfer by NAD+-dependent Sir2 histone/protein deacetylases [J]. The Proceeding of the National Academy of Science USA, 2004, 101: 8563-8568.
[38] SMITH B C, DENU J M. Sir2 Protein Deacetylases: Evidence for Chemical Intermediates and Functions of a Conserved Histidine [J]. Biochemistry, 2006, 45: 272-282.
[39] HAWSE W F, HOFF K G, FATKINS D G, et al. Structural insights into intermediate steps in the Sir2 deacetylation reaction [J]. Structure, 2008, 16: 1368-1377.
[40] ARMSTRONG C M, KAEBERLEIN M, IMAI S I, et al. Mutations in Saccharomyces cerevisiae Gene SIR2 Can Have Differential Effects on In Vivo Silencing Phenotypes and In Vitro Histone Deacetylation Activity [J]. Molecular Biological Cell, 2002, 13: 1427-1438.
[41] ZHU X, HEINE A, MONNAT F, et al. Structural Basis for Antibody Catalysis of a Cationic Cyclization Reaction [J]. Journal of Molecular Biology, 2003, 329: 69-83.
[42] SANDERS B D, ZHAO K H, SLAMA J T, et al. Structural Basis for Nicotinamide Inhibition and Base Exchange in Sir2 Enzymes [J]. Molecular Cell, 2007, 25: 463-472.