碱基对AT/GC与组氨酸/天冬酰胺侧链间氢键作用的优势位点
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摘要
采用B3LYP/6-31+G(d,p)方法优化得到18个由组氨酸(His)/天冬酰胺(Asp)侧链分别与2种Watson-Crick碱基对(AT/GC)形成稳定构型.对18个稳定构型使用M06-2X-D3/aug-cc-pVDZ方法计算得到氢键复合物的结合能.在此基础上,采用同样的量子化学计算方法加上极化连续介质(PCM)模型计算得到氢键复合物在水相中的结合能.结果表明,碱基对AT与组氨酸侧链/天冬酰胺侧链氢键作用的较稳定作用位点是site 1与site 3;碱基对GC的较稳定作用位点是site 1与site 4.分子中原子(AIM)与自然键轨道(NBO)分析计算所得的结果与结合能强弱顺序一致.
The optimal structures of eighteen hydrogen-bonded complexes,containing asparagine,histidine side chains and two Watson-Crick bases,were obtained at the B3 LYP/6-31+ G(d,p)level.The binding energies of the 18 stable hydrogen-bonded complexes were calculated using the M06-2 XD3/aug-cc-pVDZ method.On this basis,the stable structures and interaction energies of hydrogenbonded complexes in aqueous phase were calculated by using the same quantum chemistry calculation level and polarized continuum(PCM)model.The results showed that the stable sites of hydrogen bonding between Watson-Crick bases AT and asparagine and histidine side chains are site1 and site3;the stable sites of hydrogen bonding between Watson-Crick bases GC and asparagine and histidine are site1 and site4.The order of stability of the hydrogen-bonded complexes calculated from the analysis of atoms in molecules(AIM)and natural bond orbital(NBO)is consistent with the order of stability obtained from the binding energies.
The optimal structures of eighteen hydrogen-bonded complexes,containing asparagine,histidine side chains and two Watson-Crick bases,were obtained at the B3 LYP/6-31+ G(d,p)level.The binding energies of the 18 stable hydrogen-bonded complexes were calculated using the M06-2 XD3/aug-cc-pVDZ method.On this basis,the stable structures and interaction energies of hydrogenbonded complexes in aqueous phase were calculated by using the same quantum chemistry calculation level and polarized continuum(PCM)model.The results showed that the stable sites of hydrogen bonding between Watson-Crick bases AT and asparagine and histidine side chains are site1 and site3;the stable sites of hydrogen bonding between Watson-Crick bases GC and asparagine and histidine are site1 and site4.The order of stability of the hydrogen-bonded complexes calculated from the analysis of atoms in molecules(AIM)and natural bond orbital(NBO)is consistent with the order of stability obtained from the binding energies.
引文
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[2]林雪飞,孙成科,杨思娅,等.o-6-鸟嘌呤和o-4-胸腺嘧啶甲基化与DNA碱基异常氢键作用的理论研究[J].化学学报,2011,69(23):2787-2795.
[3]LI Y,WANG C S.Rapid evaluation of the binding energies between peptide amide and DNA base[J].Journal of Computational Chemistry,2011,32(13):2765-2773.
[4]LI S S,HUANG C Y,HAO J J,et al.A polarizable dipole-dipole interaction model for evaluation of the interaction energies for N-H…OC and C-H…OC hydrogen-bonded complexes[J].Journal of Computational Chemistry,2014,35(6):415-426.
[5]WANG Z X,WU C,LEI H,et al.Accurate ab initio study on the hydrogen-bond pairs in protein secondary structures[J].Journal of Chemical Theory&Computation,2007,3(4):1527.
[6]刘帅,李书实,刘冬佳,等.碱基腺嘌呤与多肽酰胺间氢键作用的最佳位点[J].物理化学学报,2013,29(12):2551-2557.
[7]LAUDO M D,AND S R W,WETMORE S D.Effects of hydrogen bonding on the acidity of uracil[J].Journal of Physical Chemistry A,2003,107(48):10406-10413.
[8]VARGAS R,GARZA J,FRIESNER R A,et al.Reply to comment on“Strength of the NH…OC bonds in formamide and N-Methylacetamide dimers”[J].Journal of Physical Chemistry A,2005,109(31).
[9]吴建盛,胡栋,晏善成,等.蛋白质-核酸复合物氢键与范德华力作用位点分析[J].东南大学学报(自然科学版),2011,41(4):778-783.
[10]SEEMAN N C,ROSENBERG J M,RICH A.Sequence-Specific recognition of double helical nucleic acids by proteins[J].Proceedings of the National Academy of Sciences of the United States of America,1976,73(3):804-812.
[11]GU J D,WANG J,LESZCZYNSKI J.Molecular basis of the recognition process:hydrogen-bonding patterns in the guanine primary recognition site of ribonuclease T1[J].Journal of Physical Chemistry B,2006,110(27):13590-13596.
[12]SUN C L,ZHANG Y,JIANG X N,et al.A new method for quick predicting the strength of intermolecular hydrogen bonds[J].中国科学:化学,2009,52(2):153-160.
[13]王长生,黄翠英.核酸碱基间氢键距离和作用能的快速预测[J].辽宁师范大学学报(自然科学版),2016,39(3):368-372.
[14]JIANG X N,SUN C L,WANG C S.A scheme for rapid prediction of cooperativity in hydrogen bond chains of formamides,cetamides,and N-Methyl formamides[J].Journal of Computational Chemistry,2010,31(7):1410-1420.
[15]PANECKA J,HAVRILA M,REBLOVA K,et al.Role of s-turn2in the structure,dynamics,and function of mitochondrial ribosomal A-site.A bioinformatics and molecular dynamics simulation study[J].Journal of Physical Chemistry B,2014,118(24):6687-6701.
[16]KRAUTBAUER R,CLAUSEN-SCHAUMANN H,GAUB H E,et al.Cisplatin changes the mechanics of single DNA molecules[J].Angewandte Chemie International Edition,2010,39(21):3912-3915.
[17]李书实,姜笑楠,王长生.含酰胺和尿嘧啶的氢键复合物的三体效应[J].高等学校化学学报,2014,35(11):2403-2409.
[18]刘冬佳,王长生.取代基对1-甲基尿嘧啶与N-甲基乙酰胺氢键复合物中氢键强度的影响[J].物理化学学报,2012,28(12):2809-2816.
[19]RADHAKRISHNAN M L,TIDOR B.Specificity in molecular design:A physical framework for probing the determinants of binding specificity and promiscuity in a biological environment[J].Journal of Physical Chemistry B,2007,111(47):13419-13454.
[20]BETANCOURT M R,THIRUMALAI D.Protein sequence design by energy landscaping[J].Journal of Physical Chemistry B,2002,106(3):599-609.
[21]樊迪,刘振明,金宏威,等.基于结合位点的辅酶A结合蛋白家族的分类[J].物理化学学报,2011,27(5):1223-1231
[22]智胜德.核酸碱基与氨基酸侧链之间氢键相互作用研究和基于药物靶标FXR的药物筛选模型的设计[D].中国科学院上海药物研究所,中国科学院上海生命科学研究院上海药物研究所,中国科学院上海生命科学研究院,2004.
[23]FRISCH M J,TRUCKS G W,SCHLEGEL H B,et al.Gaussian 09,D.01[CP].Wallingford CT:Gaussian Inc,2013.
[24]LU T,CHEN F.Multiwfn:a multifunctional wavefunction analyzer[J].Journal of Computational Chemistry,2012,33(5):580-672.