乙型流感病毒质子通道蛋白BM2的分子动力学模拟
|
摘要
流行性感冒(简称流感)是由流感病毒引起的急性呼吸道感染,每次大爆发在人群中有着显著的发病率和一定的致死率。乙型流感病毒引起的疾病占流感病毒的50%,会呈现周期性的大爆发,感染对象主要是老人、小孩以及孕妇等免疫力相对较低的人群。所以乙型流感病毒的研究非常重要。乙型流感病毒质子通道蛋白BM2是由四个单次跨膜蛋白单体组成的同源四聚体,BM2在病毒复制的过程中起了非常关键的作用。其跨膜段的HXXXW基序是M2蛋白形式其质子传递的选择性和门控性的关键氨基酸。阻断BM2的质子通道活性,将能在病毒感染早期有效控制病毒的复制,所以BM2有希望成为抗乙型流感病毒的药物靶点,所以对其的研究将成为对抗流感病毒研制的理论基础。
分子动力学模拟是建立在牛顿力学的基础上的一种分子模拟方法,通过求解牛顿力学方程可以获得一些体系随时间变化的热力学和动力学性质。分子动力学模拟是一种对膜蛋白这种通过实验手段研究比较困难的生物体系的有效的研究方法。在生物体系中较常用的力场中,本文使用GROMACS4.5软件,选择了GROMOS87力场以及OPLS力场分别对BM2蛋白进行了25ns的分子动力学模拟。通过模拟结果的对比,可以反映两个力场在膜蛋白模拟的应用上的差异和优劣,OPLS力场更加精细的描绘了蛋白的运动情况,相对更加精细的反映水分子的分布情况。希望对分子动力学模拟的力场选择方案提出了一定的建议。OPLS力场更加精细的描绘了通道半径的变化情况,以及更加精细的反映水分子的分布情况。BM2的跨膜段PHE5和TRP23的侧链将通道堵住,这些氨基酸附近的通道半径都小于水分子半径,分别起到了N端和C端的门的作用。水分子通过PHE5、HIS19和TRP23需要越过更高的能垒。
Flu is caused by influenza virus inflection, which accompanies a significant level of morbidity and mortality. Influenza virus B is an important constituent of human seasonal flu that accounts for about 50% of all influenza disease in recent years, which causes pandemic disease periodically. Due to willing to control actions in the event of a pandemic, it is very important to do some research on influenza virus B. BM2, the proton channel of influenza virus B, is a single-span membrane protein, which is a homotetramer in its native state. BM2 is responsible for acidizing virus and releasing the vRNA. The HXXXW sequence motif in the transmembrane domain is essential for pH sensing and channel gating.
Molecular dynamics simulations is a method establishing a molecular simulation on the basis of Newtonian mechanics. By solving the Newtonian mechanical equations can obtain thermodynamic and kinetic properties changing over time. We simulated BM2 for 25ns respectively under GROMOS87 and OPLS force field by using GROMACS 4.5. By the comparation of the results, we noticed that there are some similarity but also much more discrepancy in the application of the two force field. OPLS force field has better performance in simulation, because of the elavorate characteristcs of protein movements and water distribution. The side chain of PHE5 and TRP23 in BM2 transmembrane block the channel, and near these amino acids, the channel radius is smaller than the radius of the water molecules. PHE5 and TRP23 play the role of gate respectively, for the N-terminal and C-terminal . Potentials of mean force for the water along the z axis of the BM2 pore has shown that it has to pass over a much higher energy barrier, which proves the reason for water absence shown by the water density figure.
分子动力学模拟是建立在牛顿力学的基础上的一种分子模拟方法,通过求解牛顿力学方程可以获得一些体系随时间变化的热力学和动力学性质。分子动力学模拟是一种对膜蛋白这种通过实验手段研究比较困难的生物体系的有效的研究方法。在生物体系中较常用的力场中,本文使用GROMACS4.5软件,选择了GROMOS87力场以及OPLS力场分别对BM2蛋白进行了25ns的分子动力学模拟。通过模拟结果的对比,可以反映两个力场在膜蛋白模拟的应用上的差异和优劣,OPLS力场更加精细的描绘了蛋白的运动情况,相对更加精细的反映水分子的分布情况。希望对分子动力学模拟的力场选择方案提出了一定的建议。OPLS力场更加精细的描绘了通道半径的变化情况,以及更加精细的反映水分子的分布情况。BM2的跨膜段PHE5和TRP23的侧链将通道堵住,这些氨基酸附近的通道半径都小于水分子半径,分别起到了N端和C端的门的作用。水分子通过PHE5、HIS19和TRP23需要越过更高的能垒。
Flu is caused by influenza virus inflection, which accompanies a significant level of morbidity and mortality. Influenza virus B is an important constituent of human seasonal flu that accounts for about 50% of all influenza disease in recent years, which causes pandemic disease periodically. Due to willing to control actions in the event of a pandemic, it is very important to do some research on influenza virus B. BM2, the proton channel of influenza virus B, is a single-span membrane protein, which is a homotetramer in its native state. BM2 is responsible for acidizing virus and releasing the vRNA. The HXXXW sequence motif in the transmembrane domain is essential for pH sensing and channel gating.
Molecular dynamics simulations is a method establishing a molecular simulation on the basis of Newtonian mechanics. By solving the Newtonian mechanical equations can obtain thermodynamic and kinetic properties changing over time. We simulated BM2 for 25ns respectively under GROMOS87 and OPLS force field by using GROMACS 4.5. By the comparation of the results, we noticed that there are some similarity but also much more discrepancy in the application of the two force field. OPLS force field has better performance in simulation, because of the elavorate characteristcs of protein movements and water distribution. The side chain of PHE5 and TRP23 in BM2 transmembrane block the channel, and near these amino acids, the channel radius is smaller than the radius of the water molecules. PHE5 and TRP23 play the role of gate respectively, for the N-terminal and C-terminal . Potentials of mean force for the water along the z axis of the BM2 pore has shown that it has to pass over a much higher energy barrier, which proves the reason for water absence shown by the water density figure.
引文
1. Garcia-Garcia, J. and C. Ramos, [Influenza, an existing public health problem]. Salud Publica Mex, 2006. 48(3): p. 244-67.
2. Centers for Diease Control and Prevention http://www.cdc.gov/flu/about/qa/disease.htm.
3. Horsfall, F.L., et al., The nomenclature of influenza. The Lancet, 1940. 236(6110): p. 413-414.
4. Taylor, R., Studies on survival of influenza virus between epidemics and antigenic variants of the virus. American Journal of Public Health, 1949. 39(2): p. 171.
5. Taylor, R., A further note on 1233 (“influenza C”) virus. Archives of Virology, 1951.4(4): p. 485-500.
6. Potter, C.W., A history of influenza. Journal of applied microbiology, 2001. 91(4): p. 572-579.
7. Mills, C.E., J.M. Robins, and M. Lipsitch, Transmissibility of 1918 pandemic influenza.Nature, 2004. 432(7019): p. 904-6.
8. Fraser, C., et al., Influenza transmission in households during the 1918 pandemic. AmJ Epidemiol, 2011. 174(5): p. 505-14.
9. Gambotto, A., et al., Human infection with highly pathogenic H5N1 influenza virus. The Lancet, 2008. 371(9622): p. 1464-1475.
10. VG, D. and高子珍,丙型流感病毒.国外医学(微生物学分册), 1985. 1.
11. Mubareka, S. and P. Palese, Influenza virus: The biology of a changing virus. Influenza Vaccines for the Future, 2011: p. 3-26.
12. Smith, W., Cultivation of the virus of influenza. British Journal of Experimental Pathology, 1935. 16(6): p. 508.
13. Smith, W., et al., A Virus obtained from influenza patients. Reviews in Medical Virology, 1995. 5(4): p. 187-191.
14. Viruses, I.C.o.T.o., et al., Virus taxonomy: seventh report of the International Committee on Taxonomy of Viruses. 2000: Academic Press.
15. Toyoda, T., et al., Molecular assembly of the influenza virus RNA polymerase: determination of the subunit-subunit contact sites. Journal of general virology, 1996. 77(9): p.2149.
16. Biswas, S.K. and D.P. Nayak, Mutational analysis of the conserved motifs of influenzaA virus polymerase basic protein 1. Journal of virology, 1994. 68(3): p. 1819.
17. Guilligay, D., et al., The structural basis for cap binding by influenza virus polymerase subunit PB2. Nature structural & molecular biology, 2008. 15(5): p. 500-506.
18. Liu, Y.F., et al., Structure-function studies of the influenza virus RNA polymerase PA subunit. Science in China Series C: Life Sciences, 2009. 52(5): p. 450-458.
19. Fodor, E., et al., A single amino acid mutation in the PA subunit of the influenza virus RNA polymerase inhibits endonucleolytic cleavage of capped RNAs. Journal of virology, 2002. 76(18): p. 8989.
20. Kawaguchi, A., T. Naito, and K. Nagata, Involvement of influenza virus PA subunit inassembly of functional RNA polymerase complexes. Journal of virology, 2005. 79(2): p. 732.
21. Huarte, M., et al., Threonine 157 of influenza virus PA polymerase subunit modulates RNA replication in infectious viruses. Journal of virology, 2003. 77(10): p. 6007.
22. Krug, R. and R. Lamb, Orthomyxoviridae: the viruses and their replication. Fields Virology., 2001.
23. Schmitt, A.P. and R.A. Lamb, Influenza virus assembly and budding at the viral budozone. Advances in virus research, 2005. 64: p. 383-416.
24. Skehel, J.J. and D.C. Wiley, Receptor binding and membrane fusion in virus entry: the influenza hemagglutinin. Annual review of biochemistry, 2000. 69(1): p. 531-569.
25. Colman, P., J. Varghese, and W. Laver, Structure of the catalytic and antigenic sites in influenza virus neuraminidase. Nature, 1983. 303(5912): p. 41-44.
26. Memorandum, W., A revision of the system of nomenclature for influenza viruses: a WHO memorandum. Bull World Health Organ, 1980. 58: p. 585-591.
27. Hinshaw, V., et al., Antigenic and genetic characterization of a novel hemagglutinin subtype of influenza A viruses from gulls. Journal of virology, 1982. 42(3): p. 865.
28. Kawaoka, Y., et al., Molecular characterization of a new hemagglutinin, subtype H14, of influenza A virus. Virology, 1990. 179(2): p. 759-767.
29. R HM, C., et al., Characterization of a novel influenza hemagglutinin, H15: criteria for determination of influenza A subtypes. Virology, 1996. 217(2): p. 508-516.
30. Fouchier, R.A.M., et al., Characterization of a novel influenza A virus hemagglutinin subtype (H16) obtained from black-headed gulls. Journal of virology, 2005. 79(5): p. 2814.
31. Whittaker, G.R., Intracellular trafficking of influenza virus: clinical implications for molecular medicine. Expert Reviews in Molecular Medicine, 2001. 3(05): p. 1-13.
32. Lakadamyali, M., et al., Visualizing infection of individual influenza viruses. Proceedings of the National Academy of Sciences of the United States of America, 2003. 100(16): p. 9280.
33. Hay, A., et al., The molecular basis of the specific anti-influenza action of amantadine.The EMBO journal, 1985. 4(11): p. 3021.
34. Lamb, R.A., S.L. Zebedee, and C.D. Richardson, Influenza virus M2 protein is an integral membrane protein expressed on the infected-cell surface. Cell, 1985. 40(3): p. 627-633.
35. Helenius, A., Unpacking the incoming influenza virus. Cell, 1992. 69(4): p. 577.
36. Martin, K. and A. Helenius, Transport of incoming influenza virus nucleocapsids into the nucleus. Journal of virology, 1991. 65(1): p. 232.
37. Martin, K. and A. Heleniust, Nuclear transport of influenza virus ribonucleoproteins: the viral matrix protein (M1) promotes export and inhibits import. Cell, 1991. 67(1): p.117-130.
38. Sugrue, R. and A. Hay, Structural characteristics of the M2 protein of influenza a viruses: Evidence that it forms a tetrameric channe. Virology, 1991. 180(2): p. 617-624.
39. Hay, A. The action of adamantanamines against influenza A viruses: Inhibition of the M 2 ion channel protein. 1992.
40. Takeda, M., et al., Influenza a virus M2 ion channel activity is essential for efficient replication in tissue culture. Journal of virology, 2002. 76(3): p. 1391.
41. Laohpongspaisan, C., et al., Why amantadine loses its function in influenza M2 mutants: MD simulations. Journal of chemical information and modeling, 2009. 49(4): p. 847-852.
42.杨令芝, M2离子通道中金刚烷胺的作用位点研究及BM2离子通道阻断剂筛选. 2009,中国科学技术大学.
43. Treanor, J.J., et al., Efficacy and safety of the oral neuraminidase inhibitor oseltamivirin treating acute influenza. JAMA: the journal of the American Medical Association, 2000. 283(8): p. 1016.
44. Hayden, F.G., et al., Efficacy and safety of the neuraminidase inhibitor zanamivir in the treatment of influenzavirus infections. New England Journal of Medicine, 1997. 337(13): p. 874-880.
45. Read, R.C., Treating influenza with zanamivir. The Lancet, 1998. 352(9144): p. 1872-1873.
46. Grienke, U., et al., Influenza neuraminidase: A druggable target for natural products. Nat. Prod. Rep., 2011.
47. Chen, W., et al., A novel influenza A virus mitochondrial protein that induces cell death. Nature medicine, 2001. 7(12): p. 1306-1312.
48. Li, M.L., P. Rao, and R.M. Krug, The active sites of the influenza cap-dependent endonuclease are on different polymerase subunits. The EMBO journal, 2001. 20(8): p. 2078-2086.
49. Sampath, R., et al., Compositions for use in identification of bacteria. 2011, Google Patents.
50. Basler, C.F., Influenza viruses: basic biology and potential drug targets. Infectious Disorders-Drug Targets (Formerly Current Drug Targets-Infectious, 2007. 7(4): p. 282-293.
51. Pielak, R.M. and J.J. Chou, Influenza M2 proton channels. Biochimica et Biophysica Acta (BBA)-Biomembranes, 2011. 1808(2): p. 522-529.
52.万春和and刘明, A型流感病毒M2蛋白研究进展.动物医学进展, 2007. 28(7): p. 56-60.
53.尤金彪and郭潮潭,甲型流感病毒M2蛋白研究进展.国际流行病学传染病学杂志, 2009(006): p. 402-405.
54. Acharya, R., et al., Structure and mechanism of proton transport through the transmembrane tetrameric M2 protein bundle of the influenza A virus. Proceedings of the National Academy of Sciences, 2010. 107(34): p. 15075-15080.
55. Wang, J., et al., Solution structure and functional analysis of the influenza B proton channel. Nature structural & molecular biology, 2009. 16(12): p. 1267-1271.
56. Odagiri, T., H. Kariwa, and Y. Ohara. The influenza B virus BM2 protein may be involved in the ribonucleoprotein complexes through the binding with membrane protein M1. 2001: Elsevier.
57. Mould, J.A., et al., Influenza B virus BM2 protein has ion channel activity that conducts protons across membranes. Developmental cell, 2003. 5(1): p. 175-184.
58.陈凯先,蒋.,计算机辅助药物设计—原理、方法及应用.上海:上海科学技术出版社, 2000.
59.徐筱杰,侯.,计算机药物辅助分子设计.北京:化学工业出版社, 2004.
60.叶德泳,计算机辅助药物设计导论.北京:化学工业出版社, 2003.
61. Wong, C.F. and J.A. McCammon, Protein simulation and drug design. Advances in protein chemistry, 2003. 66: p. 87-121.
62.李春艳,刘华, and刘波涛,分子动力学模拟基本原理及研究进展.广州化工, 2011. 39(004): p. 11-13.
63.曹赞霞,蛋白质模拟的分子力学力场优化. 2008,中国科学技术大学.
64. Ponder, J.W. and D.A. Case, Force fields for protein simulations. Advances in proteinchemistry, 2003. 66: p. 27-85.
65.梁婉春,生物小分子及模型分子在溶液中的相互作用及质子转移研究. 2007,浙江大学.
66. Wu, Y. and G.A. Voth, Computational studies of proton transport through the M2 channel. FEBS letters, 2003. 552(1): p. 23-27.
67. Brewer, M.L., U.W. Schmitt, and G.A. Voth, The formation and dynamics of proton wires in channel environments. Biophysical journal, 2001. 80(4): p. 1691-1702.
68. Smondyrev, A.M. and G.A. Voth, Molecular dynamics simulation of proton transport through the influenza A virus M2 channel. Biophysical journal, 2002. 83(4): p. 1987-1996.
69. Chen, H., Y. Wu, and G.A. Voth, Proton transport behavior through the influenza A M2 channel: insights from molecular simulation. Biophysical journal, 2007. 93(10): p. 3470-3479.
70. Kandt, C., W.L. Ash, and D. Peter Tieleman, Setting up and running molecular dynamics simulations of membrane proteins. Methods, 2007. 41(4): p. 475-488.
71. Saiz, L. and M.L. Klein, Computer simulation studies of model biological membranes. Accounts of chemical research, 2002. 35(6): p. 482-489.
72. Smart, O.S., J.M. Goodfellow, and B. Wallace, The pore dimensions of gramicidin A. Biophysical journal, 1993. 65(6): p. 2455-2460.
73. Beckstein, O. and M.S.P. Sansom, A hydrophobic gate in an ion channel: the closed state of the nicotinic acetylcholine receptor. Physical biology, 2006. 3: p. 147.
74. Su, Y., et al., An improved method of potential of mean force for protein-protein interactions. Chinese Science Bulletin, 2008. 53(8): p. 1145-1151.
2. Centers for Diease Control and Prevention http://www.cdc.gov/flu/about/qa/disease.htm.
3. Horsfall, F.L., et al., The nomenclature of influenza. The Lancet, 1940. 236(6110): p. 413-414.
4. Taylor, R., Studies on survival of influenza virus between epidemics and antigenic variants of the virus. American Journal of Public Health, 1949. 39(2): p. 171.
5. Taylor, R., A further note on 1233 (“influenza C”) virus. Archives of Virology, 1951.4(4): p. 485-500.
6. Potter, C.W., A history of influenza. Journal of applied microbiology, 2001. 91(4): p. 572-579.
7. Mills, C.E., J.M. Robins, and M. Lipsitch, Transmissibility of 1918 pandemic influenza.Nature, 2004. 432(7019): p. 904-6.
8. Fraser, C., et al., Influenza transmission in households during the 1918 pandemic. AmJ Epidemiol, 2011. 174(5): p. 505-14.
9. Gambotto, A., et al., Human infection with highly pathogenic H5N1 influenza virus. The Lancet, 2008. 371(9622): p. 1464-1475.
10. VG, D. and高子珍,丙型流感病毒.国外医学(微生物学分册), 1985. 1.
11. Mubareka, S. and P. Palese, Influenza virus: The biology of a changing virus. Influenza Vaccines for the Future, 2011: p. 3-26.
12. Smith, W., Cultivation of the virus of influenza. British Journal of Experimental Pathology, 1935. 16(6): p. 508.
13. Smith, W., et al., A Virus obtained from influenza patients. Reviews in Medical Virology, 1995. 5(4): p. 187-191.
14. Viruses, I.C.o.T.o., et al., Virus taxonomy: seventh report of the International Committee on Taxonomy of Viruses. 2000: Academic Press.
15. Toyoda, T., et al., Molecular assembly of the influenza virus RNA polymerase: determination of the subunit-subunit contact sites. Journal of general virology, 1996. 77(9): p.2149.
16. Biswas, S.K. and D.P. Nayak, Mutational analysis of the conserved motifs of influenzaA virus polymerase basic protein 1. Journal of virology, 1994. 68(3): p. 1819.
17. Guilligay, D., et al., The structural basis for cap binding by influenza virus polymerase subunit PB2. Nature structural & molecular biology, 2008. 15(5): p. 500-506.
18. Liu, Y.F., et al., Structure-function studies of the influenza virus RNA polymerase PA subunit. Science in China Series C: Life Sciences, 2009. 52(5): p. 450-458.
19. Fodor, E., et al., A single amino acid mutation in the PA subunit of the influenza virus RNA polymerase inhibits endonucleolytic cleavage of capped RNAs. Journal of virology, 2002. 76(18): p. 8989.
20. Kawaguchi, A., T. Naito, and K. Nagata, Involvement of influenza virus PA subunit inassembly of functional RNA polymerase complexes. Journal of virology, 2005. 79(2): p. 732.
21. Huarte, M., et al., Threonine 157 of influenza virus PA polymerase subunit modulates RNA replication in infectious viruses. Journal of virology, 2003. 77(10): p. 6007.
22. Krug, R. and R. Lamb, Orthomyxoviridae: the viruses and their replication. Fields Virology., 2001.
23. Schmitt, A.P. and R.A. Lamb, Influenza virus assembly and budding at the viral budozone. Advances in virus research, 2005. 64: p. 383-416.
24. Skehel, J.J. and D.C. Wiley, Receptor binding and membrane fusion in virus entry: the influenza hemagglutinin. Annual review of biochemistry, 2000. 69(1): p. 531-569.
25. Colman, P., J. Varghese, and W. Laver, Structure of the catalytic and antigenic sites in influenza virus neuraminidase. Nature, 1983. 303(5912): p. 41-44.
26. Memorandum, W., A revision of the system of nomenclature for influenza viruses: a WHO memorandum. Bull World Health Organ, 1980. 58: p. 585-591.
27. Hinshaw, V., et al., Antigenic and genetic characterization of a novel hemagglutinin subtype of influenza A viruses from gulls. Journal of virology, 1982. 42(3): p. 865.
28. Kawaoka, Y., et al., Molecular characterization of a new hemagglutinin, subtype H14, of influenza A virus. Virology, 1990. 179(2): p. 759-767.
29. R HM, C., et al., Characterization of a novel influenza hemagglutinin, H15: criteria for determination of influenza A subtypes. Virology, 1996. 217(2): p. 508-516.
30. Fouchier, R.A.M., et al., Characterization of a novel influenza A virus hemagglutinin subtype (H16) obtained from black-headed gulls. Journal of virology, 2005. 79(5): p. 2814.
31. Whittaker, G.R., Intracellular trafficking of influenza virus: clinical implications for molecular medicine. Expert Reviews in Molecular Medicine, 2001. 3(05): p. 1-13.
32. Lakadamyali, M., et al., Visualizing infection of individual influenza viruses. Proceedings of the National Academy of Sciences of the United States of America, 2003. 100(16): p. 9280.
33. Hay, A., et al., The molecular basis of the specific anti-influenza action of amantadine.The EMBO journal, 1985. 4(11): p. 3021.
34. Lamb, R.A., S.L. Zebedee, and C.D. Richardson, Influenza virus M2 protein is an integral membrane protein expressed on the infected-cell surface. Cell, 1985. 40(3): p. 627-633.
35. Helenius, A., Unpacking the incoming influenza virus. Cell, 1992. 69(4): p. 577.
36. Martin, K. and A. Helenius, Transport of incoming influenza virus nucleocapsids into the nucleus. Journal of virology, 1991. 65(1): p. 232.
37. Martin, K. and A. Heleniust, Nuclear transport of influenza virus ribonucleoproteins: the viral matrix protein (M1) promotes export and inhibits import. Cell, 1991. 67(1): p.117-130.
38. Sugrue, R. and A. Hay, Structural characteristics of the M2 protein of influenza a viruses: Evidence that it forms a tetrameric channe. Virology, 1991. 180(2): p. 617-624.
39. Hay, A. The action of adamantanamines against influenza A viruses: Inhibition of the M 2 ion channel protein. 1992.
40. Takeda, M., et al., Influenza a virus M2 ion channel activity is essential for efficient replication in tissue culture. Journal of virology, 2002. 76(3): p. 1391.
41. Laohpongspaisan, C., et al., Why amantadine loses its function in influenza M2 mutants: MD simulations. Journal of chemical information and modeling, 2009. 49(4): p. 847-852.
42.杨令芝, M2离子通道中金刚烷胺的作用位点研究及BM2离子通道阻断剂筛选. 2009,中国科学技术大学.
43. Treanor, J.J., et al., Efficacy and safety of the oral neuraminidase inhibitor oseltamivirin treating acute influenza. JAMA: the journal of the American Medical Association, 2000. 283(8): p. 1016.
44. Hayden, F.G., et al., Efficacy and safety of the neuraminidase inhibitor zanamivir in the treatment of influenzavirus infections. New England Journal of Medicine, 1997. 337(13): p. 874-880.
45. Read, R.C., Treating influenza with zanamivir. The Lancet, 1998. 352(9144): p. 1872-1873.
46. Grienke, U., et al., Influenza neuraminidase: A druggable target for natural products. Nat. Prod. Rep., 2011.
47. Chen, W., et al., A novel influenza A virus mitochondrial protein that induces cell death. Nature medicine, 2001. 7(12): p. 1306-1312.
48. Li, M.L., P. Rao, and R.M. Krug, The active sites of the influenza cap-dependent endonuclease are on different polymerase subunits. The EMBO journal, 2001. 20(8): p. 2078-2086.
49. Sampath, R., et al., Compositions for use in identification of bacteria. 2011, Google Patents.
50. Basler, C.F., Influenza viruses: basic biology and potential drug targets. Infectious Disorders-Drug Targets (Formerly Current Drug Targets-Infectious, 2007. 7(4): p. 282-293.
51. Pielak, R.M. and J.J. Chou, Influenza M2 proton channels. Biochimica et Biophysica Acta (BBA)-Biomembranes, 2011. 1808(2): p. 522-529.
52.万春和and刘明, A型流感病毒M2蛋白研究进展.动物医学进展, 2007. 28(7): p. 56-60.
53.尤金彪and郭潮潭,甲型流感病毒M2蛋白研究进展.国际流行病学传染病学杂志, 2009(006): p. 402-405.
54. Acharya, R., et al., Structure and mechanism of proton transport through the transmembrane tetrameric M2 protein bundle of the influenza A virus. Proceedings of the National Academy of Sciences, 2010. 107(34): p. 15075-15080.
55. Wang, J., et al., Solution structure and functional analysis of the influenza B proton channel. Nature structural & molecular biology, 2009. 16(12): p. 1267-1271.
56. Odagiri, T., H. Kariwa, and Y. Ohara. The influenza B virus BM2 protein may be involved in the ribonucleoprotein complexes through the binding with membrane protein M1. 2001: Elsevier.
57. Mould, J.A., et al., Influenza B virus BM2 protein has ion channel activity that conducts protons across membranes. Developmental cell, 2003. 5(1): p. 175-184.
58.陈凯先,蒋.,计算机辅助药物设计—原理、方法及应用.上海:上海科学技术出版社, 2000.
59.徐筱杰,侯.,计算机药物辅助分子设计.北京:化学工业出版社, 2004.
60.叶德泳,计算机辅助药物设计导论.北京:化学工业出版社, 2003.
61. Wong, C.F. and J.A. McCammon, Protein simulation and drug design. Advances in protein chemistry, 2003. 66: p. 87-121.
62.李春艳,刘华, and刘波涛,分子动力学模拟基本原理及研究进展.广州化工, 2011. 39(004): p. 11-13.
63.曹赞霞,蛋白质模拟的分子力学力场优化. 2008,中国科学技术大学.
64. Ponder, J.W. and D.A. Case, Force fields for protein simulations. Advances in proteinchemistry, 2003. 66: p. 27-85.
65.梁婉春,生物小分子及模型分子在溶液中的相互作用及质子转移研究. 2007,浙江大学.
66. Wu, Y. and G.A. Voth, Computational studies of proton transport through the M2 channel. FEBS letters, 2003. 552(1): p. 23-27.
67. Brewer, M.L., U.W. Schmitt, and G.A. Voth, The formation and dynamics of proton wires in channel environments. Biophysical journal, 2001. 80(4): p. 1691-1702.
68. Smondyrev, A.M. and G.A. Voth, Molecular dynamics simulation of proton transport through the influenza A virus M2 channel. Biophysical journal, 2002. 83(4): p. 1987-1996.
69. Chen, H., Y. Wu, and G.A. Voth, Proton transport behavior through the influenza A M2 channel: insights from molecular simulation. Biophysical journal, 2007. 93(10): p. 3470-3479.
70. Kandt, C., W.L. Ash, and D. Peter Tieleman, Setting up and running molecular dynamics simulations of membrane proteins. Methods, 2007. 41(4): p. 475-488.
71. Saiz, L. and M.L. Klein, Computer simulation studies of model biological membranes. Accounts of chemical research, 2002. 35(6): p. 482-489.
72. Smart, O.S., J.M. Goodfellow, and B. Wallace, The pore dimensions of gramicidin A. Biophysical journal, 1993. 65(6): p. 2455-2460.
73. Beckstein, O. and M.S.P. Sansom, A hydrophobic gate in an ion channel: the closed state of the nicotinic acetylcholine receptor. Physical biology, 2006. 3: p. 147.
74. Su, Y., et al., An improved method of potential of mean force for protein-protein interactions. Chinese Science Bulletin, 2008. 53(8): p. 1145-1151.