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生物大分子多尺度理论和计算方法

李文飞 张建 王骏 王炜

生物大分子多尺度理论和计算方法

李文飞, 张建, 王骏, 王炜
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导出引用
  • 分子模拟是研究生物大分子的重要手段. 过去二十年来, 人们将分子模拟与实验研究相结合, 揭示出生物大分子结构和动力学方面的诸多重要性质. 传统分子模拟主要采用全原子分子模型或各种粗粒化的分子模型. 在实际应用中, 传统分子模拟方法通常存在精度或效率瓶颈, 一定程度上限制了其应用范围. 近年来, 多尺度分子模型越来越受到人们的关注. 多尺度分子模型基于统计力学原理, 将全原子模型和粗粒化模型相耦合, 有望克服传统分子模拟方法中的精度/效率瓶颈, 进而拓展分子模拟在生物大分子研究中的应用范围. 根据模型之间的耦合方式, 近年来发展起来的多尺度分子模拟方法可归纳为如下四种类型: 混合分辨多尺度模型、并行耦合多尺度模型、单向耦合多尺度模型、以及自学习多尺度模型. 本文将对上述四类多尺度模型做简要介绍, 并讨论其主要优缺点、应用范围以及进一步发展方向.
    • 基金项目: 国家自然科学基金(批准号: 11174134, 11334004, 11274157, 11174133)和江苏省自然科学基金(批准号: BK2011546)资助的课题.
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    Alberts B, Johnson A, Lewis J, Raff M, Roberts K, Walter P 2007 Molecular Biology of the Cell (1st Ed.) (New York: Garland Science, Taylor & Francis Group)

    [2]

    Abrahams J P, Leslie A G W, Lutter R, Walker J E 1994 Nature 370 621

    [3]

    Sun B, Wei K J, Zhang B, Zhang X H, Dou S X, Li M, Xi X G 2008 Embo. J. 27 3279

    [4]

    Glynn SE, Martin A, Nager AR, Baker TA, Sauer RT 2009 Cell 139 744

    [5]

    Stigler J, Ziegler F, Gieseke A, Gebhardt J C, Rief M 2011 Science 334 512

    [6]

    Lv C, Gao X, Li W, Xue B, Qin M, Burtnick L D, Zhou H, Cao Y, Robinson R C, Wang W 2014 Nat. Commun. 5 4623

    [7]

    Lindorff-Larsen K, Piana S, Dror RO, Shaw D E 2011 Science 334 517

    [8]

    Zhang J, Li W F, Wang J, Qin M, Wu L, Yan Z Q, Xu W X, Zuo G H, Wang W 2009 Iubmb Life 61 627

    [9]

    Levitt M, Warshel A 1975 Nature 253 694

    [10]

    Li W F, Zhang J, Wang J, Wang W 2008 J. Am. Chem. Soc. 130 892

    [11]

    Duan Y, Kollman P A 1998 Science 282 740

    [12]

    Zhao G P, Perilla J R, Yufenyuy E L, Meng X, Chen B, Ning J Y, Ahn J, Gronenborn A M, Schulten K, Aiken C 2013 Nature 497 643

    [13]

    Guo C, Luo Y, Zhou R H, Wei G H 2012 ACS Nano 6 3907

    [14]

    Xie L G, Luo Y, Lin D D, Xi W H, Yang X J, Wei G H 2014 Nanoscale 6 9752

    [15]

    He J B, Zhang Z Y, Shi Y Y, Liu H Y 2013 J. Chem. Phys. 119 4005

    [16]

    Li W F, Zhang J, Su Y, Wang J, Qin M, Wang W 2007 J. Phys. Chem. B 111 13814

    [17]

    Bian Y, Tan C, Wang J, Sheng Y, Zhang J, Wang W 2014 PLoS Comput. Biol. 10 e1003562

    [18]

    Inanami T, Terada T P, Sasai M 2014 Proc. Natl. Acad. Sci. USA. 111 15969

    [19]

    Huang Y D, Shuai J W 2013 J. Phys. Chem. B 7 11

    [20]

    Takada S 2012 Curr. Opin. Struct. Biol. 22 130

    [21]

    Vendruscolo M, Dobson CM 2011 Current Biology 21 R68

    [22]

    Tozzini V 2010 Q. Rev. Biophys. 43 333

    [23]

    Tozzini V 2005 Curr. Opin. Struc. Biol. 15 144

    [24]

    Xu W X, Lai Z Z, Oliveira R J, Leite V B P, Wang J 2012 J. Phys. Chem. B 116 5152

    [25]

    Yao X Q, Kenzaki H, Murakami S, Takada S 2010 Nature Commun. 1 1116

    [26]

    Moritsugu K, Smith J C 2007 Biophys. J. 93 3460

    [27]

    Marrink S J, Risselada H J, Yefimov S, Tieleman D P, de Vries A H 2007 J. Phys. Chem. B 111 7812

    [28]

    Zuo G H, Wang J, Wang W 2006 Proteins 63 165

    [29]

    Koga N, Takada S 2001 J. Mol. Biol. 313 171

    [30]

    Clementi C, Nymeyer H, Onuchic J N 2000 J. Mol. Biol. 298 937

    [31]

    Onuchic J N, Luthey-Schulten Z, Wolynes P G 1997 Annu. Rev. Phys. Chem. 48 545

    [32]

    Go N 1983 Annu. Rev. Biophys. Bioeng. 12 183

    [33]

    Zhou H X 2014 Curr. Opin. Struct. Biol. 25 67

    [34]

    Li W F, Yoshii H, Hori N, Kameda T, Takada S 2010 Methods 52 106

    [35]

    Li W F, Takada S 2010 Biophys. J. 99 3029

    [36]

    Li WF, Takada S 2009 J. Chem. Phys. 130 214108

    [37]

    Praprotnik M, Delle Site L, Krefler K 2008 Annu. Rev Phys. Chem. 59 545

    [38]

    Liu P, Shi Q, Lyman E, Voth G A 2008 J. Chem. Phys. 129 114103

    [39]

    Liu P, Voth G A 2007 J. Chem. Phys. 126 045106

    [40]

    Chu J W, Ayton G S, Izvekov S, Voth G 2007 Mol. Phys. 105 167

    [41]

    Lyman E, Zuckerman D M 2006 J. Chem. Theory Comput. 2 656

    [42]

    Lyman E, Ytreflerg F M, Zuckerman D M 2006 Phys. Rev. Lett. 96 028105

    [43]

    Christen M, van Gunsteren W F 2006 J. Chem. Phys. 124 154106

    [44]

    Neri M, Anselmi C, Cascella M, Maritan A, Carloni P 2005 Phys. Rev. Lett. 95 218102

    [45]

    Lwin T Z, Luo R 2005 J. Chem. Phys. 123 194904

    [46]

    Izvekov S, Voth G A 2005 J. Phys. Chem. B 109 2469

    [47]

    Reith D, Putz M, Muller-Plathe F 2003 J. Comput. Chem. 24 1624

    [48]

    Peter C, Krefler K 2010 Faraday Discuss 144 9

    [49]

    Peter C, Krefler K 2009 Soft Matter 5 4357

    [50]

    Praprotnik M, Delle Site L, Krefler K J. Chem. Phys. 123 224106

    [51]

    Moritsugu K, Terada T, Kidera A 2010 J. Chem. Phys. 133 224105

    [52]

    Moritsugu K, Terada T, Kidera A 2012 J. Am. Chem. Soc. 134 7094

    [53]

    Li W F, Wang W, Takada S 2014 Proc. Natl. Acad. Sci. USA 111 10550

    [54]

    Li W F, Terakawa T, Wang W, Takada S 2012 Proc. Natl. Acad. Sci. USA 109 17789

    [55]

    Li W F, Wolynes P G, Takada S 2011 Proc. Natl. Acad. Sci. USA 108 3504

    [56]

    Warshel A, Levitt M 1976 J. Mol. Biol. 103 23

    [57]

    Thorpe I F, Zhou J, Voth G A 2008 J. Phys. Chem. B 112 13079

    [58]

    Trylska J, Tozzini V, McCammon J A 2005 Biophys. J. 89 1455

    [59]

    Hori N, Takada S 2012 J. Chem. Theory Comput. 8 3384

    [60]

    Gohlke H, Kiel C, Case D A 2003 J. Mol. Biol. 330 891

    [61]

    Li W F, Wang J, Zhang J, Wang W 2014 Curr. Opin. Struct. Biol. 30 25

    [62]

    Terakawa T, Takada S 2011 Biophys. J. 101 1450

    [63]

    Bryngelson J D, Onuchic J N, Socci N D, Wolynes P G 1995 Proteins 21 167

    [64]

    Pirchi M, Ziv G, Riven I, Cohen SS, Zohar N, Barak Y, Haran G 2011 Nat. Commun. 2 493

    [65]

    King N P, Jacobitz A W, Sawaya M R, Goldschmidt L, Yeates T O 2010 Proc. Natl. Acad. Sci. USA 107 20732

    [66]

    Kenzaki H, Koga N, Hori N, Kanada R, Li W, Okazaki K I, Yao X Q, Takada S 1992 J. Chem. Theory Comput. 7 1979

    [67]

    Kumar S, Bouzida D, Swendsen R H, Kollman P A, Rosenberg J M 2013 J. Comput. Chem. 13 1011

    [68]

    Heath A P, Kavraki L E, Clementi C 2007 Proteins 68 646

    [69]

    Gront D, Kmiecik S, Kolinski A 2007 J. Comput. Chem. 28 1593

    [70]

    Canutescu A A, Shelenkov A A, Dunbrack R L 2003 Protein Sci. 12 2001

  • [1]

    Alberts B, Johnson A, Lewis J, Raff M, Roberts K, Walter P 2007 Molecular Biology of the Cell (1st Ed.) (New York: Garland Science, Taylor & Francis Group)

    [2]

    Abrahams J P, Leslie A G W, Lutter R, Walker J E 1994 Nature 370 621

    [3]

    Sun B, Wei K J, Zhang B, Zhang X H, Dou S X, Li M, Xi X G 2008 Embo. J. 27 3279

    [4]

    Glynn SE, Martin A, Nager AR, Baker TA, Sauer RT 2009 Cell 139 744

    [5]

    Stigler J, Ziegler F, Gieseke A, Gebhardt J C, Rief M 2011 Science 334 512

    [6]

    Lv C, Gao X, Li W, Xue B, Qin M, Burtnick L D, Zhou H, Cao Y, Robinson R C, Wang W 2014 Nat. Commun. 5 4623

    [7]

    Lindorff-Larsen K, Piana S, Dror RO, Shaw D E 2011 Science 334 517

    [8]

    Zhang J, Li W F, Wang J, Qin M, Wu L, Yan Z Q, Xu W X, Zuo G H, Wang W 2009 Iubmb Life 61 627

    [9]

    Levitt M, Warshel A 1975 Nature 253 694

    [10]

    Li W F, Zhang J, Wang J, Wang W 2008 J. Am. Chem. Soc. 130 892

    [11]

    Duan Y, Kollman P A 1998 Science 282 740

    [12]

    Zhao G P, Perilla J R, Yufenyuy E L, Meng X, Chen B, Ning J Y, Ahn J, Gronenborn A M, Schulten K, Aiken C 2013 Nature 497 643

    [13]

    Guo C, Luo Y, Zhou R H, Wei G H 2012 ACS Nano 6 3907

    [14]

    Xie L G, Luo Y, Lin D D, Xi W H, Yang X J, Wei G H 2014 Nanoscale 6 9752

    [15]

    He J B, Zhang Z Y, Shi Y Y, Liu H Y 2013 J. Chem. Phys. 119 4005

    [16]

    Li W F, Zhang J, Su Y, Wang J, Qin M, Wang W 2007 J. Phys. Chem. B 111 13814

    [17]

    Bian Y, Tan C, Wang J, Sheng Y, Zhang J, Wang W 2014 PLoS Comput. Biol. 10 e1003562

    [18]

    Inanami T, Terada T P, Sasai M 2014 Proc. Natl. Acad. Sci. USA. 111 15969

    [19]

    Huang Y D, Shuai J W 2013 J. Phys. Chem. B 7 11

    [20]

    Takada S 2012 Curr. Opin. Struct. Biol. 22 130

    [21]

    Vendruscolo M, Dobson CM 2011 Current Biology 21 R68

    [22]

    Tozzini V 2010 Q. Rev. Biophys. 43 333

    [23]

    Tozzini V 2005 Curr. Opin. Struc. Biol. 15 144

    [24]

    Xu W X, Lai Z Z, Oliveira R J, Leite V B P, Wang J 2012 J. Phys. Chem. B 116 5152

    [25]

    Yao X Q, Kenzaki H, Murakami S, Takada S 2010 Nature Commun. 1 1116

    [26]

    Moritsugu K, Smith J C 2007 Biophys. J. 93 3460

    [27]

    Marrink S J, Risselada H J, Yefimov S, Tieleman D P, de Vries A H 2007 J. Phys. Chem. B 111 7812

    [28]

    Zuo G H, Wang J, Wang W 2006 Proteins 63 165

    [29]

    Koga N, Takada S 2001 J. Mol. Biol. 313 171

    [30]

    Clementi C, Nymeyer H, Onuchic J N 2000 J. Mol. Biol. 298 937

    [31]

    Onuchic J N, Luthey-Schulten Z, Wolynes P G 1997 Annu. Rev. Phys. Chem. 48 545

    [32]

    Go N 1983 Annu. Rev. Biophys. Bioeng. 12 183

    [33]

    Zhou H X 2014 Curr. Opin. Struct. Biol. 25 67

    [34]

    Li W F, Yoshii H, Hori N, Kameda T, Takada S 2010 Methods 52 106

    [35]

    Li W F, Takada S 2010 Biophys. J. 99 3029

    [36]

    Li WF, Takada S 2009 J. Chem. Phys. 130 214108

    [37]

    Praprotnik M, Delle Site L, Krefler K 2008 Annu. Rev Phys. Chem. 59 545

    [38]

    Liu P, Shi Q, Lyman E, Voth G A 2008 J. Chem. Phys. 129 114103

    [39]

    Liu P, Voth G A 2007 J. Chem. Phys. 126 045106

    [40]

    Chu J W, Ayton G S, Izvekov S, Voth G 2007 Mol. Phys. 105 167

    [41]

    Lyman E, Zuckerman D M 2006 J. Chem. Theory Comput. 2 656

    [42]

    Lyman E, Ytreflerg F M, Zuckerman D M 2006 Phys. Rev. Lett. 96 028105

    [43]

    Christen M, van Gunsteren W F 2006 J. Chem. Phys. 124 154106

    [44]

    Neri M, Anselmi C, Cascella M, Maritan A, Carloni P 2005 Phys. Rev. Lett. 95 218102

    [45]

    Lwin T Z, Luo R 2005 J. Chem. Phys. 123 194904

    [46]

    Izvekov S, Voth G A 2005 J. Phys. Chem. B 109 2469

    [47]

    Reith D, Putz M, Muller-Plathe F 2003 J. Comput. Chem. 24 1624

    [48]

    Peter C, Krefler K 2010 Faraday Discuss 144 9

    [49]

    Peter C, Krefler K 2009 Soft Matter 5 4357

    [50]

    Praprotnik M, Delle Site L, Krefler K J. Chem. Phys. 123 224106

    [51]

    Moritsugu K, Terada T, Kidera A 2010 J. Chem. Phys. 133 224105

    [52]

    Moritsugu K, Terada T, Kidera A 2012 J. Am. Chem. Soc. 134 7094

    [53]

    Li W F, Wang W, Takada S 2014 Proc. Natl. Acad. Sci. USA 111 10550

    [54]

    Li W F, Terakawa T, Wang W, Takada S 2012 Proc. Natl. Acad. Sci. USA 109 17789

    [55]

    Li W F, Wolynes P G, Takada S 2011 Proc. Natl. Acad. Sci. USA 108 3504

    [56]

    Warshel A, Levitt M 1976 J. Mol. Biol. 103 23

    [57]

    Thorpe I F, Zhou J, Voth G A 2008 J. Phys. Chem. B 112 13079

    [58]

    Trylska J, Tozzini V, McCammon J A 2005 Biophys. J. 89 1455

    [59]

    Hori N, Takada S 2012 J. Chem. Theory Comput. 8 3384

    [60]

    Gohlke H, Kiel C, Case D A 2003 J. Mol. Biol. 330 891

    [61]

    Li W F, Wang J, Zhang J, Wang W 2014 Curr. Opin. Struct. Biol. 30 25

    [62]

    Terakawa T, Takada S 2011 Biophys. J. 101 1450

    [63]

    Bryngelson J D, Onuchic J N, Socci N D, Wolynes P G 1995 Proteins 21 167

    [64]

    Pirchi M, Ziv G, Riven I, Cohen SS, Zohar N, Barak Y, Haran G 2011 Nat. Commun. 2 493

    [65]

    King N P, Jacobitz A W, Sawaya M R, Goldschmidt L, Yeates T O 2010 Proc. Natl. Acad. Sci. USA 107 20732

    [66]

    Kenzaki H, Koga N, Hori N, Kanada R, Li W, Okazaki K I, Yao X Q, Takada S 1992 J. Chem. Theory Comput. 7 1979

    [67]

    Kumar S, Bouzida D, Swendsen R H, Kollman P A, Rosenberg J M 2013 J. Comput. Chem. 13 1011

    [68]

    Heath A P, Kavraki L E, Clementi C 2007 Proteins 68 646

    [69]

    Gront D, Kmiecik S, Kolinski A 2007 J. Comput. Chem. 28 1593

    [70]

    Canutescu A A, Shelenkov A A, Dunbrack R L 2003 Protein Sci. 12 2001

  • 引用本文:
    Citation:
计量
  • 文章访问数:  2774
  • PDF下载量:  796
  • 被引次数: 0
出版历程
  • 收稿日期:  2015-01-19
  • 修回日期:  2015-03-05
  • 刊出日期:  2015-05-05

生物大分子多尺度理论和计算方法

  • 1. 南京大学物理学院, 固体微结构国家实验室, 南京 210093;
  • 2. 人工微结构科学与技术协同创新中心, 南京 210093
    基金项目: 

    国家自然科学基金(批准号: 11174134, 11334004, 11274157, 11174133)和江苏省自然科学基金(批准号: BK2011546)资助的课题.

摘要: 分子模拟是研究生物大分子的重要手段. 过去二十年来, 人们将分子模拟与实验研究相结合, 揭示出生物大分子结构和动力学方面的诸多重要性质. 传统分子模拟主要采用全原子分子模型或各种粗粒化的分子模型. 在实际应用中, 传统分子模拟方法通常存在精度或效率瓶颈, 一定程度上限制了其应用范围. 近年来, 多尺度分子模型越来越受到人们的关注. 多尺度分子模型基于统计力学原理, 将全原子模型和粗粒化模型相耦合, 有望克服传统分子模拟方法中的精度/效率瓶颈, 进而拓展分子模拟在生物大分子研究中的应用范围. 根据模型之间的耦合方式, 近年来发展起来的多尺度分子模拟方法可归纳为如下四种类型: 混合分辨多尺度模型、并行耦合多尺度模型、单向耦合多尺度模型、以及自学习多尺度模型. 本文将对上述四类多尺度模型做简要介绍, 并讨论其主要优缺点、应用范围以及进一步发展方向.

English Abstract

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