Computational design of proteins with novel structure and functions

doi:10.1088/1674-1056/25/1/018702

中国物理B ›› 2016, Vol. 25 ›› Issue (1): 18702-018702.doi: 10.1088/1674-1056/25/1/018702

所属专题： TOPICAL REVIEW — 8th IUPAP International Conference on Biological Physics

• TOPICAL REVIEW—8th IUPAP International Conference on Biological Physics • 上一篇下一篇

Computational design of proteins with novel structure and functions

Wei Yang(杨为) and Lu-Hua Lai(来鲁华)

1. BNLMS, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, and Peking–Tsinghua Center for Life Sciences at College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China;
2. Center for Quantitative Biology, Peking University, Beijing 100871, China;
3. School of Life Sciences, Tsinghua University, Beijing 100084, China

收稿日期:2015-05-15 出版日期:2016-01-05 发布日期:2016-01-05
通讯作者: Lu-Hua Lai E-mail:lhlai@pku.edu.cn
基金资助:
Project supported by the National Basic Research Program of China (Grant No. 2015CB910300), the National High Technology Research and Development Program of China (Grant No. 2012AA020308), and the National Natural Science Foundation of China (Grant No. 11021463).

Computational design of proteins with novel structure and functions

Wei Yang(杨为)^1,2,3 and Lu-Hua Lai(来鲁华)^1,2

1. BNLMS, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, and Peking–Tsinghua Center for Life Sciences at College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China;
2. Center for Quantitative Biology, Peking University, Beijing 100871, China;
3. School of Life Sciences, Tsinghua University, Beijing 100084, China

Received:2015-05-15 Online:2016-01-05 Published:2016-01-05
Contact: Lu-Hua Lai E-mail:lhlai@pku.edu.cn
Supported by:
Project supported by the National Basic Research Program of China (Grant No. 2015CB910300), the National High Technology Research and Development Program of China (Grant No. 2012AA020308), and the National Natural Science Foundation of China (Grant No. 11021463).

摘要/Abstract

摘要：

Computational design of proteins is a relatively new field, where scientists search the enormous sequence space for sequences that can fold into desired structure and perform desired functions. With the computational approach, proteins can be designed, for example, as regulators of biological processes, novel enzymes, or as biotherapeutics. These approaches not only provide valuable information for understanding of sequence-structure-function relations in proteins, but also hold promise for applications to protein engineering and biomedical research. In this review, we briefly introduce the rationale for computational protein design, then summarize the recent progress in this field, including de novo protein design, enzyme design, and design of protein-protein interactions. Challenges and future prospects of this field are also discussed.

关键词: computational protein design, de novo protein design, enzyme design, protein-protein interaction

Abstract:

Key words: computational protein design, de novo protein design, enzyme design, protein-protein interaction

中图分类号: (Proteins)

87.14.E-

87.15.km (Protein-protein interactions) 87.14.ej (Enzymes)

杨为, 来鲁华. Computational design of proteins with novel structure and functions[J]. 中国物理B, 2016, 25(1): 18702-018702.

Wei Yang(杨为) and Lu-Hua Lai(来鲁华). Computational design of proteins with novel structure and functions[J]. Chin. Phys. B, 2016, 25(1): 18702-018702.

参考文献 69

[1]	Terwilliger T C, Stuart D and Yokoyama S 2009 Annu. Rev. Biophys. 38 371
[2]	Hwang I and Park S 2008 Drug. Discov. Today Techonol. 5 e43
[3]	Tiwari M K, Singh R, Singh R K, Kim I W and Lee J K 2012 Comput. Struct. Biotechnol. J. 2 e201209002
[4]	Kuhlman B and Baker D 2000 Proc. Natl. Acad. Sci. USA 97 10383
[5]	Samish I, MacDermaid C M, Perez-Aguilar J M and Saven J G 2011 Annu. Rev. Phys. Chem. 62 129
[6]	Ponder J W and Richards F M 1987 J. Mol. Biol. 193 775
[7]	Pokala N and Handel T M 2001 J. Struct. Biol. 134 269
[8]	Mandell D J and Kortemme T 2009 Nat. Chem. Biol. 5 797
[9]	Pokala N and Handel T M 2005 J. Mol. Biol. 347 203
[10]	Weiner S J, Kollman P A, Case D A, Singh U C, Ghio C, Alagona G, Profeta S and Weiner P 1984 J. Am. Chem. Soc. 106 765
[11]	Gordon D B, Marshall S A and Mayo S L 1999 Curr. Opin. Struct. Biol. 9 509
[12]	Marshall S A and Mayo S L 2001 J. Mol. Biol. 305 619
[13]	Ramachandran G N, Ramakrishnan C and Sasisekharan V 1963 J. Mol. Biol. 7 95
[14]	Georgiev I, Keedy D, Richardson J S, Richardson D C and Donald B R 2008 Bioinformatics 24 I196
[15]	Dunbrack R L 2002 Curr. Opin. Struct. Biol. 12 431
[16]	Metropolis N, Rosenbluth AW, RosenbluthMN, Teller A H and Teller E 1953 J. Chem. Phys. 21 1087
[17]	Desjarlais J R and Handel T M 1999 J. Mol. Biol. 290 305
[18]	Desmet J, Demaeyer M, Hazes B and Lasters I 1992 Nature 356 539
[19]	Kono H and Doi J 1996 J. Comput. Chem. 17 1667
[20]	Zwanzig R, Szabo A and Bagchi B 1992 Proc. Natl. Acad. Sci. USA 89 20
[21]	Das R and Baker D 2008 Annu. Rev. Biochem. 77 363
[22]	Rohl C A, Strauss C E M, Misura K M S and Baker D 2004 Method Enzymol 383 66
[23]	Liang S D, Zhang C, Liu S and Zhou Y Q 2006 Nucleic Acids Res. 34 3698
[24]	Xiong P, Wang M, Zhou X Q, Zhang T C, Zhang J H, Chen Q and Liu H Y 2014 Nat. Commun. 5 5330
[25]	Li Z X, Yang Y D, Zhan J, Dai L and Zhou Y Q 2013 Annu. Rev. Biophys. 42 315
[26]	DeGrado W F, Regan L and Ho S P 1987 Cold Spring Harb Symp. Quant. Biol. 52 521
[27]	Walsh S T R, Cheng H, Bryson J W, Roder H and DeGrado W F 1999 Proc. Natl. Acad. Sci. USA 96 5486
[28]	Dahiyat B I and Mayo S L 1997 Science 278 82
[29]	Kuhlman B, Dantas G, Ireton G C, Varani G, Stoddard B L and Baker D 2003 Science 302 1364
[30]	Liang H, Chen H, Fan K,Wei P, Guo X, Jin C, Zeng C, Tang C and Lai L 2009 Angew. Chem., Int. Ed. Engl. 48 3301
[31]	Koga N, Tatsumi-Koga R, Liu G, Xiao R, Acton T B, Montelione G T and Baker D 2012 Nature 491 222
[32]	King N P, Bale J B, Sheffler W, McNamara D E, Gonen S, Gonen T, Yeates T O and Baker D 2014 Nature 510 103
[33]	Huang P S, Oberdorfer G, Xu C, Pei X Y, Nannenga B L, Rogers J M, DiMaio F, Gonen T, Luisi B and Baker D 2014 Science 346 481
[34]	Thomson A R, Wood C W, Burton A J, Bartlett G J, Sessions R B, Brady R L and Woolfson D N 2014 Science 346 485
[35]	Joh N H, Wang T, Bhate M P, Acharya R, Wu Y, Grabe M, Hong M, Grigoryan G and DeGrado W F 2014 Science 346 1520
[36]	Lehninger A L, Nelson D L and Cox M M 2005 Lehninger Principles of Biochemistry, 4th edn. (New York: W. H. Freeman) p. 190
[37]	Lutz S 2010 Curr. Opin. Biotechnol. 21 734
[38]	Berman H M, Westbrook J, Feng Z, Gilliland G, Bhat T N, Weissig H, Shindyalov I N and Bourne P E 2000 Nucleic Acids Res. 28 235
[39]	Kiss G, Celebi-Olcum N, Moretti R, Baker D and Houk K N 2013 Angew. Chem., Int. Ed. Engl. 52 5700
[40]	Richter F, Leaver-Fay A, Khare S D, Bjelic S and Baker D 2011 PLoS One 6 e19230
[41]	Rothlisberger D, Khersonsky O,Wollacott A M, Jiang L, DeChancie J, Betker J, Gallaher J L, Althoff E A, Zanghellini A, Dym O, Albeck S, Houk K N, Tawfik D S and Baker D 2008 Nature 453 190
[42]	Jiang L, Althoff E A, Clemente F R, Doyle L, Rothlisberger D, Zanghellini A, Gallaher J L, Betker J L, Tanaka F, Barbas C F, Hilvert D, Houk K N, Stoddard B L and Baker D 2008 Science 319 1387
[43]	Siegel J B, Zanghellini A, Lovick H M, Kiss G, Lambert A R, St Clair J L, Gallaher J L, Hilvert D, Gelb M H, Stoddard B L, Houk K N, Michael F E and Baker D 2010 Science 329 309
[44]	Faiella M, Andreozzi C, de Rosales R T, Pavone V, Maglio O, Nastri F, DeGrado W F and Lombardi A 2009 Nat. Chem. Biol. 5 882
[45]	Nanda V and Koder R L 2010 Nature Chem. 2 15
[46]	Zheng F, Xue L, Hou S, Liu J, Zhan M, Yang W and Zhan C G 2014 Nat. Commun. 5 3457
[47]	Zheng F, Yang W, Xue L, Hou S, Liu J and Zhan C G 2010 Biochemistry 49 9113
[48]	Xue L, Ko M C, Tong M, Yang W, Hou S, Fang L, Liu J, Zheng F, Woods J H, Tai H H and Zhan C G 2011 Mol. Pharmacol. 79 290
[49]	Quinn D M 1987 Chem. Rev. 87 955
[50]	Rajagopalan S, Wang C, Yu K, Kuzin A P, Richter F, Lew S, Miklos A E, Matthews M L, Seetharaman J, Su M, Hunt J F, Cravatt B F and Baker D 2014 Nat. Chem. Biol. 10 386
[51]	Mills J H, Khare S D, Bolduc J M, Forouhar F, Mulligan V K, Lew S, Seetharaman J, Tong L, Stoddard B L and Baker D 2013 J. Am. Chem. Soc. 135 13393
[52]	Gordon S R, Stanley E J, Wolf S, Toland A, Wu S J, Hadidi D, Mills J H, Baker D, Pultz I S and Siegel J B 2012 J. Am. Chem. Soc. 134 20513
[53]	Eiben C B, Siegel J B, Bale J B, Cooper S, Khatib F, Shen BW, Players F, Stoddard B L, Popovic Z and Baker D 2012 Nat. Biotechnol. 30 190
[54]	Tinberg C E, Khare S D, Dou J Y, Doyle L, Nelson J W, Schena A, Jankowski W, Kalodimos C G, Johnsson K, Stoddard B L and Baker D 2013 Nature 501 212
[55]	Mills J H, Khare S D, Bolduc J M, Forouhar F, Mulligan V K, Lew S, Seetharaman J, Tong L, Stoddard B L and Baker D 2013 J. Am. Chem. Soc. 135 13393
[56]	Jones S and Thornton J M 1996 Proc. Natl. Acad. Sci. USA 93 13
[57]	Stranges P B and Kuhlman B 2013 Protein Sci. 22 74
[58]	Kortemme T and Baker D 2004 Curr. Opin. Chem. Biol. 8 91
[59]	Jardine J, Julien J P, Menis S, Ota T, Kalyuzhniy O, McGuire A, Sok D, Huang P S, MacPherson S, Jones M, Nieusma T, Mathison J, Baker D, Ward A B, Burton D R, Stamatatos L, Nemazee D, Wilson I A and Schief W R 2013 Science 340 711
[60]	Zhang C S and Lai L H 2011 Biochem. Soc. Trans. 39 1382
[61]	Shoichet B K 2004 Nature 432 862
[62]	Zhang C S and Lai L H 2011 J. Comput. Chem. 32 2598
[63]	Zhang C S and Lai L H 2012 Proteins: Struct., Funct., Bioinf. 80 1078
[64]	Zhang C S, Tang B,Wang Q and Lai L H 2014 Proteins: Struct., Funct., Bioinf. 82 2472
[65]	Liu S, Liu S, Zhu X, Liang H, Cao A, Chang Z and Lai L 2007 Proc. Natl. Acad. Sci. USA 104 5330
[66]	Fleishman S J, Whitehead T A, Ekiert D C, Dreyfus C, Corn J E, Strauch E M, Wilson I A and Baker D 2011 Science 332 816
[67]	Procko E, Hedman R, Hamilton K, Seetharaman J, Fleishman S J, Su M, Aramini J, Kornhaber G, Hunt J F, Tong L, Montelione G T and Baker D 2013 J. Mol. Biol. 425 3563
[68]	Zhang C, Shen Q, Tang B and Lai L 2013 Angew. Chem. Int. Ed. Engl. 52 11059
[69]	Correia B E, Bates J T, Loomis R J, et al. 2014 Nature 507 201

Computational design of proteins with novel structure and functions

Computational design of proteins with novel structure and functions

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