全新设计蛋白质的折叠机制

doi:10.3866/PKU.WHXB201209144

Abstract

Abstract:

Protein de novo design and protein folding are two different means to investigate“sequencestructure- function”relationship of proteins, which is one of the most important focuses in structural biology. The successful achievements in protein de novo design indicate the understanding accuracy of the knowledge in protein structure and interaction, while most of those designed proteins show different folding kinetic features from nature occurring proteins, which implies that there are still many challenges to the aim of getting them to play expected biological function. In this review, the status of research and development for protein de novo design, as well as the study progress of protein folding in experimental, theoretical and simulation aspects, have been introduced. Further, the investigations of folding mechanism of de novo designed proteins have been reviewed, and the new clue has been proposed that systematically investigation of the essence of different folding mechanism between the two types of protein would help to provide useful insight for more efficient protein rotational design.

Key words: Protein de novo design, Protein folding, Target structure, Kinetic features of folding

ZHANG Zhu-Qing. Folding Mechanism of De novo Designed Proteins[J].Acta Phys. -Chim. Sin., 2012, 28(10): 2381-2389.

References

(1) Anfinsen, C. B.; Haber, E.; Sela, M.; White, F. H., Jr. Proc. Natl. Acad. Sci. U. S. A. 1961, 47, 1309. doi: 10.1073/pnas.47.9.1309
(2) Anfinsen, C. B. Science 1973, 181, 223. doi: 10.1126/science.181.4096.223
(3) Berman, H. M.;Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T.N.;Weissig, H.; Shindyalov, I. N.; Bourne, P. E. Nucleic Acids Res. 2000, 28, 235. doi: 10.1093/nar/28.1.235
(4) Uversky, V. N. Protein Sci. 2002, 11, 739. doi: 10.1110/ps.4210102
(5) Huang, Y. Q.; Liu, Z. R. Acta Phys. -Chim. Sin. 2010, 26, 2061.[黄永棋, 刘志荣. 物理化学学报, 2010, 26, 2061.]
(6) Moult, J.; Pedersen, J. T.; Judson, R.; Fidelis, K. Proteins 1995,23, R2.
(7) Minton, A. P. Curr. Opin. Struct. Biol. 2000, 10, 34. doi: 10.1016/S0959-440X(99)00045-7
(8) Jackson, S. E.; Fersht, A. R. Biochemistry 1991, 30, 10428. doi: 10.1021/bi00107a010
(9) Leopold, P. E.; Montal, M.; Onuchic, J. N. Proc. Natl. Acad. Sci. U. S. A. 1992, 89, 8721. doi: 10.1073/pnas.89.18.8721
(10) Dill, K. A.; Chan, H. S. Nat. Struct. Biol. 1997, 4, 10. doi: 10.1038/nsb0197-10
(11) Duan, Y.; Kollman, P. A. Science 1998, 282, 740. doi: 10.1126/science.282.5389.740
(12) Shaw, D. E.; Maragakis, P.; Lindorff-Larsen, K.; Piana, S.; Dror,R. O.; Eastwood, M. P.; Bank, J. A.; Jumper, J. M.; Salmon, J.K.; Shan, Y.;Wriggers,W. Science 2010, 330, 341. doi: 10.1126/science.1187409
(13) Lindorff-Larse, K.; Piana, S.; Dror, R. O.; Shaw, D. E. Science2011, 334, 517. doi: 10.1126/science.1208351
(14) Shortle, D.; Dimaio, D.; Nathans, D. Annu. Rev. Genet. 1981,15, 265. doi: 10.1146/annurev.ge.15.120181.001405
(15) Leatherbarrow, R. J.; Fersht, A. R. Protein Eng. 1986, 1, 7. doi: 10.1093/protein/1.1.7
(16) Ho, S. P.; DeGrado,W. F. J. Am. Chem. Soc. 1987, 109, 6751.doi: 10.1021/ja00256a032
(17) Ramirez-Alvarado, M.; Blanco, F. J.; Serrano, L. Nat. Struct. Biol. 1996, 3, 604. doi: 10.1038/nsb0796-604
(18) Floudas, C. A. Biotechnol. Bioeng. 2007, 97, 207. doi: 10.1002/bit.21411
(19) Zhang, Y. Curr. Opin. Struct. Biol. 2008, 18, 342. doi: 10.1016/j.sbi.2008.02.004
(20) Floudas, C. A.; Fung, H. K.; McAllister, S. R.; Monnigmann,M.; Rajgaria, R. Chem. Eng. Sci. 2006, 61, 966.
(21) Shakhnovich, E. Chem. Rev. 2006, 106, 1559. doi: 10.1021/cr040425u
(22) Dill, K. A.; Ozkan, S. B.; Shell, M. S.; Thomas, R.W. Annu. Rev. Biophys. 2008, 37, 289. doi: 10.1146/annurev.biophys.37.092707.153558
(23) Thirumalai, D.; O'Brien E. P.; Morrison, G.; Hyeon, C. Annu. Rev. Biophys. 2010, 39, 159. doi: 10.1146/annurev-biophys-051309-103835
(24) Butterfoss, G. L.; Kuhlman, B. Annu. Rev. Biophys. Biomol. Struct. 2006, 35, 49. doi: 10.1146/annurev.biohhys.35.040405.102046
(25) Pantazes, R. J.; Grisewood, M. J.; Maranas, C. D. Curr. Opin. Struct. Biol. 2011, 21, 467. doi: 10.1016/j.sbi.2011.04.005
(26) Lai, L. H. Structure Prediction and Molecular Design of Proteins; Peking University Press: Beijing, 1993. [来鲁华.蛋白质的结构预测与分子设计. 北京: 北京大学出版社,1993.]
(27) Chou, P. Y.; Fasman, G. D. Biochemistry 1974, 13, 222. doi: 10.1021/bi00699a002
(28) Richardson, J. S.; Richardson, D. C. Science 1988, 240, 1648.doi: 10.1126/science.3381086
(29) Kumar, S.; Bansal, M. Proteins 1998, 31, 460. doi: 10.1002/(SICI)1097-0134(19980601)31:4<460::AID-PROT12>3.0.CO;2-D
(30) Goliaei, B.; Minuchehr, Z. FEBS Lett. 2003, 537, 121. doi: 10.1016/S0014-5793(03)00105-4
(31) Fonseca, N. A.; Camacho, R.; Magalhaes, A. L. Proteins 2008,70, 188.
(32) Qi, Y. F.; Liang, H. H.; Han, X. F.; Lai, L. L. Protein Pept. Lett.2012, 19, 345. doi: 10.2174/092986612799363118
(33) Ho, S. P.; DeGrado,W. F. J. Am. Chem. Soc. 1987, 109, 6751.doi: 10.1021/ja00256a032
(34) Hecht, M. H.; Richardson, J. S.; Richardson, D. C.; Ogden, R.C. Science 1990, 249, 884. doi: 10.1126/science.2392678
(35) Fezoui, Y.;Weaver, D. L.; Osterhout, J. J. Proc. Natl. Acad. Sci. U. S. A. 1994, 91, 3675. doi: 10.1073/pnas.91.9.3675
(36) Bryson, J.W.; Desjarlais, J. R.; Handel, T. M.; DeGrado,W. F.Protein Sci. 1998, 7, 1404. doi: 10.1002/pro.5560070617
(37) Moser, R.; Thomas, R. M.; Gutte, B. FEBS Lett. 1983, 157,247. doi: 10.1016/0014-5793(83)80555-9
(38) Blanco, F. J.; Jimenez, M. A.; Herranz, J.; Rico, M.; Santoro, J.;Nieto, J. L. J. Am. Chem. Soc. 1993, 115, 5887. doi: 10.1021/ja00066a092
(39) Blanco, F. J.; Rivas, G.; Serrano, L. Nat. Struct. Biol. 1994, 1,584. doi: 10.1038/nsb0994-584
(40) Ramirez-Alvarado, M.; Blanco, F. J.; Serrano, L. Nat. Struct. Biol. 1996, 3, 604. doi: 10.1038/nsb0796-604
(41) Kortemme, T.; Ramirez-Alvarado, M.; Serrano, L. Science1998, 281, 253. doi: 10.1126/science.281.5374.253
(42) Carulla, N.;Woodward, C.; Barany, G. Protein. Sci. 2002, 11,1539. doi: 10.1110/ps.4440102
(43) Dahiyat, B. I.; Mayo, S. L. Science 1997, 278, 82. doi: 10.1126/science.278.5335.82
(44) Riddle, D. S.; Santiago, J. V.; Bray-Hall, S. T.; Doshi, N.;Grantcharova, V. P.; Yi, Q.; Baker, D. Nat. Struct. Biol. 1997, 4,805. doi: 10.1038/nsb1097-805
(45) Kim, D. E.; Gu, H.; Baker, D. Proc. Natl. Acad. Sci. U. S. A.1998, 95, 4982. doi: 10.1073/pnas.95.9.4982
(46) Dantas, G.; Kuhlman, B.; Callender, D.;Wong, M.; Baker, D.J. Mol. Biol. 2003, 332, 449. doi: 10.1016/S0022-2836(03)00888-X
(47) Kuhlman, B.; Dantas, G.; Ireton, G. C.; Varani, G.; Stoddard, B.L.; Baker, D. Science 2003, 302, 1364. doi: 10.1126/science.1089427
(48) Liang, H.; Chen, H.; Fan, K.;Wei, P.; Guo, X.; Jin, C.; Zeng, C.;Tang, C.; Lai, L. Angew. Chem. Int. Edit. 2009, 48, 3301. doi: 10.1002/anie.200805476
(49) Zhu, C.; Zhang, C.; Liang, H.; Lai, L. Protein & Cell 2011, 2,1006. doi: 10.1007/s13238-011-1121-3
(50) Samish, I.; MacDermaid, M.; Perez-Aguilar, J. M.; Saven, J. G.Annu. Rev. Phys. Chem. 2011, 62, 129. doi: 10.1146/annurevphyschem-032210-103509
(51) Li, H.; Helling, R.; Tang, C.;Wingreen, N. Science 1996, 273,666. doi: 10.1126/science.273.5275.666
(52) Saven, J. G. Chem. Rev. 2011, 101, 3113.
(53) Hellinga, H.W. Proc. Natl. Acad. Sci. U. S. A. 1997, 94, 10015.doi: 10.1073/pnas.94.19.10015
(54) Zhang, C. S.; Lai, L. H. Biochem. Soc. Trans. 2011, 39, 1382.doi: 10.1042/BST0391382
(55) Zhang, C. S.; Lai, L. H. Proteins 2012, 80, 1078. doi: 10.1002/prot.24009
(56) Robertson, D. E.; Farid, R. S.; Moser, C. C.; Urbauer, J. L.;Mulholland, S. E.; Pidikiti, R.; Lear, J. D.;Wand, A. J.;DeGrado,W. F.; Dutton, P. L. Nature 1994, 368, 425. doi: 10.1038/368425a0
(57) Reynolds, K. A.; Hanes, M. S.; Thomson, J. M.; Antczak, A. J.;Berger, J. M.; Bonomo, R. A.; Kirsch, J. F.; Handel, T. M.J. Mol. Biol. 2008, 382, 1265. doi: 10.1016/j.jmb.2008.05.051
(58) Liu, S.; Zhu, X.; Liang, H.; Cao, A.; Chang, Z.; Lai, L. Proc. Natl. Acad. Sci. U. S. A. 2007, 104, 5330. doi: 10.1073/pnas.0606198104
(59) Bai, H. J.; Lai, L. H. Acta Phys. -Chim. Sin. 2010, 26, 1988.[白红军, 来鲁华. 物理化学学报, 2010, 26, 1988.] doi: 10.3866/PKU.WHXB20100725
(60) 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., III; Hilvert, D.; Houk, K. N.;Stoddard, B. L.; Baker, D. Science 2008, 319, 1387. doi: 10.1126/science.1152692
(61) Stefani, M.; Dobson, C. M. J. Mol. Med. 2003, 81, 678. doi: 10.1007/s00109-003-0464-5
(62) Levinthal, C. J. Chem. Phys. 1968, 65, 44.
(63) Viguera, A. R.; Martinez, J. C.; Filimonov, V. V.; Mateo, P. L.;Serrano, L. Biochemistry 1994, 33, 2142. doi: 10.1021/bi00174a022
(64) Otzen, D. E.; Kristensen, O.; Proctor, M.; Oliveberg, M.Biochemistry 1999, 38, 6499. doi: 10.1021/bi982819j
(65) Plaxco, K.W.; Baker, D. Proc. Natl. Acad. Sci. U. S. A. 1998,95, 13591. doi: 10.1073/pnas.95.23.13591
(66) Taverna, D. M.; Goldstein, R. A. Proteins 2002, 46, 105. doi: 10.1002/prot.10016
(67) Matouschek, A.; Kellis, J. T.; Serrano, L.; Fersht, A. R. Nature1989, 340, 122. doi: 10.1038/340122a0
(68) Fersht, A. R.; Matouschek, A.; Serrano, L. J. Mol. Biol. 1992,224, 771. doi: 10.1016/0022-2836(92)90561-W
(69) Scaloni, F.; Federici, L.; Brunori, M.; Gianni, S. Proc. Natl. Acad. Sci. U. S. A. 2010, 95, 4982.
(70) Morris, E. R.; Searle, M. S. Curr. Protoc. Protein. Sci. 2012, 28,Unit 28.2.1.
(71) Gomez-Hens, A.; Perez-Bendito, D. Anal. Chim. Acta 1991,242, 147. doi: 10.1016/0003-2670(91)87060-K
(72) Bai, Y.W.; Sosnick, T. R.; Mayne, L.; Englander, S.W. Science1995, 269, 192. doi: 10.1126/science.7618079
(73) Gai, F.; Du, D.; Xu, Y. Methods. Mol. Biol. 2007, 350, 1.
(74) Borgia, A.;Williams, P. M.; Clarke, J. Annu. Rev. Biochem.2008, 77, 101. doi: 10.1146/annurev.biochem.77.060706.093102
(75) Chung, H. S.; McHale, K.; Louis, J. M.; Eaton,W. A. Science2012, 335, 981. doi: 10.1126/science.1215768
(76) Onuchic, J. N.; Luthey-Schulten, Z.;Wolynes, P. G. Annu. Rev. Phys. Chem. 1997, 48, 545. doi: 10.1146/annurev.physchem.48.1.545
(77) Gsponer, J.; Vendruscolo, M. Protein Pept. Lett. 2006, 13, 287.doi: 10.2174/092986606775338407
(78) Dill, K. A. Biochemistry 1985, 24, 1501. doi: 10.1021/bi00327a032
(79) Clementi, C. Curr. Opin. Struct. Biol. 2008, 18, 10. doi: 10.1016/j.sbi.2007.10.005
(80) Ueeda, Y.; Taketomi, H.; Gō, N. Biopolymers 1978, 17, 1531.doi: 10.1002/bip.1978.360170612
(81) Plaxco, K.W.; Simons, K. T.; Baker, D. J. Mol. Biol. 1998, 277,985. doi: 10.1006/jmbi.1998.1645
(82) Clementi, C.; Nymeyer, H.; Onuchic, J. N. J. Mol. Biol. 2000,298, 937. doi: 10.1006/jmbi.2000.3693
(83) Hills, R. D., Jr.; Brooks, C. L., III. Int. J. Mol. Sci. 2009, 10,889. doi: 10.3390/ijms10030889
(84) Chan, H. S.; Zhang, Z.;Wallin, S.; Liu, Z. Annu. Rev. Phys. Chem. 2011, 62, 301. doi: 10.1146/annurev-physchem-032210-103405
(85) Cho, S. S.; Levy, Y.;Wolynes, P. G. Proc. Natl. Acad. Sci. U. S. A. 2009, 106, 434. doi: 10.1073/pnas.0810218105
(86) Cho, S. S.;Weinkam, P.;Wolynes, P. G. Proc. Natl. Acad. Sci. U. S. A. 2008, 105, 118. doi: 10.1073/pnas.0709376104
(87) Zuo, G.;Wang, J.;Wang,W. Proteins 2006, 63, 165. doi: 10.1002/prot.20857
(88) Badasyan, A.; Liu, Z.; Chan, H. S. J. Mol. Biol. 2008, 384, 512.doi: 10.1016/j.jmb.2008.09.023
(89) Liu, Z.; Chan, H. S. J. Mol. Biol. 2005, 349, 872. doi: 10.1016/j.jmb.2005.03.084
(90) Ferguson, A.; Liu, Z.; Chan, H. S. J. Mol. Biol. 2009, 389, 619.doi: 10.1016/j.jmb.2009.04.011
(91) Zarrine-Afsar, A.;Wallin, S.; Neculai, A. M.; Neudecker, P.;Howell, P. L.; Davidson, A. R.; Chan, H. S. Proc. Natl. Acad. Sci. U. S. A. 2008, 105, 9999. doi: 10.1073/pnas.0801874105
(92) Zarrine-Afsar, A.; Zhang, Z.; Schweiker, K. L.; Makhatadze, G.I.; Davidson, A. R.; Chan, H. S. Proteins 2012, 80, 858. doi: 10.1002/prot.23243
(93) Su, J. G.; Chen,W. Z.;Wang, C. X. Proteins 2010, 78, 2157.
(94) Azia, A.; Levy, Y. J. Mol. Biol. 2009, 393, 527. doi: 10.1016/j.jmb.2009.08.010
(95) Liu, Z.; Reddy, G.; O'Brien, E. P.; Thirumalai, D. Proc. Natl. Acad. Sci. U. S. A. 2011, 108, 7787. doi: 10.1073/pnas.1019500108
(96) Liu, Z.; Reddy, G.; Thirumalai, D. J. Phys. Chem. B 2012, 116,6707. doi: 10.1021/jp211941b
(97) Wu, L.; Li,W.; Liu, F.; Zhang, J.;Wang, J.;Wang,W. J. Chem. Phys. 2009, 131, 065105. doi: 10.1063/1.3200952
(98) Wu, L.; Zhang, J.;Wang, J.; Li,W. F.;Wang,W. Phys. Rev. E2007, 75, 031914. doi: 10.1103/PhysRevE.75.031914
(99) Wu, L.; Zhang, J.; Qin, M.; Liu, F.;Wang,W. J. Chem. Phys.2008, 128, 235103. doi: 10.1063/1.2943202
(100) McCammon, J. A.; Gelin, B. R.; Karplus, M. Nature 1977,267, 585. doi: 10.1038/267585a0
(101) Zhu, Y.; Alonso, D. O.; Maki, K.; Huang, C. Y.; Lahr, S. J.;Daggett, V.; Roder, H.; DeGrado,W. F.; Gai, F. Proc. Natl. Acad. Sci. U. S. A. 2003, 100, 15486. doi: 10.1073/pnas.2136623100
(102) Zhu, Y.; Fu, X.;Wang, T.; Tamura, A.; Takada, S.; Saven, J. G.;Gai, F. Chem. Phys. 2004, 307, 99. doi: 10.1016/j.chemphys.2004.05.008
(103) Wang, T.; Zhu, Y.; Gai, F. J. Phys. Chem. B 2004, 108, 3694.doi: 10.1021/jp049652q
(104) Gillespie, B.; Vu, D. M.; Shah, P. S.; Marshall, S. A.; Dyer, R.B.; Mayo, S. L.; Plaxco, K.W. J. Mol. Biol. 2003, 330, 813.doi: 10.1016/S0022-2836(03)00616-8
(105) Scalley-Kim, M.; Baker, D. J. Mol. Biol. 2004, 338, 573. doi: 10.1016/j.jmb.2004.02.055
(106) Sadqi, M.; de Alba, E.; Perez-Jimenez, R.; Sanchez-Ruiz, J.M.; Muñoz, V. Proc. Natl. Acad. Sci. U. S. A. 2009, 106, 4127.doi: 10.1073/pnas.0812108106
(107) Watters, A. L.; Deka, P.; Corrent, C.; Callender, D.; Varani, G.;Sosnick, T.; Baker, D. Cell 2007, 128, 613. doi: 10.1016/j.cell.2006.12.042
(108) Zhang, Z.; Chan, H. S. Biophys. J. 2009, 96, L25.
(109) Zhang, Z.; Chan, H. S. Proc. Natl. Acad. Sci. U. S. A. 2010,107, 2920. doi: 10.1073/pnas.0911844107
(110) Qi, Y.; Huang, Y.; Liang, H.; Liu, Z.; Lai, L. Biophys. J. 2010,98, 321. doi: 10.1016/j.bpj.2009.10.018

[1]	Aoneng Cao. "Confined Lowest Energy Structure Fragments (CLESFs)" Hypothesis for Protein Structure and the "Stone Age" of Protein Prebiotic Evolution [J]. Acta Physico-Chimica Sinica, 2020, 36(1): 1907002-.
[2]	LI Yong, ZHOU Wei, DAI Zhi-Jun, CHEN Yuan, WANG Zhi-Ming, YUAN Zhe-Ming. Predicting the Protein Folding Rate Based on Sequence Feature Screening and Support Vector Regression [J]. Acta Phys. -Chim. Sin., 2014, 30(6): 1091-1098.
[3]	ZHI Ze-Yong, LIU Peng-Cheng, HUANG Yan-Yi, ZHAO Xin-Sheng. A Microfluidic Mixer for Single-Molecule Kinetics Experiments [J]. Acta Phys. -Chim. Sin., 2011, 27(08): 1990-1995.
[4]	HUANG Yong-Qi, LIU Zhi-Rong. Intrinsically Disordered Proteins: the New [J]. Acta Phys. -Chim. Sin., 2010, 26(08): 2061-2072.
[5]	GAO Meng, YAO Xin-Qiu, SHE Zhen-Su, LIU Zhi-Rong, ZHU Huai-Qiu. Intermediate Structure and Slow HydrationWater Dynamics in Protein Folding Process [J]. Acta Phys. -Chim. Sin., 2010, 26(07): 1998-2006.
[6]	WANG Zheng, LAI Bing, CAO Jie, LI Zhu, QU Li-Li, CAO Ao-Neng, LAI Lu-Hua. Hierarchical Unfolding of Mj HSP16.5 [J]. Acta Phys. -Chim. Sin., 2008, 24(10): 1745-1750.

Folding Mechanism of De novo Designed Proteins

PDF

Like

Knowledge

Abstract

Cite this article

share this article

References

Related Articles 6

Metrics

Recommended 0