Predicting protein folding rate from amino acid sequence

Progress in Biochemistry and Biophysics

Volumn 37, Issue 12, 2010, Pages 1331-1338

  Guo, Jian Xiu ^a   Rao, Ni Ni ^a   Liu, Guang Xiong ^a   Li, Jie ^a   Wang, Yun He ^a  

^a UNIVERSITY OF ELECTRONIC SCIENCE AND TECHNOLOGY OF CHINA   (China)

Author keywords

Monte Carlo method; Prediction of folding rate; Protein folding; Pseudo amino acid composition

Indexed keywords

EID: 79951925211     PISSN: 10003282     EISSN: None     Source Type: Journal    
DOI: 10.3724/SP.J.1206.2010.00380     Document Type: Article

References (50)

1. Taubes G. Misfolding the way to disease. Science, 1996, 271(5255): 1493-1495 (Pubitemid 26097206)
2. Fabian H, Naumann D. Methods to study protein folding by stopped-flow FT-IR. Methods, 2004, 34(1): 28-40 (Pubitemid 38993206)
3. Zeeb M, Balbach J. Protein folding studied by real-time NMR spectroscopy. Methods, 2004, 34(1): 65-74 (Pubitemid 38993209)
4. Maity H, Maity M, Krishna M M G, et al. Protein folding: the stepwise assembly of foldon units. Proc Nat Acad Sci USA, 2005, 102(13): 4741-4746 (Pubitemid 40471524)
5. Xiao H, Hoerner J K, Eyles S J, et al. Mapping protein energy landscapes with amide hydrogen exchange and mass spectrometry: I. A generalized model for a two-state protein and comparison with experiment. Protein Sci, 2005, 14(2): 543-557 (Pubitemid 40194607)
6. Maxwell K L, Wildes D, Zarrine-Afsar A, et al. Protein folding: defining a "standard" set of experimental conditions and a preliminary kinetic data set of two-state proteins. Protein Sci, 2005, 14(3): 602-616 (Pubitemid 40283898)
7. Guo J X, Ma B G, Zhang H Y. Acta Biophys Sin, 2006, 22(2): 89-95
8. Gromiha M M, Selvaraj S. Bioinformatics approaches for understanding and predicting protein folding rates. Current Bioinformatics, 2008, 3(1): 1-9 (Pubitemid 351223144)
9. Plaxco K W, Simons K T, Baker D. Contact order, transition state placement and the refolding rates of single domain proteins. J Mol Biol, 1998, 277(4): 985-994 (Pubitemid 28195995)
10. Gromiha M M, Selvaraj S. Comparison between long-range interactions and contact order in determining the folding rate of two-state proteins: application of long-range order to folding rate prediction. J Mol Biol, 2001, 310(1): 27-32 (Pubitemid 32619950)
11. Zhou H, Zhou Y. Folding rate prediction using total contact distance. Biophys J, 2002, 82(1): 458-463 (Pubitemid 34289818)
12. Nölting B, Schälike W, Hampel P, et al. Structural determinants of the rate of protein folding. J Theor Biol, 2003, 223(3): 299-307 (Pubitemid 36808925)
13. Weikl T R, Dill K A Folding kinetics of two-state proteins: Effect of circularization, permutation, and crosslinks. J Mol Biol, 2003, 332(4): 953-963 (Pubitemid 37101380)
14. Ivankov D N, Garbuzynskiy S O, Alm E, et al. Contact order revisited: influence of protein size on the folding rate. Protein Sci, 2003, 12(9): 2057-2062 (Pubitemid 37022826)
15. Mirny L, Shakhnovich E. Protein folding theory: from lattice to all-atom models. Annu Rev Biophys Biomol Struct, 2001, 30(1): 361-396 (Pubitemid 32566168)
16. Gong H, Isom D G, Srinivasan R, et al. Local secondary structure content predicts folding rates for simple two-state proteins. J Mol Biol, 2003, 327(5): 1149-1154 (Pubitemid 36363719)
17. Ivankov D N, Finkelstein A V. Prediction of protein folding rates from the amino acid sequence-predicted secondary structure. Proc Nat Acad Sci USA, 2004, 101(24): 8942-8944 (Pubitemid 38781590)
18. Fleming P J, Gong H P, Rose G D. Secondary structure determines protein topology. Protein Sci, 2006, 15(8): 1829-1834 (Pubitemid 44141500)
19. Huang J T, Cheng J P, Chen H. Secondary structure length as a determinant of folding rate of proteins with two- and three-state kinetics. Proteins, 2007, 67(1): 12-17 (Pubitemid 46340122)
20. Prabhu N P, Bhuyan A K. Prediction of folding rates of small proteins: empirical relations based on length, secondary structure content, residue type, and stability. Biochemistry, 2006, 45 (11): 3805-3812
21. Shao H, Peng Y, Zeng Z H. A simple parameter relating sequences with folding rates of small helical proteins. Protein Pept Lett, 2003, 10(3): 277-280 (Pubitemid 36614852)
22. Galzitskaya O V, Garbuzynskiy S O, Ivankov D N, et al. Chain length is the main determinant of the folding rate for proteins with three-state folding kinetics. Proteins, 2003, 51(2): 162-166 (Pubitemid 36397749)
23. Huang J T, Jing T. Amino acid sequence predicts folding rate for middle-size two-state proteins. Proteins, 2006, 63(3): 551-554
24. Gromiha M M. A statistical model for predicting protein folding rates from amino acid sequence with structural class information. J Chem Inf Model, 2005, 45(2): 494-501 (Pubitemid 40635357)
25. Ma B G, Guo J X, Zhang H Y. Direct correlation between proteins' folding rates and their amino acid compositions: an ab initio folding rate prediction. Proteins, 2006, 65(2): 362-372
26. Gromiha M M, Thangakani A M, Selvaraj S. FOLD-RATE: prediction of protein folding rates from amino acid sequence. Nucleic Acids Res, 2006, 34(suppl-2): 70-74
27. OuYang Z, Liang J. Predicting protein folding rates from geometric contact and amino acid sequence. Protein Sci, 2008, 17(7): 1256-1263 (Pubitemid 351930923)
28. Huang L T, Gromiha M M. Analysis and prediction of protein folding rates using quadratic responde surface models. J Comput Chem, 2008, 29(10): 1675-1683
29. Shen H B, Song J N, Chou K C. Prediction of protein folding rates from primary sequence by fusing multiple sequential features. J Biomedical Science and Engineering, 2009, 2(3): 136-143
30. Jiang Y, Iglinski P, Kurgan L. Prediction of protein folding rates from primary sequences using hybrid sequence representation. J Comput Chem, 2009, 30(5): 772-783
31. Chou K C. Prediction of protein cellular attributes using pesudo-amino acid composition. Proteins, 2001, 43(2): 246-255
32. Fulton K F, Bate M A, Faux N G, et al. Protein Folding Database (PFD 2.0): an online environment for the International Foldeomics Consortium. Nucleic Acids Res, 2007, 35(Database issue): D304-D307 (Pubitemid 46056220)
33. Bogatyreva N S, Osypov A A, Ivankov D N. KineticDB: a database of protein folding kinetics. Nucleic Acids Res, 2009, 37(Database issue): D342-346
34. Gutin A M, Abkevich V I, Shakhnovich E I. Chain length scaling of protein folding Time. Phys Rev Lett, 1996, 77(27): 5433-5436
35. Thirumalai D. From minimal models to real proteins: time scales for protein folding kinetics. J Phys I, 1995, 5(11): 1457-1467
36. Finkelstein A V, Badretdinov A Y. Rate of protein folding near the point of thermodynamic equilibrium between the coil and the most stable chain fold. Fold Des, 1997, 2(2): 115-121 (Pubitemid 127740460)
37. Chou K C, Zhang C T. Review: Prediction of protein structural classes. Crit Rev Biochem Mol Biol, 1995, 30(4): 275-349
38. Chou K C, Shen H B. Recent progress in protein subcellular location prediction. Anal Biochem, 2007, 370(1): 1-16
39. Chou K C, Shen H B. Cell-PLoc: a package of Web servers for predicting subcellular localization of proteins in various organisms. Nature Protocols, 2008, 3(2): 153-162
40. Viguera A R, Vega C, Serrano L. Unspecific hydrophobic stabilization of folding transition states. Proc Nat Acad Sci USA, 2002, 99(8): 5349-5354 (Pubitemid 34411551)
41. Cranz-Mileva S, T. Friel C, E. Radford S. Helix stability and hydrophobicity in the folding mechanism of the bacterial immunity protein Im9. Protein Eng Des Sel, 2005, 18(1): 41-50 (Pubitemid 40516990)
42. Muñoz V, Eaton W A. A simple model for calculating the kinetics of protein folding from three-dimensional structures. Proc Nat Acad Sci USA, 1999, 96(20): 11311-11316 (Pubitemid 29487377)
43. Northey J G B, Nardo A A D, Davidson A R. Hydrophobic core packing in the SH3 domain folding transition state. Nat Struct Biol, 2002, 9(2): 126-130 (Pubitemid 34132415)
44. Dias C L, Ala-Nissila T, Wong-ekkabut J, et al. The hydrophobic effect and its role in cold denaturation. Cryobiology, 2010, 60(1): 91-99
45. Lee S, Lee B C, Kim D. Prediction of protein secondary structure content using amino acid composition and evolutionary information. Proteins, 2006, 62(4): 1107-1114 (Pubitemid 43364173)
46. Mines G A, Pascher T, Lee S C, et al Cytochrome c folding triggered by electron transfer. Chemistry & Biology, 1996, 3(6): 491-497 (Pubitemid 126663349)
47. Wang T, Zhu Y, Gai F. Folding of a three-helix bundle at the folding speed limit. J Physi Chem B, 2004, 108(12): 3694-3697
48. Muñoz V, Thompson P A, Hofrichter J, et al. Folding dynamics and mechanism of β-hairpin formation. Nature, 1997, 390(13): 196-199 (Pubitemid 27507992)
49. Qiu L, Pabit S A, Roitberg A E, et al. Smaller and faster: the 20-residue trp-cage protein folds in 4 μs. J. Am Chem Soc, 2002, 124(44): 12952-12953 (Pubitemid 35247099)
50. Kawashima S, Ogata H, Kanehisa M. AAindex: Amino acid index database. Nucleic Acids Res, 1999, 27(1): 368-369 (Pubitemid 29209488)