Predicting protein folding pathways at the mesoscopic level based on native interactions between secondary structure elements

BMC Bioinformatics

Volumn 9, Issue , 2008, Pages

  Yang, Qingwu ^a   Sze, Sing Hoi ^a  

^a TEXAS A AND M UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACCURATE PREDICTION; COMPUTATIONAL TECHNIQUE; EXPERIMENTAL DETERMINATION; FOLDED STRUCTURES; INTERMEDIATE CONFORMATION; INTERMEDIATE FOLDING; PHOSPHOGLYCERATE KINASE; SECONDARY STRUCTURE ELEMENTS;

FORECASTING; PROTEIN FOLDING; SUPERCONDUCTING MATERIALS;

PROTEINS;

BACTERIAL PROTEIN; PHOSPHOGLYCERATE KINASE; PROTEIN G; PROTEIN L; PROTEIN NUG1; PROTEIN NUG2; IGG FC BINDING PROTEIN, STREPTOCOCCUS; IGG FC-BINDING PROTEIN, STREPTOCOCCUS;

ACCURACY; ANIMAL TISSUE; ARTICLE; CONFORMATIONAL TRANSITION; CONTROLLED STUDY; NONHUMAN; PREDICTION; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN PROTEIN INTERACTION; PROTEIN SECONDARY STRUCTURE; RESIDUE ANALYSIS; STRUCTURE ANALYSIS; SWINE; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; GENETIC VARIABILITY; GENETICS; STREPTOCOCCACEAE;

SUIDAE;

BACTERIAL PROTEINS; COMPUTER SIMULATION; MODELS, MOLECULAR; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; STREPTOCOCCACEAE; VARIATION (GENETICS);

EID: 51049105080     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-9-320     Document Type: Article

References (59)

1. Levinthal C Are there pathways for protein folding? J Chim Phys 1968, 65:44-45.
2. Anfinsen C B Scheraga H A Experimental and theoretical aspects of protein folding Adv Protein Chem 1975, 29:205-300. 237413
3. Kim P S Baldwin R L Intermediates in the folding reactions of small proteins Ann Rev Biochem 1990, 59:631-660. 2197986
4. Matthews C R Pathways of protein folding Ann Rev Biochem 1993, 62:653-683. 8352599
5. Dill K A Chan H S From Levinthal to pathways to funnels Nat Struct Biol 1997, 4:10-19. 8989315
6. Gruebele M Protein folding: The free energy surface Curr Opin Struct Biol 2002, 12:161-168. 11959492
7. Eaton WA Muñoz V Thompson PA Chan CK Hofrichter J Submillisecond kinetics of protein folding Curr Opin Struct Biol 1997, 7:10-14. 9032067
8. Nölting B Golbik R Neira J L Soler Gonzalez A S Schreiber G Fersht A R The folding pathway of a protein at high resolution from microseconds to seconds Proc Natl Acad Sci USA 1997, 94:826-830. 19598 9023341
9. Levitt M Protein folding by restrained energy minimization and molecular dynamics J Mol Biol 1983, 170:723-764. 6195346
10. Daggett V Levitt M Realistic simulations of native-protein dynamics in solution and beyond Ann Rev Biophys Biomol Struct 1993, 22:353-380.
11. Duan Y Kollman P A Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution Science 1998, 282:740-744. 9784131
12. Daggett V Molecular dynamics simulations of the protein unfolding/ folding reaction Acc Chem Res 2002, 35:422-429. 12069627
13. Kolinski A Skolnick J Monte Carlo simulations of protein folding. I. Lattice model and interaction scheme Proteins 1994, 18:338-352. 8208726
14. Yue K Dill K A Folding proteins with a simple energy function and extensive conformational searching Protein Sci 1996, 5:254-261. 2143350 8745403
15. Alm E Baker D Prediction of protein-folding mechanisms from free-energy landscapes derived from native structures Proc Natl Acad Sci USA 1999, 96:11305-11310. 18029 10500172
16. Muñoz V Eaton W A A simple model for calculating the kinetics of protein folding from three-dimensional structures Proc Natl Acad Sci USA 1999, 96:11311-11316. 18030 10500173
17. Amato N M Song G Using motion planning to study protein folding pathways J Comput Biol 2002, 9:149-168. 12015875
18. Liwo A Khalili M Scheraga HA Ab initio simulations of protein-folding pathways by molecular dynamics with the united-residue model of polypeptide chains Proc Natl Acad Sci USA 2005, 102:2362-2367. 548970 15677316
19. Kmiecik S Kolinski A Characterization of protein-folding pathways by reduced-space modeling Proc Natl Acad Sci USA 2007, 104:12330-12335. 1941469 17636132
20. Kmiecik S Kolinski A Folding pathway of the B1 domain of protein G explored by multiscale modeling Biophys J 2008, 94:726-736. 17890394
21. Berman H M Westbrook J Feng Z Gilliland G Bhat T N Weissig H Shindyalov I N Bourne P E The Protein Data Bank Nucleic Acids Res 2000, 28:235-242. 102472 10592235
22. Nölting B Andert K Mechanism of protein folding Proteins 2000, 41:288-298. 11025541
23. Eyrich V A Standley D M Felts A K Friesner R A Protein tertiary structure prediction using a branch and bound algorithm Proteins 1999, 35:41-57. 10090285
24. Apaydin M S Singh A P Brutlag D L Latombe J C Capturing molecular energy landscapes with probabilistic conformational roadmaps Proceedings of the IEEE International Conference on Robotics and Automation 2001:932-939.
25. Zaki M J Nadimpally V Bardhan D Bystroff C Predicting protein folding pathways Bioinformatics 2004, 20(Suppl 1):386-393.
26. Kabsch W Sander C Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features Biopolymers 1983, 22:2577-2637. 6667333
27. Rohl C A Strauss C E M Misura K M S Baker D Protein structure prediction using Rosetta Methods Enzymol 2004, 383:66-93. 15063647
28. Simons K T Ruczinski I Kooperberg C Fox B A Bystroff C Baker D Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins Proteins 1999, 34:82-95. 10336385
29. Song G Thomas S Dill K A Scholtz J M Amato N M A path planning-based study of protein folding with a case study of hairpin formation in protein G and L Pacific Symposium on Biocomputing 2003:240-251. 12603032
30. Alexander P Orban J Bryan P Kinetic analysis of folding and unfolding the 56 amino acid IgG-binding domain of streptococcal protein G Biochemistry 1992, 31:7243-7248. 1510916
31. Blanco FJ Rivas G Serrano L A short linear peptide that folds into a native stableβ-hairpin in aqueous solution Nat Struct Biol 1994, 1:584-590. 7634098
32. Gallagher T Alexander P Bryan P Gilliland G L Two crystal structures of the B1 immunoglobulin-binding domain of streptococcal protein G and comparison with NMR Biochemistry 1994, 33:4721-4729. 8161530
33. Blanco FJ Serrano L Folding of protein G B1 domain studied by the conformationalcharacterization of fragments comprising its secondary structureelements Eur J Biochem 1995, 230:634-649. 7607238
34. Kim D E Fisher C Baker D A breakdown of symmetry in the folding transition state of protein L J Mol Biol 2000, 298:971-984. 10801362
35. McCallister EL Alm E Baker D Critical role of β-hairpin formation in protein G folding Nat Struct Biol 2000, 7:669-673. 10932252
36. Nauli S Kuhlman B Baker D Computer-based redesign of a protein folding pathway Nat Struct Biol 2001, 8:602-605. 11427890
37. Tunnicliffe R B Waby J L Williams R J Williamson M P An experimental investigation of conformational fluctuations in proteins G and L Structure 2005, 13:1677-1684. 16271891
38. Islam S A Karplus M Weaver D L The role of sequence and structure in protein folding kinetics: The diffusion-collision model applied to proteins L and G Structure 2004, 12:1833-1845. 15458632
39. Yi Q Scalley Kim M L Alm E J Baker D NMR characterization of residual structure in the denatured state of protein L J Mol Biol 2000, 299:1341-1351. 10873457
40. Thomas S Tang X Tapia L Amato N M Simulating protein motions with rigidity analysis J Comput Biol 2007, 14:839-855. 17691897
41. Nauli S Kuhlman B Le Trong I Stenkamp R E Teller D Baker D Crystal structures and increased stabilization of the protein G variants with switched folding pathways NuG1 and NuG2 Protein Sci 2002, 11:2924-2931. 2373753 12441390
42. Parker M J Spencer J Jackson G S Burston S G Hosszu L L Craven C J Waltho J P Clarke A R Domain behavior during the folding of a thermostable phosphoglycerate kinase Biochemistry 1996, 35:15740-15752. 8961937
43. Kovári Z Flachner B Náray Szabó G Vas M Crystallographic and thiol-reactivity studies on the complex of pigmuscle phosphoglycerate kinase with ATP analogues: Correlation betweennucleotide binding mode and helix flexibility Biochemistry 2002, 41:8796-8806. 12102622
44. Osváth S Köhler G Závodszky P Fidy J Asymmetric effect of domain interactions on the kinetics of folding in yeast phosphoglycerate kinase Protein Sci 2005, 14:1609-1616. 2253372 15883189
45. Szilágyi A N Vas M Sequential domain refolding of pig muscle 3-phosphoglycerate kinase: Kinetic analysis of reactivation Fold Des 1998, 3:565-575. 9889168
46. Li R Woodward C The hydrogen exchange core and protein folding Protein Sci 1999, 8:1571-1590. 2144413 10452602
47. Itoh K Sasai M Flexibly varying folding mechanism of a nearly symmetrical protein: B domain of protein A Proc Natl Acad Sci USA 2006, 103:7298-7303. 1564280 16648265
48. Nishimura C Prytulla S Dyson H J Wright P E Conservation of folding pathways in evolutionarily distant globin sequences Nat Struct Biol 2000, 7:679-686. 10932254
49. Lazaridis T Karplus M "New view" of protein folding reconciled with the old through multiple unfolding simulations Science 1997, 278:1928-1931. 9395391
50. Sivaraman T Kumar T K Chang D K Lin W Y Yu C Events in the kinetic folding pathway of a small, allβ-sheet protein J Biol Chem 1998, 273:10181-10189. 9553067
51. Weissman J S Kim P S A kinetic explanation for the rearrangement pathway of BPTI folding Nat Struct Biol 1995, 2:1123-1130. 8846225
52. Zhang J X Goldenberg D P Mutational analysis of the BPTI folding pathway: I. Effects ofaromatic & leucine substitutions on the distributionof folding intermediates Protein Sci 1997, 6:1549-1562. 2143733 9232656
53. Kazmirski SL Daggett V Simulations of the structural and dynamical properties of denatured proteins: The "molten coil" state of bovine pancreatic trypsin inhibitor J Mol Biol 1998, 277:487-506. 9514766
54. Karplus M Weaver D L Protein folding dynamics: The diffusion-collision model and experimental data Protein Sci 1994, 3:650-668. 2142854 8003983
55. Abkevich V I Gutin A M Shakhnovich E I Specific nucleus as the transition state for protein folding: Evidence from the lattice model Biochemistry 1994, 33:10026-10036. 8060971
56. Fersht A R Optimization of rates of protein folding: The nucleation-condensation mechanism and its implications Proc Natl Acad Sci USA 1995, 92:10869-10873. 40532 7479900
57. Viguera A R Serrano L Wilmanns M Different folding transition states may result in the same native structure Nat Struct Biol 1996, 3:874-880. 8836105
58. Dobson C M Protein folding and misfolding Nature 2003, 426:884-890. 14685248
59. Rao F Caflisch A The protein folding network J Mol Biol 2004, 342:299-306. 15313625