Multiscale approach to protein folding dynamics

Multiscale Approaches to Protein Modeling: Structure Prediction, Dynamics, Thermodynamics and Macromolecular Assemblies

Volumn , Issue , 2011, Pages 281-293

  Kmiecik, Sebastian ^a   Jamroz, Michał ^a   Kolinski, Andrzej ^a  

^a UNIVERSITY OF WARSAW   (Poland)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84919835803     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/978-1-4419-6889-0_12     Document Type: Chapter

References (67)

1. Arcus VL, Vuilleumier S et al (1995) A comparison of the pH, urea, and temperature-denatured states of barnase by heteronuclear NMR: implications for the initiation of protein folding. J Mol Biol 254:305-321
2. Blanco FJ, Ortiz AR et al (1997) Role of a nonnative interaction in the folding of the protein G B1 domain as inferred from the conformational analysis of the alpha-helix fragment. Fold Des 2:123-133
3. Blanco FJ, Serrano L et al (1998) High populations of non-native structures in the denatured state are compatible with the formation of the native folded state. J Mol Biol 284:1153-1164
4. Bond CJ, Wong KB et al (1997) Characterization of residual structure in the thermally denatured state of barnase by simulation and experiment: description of the folding pathway. Proc Natl Acad Sci USA 94:13409-13413
5. Bradley P, Malmstrom L et al (2005a) Free modeling with ROSETTA in CASP6. Proteins 61(S7):128-134
6. Bradley P, Misura KM et al (2005b) Toward high-resolution de novo structure prediction for small proteins. Science 309:1868-1871
7. Bycroft M, Ludvigsen S et al (1991) Determination of the three-dimensional solution structure of barnase using nuclear magnetic resonance spectroscopy. Biochemistry 30:8697-8701
8. Chan HS, Dill KA (1990) Origins of structure in globular proteins. Proc Natl Acad Sci USA 87:6388-6392
9. Daggett V, Fersht AR (2003a) The present view of the mechanism of protein folding. Nat Rev Mol Cell Biol 4:497-502
10. Daggett V, Fersht AR (2003b) Is there a unifying mechanism for protein folding? Trends Biochem Sci 28:18-25
11. De Prat Gay, Ruiz-Sanz GJ et al (1995) Conformational pathway of the polypeptide chain of chymotrypsin inhibitor-2 growing from its N terminus in vitro. Parallels with the protein folding pathway. J Mol Biol 254:968-979
12. Di Maio F, Tyka MD et al (2009) Refinement of protein structures into low-resolution density maps using ROSETTA. J Mol Biol 392:181-190
13. Dobson CM (1994) Protein folding. Solid evidence for molten globules. Curr Biol 4:636-640.
14. Ferrara P, Apostolakis J et al (2000a) Computer simulations of protein folding by targeted molecular dynamics. Proteins 39:252-260
15. Ferrara P, Apostolakis J et al (2000b) Targeted molecular dynamics simulations of protein unfolding J Phys Chem B 104:4511-4518
16. Fersht AR (1993) The sixth Datta Lecture. Protein folding and stability: the pathway of folding of barnase. FEBS Lett 325(1-2):5-16
17. Forster F, Webb B et al (2008) Integration of small-angle X-ray scattering data into structural modeling of proteins and their assemblies. J Mol Biol 382:1089-1106
18. Frank MK, Clore GM et al (1995) Structural and dynamic characterization of the urea denatured state of the immunoglobulin binding domain of streptococcal protein G by multidimensional heteronuclear NMR spectroscopy. Protein Sci 4:2605-2615
19. Freund SM, Wong KB et al (1996) Initiation sites of protein folding by NMR analysis. Proc Natl Acad Sci USA 93:10600-10603
20. Gront D, Kmiecik S et al (2007) Backbone building from quadrilaterals: A fast and accurate algorithm for protein backbone reconstruction from alpha carbon coordinates. J Comput Chem 28:1593-1597
21. Hubner IA, Shimada J et al (2004) Commitment and nucleation in the protein G transition state. J Mol Biol 336:745-761
22. Jackson SE (1998) How do small single-domain proteins fold? Fold Des 3:R81-R91
23. Jackson SE, El Masry N et al (1993) Structure of the hydrophobic core in the transition state for folding of chymotrypsin inhibitor 2: a critical test of the protein engineering method of analysis. Biochemistry 32:11270-11278
24. Jackson SE, Fersht AR (1991) Folding of chymotrypsin inhibitor 2.1. Evidence for a two-state transition. Biochemistry 30:10428-10435
25. Jonic S, Venien-Bryan C (2009) Protein structure determination by electron cryo-microscopy. Curr Opin Pharmacol 9:636-642
26. Kazmirski SL, Wong KB et al (2001) Protein folding from a highly disordered denatured state: the folding pathway of chymotrypsin inhibitor 2 at atomic resolution. Proc Natl Acad Sci USA 98:4349-4354
27. Klein-Seetharaman J, Oikawa M et al (2002) Long-range interactions within a nonnative protein. Science 295(5560):1719-1722
28. Klepeis JL, Lindorff-Larsen K et al (2009) Long-timescale molecular dynamics simulations of protein structure and function. Curr Opin Struct Biol 19:120-127
29. Kmiecik S, Gront D et al (2007b) Towards the high-resolution protein structure prediction. Fast refinement of reduced models with all-atom force field. BMC Structural Biology 7:43
30. Kmiecik S, Kolinski A (2007a) Characterization of protein-folding pathways by reduced-space modeling. Proc Natl Acad Sci USA 104:12330-12335
31. Kmiecik S, Kolinski A (2008) Folding pathway of the B1 domain of protein G explored by multiscale modeling. Biophys J 94:726-736
32. Kolinski A (2004) Protein modeling and structure prediction with a reduced representation. Acta Biochim Pol 51:349-371
33. Kolinski A, Bujnicki JM (2005) Generalized protein structure prediction based on combination of fold-recognition with de novo folding and evaluation of models. Proteins 61:84-90.
34. Kolinski A, Skolnick J (2004) Reduced models of proteins and their applications. Polymer 45:511-524
35. Krantz BA, Mayne L et al (2002) Fast and slow intermediate accumulation and the initial barrier mechanism in protein folding. J Mol Biol 324:359-371
36. Krukenberg KA, Forster F et al (2008) Multiple conformations of E. coli Hsp90 in solution: insights into the conformational dynamics of Hsp90. Structure 16:755-765
37. Kuszewski J, Clore GM et al (1994) Fast folding of a prototypic polypeptide: the immunoglobulin binding domain of streptococcal protein G. Protein Sci 3:1945-1952
38. Kuwajima K (1989) The molten globule state as a clue for understanding the folding and cooperativity of globular-protein structure. Proteins 6:87-103
39. Lazaridis T, Karplus M (1997) "New view" of protein folding reconciled with the old through multiple unfolding simulations. Science 278(5345):1928-1931
40. Lee SY, Fujitsuka Y et al (2004) Roles of physical interactions in determining protein-folding mechanisms: molecular simulation of protein G and alpha spectrin SH3. Proteins 55:128-138
41. Levinthal C (1968) Mossbauer Spectroscopy in Biological Systems. In: Debrunner P, Tsibris J, Munck E (eds) Proceedings of a meeting held at Allerton house, Monticello, Illinois. University of Illinois Press, Urbana, Illinois, pp 22-24
42. Li A, Daggett V (1998) Molecular dynamics simulation of the unfolding of barnase: characterization of the major intermediate. J Mol Biol 275:677-694
43. Li L, Shakhnovich EI (2001) Constructing, verifying, and dissecting the folding transition state of chymotrypsin inhibitor 2 with all-atom simulations. Proc Natl Acad Sci USA 98:13014-13018
44. Liwo A, Khalili M et al (2005) Ab initio simulations of protein-folding pathways by molecular dynamics with the united-residue model of polypeptide chains. Proc Natl Acad Sci USA 102:2362-2367
45. Matouschek A, Kellis JT Jr et al (1989) Mapping the transition state and pathway of protein folding by protein engineering. Nature 340(6229):122-126
46. Matouschek A, Serrano L et al (1992) The folding of an enzyme. IV. Structure of an intermediate in the refolding of barnase analysed by a protein engineering procedure. J Mol Biol 224:819-835
47. McCallister EL, Alm E et al (2000) Critical role of beta-hairpin formation in protein G folding. Nat Struct Biol 7:669-673
48. Mittermaier A, Kay LE (2006) New tools provide new insights in NMR studies of protein dynamics. Science 312(5771):224-228
49. Otzen DE, Itzhaki LS et al (1994) Structure of the transition state for the folding/unfolding of the barley chymotrypsin inhibitor 2 and its implications for mechanisms of protein folding. Proc Natl Acad Sci USA 91:10422-10425
50. Park SH, Shastry MC et al (1999) Folding dynamics of the B1 domain of protein G explored by ultrarapid mixing. Nat Struct Biol 6:943-947
51. Prieto L, De Sancho D et al (2005) Thermodynamics of Go-type models for protein folding. J Chem Phys 123:154903
52. Ptitsyn OB (1995) Molten globule and protein folding. Adv Protein Chem 47:83-229
53. Reich L, Weikl TR (2006) Substructural cooperativity and parallel versus sequential events during protein unfolding. Proteins 63:1052-1058
54. Roder H, Maki K et al (2006) Early events in protein folding explored by rapid mixing methods. Chem Rev 106:1836-1861
55. Rothwarf DM, Scheraga HA (1996) Role of non-native aromatic and hydrophobic interactions in the folding of hen egg white lysozyme. Biochemistry 35:13797-13807
56. Rueda M, Ferrer-Costa C et al (2007) A consensus view of protein dynamics. Proc Natl Acad Sci USA 104:796-801
57. Russel D, Lasker K et al (2009) The structural dynamics of macromolecular processes. Curr Opin Cell Biol 21:97-108
58. Salvatella X, Dobson CM et al (2005) Determination of the folding transition states of barnase by using PhiI-value-restrained simulations validated by double mutant PhiIJ-values. Proc Natl Acad Sci USA 102:12389-12394
59. Schaeffer RD, Fersht A et al (2008) Combining experiment and simulation in protein folding: closing the gap for small model systems. Curr Opin Struct Biol 18:4-9
60. Scheraga HA, Khalili M et al (2007) Protein-folding dynamics: overview of molecular simulation techniques. Annu Rev Phys Chem 58:57-83
61. Serrano L, Matouschek A et al (1992) The folding of an enzyme. III. Structure of the transition state for unfolding of barnase analysed by a protein engineering procedure. J Mol Biol 224:805-818
62. Shimada J, Shakhnovich EI (2002) The ensemble folding kinetics of protein G from an all-atom Monte Carlo simulation. Proc Natl Acad Sci USA 99:11175-11180
63. Shortle D (1996) The denatured state (the other half of the folding equation) and its role in protein stability. Faseb J 10:27-34
64. Shortle D, Ackerman MS (2001) Persistence of native-like topology in a denatured protein in 8 M urea. Science 293(5529):487-489
65. Thirumalai D, Klimov DK (1999) Deciphering the timescales and mechanisms of protein folding using minimal off-lattice models. Curr Opin Struct Biol 9:197-207
66. Udgaonkar JB, Baldwin RL (1988) NMR evidence for an early framework intermediate on the folding pathway of ribonuclease A. Nature 335(6192):694-699
67. Wong KB, Clarke J et al. (2000) Towards a complete description of the structural and dynamic properties of the denatured state of barnase and the role of residual structure in folding. J Mol Biol 296:1257-1282