A Framework for Describing Topological Frustration in Models of Protein Folding

Journal of Molecular Biology

Volumn 362, Issue 3, 2006, Pages 605-621

  Norcross, Todd S ^a   Yeates, Todd O ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Delaunay tessellation; dynamic programming algorithm; knotted proteins; protein folding; topological frustration

Indexed keywords

AMINO TERMINAL SEQUENCE; ARTICLE; MATHEMATICAL MODEL; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN FOLDING; PROTEIN FUNCTION; PROTEIN LOCALIZATION; PROTEIN STRUCTURE;

EID: 33748123253     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2006.07.054     Document Type: Article

References (64)

1. Mirny L., and Shakhnovich E. Protein folding theory: from lattice to all-atom models. Annu. Rev. Biophys. Biomol. Struct. 30 (2001) 361-396
2. Grantcharova V., Alm E.J., Baker D., and Horwich A.L. Mechanisms of protein folding. Curr. Opin. Struct. Biol. 11 (2001) 70-82
3. Fersht A.R., and Dagget V. Protein folding and unfolding at atomic resolution. Cell 108 (2002) 573-582
4. Gruebele M. Protein folding: the free energy surface. Curr. Opin. Struct. Biol. 12 (2002) 161-168
5. Vendruscolo M., and Paci E. Protein folding: bringing theory and experiment closer together. Curr. Opin. Struct. Biol. 13 (2003) 82-87
6. Daggett V., and Fersht A.R. Is there a unifying mechanism for protein folding?. Trends Biochem. Sci. 28 (2003) 18-25
7. Ferguson N., and Fersht A.R. Early events in protein folding. Curr. Opin. Struct. Biol. 13 (2003) 75-81
8. Dagget V., and Fersht A. The present view of the mechanism of protein folding. Nature Rev. Mol. Cell Biol. 4 (2003) 497-502
9. Onuchic J.N., and Wolynes P.G. Theory of protein folding. Curr. Opin. Struct. Biol. 14 (2004) 70-75
10. Alm E., and Baker D. Prediction of protein-folding mechanisms from free-energy landscapes derived from native structures. Proc. Natl Acad. Sci. USA 96 (1999) 11305-11310
11. Debe D.A., and Goddard W.A. First principles prediction of protein folding rates. J. Mol. Biol. 294 (1999) 619-625
12. Gromiha M.M., and 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. 310 (2001) 27-32
13. Ivankov D.N., and Finkelstein A.V. Theoretical study of a landscape of protein folding-unfolding pathways. Folding rates at midtransition. Biochemistry 40 (2001) 9957-9961
14. Munoz V., and Eaton W.A. A simple model for calculating the kinetics of protein folding from three-dimensional structures. Proc. Natl Acad. Sci. USA 96 (1999) 11311-11316
15. Plaxco K.W., Simons K.T., and Baker D. Contact order, transition state placement and the refolding rates of single domain proteins. J. Mol. Biol. 277 (1998) 985-994
16. Plaxco K.W., Simons K.T., Ruczinski I., and Baker D. Topology, stability, sequence, and length: defining the determinants of two-state protein folding kinetics. Biochemistry 37 (2000) 11177-11183
17. Zhou H.Y., and Zhou Y.Q. Folding rate prediction using total contact distance. Biophys. J. 82 (2002) 458-463
18. Mansfield M.L. Are there knots in proteins?. Nature Struct. Biol. 1 (1994) 213-214
19. Taylor W.R., and Lin K. Protein knots: a tangled problem. Nature 421 (2003) 25
20. Taylor W.R. A deeply knotted protein structure and how it might fold. Nature 406 (2000) 916-919
21. Wagner J.R., Brunzelle J.S., Forest K.T., and Vierstra R.D. A light-sensing knot revealed by the structure of the chromophore-binding domain of phytochrome. Nature 438 (2005) 325-331
22. Duan Y., and Kollman P.A. Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution. Science 282 (1998) 740-744
23. Duan Y., Wang L., and Kollman P.A. The early stage of folding of villin headpiece subdomain observed in a 200-nanosecond fully solvated molecular dynamics simulation. Proc. Natl Acad. Sci. USA 95 (1998) 9897-9902
24. Sato S., Religa T.L., Dagget V., and Fersht A.R. Testing protein-folding simulations by experiment: B domain of protein A. Proc. Natl Acad. Sci. USA 101 (2004) 6952-6956
25. Alm E., and Baker D. Prediction of protein-folding mechanisms from free-energy landscapes derived from native structures. Proc. Natl Acad. Sci. USA 96 (1999) 11305-11310
26. Munoz V., and Eaton W.A. A simple model for calculating the kinetics of protein folding from three-dimensional structures. Proc. Natl Acad. Sci. USA 96 (1999) 11311-11316
27. Ivankov D.N., and Finkelstein A.V. Theoretical study of a landscape of protein folding-unfolding pathways. Folding rates at midtransition. Biochemistry 40 (2001) 9957-9961
28. Shea J., Onuchic J.N., and Brooks C.L. Exploring the origins of topological frustration: design of a minimally frustrated model of fragment B of protein A. Proc. Natl Acad. Sci. USA 96 (1999) 12512-12517
29. Nymeyer H., Socci N.D., and Onuchic J.N. Landscape approaches for determining the ensemble of folding transition states: Success and failure hinge on the degree of frustration. Proc. Natl Acad. Sci. USA 97 (2000) 634-639
30. Clementi C., Nymeyer H., and Onuchic J.N. Topological and energetic factors: what determines the structural details of the transition state ensemble and "en-route" intermediates for protein folding?. J. Mol. Biol. 298 (2000) 937-953
31. Clementi C., Jennings P.A., and Onuchic J.N. How native-state topology affects the folding of dihydrofolate reductase and interleukin-1β. Proc. Natl Acad. Sci. USA 97 (2000) 5871-5876
32. Thirumalai D., and Woodson S.A. Kinetics of folding of proteins and RNA. Acc. Chem. Res. 29 (1996) 433-439
33. Thirumalai D., and Hyeon C. RNA and protein folding: common themes and variations. Biochemistry 44 (2005) 4957-4970
34. Connolly M.L., Kuntz I.D., and Crippen G.M. Linked and threaded loops in proteins. Biopolymers 19 (1980) 1167-1182
35. Needleman S.B., and Wunsch C.D. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol. 48 (1970) 443-453
36. Smith T.F., and Waterman M.S. Identification of common molecular subsequences. J. Mol. Biol. 147 (1981) 195-197
37. Orengo C.A., and Taylor W.R. SSAP: sequential structure alignment program for protein structure comparison. Methods Enzymol. 266 (1996) 617-635
38. Chang J.Y., and Li L. Divergent folding pathways of two homologous proteins, BPTI and tick anticoagulant peptide: compartmentalization of folding intermediates and identification of kinetic traps. Arch. Biochem. Biophys. 437 (2005) 85-95
39. Faraone-Mennella J., Gray H.B., and Winkler J.R. Early events in the folding of four-helix-bundle heme proteins. Proc. Natl Acad. Sci. USA 102 (2005) 6315-6319
40. 8-barrel enzyme fold. Chem. Rev. 105 (2005) 4038-4055
41. Fedorov A.N., and Baldwin T.O. Cotranslational protein folding. J. Biol. Chem. 272 (1997) 32715-32718
42. Kramer G., Ramachandiran V., and Hardesty B. Cotranslational folding-Omnia mea mecum porto?. Int. J. Biochem. Cell Biol. 33 (2001) 541-553
43. Hardesty B., and Kramer G. Folding of a nascent peptide on the ribosome. Prog. Nucl. Acid Res. Mol. Biol. 66 (2001) 41-66
44. Guo Z., and Thirumalai D. The nucleation-collapse mechanism in protein folding: evidence for the non-uniqueness of the folding nucleus. Fold. Des. 2 (1997) 377-391
45. Shakhnovich E.I. Folding nucleus: specific or multiple? Insights from lattice models and experiments. Fold. Des. 3 (1998) R108-R111
46. Thirumalai D., and Klimov D.K. Fishing for folding nuclei in lattice models and proteins. Fold. Des. 3 (1998) R112-R118
47. Ivankov D.N., Garbuzynskiy S.O., Alm E., Plaxco K.W., Baker D., and Finkelstein A.V. Contact order revisited: Influence of protein size on the folding rate. Protein Sci. 12 (2003) 2057-2062
48. Anfinsen C.B. Principles that govern the folding of protein chains. Science 181 (1973) 223-230
49. Weissman J.S., and Kim P.S. Kinetic role of nonnative species in the folding of bovine pancreatic trypsin inhibitor. Proc. Natl Acad. Sci. USA 89 (1992) 9900-9904
50. Jones M.D., Narhi L.O., Chang W., and Lu H.S. Refolding and oxidation of recombinant human stem cell factor produced in Escherichia coli. J. Biol. Chem. 271 (1996) 11301-11308
51. Rothwarf D.M., Li Y., and Scheraga H.A. Regeneration of bovine pancreatic ribonuclease A: detailed kinetic analysis of two independent folding pathways. Biochemistry 37 (1998) 3767-3776
52. van den Berg B., Chung E.W., Robinson C.V., Mateo P.L., and Dobson C.M. The oxidative refolding of hen lysozyme and its catalysis by protein disulfide isomerase. EMBO J. 18 (1999) 4794-4803
53. Ruoppolo M., Talamo F., Pucci P., Moutiez M., Quemeneur E., Menez A., and Marino G. Slow folding of three-fingered toxins is associated with the accumulation of native disulfide-bonded intermediates. Biochemistry 40 (2001) 15257-15266
54. Chang J., Li L., and Lai P. A major kinetic trap for the oxidative folding of human epidermal growth factor. J. Biol. Chem. 276 (2001) 4845-4852
55. Welker E., Narayan M., Volles M.J., and Scheraga H.A. Two new structured intermediates in the oxidative folding of RNase A. FEBS Letters 460 (1999) 477-479
56. Vanselow D.G. Role of constraint in catalysis and high-affinity binding by proteins. Biophys. J. 82 (2002) 2293-2303
57. Jacobs S.A., Harp J.M., Devarakonda S., Kim Y., Rastinejad F., and Khorasanizadeh S. The active site of the SET domain is constructed on a knot. Nature Struct. Biol. 9 (2002) 833-838
58. Fersht A.R., Matouschek A., and Serrano L. The folding of an enzyme. I. Theory of protein engineering analysis of stability and pathway of protein folding. J. Mol. Biol. 224 (1992) 771-782
59. Jansens A., van Duijn E., and Braakman I. Coordinate nonvectorial folding in a newly synthesized multidomain protein. Science 298 (2002) 2401-2403
60. Norberg J., and Nilsson L. Advances in biomolecular simulations: methodology and recent applications. Quart. Rev. Biophys. 36 (2003) 257-306
61. Hobohm U., Scharf M., Schneider R., and Sander C. Selection of representative protein data sets. Protein Sci. 1 (1992) 409-417
62. Collaborative Computational Project, Number 4. The CCP4 suite: programs for protein crystallography. Acta Crystallog. sect. D 50 (1994) 760-763
63. Yeates T.O. Algorithms for evaluating the long-range accessibility of protein surfaces. J. Mol. Biol. 249 (1995) 804-815
64. Orengo C.A., Michie A.D., Jones S., Jones D.T., Swindells M.B., and Thornton J.M. CATH-a hierarchic classification of protein domain structures. Structure 5 (1997) 1093-1108