Folding funnels, binding funnels, and protein function

Protein Science

Volumn 8, Issue 6, 1999, Pages 1181-1190

  Tsai, Chung Jung ^a   Kumar, Sandeep ^b   Ma, Buyong ^a   Nussinov, Ruth ^a,b,c  

^a NATIONAL CANCER INSTITUTE   (United States)

^b SAIC FREDERICK INC   (United States)

^c TEL AVIV UNIVERSITY   (Israel)

Author keywords

Binding funnels; Conformational ensembles; Energy landscape; Folding funnels; Function; Misfolding

Indexed keywords

ENDONUCLEASE; PROTEIN;

CONFORMATIONAL TRANSITION; ENZYME BINDING; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; PRIORITY JOURNAL; PROTEIN FOLDING; REVIEW; THERMODYNAMICS;

EID: 0033056708     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1110/ps.8.6.1181     Document Type: Review

References (66)

1. Baker D, Agard DA. 1994. Kinetics versus thermodynamics in protein folding. Biochemistry 33:7505-1509.
2. Baldwin RL. 1994. Matching speed and stability. Nature 369:183-184.
3. Baldwin RL. 1995. The nature of protein folding pathways: The classical versus the new view. J Biomol NMR 5:103-109.
4. Baldwin RL, Rose GD. 1999. Is protein folding hierarchic? I. Local structure and peptide folding. Trends Biochem Sci 24:26-33.
5. Ballew RM, Sabelko J, Gruebele M. 1996. Direct observation of fast protein folding: The initial collapse of apomyoglobin. Proc Natl Acad Sci USA 93:5759-5764.
6. Barrett AJ, Rawlings ND, Woessner JF. 1998. Handbook of proteolytic enzymes. San Diego, California: Academic Press.
7. Becker OM, Karplus M. 1997. The topology of multidimensional potential energy surfaces: Theory and application to peptide structure and kinetics. J Chem Phys 106:1495-1517.
8. Bennett MJ, Choe S, Eisenberg D. 1994. Domain swapping: Entangling alliances between proteins. Proc Natl Acad Sci USA 91:3127-3131.
9. Bennett MJ, Schlunegger MP, Eisenberg D. 1995. 3D domain swapping: A mechanism for oligomer assembly. Protein Sci 4:2455-2468.
10. Bryngelson JD, Wolynes PG. 1989. Intermediates and barrier crossing in a random energy model (with applications to protein folding). J Phys Chem 93:6902-6915.
11. Chaffotte AF, Li JH, Georgescu RE, Goldberg ME, Tasayco ML. 1997. Recognition between disordered states: Kinetics of the self-assembly of thioredoxin fragments. Biochemistry 36:16040-16048.
12. Chan HS, Dill KA. 1994. Transition states and folding dynamics of proteins and heteropolymers. J Chem Phys 100:9238-9257.
13. Chan HS, Dill KA. 1998. Protein folding in the landscape perspective: Chevron plots and non-Arrhenius kinetics. Proteins 30:2-33.
14. Cherfils J, Janin J. 1993. Protein docking algorithms: Simulating molecular recognition. Curr Opin Struct Biol 3:265-269.
15. Creighton TE. 1993. Proteins: Structure and molecular properties, 2nd ed. New York: WH Freeman and Company.
16. D'Alessio G. 1995. Oligomer evolution in action. Nat Struct Biol 2:11-13.
17. Dill KA. 1999. Polymer principles and protein folding. Protein Sci 8:1166-1180.
18. Dill KA, Chan HS. 1997. From Levinthal to pathways to funnels. Nat Struct Biol 4:10-19.
19. Dill KA, Phillips, AT, Rosen JB. 1997. Protein structure and energy landscape dependence on sequence using a continuous energy function. J Comp Biol 4:227-239.
20. Dunbrack RL, Gerloff DL, Bower M, Chen X, Lichtarge O, Cohen FE. 1997. Meeting review: The second meeting on the critical assessment of techniques for protein structure prediction (CASP2), Asilomar, California, December 13-16, 1996. Folding Design 2:R27-R42.
21. Eaton WA, Munoz V, Thompson PA, Chan CK, Hofrichter J. 1997. Submillisecond kinetics of protein folding. Curr Opin Struct Biol 7:10-14.
22. Fersht AR. 1997. Nucleation mechanisms in protein folding. Curr Opin Struct Biol 7:3-9.
23. Fischer D, Lin SL, Wolfson HJ, Nussinov, R. 1995. A geometry-based suite of molecular docking processes. J Mol Biol 248:459-411.
24. Fischer E. 1894. Ber Dt Chem Ges 27:2985-2991.
25. Foote J, Milstein C. 1994. Conformational isomerism and the diversity of antibodies. Proc Natl Acad Sci USA 91:10370-10374.
26. Frauenfelder H, Leeson DT. 1998. The energy landscape in non-biological molecules. Nat Struct Biol 5:757-759.
27. Frauenfelder H, Sligar SG, Wolynes PG. 1991. The energy landscapes and motions of proteins. Science 254:1598-1603.
28. Gruebele M, Wolynes P. 1998. Satisfying turns in folding transitions. Nat Struct Biol 5:662-665.
29. Jarrett JT, Lansbury PT Jr. 1993. Seeding "one-dimensional crystallization" of amyloid: A pathogenic mechanism in Alzheimer's disease and scrapie? Cell 73:1055-1058.
30. Karplus M. 1997. The Levinthal paradox: yesterday and today. Folding Design 2:S69-S75.
31. Karplus M, Sali A, Shakhnovitch E. 1995. Comment: Kinetics of protein folding. Nature 373:664-665.
32. Karplus M, Shakhnovitch E. 1992. Protein folding: Theoretical studies of thermodynamics and dynamics. In: Creighton T, ed. Protein folding. New York: WH Freeman & Sons, pp 127-195.
33. Katchalski-Katzir E, Shariv I, Eisenstein M, Friesem AA, Aflalo C, Vakser IA. 1992. Molecular surface recognition: Determination of geometric fit between protein and their ligands by correlation techniques. Proc Natl Acad Sci USA 89:2195-2199.
34. Koshland DE Jr. 1958. Application of a theory of enzyme specificity to protein synthesis. Proc Natl Acad Sci USA 44:98-123.
35. Ladurner AG, Itzhaki LS, Gay FDP, Fersht AR. 1997. Complementation of peptide fragments of the single domain protein chymotrypsin inhibitor 2. J Mol Biol 273:317-329.
36. Lazaridis T, Karplus M. 1997. "New view" of protein folding reconciled with the old through multiple unfolding simulations. Science 274:1928-1931.
37. Lee AY, Gulnik SV, Erickson JW. 1998. Conformational switching in an aspartic proteinase. Nat Struct Biol 5:866-871.
38. Levinthal C. 1969. How to fold graciously. In: Debrunner P, Tsibris JCM, Munck E, eds. Mossbauer spectroscopy in biological systems (Proceedings of a meeting held at Allerton House, Monticello, Illinois). Urbana, Illinois: University of Illinois Press. p 22.
39. Martinez JC, Pisabarro MT, Serrano L. 1998. Obligatory steps in protein folding and the conformational diversity of the transition state. Nat Struct Biol 5:721-729.
40. Miller DW, Dill KA. 1997. Ligand binding to proteins: The binding landscape model. Protein Sci 6:2166-2179.
41. Muller Y, Kelley RF, De Vos AM. 1998. Hinge bending within the cytokine receptor superfamily revealed by the 2.4 Å crystal structure of the extracellular domain of the rabbit tissue factor. Protein Sci 7:1106-1115.
42. Netzer WJ, Hartl FU. 1997. Recombination of protein domains facilitated by co-translational folding in eukaryotes. Nature 388:343-349.
43. Norel R, Lin SL, Wolfson H, Nussinov R. 1994. Shape complementarity at protein-protein interfaces. Biopolymers 34:933-940.
44. Norel R, Lin SL, Wolfson H, Nussinov R. 1995. Molecular surface complementarity at protein-protein interfaces: The critical role played by surface normals at well placed, sparse, points in docking. J Mol Biol 252:263-273.
45. Northrup SH, Erickson HP. 1992. Kinetics of protein-protein association explained by Brownian dynamics computer simulation. Proc Natl Acad Sci USA 89:3338-3342.
46. Onuchic JN, Wolynes PG, Luthey-Schulten Z, Socci ND. 1995. Towards an outline of the topography of a realistic protein folding funnel. Proc Natl Acad Sci USA 92:3626-3630.
47. Perona JJ, Craik CS. 1995. Structural basis of substrate specificity in the serine proteases. Protein Sci 4:337-360.
48. Piccoli R, Tamburrini M, Piccialli G, Di Donato A, Parente A, D'Alessio G. 1992. The dual-mode quaternary structure of seminal rnase. Proc Natl Acad Sci USA 89:1870-1874.
49. Prusiner SB. 1991. Molecular biology of prion diseases. Science 252:1515-1522.
50. Tasayco ML, Chao K. 1995. NMR study of the reconstitution of the β-sheet of thioredoxin by fragment complementation. Proteins SFG 22:41-44.
51. Tsai CJ, Lin SL, Wolfson, H, Nussinov R. 1996. Protein-protein interfaces: Architectures and interactions in protein-protein interfaces and in protein cores. Their similarities and differences. Critic Rev Biochem Mol Biol 31:127-152.
52. Tsai CJ, Lin SL, Wolfson, H, Nussinov R. 1997a. Studies of protein-protein interfaces: Statistical analysis of the hydrophobic effect. Protein Sci 6:53-64.
53. Tsai CJ, Maizel JV Jr, Nussinov R. 1999. Distinguishing between sequential and non-sequentially folded protein: Implications for folding and misfolding. Protein Sci. In press.
54. Tsai CJ, Nussinov R. 1997. Hydrophobic folding units derived from dissimilar monomer structures and their interactions. Protein Sci 6:24-42.
55. Tsai CJ, Xu D, Nussinov R. 1997b. Structural motifs at protein-protein interfaces: Protein cores versus two-state and three-state model complexes. Protein Sci 6:1793-1805.
56. Tsai CJ, Xu D, Nussinov R. 1998. Protein folding via binding, and vice versa. Folding Design 3:R71-R80.
57. Verkhivker GM, Rejto PA, Gehlhaar DK, Freer ST. 1996. Exploring the energy landscapes of molecular recognition by a genetic algorithm: Analysis of the requirements for robust docking of HIV-1 protease and FKBP-12 complexes. Proteins SFG 250:342-352.
58. Wales DJ, Miller MA, Walsh TR. 1998. Archetypal energy landscapes. Nature 394:758-760.
59. Wang Y, Shortle D. 1996. A dynamic bundle of four adjacent hydrophobic segments in the denatured state of staphylococcal nuclease. Protein Sci 5:1898-1906.
60. Wedemayer GJ, Patten PA, Wang LH, Schultz PG, Stevens RC. 1997. Structural insights into the evolution of an antibody combining site. Nat Struct Biol 276:1665-1669.
61. Wells JA. 1996. Binding in the growth hormone receptor complex. Proc Natl Acad Sci USA 93:1-6.
62. Wolynes PG, Onuchic JN, Thirumalai D. 1995. Navigating the folding routes. Science 267:1619-1620.
63. Yue K, Dill KA. 1995. Forces of tertiary structural organization in globular proteins. Proc Natl Acad Sci USA 92:146-150.
64. Xu D, Lin SL, Nussinov R. 1997. Protein binding versus protein folding: The role of hydrophilic bridges in protein association. J Mol Biol 265:68-84.
65. Xu D, Tsai CJ, Nussinov R. 1998. Mechanism and evolution of protein dimerization. Protein Sci 7:533-544.
66. Zhang C, Chen J, DeLisi C. 1999. Protein-protein recognition: Exploring the energy funnels near the binding sites. Proteins SFG 34:255-267.