Protein folding via binding and vice versa

Folding and Design

Volumn 3, Issue 4, 1998, Pages

  Tsai, Chung Jung ^a   Xu, Dong ^b   Nussinov, Ruth ^b,c  

^a NATIONAL CANCER INSTITUTE   (United States)

^b SAIC FREDERICK INC   (United States)

^c TEL AVIV UNIVERSITY   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; BINDING AFFINITY; DRUG RECEPTOR BINDING; ENERGY TRANSFER; HYDROPHOBICITY; MOLECULAR RECOGNITION; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN PROTEIN INTERACTION; PROTEIN STABILITY; REVIEW;

EID: 0031868211     PISSN: 13590278     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1359-0278(98)00032-7     Document Type: Article

References (90)

1. Argos, P. (1988). An investigation of protein submits and domain interfaces. Protein Eng. 2, 101-113.
2. Janin, J., Miller, S. & Chothia, C. (1988). Surface, subunit interfaces and interior of oligomeric proteins. J. Mol. Biol. 204, 155-164.
3. Janin, J. & Chothia, C. (1990). The structure of protein-protein recognition sites. J. Biol. Chem. 265, 16027-16030.
4. Wu, L.C., Grandori, R. & Carey, J. (1994). Autonomous subdomains in protein folding. Protein Sci. 3, 359-371.
5. Jones, S. & Thornton, J.M. (1996). Principles of protein-protein interactions. Proc. Natl Acad. Sci. USA 93, 13-20.
6. Kippen, A.D., Sancho, J. & Fersht, A.R. (1994). Folding of barnase in parts. Biochemistry 33, 3778-3786.
7. Liang, H., Sandberg, W.S. & Terwillinger, T.C. (1993). Genetic fusion of subunits of a dimeric protein substantially enhances its stability and rate of folding. Proc. Natl Acad. Sci. USA 90, 7010-7014.
8. Cheng, Y.S., Yin, F.H., Foundling, S., Blomstrom, D. & Kettner, C.A. (1990). Stability and activity of human immunodeficiency virus protease: comparison of the natural dimer with a homologous, single-chain tethered dimer. Proc. Natl Acad. Sci. USA 87, 9660-9664.
9. Nussinov, R. & Wolfson, H J. (1991). Efficient detection of motifs in biological macromolecules by computer vision techniques. Proc. Natl Acad. Sci. USA 88, 10495-10499.
10. Bachar, O., Fischer, D., Nussinov, R. & Wolfson, H.J. (1993). A computer vision based technique for 3-D sequence independent structural comparison of proteins. Protein Eng. 6, 279-288.
11. Fischer, D., Lin, S.L., Wolfson, H.J. & Nussinov, R. (1994). 3-D, sequence-order independent structural comparison of trypsin against the crystallographic database reveals active site similarities to subtilisin-like and sulfhydryl proteases: potential implications. Protein Sci. 3, 769-778.
12. Tsai, C.J., Lin, S.L., Wolfson, H. & Nussinov, R. (1996). A dataset of protein-protein interfaces generated with a sequence-order-independent comparison technique. J. Mol. Biol. 260, 604-620.
13. Crippen, G.M. (1978). The tree structural organization of proteins. J. Mol. Biol. 126, 315-332.
14. Lesk, A.M. & Rose, G.D. (1981). Folding units in globular proteins. Proc. Natl Acad. Sci. USA 78, 4304-4308.
15. Rashin, A.A. (1981). Location of domains in globular proteins. Nature 291, 85-87.
16. Wodak, S.J. & Janin, J. (1981). Location of structural domains in proteins. Biochemistry 20, 6544-6552.
17. Zehfus, M.H. & Rose, G.D. (1986). Compact units in proteins. Biochemistry 25, 5759-5765.
18. Segawa, S. & Richards, P.M. (1988). Identification of regions of potential flexibility in protein structures: folding units and correlations with intron positions. Biopolymers 27, 23-40.
19. Moult, J. & Unger, R. (1991). An analysis of protein folding pathways. Biochemistry 30, 3816-3824.
20. Murphy, K., Bhakuni, V., Vie, D. & Freire, E. (1992). Molecular basis of cooperativity in protein folding. II. Structural identification of cooperative folding units and folding intermediates. J. Mol. Biol. 227, 293-306.
21. Zehfus, M.H. (1993). Improved calculations of compactness and a reevaluation of continuous compact units. Proteins 16, 293-300.
22. Holm, L. & Sander, C. (1994). Parser for protein folding units. Proteins 19, 256-268.
23. Islam, S.A., Luo, J. & Sternberg, M.J. (1995). Identification and analysis of domains in proteins. Protein Eng. 8, 513-525.
24. Siddiqui, A.S. & Barton, G.J. (1995). Continuous and discontinuous domains: an algorithm for the automatic generation of reliable protein domain definitions. Protein Sci. 4, 872-884.
25. Sowdhamini, R. & Blundell, T.L. (1995). An automatic method involving cluster analysis of secondary structures for the identification of domains in proteins. Protein Sci. 4, 506-520.
26. Swindell, M.B. (1995). A procedure for detecting structural domains in proteins. Protein Sci. 4, 103-112.
27. Panachenko, A.R., Luthey-Schulten, Z. & Wolynes, P.G. (1996). Foldons, protein structural modules and exons. Proc. Natl Acad. Sci. USA 93, 2008-2013.
28. Tsai, C.J. & Nussinov, R. (1997). Hydrophobic folding units derived from dissimilar structures and their interactions. Protein Sci. 6, 24-42.
29. Karplus, M. & Weaver, D.L. (1994). Protein folding dynamics: the diffusion-collision model and experimental data. Protein Sci. 3, 650-668.
30. Dill, K.A. (1990). Dominant forces in protein folding. Biochemistry 31, 7134-7155.
31. Garel, J.R. (1992). Folding of large proteins: multidomain and multisubunit proteins. In Protein Folding (Creighton, T.E., ed.), pp 405-454. W.H. Freeman and Company, New York.
32. Neet, K.E. & Timm, D.E. (1994). Conformational stability of dimeric proteins: quantitative studies by equilibrium denaturation. Protein Sci. 3, 2167-2174.
33. Wolynes, P.G., Onuchic, J.N. & Thirumalai, D. (1995). Navigating the folding routes. Science 267, 1619-1620.
34. Park, B.H., Huang, E.S. & Levitt, M. (1997). Factors affecting the ability of energy functions to discriminate correct from incorrect folds. J. Mol. Biol. 266, 831-846.
35. Honig, B. & Cohen, F.E. (1996). Adding backbone to protein folding: why proteins are polypeptides. Fold. Des. 1, R17-R20.
36. Shortle, D., Wang, Y., Gillespie, J.R. & Wrabl, J.O. (1996). Protein folding for realists: a timeless phenomenon. Protein Sci. 5, 991-1000.
37. Otzen, D.E., Itzhaki, L.S., ElMasry, N.F., Jackson, S.E. & Fersht, A.R. (1994). Structure of the transition state for the folding state for the folding/unfolding of the barley chymotrypsin inhibitor 2 and its implications for the mechanism of protein folding. Proc. Natl Acad. Sci. USA 91, 10422-10425.
38. Bryngelson, J.D., Onuchic, J.N., Socci, N.D. & Wolynes, P.G. (1995). Funnels, pathways and the energy landscape of protein folding. Proteins 21, 167-195.
39. Onuchic, J.N., Wolnyes, P.G., Luthey-Schulten, Z. & Socci, N.D. (1995). Towards an outline of the topography of a realistic protein folding funnel. Proc. Natl Acad. Sci. USA 92, 3626-3630.
40. Yue, K. & Dill, K.A. (1996). Folding proteins with a simple energy function and extensive conformational searching. Protein Sci. 5, 254-261.
41. Xu, D., Lin, S.L. & Nussinov, R. (1997). Protein binding versus protein folding: the role of hydrophilic bridges in protein associations, J. Mol. Biol. 265, 68-84.
42. Fersht, A.R. (1994). Characterizing transition states in protein folding: an essential step in the puzzle. Curr. Opin. Struct. Biol. 5, 79-84.
43. Fersht, A.R. (1994). Optimization of rates of protein folding: the nucleation-condensation mechanism and its implications. Proc. Natl Acad. Sci. USA 92, 10869-10873.
44. Tsai, C.J., Lin, S.L., Wolfson, H. & Nussinov, R. (1997). Studies of protein-protein interfaces: a statistical analysis of the Hydrophobic effect. Protein Sci. 6, 53-64.
45. Dill, K.A. & Chan, S.H. (1997). From Levinthal to pathways to funnels. Nat. Struct. Biol. 4, 10-19.
46. Tsai, C.J., Xu, D. & Nussinov, R. (1997). Structural motifs at protein-protein interfaces: protein cores versus two-state and three-state model complexes. Protein Sci. 6, 1793-1805.
47. Walls, P.M. & Sternberg, M.J.E. (1992). New algorithm to model protein-protein recognition based on surface complementarity. J. Mol. Biol. 228, 277-297.
48. Yu, M.H., Lee, K.N. & Kim, J. (1995). The Z type variation of human alpha 1-antitrypsin causes a protein folding defect. Nat. Struct. Biol. 2, 363-367.
49. Ruddon, R.W., Sherman, S.A. & Bedows, E. (1996). Protein folding in the endoplasmic reticulum: lessons from the human chorionic gonadotropin beta subunit. Protein Sci. 5, 1443-1452.
50. McCormack, A.L., Mononen, I., Kaartinen, V. & Yates, J.R. (1995). Localization of the disulfide bond involved in post-translational processing of glycosylasparaginase and disrupted by a mutation in the Finnish-type aspartylglycosaminuria. J. Biol. Chem. 270, 3212-3215.
51. Stott, K., Blackburn, J.M., Butler, P.J.G. & Perutz, M. (1995). Incorporation of glutamine repeats makes protein oligomerize: implications to neurodegenerative diseases. Proc. Natl Acad. Sci. USA 92, 6509-6513.
52. Soto, C., Castano, E.M., Frangione, B. & Inestrosa, N.C. (1995). Tha alpha-helical to beta-strand transition in the amino-terminal fragment of the amyloid beta-peptide modulates amyloid formation. J. Biol. Chem. 270, 3036-3067.
53. Ekiel, I., et al., & Gehring, K. (1997). NMR structural studies of human cystatin C dimers and monomers. J. Mol. Biol. 271, 266-277.
54. Bennett, M.J., Schlunegger, M.P. & Eisenberg, D. (1995). 3D domain swapping: a mechanism for oligomer assembly. Protein Sci. 4, 2455-2468.
55. Xu, D., Tsai, C.J. & Nussinov, R. (1998). Mechanism and evolution of protein dimerization. Protein Sci. 7, 533-544.
56. Bernstein, F.C., et al., & Tasumi M. (1977). The protein databank: a computer-based archival file for macromolecular structures. J. Mol. Biol. 112, 535-542.
57. Tsai, C.J., Lin, S.L., Wolfson, H. & Nussinov, R. (1996). Protein-protein interfaces: architectures and interactions in protein-protein interfaces and in protein cores. Their similarities and differences. CRC Crit. Rev. Biochem. Mol. Biol. 31, 127-152.
58. Rossmann, M.G., Liljas, A., Branden, C.I. & Banaszak, L.J. (1975). Evolutionary and structural relationships among dehydrogenases. Enzymes 11, 61-102.
59. Lesk, A. & Chothia, C. (1980). How different amino acid sequences determine similar protein structures: the structure and evolutionary dynamics of the globin fold. J. Mol. Biol. 136, 225-270.
60. Miller, S. (1989). Structure of interfaces between subunits of dimeric and tetrameric proteins. Protein Eng. 3, 77-83.
61. Grindley, H.M., Artymiuk, P.J., Rice, D.W. & Willet, P. (1993). Identification of tertiary structure resemblance in proteins using a maximal common subgraph isomorphism algorithm. J. Mol. Biol. 229, 707-721.
62. Orengo, C.A., Flores, T.P., Taylor, W.R. & Thornton, J.M. (1993). Identification and classification of protein fold families. J. Mol. Biol. 6, 485-500.
63. Slingsby, C., Bateman, O.A. & Simpson, A. (1993). Motifs in protein-protein interactions. Mol. Biol. Rep. 17, 185-195.
64. Fischer, D., Tsai, C.J., Wolfson, H. & Nussinov, R. (1995). A 3D sequence-independent representation of the protein data bank. Protein Eng. 8, 981-997.
65. Murzin, A.G., Brenner, S.E., Hubbard, T. & Chothia, C. (1995). SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247, 536-540.
66. Hutchinson, E.G. & Thornton, J.M. (1996). PROMOTIF - a program to identify and analyze structural motifs in proteins. Protein Sci. 5, 212-220.
67. Finkelstein, A.V. & Ptitsyn, O.B. (1987). Why do globular proteins fit the limited set of folding patterns? Prog. Biophys. Mol. Biol. 50, 171-190.
68. Chothia, C. (1992). One thousand families for the molecular biologist. Nature 357, 543-544.
69. Crippen, G.M. & Maiorov, V.N. (1995). How many protein folding motifs are there? J. Mol. Biol. 252, 144-151.
70. Lin, S.L., Tsai, C.J. & Nussinov, R. (1995). A study of four-helix bundles: investigating protein folding via similar architectural motifs in protein cores and in subunit interfaces. J. Mol. Biol. 248, 151-161.
71. Harris, N.L., Presnell, S.R. & Cohen, F.E. (1994). Four-helix bundle diversity in globular proteins. J. Mol. Biol. 236, 1356-1368.
72. Tsai, C.J. & Nussinov, R. (1997). Hydrophobic folding units at protein-protein interfaces: implications to protein folding and to protein-protein association. Protein Sci. 6, 1426-1437.
73. Viguera, A.R., Blanco, F.J. & Serrano, L. (1995). The order of secondary structure elements does not determine the structure of a protein but does affect its folding kinetics. J. Mol. Biol. 247, 670-681.
74. Garrett, J.B., Mullins, L.S. & Raushel, P.M. (1996). Are turns required for the folding of ribonuclease T1? Protein Sci. 5, 204-211.
75. Pieper, U., Hayakawa, K., Li, Z. & Herzberg, O. (1997). Circularly permuted beta-lactamase from Staphylococcus aureus PC1. Biochemistry 36, 8767-8774.
76. Korn, A.P. & Burnett, R.M. (1991). Distribution and complementarity of hydropathy in multisubunit proteins. Proteins 9, 37-55.
77. Vakser, I.A. & Aflalo, C. (1994). Hydrophobic docking: a proposed enhancement to molecular recognition techniques. Proteins 20, 320-329.
78. Young, L., Jernigan, R.L. & Covell, D.G. (1994). A role for surface hydrophobicity in protein-protein recognition. Protein Sci. 3, 717-729.
79. Le Bras, G., Auzat, I. & Garel, J.R. (1995). Tetramer-dimer equilibrium of phosphofruktokinase and formation of hybrid tetramers. Biochemistry 34, 13203-13210.
80. Hendsch, B.Z.S. & Tidor, B. (1994). Do salt bridges stabilize proteins? A continuum electrostatic analysis. Protein Sci. 3, 211-226.
81. Horton, N. & Lewis, M. (1992). Calculation of the free energy of association for protein complexes. Protein Sci. 1, 169-181.
82. Xu, D., Tsai, C.J. & Nussinov, R. (1997). Hydrogen bonds and salt bridges across protein-protein interfaces. Protein Eng. 10, 999-1012.
83. Bowie, J.U., Reidhaar-Olson, J.F., Lim, W.A. & Sauer, R.T. (1990). Deciphering the message in protein sequences: tolerance to amino acid substitutions. Science 247, 1306-1310.
84. Xie, D. & Freire, E. (1994). Structure based prediction of protein folding intermediates. J. Mol. Biol. 242, 62-80.
85. Luque, I., Mayorga, O.L. & Freire, E. (1996). Structure-based thermodynamic scale of α-helix propensities in amino acids. Biochemistry 35, 13681-13688.
86. Hilser, V.J. & Freire, E. (1997). Predicting the equilibrium protein folding pathway: structure-based analysis of staphylococcal nuclease. Proteins 27, 171-183.
87. Weng, Z., DeLisi, C. & Vajda, S. (1997). Empirical free energy calculation: comparison to calorimetric data. Protein Sci. 6, 1976-1984.
88. Gomez, J. & Freire, E. (1995). Thermodynamic mapping of the inhibitor site of the aspartic protease endothiapepsin. J. Mol. Biol. 252, 337-350.
89. Sternberg, M.J.E. & Chickos, J.S. (1994). Protein sidechain conformational entropy derived from fusion data - comparison with other empirical scales. Protein Eng. 7, 149-155.
90. Zhang, C., Cornette, J.L. & DeLisi, C. (1997). Consistency in structural energetics of protein folding and peptide recognition. Protein Sci. 6, 1057-1064.