A strategy for detecting the conservation of folding-nucleus residues in protein superfamilies

Folding and Design

Volumn 3, Issue 4, 1998, Pages 239-251

  Michnick, Stephen W ^a   Shakhnovich, Eugene ^b  

^a UNIVERSITÉ DE MONTRÉAL   (Canada)

^b HARVARD UNIVERSITY   (United States)

Author keywords

Folding nucleus; Protein folding; Protein superfamilies; Sequence design

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; GENETIC CONSERVATION; GENETIC ENGINEERING; HYDROPHOBICITY; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN FAMILY; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE; PROTEIN STABILITY; RESIDUE ANALYSIS;

EID: 0031867090     PISSN: 13590278     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1359-0278(98)00035-2     Document Type: Article

References (67)

1. Doolittle, R.F. (1995). The multiplicity of domains in proteins. Annu. Rev. Biochem. 64, 287-314.
2. Doolittle, R.F., Feng, D.F., Tsang, S., Cho, G. & Little, E. (1996). Determining divergence times of the major kingdoms of living organisms with a protein clock. Science 271, 470-477.
3. Holm, L. & Sander, C. (1993). Protein structure comparison by alignment of distance matrices. J. Mol. Biol. 233, 123-138.
4. Holm, L. & Sander, C. (1996). Alignment of three-dimensional protein structures: network server for database searching. Methods Enzymol. 266, 653-662.
5. Ponting, C.P. & Benjamin, D.R. (1996). A novel family of Ras-binding domains. Trends Biochem. Sci. 21, 422-425.
6. Russell, R.B., Copley, R.R. & Barton, G.J. (1996). Protein fold recognition by mapping predicted secondary structures. J. Mol. Biol. 259, 349-365.
7. Abkevich, V.I., Gutin, A.M. & Shakhnovich, E.I. (1994). Specific nucleus as the transition state for protein folding: evidence from the lattice model. Biochemistry 33, 10026-10036.
8. Guo, Z.Y. & Thirumalai, D. (1995). Kinetics of protein folding - nucleation mechanism, time scales, and pathways. Biopolymers 36, 83-102.
9. Alexander, P., Orban, J. & Bryan, P. (1992). Kinetic analysis of folding and unfolding the 56 amino acid IgG-binding domain of streptococcal protein G. Biochemistry 31, 7243-7248.
10. Johnson, B.H. & Hecht, M.H. (1994). Recombinant proteins can be isolated from E. coli cells by repeated cycles of freezing and thawing. BioTechnology 12, 1357-1360.
11. Schindler, T., Herrler, M., Marahiel, M.A. & Schmid, F.X. (1995). Extremely rapid protein folding in the absence of intermediates. Nat. Struct. Biol. 2, 663-673.
12. Shakhnovich, E.I., Abkevich, V. & Ptitsyn, O. (1996). Conserved residues and the mechanism of protein folding. Nature 379, 96-98.
13. Shakhnovich, E.I. (1997). Theoretical studies of protein-folding thermodynamics and kinetics. Curr. Opin. Struct. Biol. 7, 29-40.
14. Sosnick, T.R., Mayne, L., Hiller, R. & Englander, S.W. (1994). The barriers in protein folding. Nat. Struct. Biol. 1, 149-156.
15. 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.
16. Perl, D., et al., & Schmid, F.X. (1998). Conservation of rapid two-state folding in mesophilic, thermophilic and hyperthermophilic cold shock proteins. Nat. Struct. Biol. 5, 229-235.
17. Itzhaki, L.S., Otzen, D.E. & Fersht, A.R. (1995). The structure of the transition state for folding of chymotrypsin inhibitor 2 analysed by protein engineering methods: evidence for a nucleation-condensation mechanism for protein folding. J. Mol. Biol. 254, 260-288.
18. Lopez-Hernandez, E. & Serrano, L. (1996). Structure of the transition state for folding of the 129 aa protein CheY resembles that of a smaller protein, Cl-2. Fold. Des. 1, 43-55.
19. Jackson, S.E., Main, E.R.G. & Fulton, K.F. (1998). Folding of FKBP12: pathway of folding and thermodynamic analysis of the transition state for folding. Biochemistry, in press.
20. de Prat Gay, G., Ruiz-Sanz, J., Davis, B. & Fersht, A.R. (1994). The structure of the transition state for the association of two fragments of the barley chymotrypsin inhibitor 2 to generate native-like protein: implications for mechanisms of protein folding. Proc. Natl Acad. Sci. USA 91, 10943-10946.
21. Fersht, A.R. (1995). Optimization of rates of protein folding - the nucleation-condensation mechanism and its implications. Proc. Natl Acad. Sci. USA 92, 10869-10873.
22. Itzhaki, L.S., Otzen, D.E. & Fersht, A.R. (1995). The structure of the transition state for folding of chymotrypsin inhibitor 2 analysed by protein engineering methods - evidence for a nucleation-condensation mechanism for protein folding. J. Mol. Biol. 254, 260-288.
23. Ruiz-Sanz, J., de Prat Gay, G., Otzen, D.E. & Fersht, A.R. (1995). Protein fragments as models for events in protein folding pathways: protein engineering analysis of the association of two complementary fragments of the barley chymotrypsin inhibitor 2 (Cl-2). Biochemistry 34, 1695-1701.
24. Nassar, N., et al., & Wittinghofer, A. (1995). The 2.2 Å crystal structure of the Ras-binding domain of the serine/threonine kinase c-Raf1 in complex with Rap1A and a GTP analogue. Nature 375, 554-560.
25. Vijay-Kumar, S., Bugg, C.E. & Cook, W.J. (1987). Structure of ubiquitin refined at 1.8 Å resolution. J. Mol. Biol. 194, 531-544.
26. Emerson, S.D., et al., & Fry, D.C. (1994). Chemical shift assignments and folding topology of the Ras-binding domain of human Raf-1 as determined by heteronuclear three-dimensional NMR spectroscopy. Biochemistry 33, 7745-7752.
27. Emerson, S.D., et al., & Fry, D.C. (1995). Solution structure of the Ras-binding domain of c-Raf-1 and identification of its Ras interaction surface. Biochemistry 34, 6911-6918.
28. 1H NMR study of human ubiquitin: a main chain directed assignment and structure analysis. Biochemistry 26, 7272-7281.
29. Briggs, M.S. & Roder, H. (1992). Early hydrogen-bonding events in the folding reaction of ubiquitin. Proc. Natl Acad. Sci. USA 89, 2017-2021.
30. Cox, J.P., Evans, P.A., Packman, L.C., Williams, D.H. & Woolfson, D.N. (1993). Dissecting the structure of a partially folded protein. Circular dichroism and nuclear magnetic resonance studies of peptides from ubiquitin. J. Mol. Biol. 234, 483-492.
31. Harding, M.M., Williams, D.H. & Woolfson, D.N. (1991). Characterization of a partially denatured state of a protein by two-dimensional NMR: reduction of the hydrophobic interactions in ubiquitin. Biochemistry 30, 3120-3128.
32. Khorasanizadeh, S., Peters, I.D., Butt, T.R. & Roder, H. (1993). Folding and stability of a tryptophan-containing mutant of ubiquitin. Biochemistry 32, 7054-7063.
33. Khorasanizadeh, S., Peters, I.D. & Roder, H. (1996). Evidence for a three-state model of protein folding from kinetic analysis of ubiquitin variants with altered core residues. Nat. Struct. Biol. 3, 193-205.
34. Stockman, B.J., Euvrard, A. & Scahill, T.A. (1993). Heteronuclear three-dimensional NMR spectroscopy of a partially denatured protein: the A-state of human ubiquitin. J. Biomol. NMR 3, 285-296.
35. Wintrode, P.L., Makhatadze, G.I. & Privalov, P.L. (1994). Thermodynamics of ubiquitin unfolding. Proteins 18, 246-253.
36. Woolfson, D.N., Cooper, A., Harding, M.M., Williams, D.H. & Evans, P.A. (1993). Protein folding in the absence of the solvent ordering contribution to the hydrophobic interaction. J. Mol. Biol. 229, 502-511.
37. Ptitsyn, O. (1998). Protein folding and protein evolution: common folding nucleus in different subfamilies of c-type cytochromes. J. Mol. Biol. 278, 655-666.
38. Mirny, LA. & Shakhnovich, E.I. (1996). How to derive a protein folding potential? A new approach to an old problem. J. Mol. Biol. 264, 1164-1179.
39. Varshavsky, A. (1996). The N-end rule: functions, mysteries, uses. Proc. Natl Acad. Sci. USA 93, 12142-12149.
40. Smith, S.E., Koegl, M. & Jentsch, S. (1996). Role of the ubiquitin/proteasome system in regulated protein degradation in Saccharomyces cerevisiae. Biol. Chem. 377, 437-446.
41. Hershko, A. (1996). Lessons from the discovery of the ubiquitin system. Trends Biochem. Sci. 21, 445-449.
42. Wittinghofer, A. & Nassar, N. (1996). How Ras-related proteins talk to their effectors. Trends Biochem. Sci. 21, 488-491.
43. Avruch, J., Zhang, X.F. & Kyriakis, J.M. (1994). Raf meets Ras: completing the framework of a signal transduction pathway. Trends Biochem. Sci. 19, 279-283.
44. Shakhnovich, E.I. & Gutin, A.M. (1993). A new approach to the design of stable proteins. Protein Eng. 6, 793-800.
45. Shakhnovich, E.I. & Gutin, A.M. (1993). Engineering of stable and fast-folding sequences of model proteins. Proc. Natl Acad. Sci. USA 90, 7195-7199.
46. Tisi, L.C. & Evans, P.A. (1995). Conserved structural features on protein surfaces: small exterior hydrophobic clusters. J. Mol. Biol. 249, 251-258.
47. Minor, D., Jr. & Kim, P.S. (1994). Measurement of the beta-sheet-forming propensities of amino acids. Nature 367, 660-663.
48. Minor, D., Jr. & Kim, P.S. (1994). Context is a major determinant of beta-sheet propensity. Nature 371, 264-267.
49. Smith, C.K., Withka, J.M. & Regan, L. (1994). A thermodynamic scale for the beta-sheet forming tendencies of the amino acids. Biochemistry 33, 5510-5517.
50. Smith, C.K. & Regan, L. (1995). Guidelines for protein design: the energetics of beta sheet side chain interactions. Science 270, 980-982.
51. Wikstrom, M., Drakenberg, T., Forsen, S., Sjobring, U. & Bjorck, L. (1994). Three-dimensional solution structure of an immunoglobulin light chain-binding domain of protein L. Comparison with the IgG-binding domains of protein G. Biochemistry 33, 14011-14017.
52. Gronenborn, A.A., et al., & Clore, G.M. (1991). A novel, highly stable fold of the immunoglobulin binding domain of streptococcal protein G. Science 253, 657-661.
53. Achari, A., et al., & Whitlow, M. (1992). 1.67-Å X-ray structure of the B2 immunoglobulin-binding domain of streptococcal protein G and comparison to the NMR structure of the B1 domain. Biochemistry 31, 10449-10457.
54. Jacobson, B.L, Chae, Y.K., Markley, J.L, Rayment, I. & Holden, H.M. (1993). Molecular structure of the oxidized, recombinant, heterocyst [2Fe-2S] ferredoxin from Anabaena 7120 determined to 1.7-Å resolution. Biochemistry 32, 6788-6793.
55. Romao, M.J., et al., & Huber, R. (1995). Crystal structure of the xanthine oxidase-related aldehyde oxido-reductase from D. gigas. Science 270, 1170-1176.
56. Swaminathan, S., Furey, W., Pletcher, J. & Sax, M. (1992). Crystal structure of staphylococcal enterotoxin B, a superantigen. Nature 359, 801-806.
57. 1H NMR sequential assignments and identification of secondary structural elements in oxidized putidaredoxin, an electron-transfer protein from Pseudomonas. Biochemistry 31, 1961-1968.
58. Minor, D., Jr. & Kim, P.S. (1996). Context-dependent secondary structure formation of a designed protein sequence. Nature 380, 730-734.
59. Sander, C. & Schneider, R. (1991). Database of homology-derived protein structures and the structural meaning of sequence alignment. Proteins 9, 56-68.
60. Shoemaker, B.A., Wang, J. & Wolynes, P.G. (1997). Structural correlations in protein folding funnels. Proc. Natl Acad. Sci. USA 94, 777-782.
61. Beasley, J.R. & Hecht, M.H. (1997). Protein design: the choice of de novo sequences. J. Biol. Chem. 272, 2031-2034.
62. Kamtekar, S., Schiffer, J.M., Xiong, H., Babik, J.M. & Hecht, M.H. (1993). Protein design by binary patterning of polar and nonpolar amino acids. Science 262, 1680-1685.
63. Dalal, S., Balasubramanian, S. & Regan, L. (1997). Protein alchemy - changing beta-sheet into alpha-helix. Nat. Struct. Biol. 4, 548-552.
64. Holm, L. & Sander, C. (1997). Dali/FSSP classification of three-dimensional protein folds. Nucleic Acids Res. 25, 231-234.
65. Holm, L. & Sander, C. (1995). Dali: a network tool for protein structure comparison. Trends Biochem. Sci. 20, 478-480.
66. Kabsch, W. & Sander, C. (1983). Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22, 2577-2637.
67. Kraulis, P.J. (1991). MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr. 24, 946-950.