Relationship between sequence determinants of stability for two natural homologous proteins with different folds

Biochemistry

Volumn 45, Issue 35, 2006, Pages 10542-10553

  Van Dorn, Laura O ^a   Newlove, Tracey ^a   Chang, Saemin ^a   Ingram, Wendy M ^a   Cordes, Matthew H J ^a  

^a UNIVERSITY OF ARIZONA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; BIOCHEMISTRY; CONFORMATIONS; MOLECULAR STRUCTURE; MUTAGENESIS; NUCLEAR MAGNETIC RESONANCE;

EVOLUTIONARY TRANSITIONS; HOMOLOGOUS PROTEINS; SECONDARY STRUCTURE; STABILITY DETERMINANTS;

PROTEINS;

MUTANT PROTEIN; PROTEIN; PROTEIN CRO; PROTEIN LAMBDA CRO; PROTEIN P22 CRO; UNCLASSIFIED DRUG;

ALPHA HELIX; AMINO ACID SEQUENCE; ARTICLE; BETA SHEET; CARBOXY TERMINAL SEQUENCE; MOLECULAR EVOLUTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN STABILITY; PROTEIN STRUCTURE; SEQUENCE HOMOLOGY; STRUCTURE ANALYSIS; WILD TYPE;

ALANINE; AMINO ACID MOTIFS; AMINO ACID SEQUENCE; DNA-BINDING PROTEINS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MUTAGENESIS; PROTEIN FOLDING; PROTEIN STRUCTURE, TERTIARY; PROTEINS; REPRESSOR PROTEINS; SEQUENCE HOMOLOGY, AMINO ACID; STRUCTURAL HOMOLOGY, PROTEIN; VIRAL PROTEINS;

EID: 33748269731     PISSN: 00062960     EISSN: None     Source Type: Journal    
DOI: 10.1021/bi060853p     Document Type: Article

References (42)

1. Andreeva, A., Howorth, D., Brenner, S. E., Hubbard, T. J., Chothia, C., and Murzin, A. G. (2004) SCOP database in 2004: Refinements integrate structure and sequence family data, Nucleic Acids Res. 32, D226-9.
2. Grishin, N. V. (2001) Fold change in evolution of protein structures, J. Struct. Biol. 134, 167-85.
3. Lauber, T., Schulz, A., Schweimer, K., Adermann, K., and Marx, U. C. (2003) Homologous proteins with different folds: The three-dimensional structures of domains 1 and 6 of the multiple Kazal-type inhibitor LEKTI, J. Mol. Biol. 328, 205-19.
4. Newlove, T., Konieczka, J. H., and Cordes, M. H. (2004) Secondary structure switching in Cro protein evolution, Structure 12, 569-81.
5. Babajide, A., Hofacker, I. L., Sippl, M. J., and Stadler, P. F. (1997) Neutral networks in protein space: A computational study based on knowledge-based potentials of mean force, Folding Des. 2, 261-9.
6. Bornberg-Bauer, E. (1997) How are model protein structures distributed in sequence space? Biophys. J. 73, 2393-403.
7. Govindarajan, S., and Goldstein, R. A. (1997) The foldability landscape of model proteins, Biopolymers 42, 427-38.
8. Babajide, A., Farber, R., Hofacker, I. L., Inman, J., Lapedes, A. S., and Stadler, P. F. (2001) Exploring protein sequence space using knowledge-based potentials, J. Theor. Biol. 212, 35-46.
9. Cui, Y., Wong, W. H., Bornberg-Bauer, E., and Chan, H. S. (2002) Recombinatoric exploration of novel folded structures: A heteropolymer-based model of protein evolutionary landscapes, Proc. Natl. Acad. Sci. U.S.A. 99, 809-14.
10. Dalal, S., and Regan, L. (2000) Understanding the sequence determinants of conformational switching using protein design, Protein Sci. 9, 1651-9.
11. Dalal, S., Balasubramanian, S., and Regan, L. (1997) Protein alchemy: Changing β-sheet into α-helix, Nat. Struct. Biol. 4, 548-52.
12. Alexander, P. A., Rozak, D. A., Orban, J., and Bryan, P. N. (2005) Directed evolution of highly homologous proteins with different folds by phage display: Implications for the protein folding code, Biochemistry 44, 14045-54.
13. Cordes, M. H., Walsh, N. P., McKnight, C. J., and Sauer, R. T. (1999) Evolution of a protein fold in vitro, Science 284, 325-8.
14. Cerasoli, E., Sharpe, B. K., and Woolfson, D. N. (2005) ZiCo: A peptide designed to switch folded state upon binding zinc, J. Am. Chem. Soc. 127, 15008-9.
15. Cordes, M. H., Burton, R. E., Walsh, N. P., McKnight, C. J., and Sauer, R. T. (2000) An evolutionary bridge to a new protein fold, Nat. Struct. Biol. 7, 1129-32.
16. Ambroggio, X. I., and Kuhlman, B. (2006) Computational design of a single amino acid sequence that can switch between two distinct protein folds, J. Am. Chem. Soc. 128, 1154-61.
17. Ohlendorf, D. H., Tronrud, D. E., and Matthews, B. W. (1998) Refined structure of Cro repressor protein from bacteriophage λ suggests both flexibility and plasticity, J. Mol. Biol. 280, 129-36.
18. LeFevre, K. R., and Cordes, M. H. (2003) Retroevolution of λ Cro toward a stable monomer, Proc. Natl. Acad. Sci. U.S.A. 100, 2345-50.
19. Milla, M. E., Brown, B. M., and Sauer, R. T. (1993) P22 Arc repressor: Enhanced expression of unstable mutants by addition of polar C-terminal sequences, Protein Sci. 2, 2198-205.
20. Myers, J. K., Pace, C. N., and Scholtz, J. M. (1995) Denaturant m values and heat capacity changes: Relation to changes in accessible surface areas of protein unfolding, Protein Sci. 4, 2138-48.
21. Delaglio, F., Grzesiek, S., Vuister, G. W., Zhu, G., Pfeifer, J., and Bax, A. (1995) NMRPipe: A multidimensional spectral processing system based on UNIX pipes, J. Biomol. NMR 6, 277-93.
22. Johnson, B. A., and Blevins, R. (1994) NMRView. A computer program for the visualization and analysis of NMR data, J. Biomol. NMR 4, 603-14.
23. Newlove, T., Atkinson, K. R., Van Dorn, L. O., and Cordes, M. H. (2006) A trade between similar but nonequivalent intrasubunit and intersubunit contacts in Cro dimer evolution, Biochemistry 45, 6379-91.
24. 15N chemical shift referencing in biomolecular NMR, J. Biomol. NMR 6, 135-40.
25. Wuthrich, K. (1986) NMR of Proteins and Nucleic Acids, John Wiley and Sons, New York.
26. Yu, M. H., Weissman, J. S., and Kim, P. S. (1995) Contribution of individual side-chains to the stability of BPTI examined by alanine-scanning mutagenesis, J. Mol. Biol. 249, 388-97.
27. Milla, M. E., Brown, B. M., and Sauer, R. T. (1994) Protein stability effects of a complete set of alanine substitutions in Arc repressor, Nat. Struct. Biol. 1, 518-23.
28. Mossing, M. C., and Sauer, R. T. (1990) Stable, monomeric variants of λ Cro obtained by insertion of a designed β-hairpin sequence, Science 250, 1712-5.
29. Jana, R., Hazbun, T. R., Mollah, A. K., and Mossing, M. C. (1997) A folded monomeric intermediate in the formation of λ Cro dimer-DNA complexes, J. Mol. Biol. 273, 402-16.
30. Darling, P. J., Holt, J. M., and Ackers, G. K. (2000) Coupled energetics of λ cro repressor self-assembly and site-specific DNA operator binding I: Analysis of cro dimerization from nanomolar to micromolar concentrations, Biochemistry 39, 11500-7.
31. Albright, R. A., and Matthews, B. W. (1998) Crystal structure of A-Cro bound to a consensus operator at 3.0 Å resolution, J. Mol. Biol. 280, 137-51.
32. Viguera, A. R., and Serrano, L. (1999) Stable proline box motif at the N-terminal end of α-helices, Protein Sci. 8, 1733-42.
33. Aurora, R., and Rose, G. D. (1998) Helix capping, Protein Sci. 7, 21-38.
34. Aurora, R., Srinivasan, R., and Rose, G. D. (1994) Rules for α-helix termination by glycine, Science 264, 1126-30.
35. Hutchinson, E. G., and Thornton, J. M. (1994) A revised set of potentials for β-turn formation in proteins, Protein Sci. 3, 2207-16.
36. Lattman, E. E., and Rose, G. D. (1993) Protein folding: What is the question? Proc. Natl. Acad. Sci. U.S.A. 90, 439-41.
37. Aggarwal, A. K., Rodgers, D. W., Drottar, M., Ptashne, M., and Harrison, S. C. (1988) Recognition of a DNA operator by the repressor of phage 434: A view at high resolution, Science 242, 899-907.
38. Beamer, L. J., and Pabo, C. O. (1992) Refined 1.8 Å crystal structure of the λ repressor-operator complex, J. Mol. Biol. 227, 177-96.
39. Mondragon, A., and Harrison, S. C. (1991) The phage 434 Cro/OR1 complex at 2.5 Å resolution, J. Mol. Biol. 219, 321-34.
40. Minor, D. L., Jr., and Kim, P. S. (1996) Context-dependent secondary structure formation of a designed protein sequence, Nature 380, 730-4.
41. Kraulis, P. J. (1991) MOLSCRIPT: A program to produce both detailed and schematic plots of protein structures, J. Appl. Crystallogr. 24, 946-50.
42. Merritt, E. A., and Bacon, D. J. (1997) Raster3D: Photorealistic Molecular Graphics, Methods Enzymol. 277, 505-24.