A stability pattern of protein hydrophobic mutations that reflects evolutionary structural optimization

Biophysical Journal

Volumn 89, Issue 5, 2005, Pages 3320-3331

  Godoy Ruiz, Raquel ^a   Perez Jimenez, Raul ^a   Ibarra Molero, Beatriz ^a   Sanchez Ruiz, Jose M ^a  

^a UNIVERSITY OF GRANADA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

ISOLEUCINE; THIOREDOXIN; VALINE;

AMINO ACID SUBSTITUTION; ARTICLE; ENERGY TRANSFER; ESCHERICHIA COLI; EVOLUTION; HYDROPHOBICITY; MOLECULAR MODEL; MUTATION; NONHUMAN; PROTEIN STABILITY; PROTEIN STRUCTURE;

ESCHERICHIA COLI;

EID: 27744443713     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1529/biophysj.105.067025     Document Type: Article

References (30)

1. Godoy-Ruiz, R., R. Perez-Jimenez, B. Ibarra-Molero, and J. M. Sanchez-Ruiz. 2004. Relation between protein stability, evolution and structure, as probed by carboxylic acid mutations. J. Mol. Biol. 336: 313-318.
2. Sanchez-Ruiz, J. M. 1995. Differential Scanning Calorimetry of Proteins. B. B. R. S. Biswas, editor. Plenum Press, New York, NY.
3. Lumb, K. J., and P. S. Kim. 1995. A buried polar interaction imparts structural uniqueness in a designed heterodimeric coiled coil. Biochemistry. 34:8642-8648.
4. Knappenberger, J. E., J. E. Smith, S. H. Thorpe, J. Z. Zitzewitz, and C. R. Matthews. 2002. A buried polar residue in the hydrophobic interface of a coiled-coil peptide, GNC4-p1, plays a thermodynamic, not a kinetic role. J. Mol. Biol. 321:1-6.
5. George, D. G., W. C. Baker, and L. T. Hunt. 1990. Mutation data matrix and its uses. Methods Enzymol. 183:333-351.
6. Dokholyan, N. V., and E. I. Shakhnovich. 2001. Understanding hierarchical protein evolution from first principles. J. Mol. Biol. 312:289-307.
7. Perez-Jimenez, R., R. Godoy-Ruiz, B. Ibarra-Molero, and J. M. Sanchez-Ruiz. 2004. The efficiency of different salts to screen charge interactions in proteins: a Hofmeister effect? Biophys. J. 86:2414-2429.
8. Georgescu, R. E., M. M. Garcia-Mira, M. L. Tasayco, and J. M. Sanchez-Ruiz. 2001. Heat capacity analysis of oxidized Escherichia coli thioredoxin fragments (1-73, 74-108) and their noncovalent complex. Evidence for the burial of apolar surface in protein unfolded states. Eur. J. Biochem. 268:1477-1485.
9. Ladbury, J. E., R. Wynn, H. W. Hellinga, and J. M. Sturtevant. 1993. Stability of oxidized Escherichia coli thioredoxin and its dependence on protonation of the aspartic acid residue in the 26 position. Biochemistry. 32:7526-7530.
10. Munoz, V., and J. M. Sanchez-Ruiz. 2004. Exploring protein-folding ensembles: a variable-barrier model for the analysis of equilibrium unfolding experiments. Proc. Natl. Acad. Sci. USA. 101:17646-17651.
11. Shrake, A., and J. A. Rupley. 1973. Environment and exposure to solvent of protein atoms. Lysozyme and insulin. J. Mol. Biol. 79: 351-371.
12. Chothia, C. 1975. Structural invariants in protein folding. Nature. 254: 304-308.
13. Shortle, D. 2003. Propensities, probabilities, and the Boltzmann hypothesis. Protein Sci. 12:1298-1302.
14. Lehmann, M., L. Pasamontes, S. F. Lassen, and M. Wyss. 2000. The consensus concept for thermostability engineering of proteins. Biochim. Biophys. Acta. 1543:408-415.
15. Ewens, W. J., and G. R. Grant. 2001. Statistical Methods in Bioinformatics: An introduction. Springer, New York, NY.
16. Lawrence, C. E., S. F. Altschul, M. S. Boguski, J. S. Liu, A. F. Neuwald, and J. C. Wootton. 1993. Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment. Science. 262: 208-214.
17. Loladze, V. V., D. N. Ermolenko, and G. I. Makhatadze. 2002. Thermodynamic consequences of burial of polar and non-polar amino acid residues in the protein interior. J. Mol. Biol. 320:343-357.
18. Takano, K., J. M. Scholtz, J. C. Sacchettini, and C. N. Pace. 2003. The contribution of polar group burial to protein stability is strongly context-dependent. J. Biol. Chem. 278:31790-31795.
19. Steiner, E. 1996. The Chemistry Math Book. Oxford University Press, Oxford, UK.
20. Eriksson, A. E., W. A. Baase, X. J. Zhang, D. W. Heinz, M. Blaber, E. P. Baldwin, and B. W. Matthews. 1992. Response of a protein structure to cavity-creating mutations and its relation to the hydrophobic effect. Science. 255:178-183.
21. Robic, S., M. Guzman-Casado, J. M. Sanchez-Ruiz, and S. Marqusee. 2003. Role of residual structure in the unfolded state of a thermophilic protein. Proc. Natl. Acad. Sci. USA. 100:11345-11349.
22. Yohannan, S., S. Faham, D. Yang, J. P. Whitelegge, and J. U. Bowie. 2004. The evolution of transmembrane helix kinks and the structural diversity of G protein-coupled receptors. Proc. Natl. Acad. Sci. USA. 101:959-963.
23. Baldwin, E., J. Xu, O. Hajiseyedjavadi, W. A, Baase, and B. W. Matthews. 1996. Thermodynamic and structural compensation in "size-switch" core repacking variants of bacteriophage T4 lysozyme. J. Mol. Biol. 259:542-559.
24. Malakauskas, S. M., and S. L. Mayo. 1998. Design, structure and stability of a hyperthermophilic protein variant. Nat. Struct. Biol. 5: 470-475.
25. Korkegian, A., M. E. Black, D. Baker, and B. L. Stoddard. 2005. Computational thermostabilization of an enzyme. Science. 308: 857-860.
26. Ibarra-Molero, B., and J. M. Sanchez-Ruiz. 2002. Genetic algorithm to design stabilizing surface-charge distributions in proteins. J. Phys. Chem. B. 106:6609-6613.
27. Taverna, D. M., and R. A. Goldstein. 2002. Why are proteins marginally stable? Proteins. 46:105-109.
28. Wolynes, P. G., J. N. Onuchic, and D. Thirumalai. 1995. Navigating the folding routes. Science. 267:1619-1620.
29. Chan, H. S., S. Shimizu, and H. Kaya. 2004. Cooperativity principles in protein folding. Methods Enzymol. 380:350-379.
30. Scalley-Kim, M., and D. Baker. 2004. Characterization of the folding energy landscapes of computer generated proteins suggests high folding free energy barriers and cooperativity may be consequences of natural selection. J. Mol. Biol. 338:573-583.