Functionality of wrapping defects in soluble proteins: What cannot be kept dry must be conserved

Journal of Molecular Biology

Volumn 337, Issue 2, 2004, Pages 477-483

  Fernández, Ariel ^a  

^a Indiana University   (United States)

Author keywords

DIP, database of interacting proteins; Hydrogen bond; Molecular evolution; Protein interactivity; Protein structure; Wrapping

Indexed keywords

PROTEOME;

ARTICLE; BINDING SITE; CORRELATION ANALYSIS; HYBRID; HYDROGEN BOND; MUTATION; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN STRUCTURE; SCALE UP; SOLUBILITY; STATISTICAL ANALYSIS;

EID: 18544394624     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2004.01.050     Document Type: Article

References (28)

1. Nemethy G., Steinberg I.Z., Scheraga H.A. The influence of water structure and hydrophobic contacts on the strength of side-chain hydrogen bonds in proteins. Biopolymers. 1:1963;43-69.
2. Vila J.A., Ripoll D.R., Scheraga H.A. Physical reasons for the unusual alpha-helix stabilization afforded by charged or neutral polar residues in alanine-rich peptides. Proc. Natl Acad. Sci. USA. 97:2000;13075-13079.
3. Fernández A., Sosnick T., Colubri A. Dynamics of hydrogen bond desolvation in protein folding. J. Mol. Biol. 321:2002;659-675.
4. Fernández A., Scheraga H.A. Insufficiently dehydrated hydrogen bonds as determinants of protein interactions. Proc. Natl Acad. Sci. USA. 100:2003;113-118.
5. Fernández A., Kardos J., Scott L.R., Goto Y., Berry R.S. Structural defects and the diagnosis of amyloidogenic propensity. Proc. Natl Acad. Sci. USA. 100:2003;6446-6451.
6. Fernández A., Scott L.R. Dehydron: a structurally encoded signal for protein interaction. Biophys. J. 85:2003;1914-1928.
7. Fernández A., Scott L.R. Adherence of packing defects in soluble proteins. Phys. Rev. Letters. 91:2003;018102.
8. Fernández A., Berry R.S. Proteins with H-bond packing defects are highly interactive with lipid bilayers: implications for amyloidogenesis. Proc. Natl Acad. Sci. USA. 100:2003;2391-2396.
9. Editors of Bourne P.E., Weissig H. Structural Bioinformatics. 2003;Wiley, New York.
10. Bleasby A.J., Akrigg D., Attwood T.K. OWL: a nonredundant composite protein sequence database. Nucl. Acids Res. 22:1994;3574-3577.
11. Ball P. Keeping dry in water. Nature. 423:2003;25-26.
12. Warshel A. Electrostatic origin of the catalytic power of enzymes and the role of pre-organized active sites. J. Biol. Chem. 273:1998;27035-27038.
13. Sham Y.Y., Chou Z.T., Tao H., Warshel A. Examining methods for calculations of binding free energies: LRA, LIE, PDLD-LRA, and PDLD/S-LRA calculations for ligand binding to an HIV protease. Proteins: Struct. Funct. Genet. 39:2000;393-407.
14. Muegge I., Schweins T., Warshel A. Electrostatic contributions to protein-protein binding affinities: application to Rap/Raf interaction. Proteins: Struct. Funct. Genet. 30:1998;407-423.
15. Fernández A., Scott L.R., Scheraga H.A. Amino acid residues at protein-protein interfaces: why is propensity so different from relative abundance? J. Phys. Chem. ser. B. 107:2003;9929-9932.
16. Xenarios I., Salwinski L., Duan X.J., Higney P., Kim S.M., Eisenberg D. DIP, the database of interacting proteins: a research tool for studying cellular networks of protein interactions. Nucl. Acids Res. 30:2002;303-305.
17. Kragelund B.B., Osmark P., Neergaard T., Schiot J., Kristiansen K., Knudsen J., Poulsen F.M. The formation of native-like structure containing eight conserved hydrophobic residues is rate limiting in two-state protein fold of acbp. Nature Struct. Biol. 6:1999;594-601.
18. Mirny L., Shakhnovich E. Universally conserved positions in protein folds: reading evolutionary signals about stability, folding kinetics and function. J. Mol. Biol. 291:1999;177-196.
19. Plaxco K., Larson S., Ruczinski I., Riddle D.S., Thayer E.C., Buchwitz B., et al. Evolutionary conservation in protein folding kinetics. J. Mol. Biol. 298:2000;303-312.
20. Altschul S.F., et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucl. Acids Res. 25:1997;3389-3402.
21. Higgins D.G., Thompson J.D., Gibson T.J. Using CLUSTAL for multiple sequence alignments. Methods Enzymol. 266:1996;383-402.
22. Shenkin S.P., Erman B., Mastrandrea L.D. Information-theoretical entropy as a measure of sequence variability. Proteins: Struct. Funct. Genet. 11:1991;297-313.
23. Voet D., Voet J.G. Biochemistry. 1995;Wiley, New York.
24. Wilson A.C. The molecular basis of evolution. Sci. Am. 253:1985;164-173.
25. Moore G.R., Pettigrew G.W. Cytochromes c. Evolutionary, Structural and Physico-Chemical Aspects. 1990;Springer, Berlin.
26. Brown C., Takayama S., Campen A.M., Vise P., Marshall T.W., Oldfield C.J., et al. Evolutionary rate heterogeneity in proteins with long disordered regions. J. Mol. Evol. 55:2002;104-110.
27. Fernández A. What caliber pore is like a pipe? Nanotubes as modulators of ionic gradients. J. Chem. Phys. 119:2003;5315-5319.
28. Ma B., Elkayam T., Wolfson H., Nussinov R. Protein-protein interactions: structurally conserved residues distinguish between binding sites and exposed protein surfaces. Proc. Natl Acad. Sci. USA. 100:2003;5772-5777.