Cysteine Function Governs Its Conservation and Degeneration and Restricts Its Utilization on Protein Surfaces

Journal of Molecular Biology

Volumn 404, Issue 5, 2010, Pages 902-916

  Marino, Stefano M ^a   Gladyshev, Vadim N ^a  

^a HARVARD MEDICAL SCHOOL   (United States)

Author keywords

Amino acid conservation; Cysteine; Exposure; Hydrophobic scales; Reactive thiols

Indexed keywords

CYSTEINE;

AMINO ACID ANALYSIS; ARTICLE; GENETIC CONSERVATION; HUMAN; HYDROPHOBICITY; MOLECULAR EVOLUTION; NONHUMAN; PHYSICAL CHEMISTRY; PKA; PRIORITY JOURNAL; PROTEIN FUNCTION; PROTEIN LOCALIZATION; PROTEIN STRUCTURE; STATISTICAL ANALYSIS;

EID: 78649529306     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2010.09.027     Document Type: Article

References (23)

1. Trifonov E.N. The triplet code from first principles. J. Biomol. Struct. Dyn. 2004, 22:1-11.
2. Jordan I.K., Kondrashov F.A., Adzhubei I.A., Wolf Y.I., Koonin E.V., Kondrashov A.S., Sunyaev S. A universal trend of amino acid gain and loss in protein evolution. Nature 2005, 433:633-638.
3. Wu H., Ma B.G., Zhao J.T., Zhang H.Y. How similar are amino acid mutations in human genetic diseases and evolution. Biochem. Biophys. Res. Commun. 2007, 362:233-237.
4. Fomenko D.E., Xing W., Adair B.M., Thomas D.J., Gladyshev V.N. High-throughput identification of catalytic redox-active cysteine residues. Science 2007, 315:387-389.
5. Zhang Y., Baranov P.V., Atkins J.F., Gladyshev V.N. Pyrrolysine and selenocysteine use dissimilar decoding strategies. J. Biol. Chem. 2005, 280:20740-20751.
6. Janin J. Surface and inside volumes in globular proteins. Nature 1979, 277:491-492.
7. Rose G.D., Geselowitz A.R., Lesser G.J., Lee R.H., Zehfus M.H. Hydrophobicity of amino acid residues in globular proteins. Science 1985, 229:834-838.
8. Kyte J., Doolittle R.F. A simple method for displaying the hydropathic character of a protein. J. Mol. Biol. 1982, 157:105-132.
9. Damodaran S., Song K.B. The role of solvent polarity in the free energy of transfer of amino acid side chains from water to organic solvents. J. Biol. Chem. 1986, 261:7220-7222.
10. Fauchere J.L., Pliska V. Hydrophobic parameters pi of amino-acid side chains from the partitioning of N-acetyl-amino-acid amides. Eur. J. Med. Chem. 1983, 18:369-375.
11. Radzicka A., Wolfenden R. Comparing the polarities of the amino acids: side-chain distribution coefficients between the vapor phase, cyclohexane, 1-octanol, and neutral aqueous solution. Biochemistry 1988, 27:1664-1670.
12. Karplus P.A. Hydrophobicity regained. Protein Sci. 1997, 6:1302-1307.
13. Thomas A., Milon A., Brasseur R. Partial atomic charges of amino acids in proteins. Proteins 2004, 56:102-109.
14. Iqbalsyah T.M., Moutevelis E., Warwicker J., Errington N., Doig A.J. The CXXC motif at the N terminus of an alpha-helical peptide. Protein Sci. 2006, 15:1945-1950.
15. Salsbury F.R., Knutson S.T., Poole L.B., Fetrow J.S. Functional site profiling and electrostatic analysis of cysteines modifiable to cysteine sulfenic acid. Protein Sci. 2008, 17:299-312.
16. Marino S.M., Gladyshev V.N. A structure-based approach for detection of thiol oxidoreductases and their catalytic redox-active cysteine residues. PLoS Comput. Biol. 2009, 5:e1000383.
17. Ondrechen M.J., Clifton J.G., Ringe D. THEMATICS: a simple computational predictor of enzyme function from structure. Proc. Natl Acad. Sci. USA 2001, 98:12473-12478.
18. Beeby M., O'Connor B.D., Ryttersgaard C., Boutz D.R., Perry L.J., Yeates T.O. The genomics of disulfide bonding and protein stabilization in thermophiles. PloS Biol. 2005, 3:e309.
19. Mallick P., Boutz D.R., Eisenberg D., Yeates T.O. Genomic evidence that the intracellular proteins of archaeal microbes contain disulfide bonds. Proc. Natl Acad. Sci. USA 2002, 99:9679-9684.
20. Kim H.Y., Gladyshev V.N. Different catalytic mechanisms in mammalian selenocysteine- and cysteine-containing methionine-R-sulfoxide reductases. PLoS Biol. 2005, 3:e375.
21. Cammer S.A., Hoffman B.T., Speir J.A., Canady M.A., Nelson M.R., Knutson S., et al. Structure-based active site profiles for genome analysis and functional family subclassification. J. Mol. Biol. 2003, 334:387-401.
22. Overington J., Donnelly D., Johnson M.S., Sali A., Blundell T.L. Environment-specific amino acid substitution tables: tertiary templates and prediction of protein folds. Protein Sci. 1992, 1:216-226.
23. Bryliński M., Prymula K., Jurkowski W., Kochańczyk M., Stawowczyk E., Konieczny L., Roterman I. Prediction of functional sites based on the fuzzy oil drop model. PLoS Comput. Biol. 2007, 3:e94.