Application of amino acid distribution along the sequence for discriminating mesophilic and thermophilic proteins

Process Biochemistry

Volumn 41, Issue 8, 2006, Pages 1792-1798

  Zhang, Guangya ^a   Fang, Baishan ^a  

^a HUAQIAO UNIVERSITY   (China)

Author keywords

Amino acid composition; Dipeptide composition; Discrimination; Protein thermostability

Indexed keywords

DATABASE SYSTEMS; NUMERICAL METHODS; PROTEINS; THERMODYNAMIC STABILITY;

AMINO ACID COMPOSITION; DIPEPTIDE COMPOSITION; DISCRIMINATION; PROTEIN THERMOSTABILITY;

AMINO ACIDS;

EID: 33646789420     PISSN: 13595113     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.procbio.2006.03.026     Document Type: Article

References (22)

1. Pokala N., and Handel T.M. Protein design-where we were, where we are, where we're going. J Struct Biol 134 (2001) 269-281
2. Malakauskas S.M., and Mayo S.L. Design, structure and stability of a hyperthermophilic protein variant. Nat Struct Biol 5 (1998) 470-475
3. Kumar S., and Nussinov R. How do thermophilic proteins deal with heat?. Cell Mol Life Sci 58 (2001) 1216-1233
4. Szilagyi A., and Zavodsky P. Structural differences between mesophilic, moderately thermophilic and extremely thermophilic protein subunits: results of a comprehensive survey. Struct Fold Des 8 5 (2000) 493-504
5. Vieille C., and Zeikus G.J. Hyperthermophilic enzymes: sources, uses, and molecular mechanisms for thermostability. Microbiol Mol Biol Rev 65 (2001) 1-43
6. Haney P.J., Jonathan H.B., Gerald L.B., Claudia I.R., Carl R.W., and Gary J.O. Thermal adaptation analyzed by comparison of protein sequences from mesophilic and extremely thermophilic Methanococcus species. PNAS 96 (1999) 3578-3583
7. Suhre K., and Claverie J.M. Genomic correlaties of hyperthermostability, an update. J Biol Chem 278 19 (2003) 17198-17202
8. Gromiha M.M., Oobatake M., and Sari A. Important amino acid properties for enhanced thermostability from mesophilic to thermophilic proteins. Biophys Chem 82 1 (1999) 51-67
9. Ding Y.R., Cai Y.J., Zhang G.X., and Xu W.B. The influence of dipeptide composition on protein thermostability. FEBS Lett 569 (2004) 284-288
10. Chou K.C. Prediction of protein structural classes and subcellular locations. Curr Protein Pept Sci 1 (2000) 171-208
11. Mozo-Villarias A., Cedano J., and Querol E. A simple electrostatic criterion for predicting the thermal stability of proteins. Protein Eng 16 (2003) 279-286
12. Gromiha M.M., Oobatake M., Kono H., Uedaira H., and Sarai A. Relationship between amino acid properties and protein stability: buried mutations. J Protein Chem 18 (1999) 565-578
13. Robert J.H., Jorg B., Marie L.A., Marian Y.H., Jonathan M.J., Jost V., et al. Combining computational and experimental screening for rapid optimization of protein properties. Proc Natl Acad Sci USA 99 (2002) 15926-15931
14. Bairoch A., Apweiler R., Wu C.H., Barker W.C., Boeckmann B., Ferro S., et al. The universal protein resource (UniProt). Nucleic Acids Res 33 (2005) 154-159
15. Gromiha M.M., Ahmad S., and Suwa M. Application of residue distribution along the sequence for discriminating outer membrane proteins. Comput Biol Chem 29 (2005) 135-142
16. Fredj T., Edouard Y., and Bernard D. Amino acid composition of genomes, lifestyles of organisms, and evolutionary trends: a global picture with correspondence analysis. Gene 297 (2002) 51-60
17. David J.L., Gregory A.C., Singer, and Donal A.H. Synonymous codon usage is subject to selection in thermophilic bacteria. Nucleic Acids Res 30 (2002) 4272-4277
18. Zhang G.Y., and Fang B.S. Discrimination of thermophilic and mesophilic proteins via pattern recognition methods. Process Biochem 41 (2006) 552-556
19. Das R., and Gerstein M. The stability of thermophilic proteins: a study based on comprehensive genome comparison. Funct Integr Genomics 1 (2000) 76-88
20. Querol E., Perez-Pons J.A., and Mozo-Villarias A. Analysis of protein conformational characteristics related to thermostability. Protein Eng 9 (1996) 265-271
21. Seung P.P., and Young J.Y. Protein thermostability: structure-based difference of amino acid between thermophilic and mesophilic proteins. J Biotech 111 (2004) 269-277
22. Kumar S., Tsai C.J., and Nussinov R. Factors enhancing protein thermostability. Protein Eng 13 (2000) 179-191