The effects of added salt on the second virial coefficients of the complete proteome of E. coli

Journal of Chemical Physics

Volumn 118, Issue 11, 2003, Pages 5157-5161

  Sear, Richard P ^a  

^a UNIVERSITY OF SURREY   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; COMPOSITION EFFECTS; ESCHERICHIA COLI; MIXTURES; PROTONS; SALTS; VOLUME FRACTION;

GAUSSIAN FUNCTION; PROTEOME; SECOND VIRIAL COEFFICIENT;

PROTEINS;

EID: 0037444490     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.1544556     Document Type: Article

References (25)

1. A brid introduction to the biological nomenclature: an organism's DNA contains many genes, each of which codes for a protein. The complete set of genes is called the organism's genome and we will refer to the complete set of proteins as its proteome. Some authors use the word proteome somewhat differently; they use it to denote the set of proteins present in the cytosol of an organism at a particular time. See, for example, Ref. 13, for a a more detailed definition of a genome.
2. S. Cayley, B. A. Lewis, H. J. Guttman, and M. T. Record, Jr., J. Mol. Biol. 222, 281 (1991).
3. W. C. K. Poon, S. U. Egelhaaf, P. A. Beales, A. Salonen, and L. Sawyer, J. Phys.: Condens. Matter 12, L569 (2000).
4. M. Muschol and F. Rosenberger, J. Chem. Phys. 107, 1953 (1997).
5. P. B. Warren, J. Phys.: Condens. Matter 14, 7617 (2002).
6. O. D. Velev, E. W. Kaler, and A. M. Lenhoff, Biophys. J. 75, 2682 (1998).
7. B. Guo, S. Kao, H. McDonald, A. Asanov, L. L. Combs, and W. W. Wilson, J. Cryst. Growth 196, 424 (1999).
8. D. F. Rosenbaum, A. Kulkarni, S. Ramakrishnan, and C. F. Zukoski, J. Chem. Phys. 111, 9822 (1999).
9. R. Piazza and M. Pierno, J. Phys.: Condens. Matter 12, A443 (2000).
10. K. Runcong and S. Mitaku, Genome Informatics 12, 364 (2001).
11. F. R. Blattner et al., Science 277, 1453 (1997).
12. The complete proteome of E. coli K-12, i.e., the amino-acid sequences of all its proteins, can be downloaded from databases such as that at the European Bioinformatics Institute (http://www.ebi.ac.uk/proteome). E. coli K-12 was sequenced by Blattner et al. (Ref. 11).
13. B. Alberts, D. Bray, J. Lewis, M. Raff, K. Roberts, and J. D. Watson, Molecular Biology of The Cell, 3rd ed. (Garland, New York, 1994).
14. L. Stryer, Biochemistry, 4th ed. (Freeman, New York, 1995).
15. The sequence used to determine this charge has a Protein Data Bank ID (Ref. 25) of 1GWD.
16. This value is obtained from Fig. 1 of C. Tanford and R. Roxby, Biochemistry 11, 2192 (1972).
17. M. Gerstein and H. Hegyi, FEMS Microbiol. Rev. 22, 277 (1998).
18. S. Mitaku, M. Ono, T. Hirokawa, S. Boon-Chieng, and M. Sonoyama, Biophys. Chem. 82, 165 (1999).
19. R. P. Sear (unpublished).
20. M. T. Madigan, J. M. Martinko, and J. Parker, Brock Biology of Microorganisms (Prentice-Hall, New Jersey, 1997).
21. V. Lobaskin, A. Lyubartsev, and P. Linse, Phys. Rev. E 63, 020401 (2001).
22. P.B. Warren, J. Chem. Phys. 112, 4683 (2000).
23. S. D. Durbin and G. Feher, Annu. Rev. Phys. Chem. 47, 171 (1996).
24. F. C. Neidhardt, "Chemical composition of E. coli," in E. coli and S. typhimurium: Cellular and Molecular Biology, edited by F. C. Neidhardt, J. L. Ingraham, K. B. Low, B. Magasanik, and H. E. Umbarger (American Society for Microbiology, Washington, D.C., 1987).
25. H. M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T. N. Bhat, H. Weissig, I. N. Shindyalov, and P. E. Bourne, Nucleic Acids Res. 28, 235 (2000). Web site: http://www.rcsb.org/pdb/