Cellular proteomes have broad distributions of protein stability

Biophysical Journal

Volumn 99, Issue 12, 2010, Pages 3996-4002

  Ghosh, Kingshuk ^a   Dill, Ken ^b  

^a UNIVERSITY OF DENVER   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CAENORHABDITIS ELEGANS; ESCHERICHIA COLI;

EID: 78650217130     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2010.10.036     Document Type: Article

References (41)

1. Weinberg, R. 2007. The Biology of Cancer. Garland Science, London.
2. Coffey, D. S., R. H. Getzenberg, and T. L. DeWeese. 2006. Hyperthermic biology and cancer therapies: a hypothesis for the "Lance Armstrong effect". JAMA. 296:445-448.
3. Vertrees, R. A., J. B. Zwischenberger, ., S. D. Pencil. 2000. Oncogenic ras results in increased cell kill due to defective thermoprotection in lung cancer cells. Ann. Thorac. Surg. 69:1675-1680.
4. Ferguson, M. W., and T. Joanen. 1982. Temperature of egg incubation determines sex in Alligator mississippiensis. Nature. 296:850-853.
5. Webb, G., and H. Cooper-Preston. 1989. Effects of incubation temperature on crocodiles and the evolution of reptilian oviparity. Am. Zool. 29:953-971.
6. Kennett, J., and L. Stott. 1991. Abrupt deep-sea warming, palaeoceanographic changes and benthic extinctions at the end of the Palaeocene.Nature. 353:225-229.
7. Ivany, L. C.,W. P. Patterson, and K. C. Lohmann. 2000. Cooler winters as a possible cause of mass extinctions at the Eocene/Oligocene boundary. Nature. 407:887-890.
8. Allen, A. P., J. F. Gillooly, ., J. H. Brown. 2006. Kinetic effects of temperature on rates of genetic divergence and speciation. Proc. Natl. Acad. Sci. USA. 103:9130-9135.
9. Brett, J. 1971. Energetic responses of salmon to temperature-study of some thermal relations in physiology and freshwater ecology of sockeye salmon (Oncorhynchus nerka). Am. Zool. 11:99-113.
10. Balch, W. E., R. I. Morimoto, ., J. W. Kelly. 2008. Adapting proteostasis for disease intervention. Science. 319:916-919.
11. Dobson, C. M. 2003. Protein folding and misfolding. Nature. 426: 884-890.
12. Rutherford, S. L., and S. Lindquist. 1998. Hsp90 as a capacitor for morphological evolution. Nature. 396:336-342.
13. Queitsch, C., T. A. Sangster, and S. Lindquist. 2002. Hsp90 as a capacitor of phenotypic variation. Nature. 417:618-624.
14. Lepock, J. R. 2005. Measurement of protein stability and protein denaturation in cells using differential scanning calorimetry. Methods. 35:117-125.
15. Westra, A., and W. C. Dewey. 1971. Variation in sensitivity to heat shock during the cell-cycle of Chinese hamster cells in vitro. Int. J. Radiat. Biol. Relat. Stud. Phys. Chem. Med. 19:467-477.
16. Robertson, A. D., and K. P. Murphy. 1997. Protein structure and the energetics of protein stability. Chem. Rev. 97:1251-1268.
17. Ghosh, K., and K. A. Dill. 2009. Computing protein stabilities from their chain lengths. Proc. Natl. Acad. Sci. USA. 106:10649-10654.
18. Zhang, J. 2000. Protein-length distributions for the three domains of life. Trends Genet. 16:107-109.
19. Kumar, M. D., K. A. Bava, ., A. Sarai. 2006. ProTherm and ProNIT: thermodynamic databases for proteins and protein-nucleic acid interactions. Nucleic Acids Res. 34(Database issue):D204-D206.
20. Zeldovich, K. B., P. Chen, and E. I. Shakhnovich. 2007. Protein stability imposes limits on organism complexity and speed of molecular evolution. Proc. Natl. Acad. Sci. USA. 104:16152-16157.
21. Ratkowsky, D. A., R. K. Lowry, ., R. E. Chandler. 1983. Model for bacterial culture growth rate throughout the entire biokinetic temperature range. J. Bacteriol. 154:1222-1226.
22. Shoichet, B. K.,W. A. Baase,., B.W. Matthews. 1995. A relationship between protein stability and protein function. Proc. Natl. Acad. Sci. USA. 92:452-456.
23. Moeckel, G. W., L. Zhang, ., M. D. Breyer. 2003. COX2 activity promotes organic osmolyte accumulation and adaptation of renal medullary interstitial cells to hypertonic stress. J. Biol. Chem. 278:19352-19357.
24. Mulhern, M. L., C. J. Madson, ., T. Shinohara. 2007. Cellular osmolytes reduce lens epithelial cell death and alleviate cataract formation in galactosemic rats. Mol. Vis. 13:1397-1405.
25. Yancey, P. H., M. E. Clark,., G. N. Somero. 1982. Living with water stress: evolution of osmolyte systems. Science. 217:1214-1222.
26. Chen, P., and E. I. Shakhnovich. 2010. Thermal adaptation of viruses and bacteria. Biophys. J. 98:1109-1118.
27. Ratkowsky, D. A., J. Olley, and T. Ross. 2005. Unifying temperature effects on the growth rate of bacteria and the stability of globular proteins. J. Theor. Biol. 233:351-362.
28. Salter, M. A., T. Ross, and T. A. McMeekin. 1998. Applicability of a model for non-pathogenic Escherichia coli for predicting the growth of pathogenic Escherichia coli. J. Appl. Microbiol. 85:357-364.
29. Baba, T., T. Ara, M. Hasegawa, Y. Takai, Y. Okumura, M. Baba, K. Datsenko, M. Tomita, B. Wanner, and H. Mori. 2006. Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol. Syst. Biol. 2:2006.0008.
30. Vogel, C., M. Bashton, ., S. A. Teichmann. 2004. Structure, function and evolution of multidomain proteins. Curr. Opin. Struct. Biol. 14:208-216.
31. Teichmann, S. A., J. Park, and C. Chothia. 1998. Structural assignments to the Mycoplasma genitalium proteins show extensive gene duplications and domain rearrangements. Proc. Natl. Acad. Sci. USA. 95:14658-14663.
32. Gerstein, M. 1998. How representative are the known structures of the proteins in a complete genome? A comprehensive structural census. Fold. Des. 3:497-512.
33. Lipman, D. J., A. Souvorov,., T. A. Tatusova. 2002. The relationship of protein conservation and sequence length. BMC Evol. Biol. 2:20.
34. Wheelan, S. J., A. Marchler-Bauer, and S. H. Bryant. 2000. Domain size distributions can predict domain boundaries. Bioinformatics. 16:613-618.
35. Ku, T., P. Lu, ., N. Hsiao. 2009. Predicting melting temperature directly from protein sequences. Comput. Biol. Chem. 33:445-450.
36. Warringer, J., and A. Blomberg. 2006. Evolutionary constraint on yeast protein size. BMC Evol. Biol. 6:61.
37. Ghaemmaghami, S.,W. K. Huh,., J. S.Weissman. 2003. Global analysis of protein expression in yeast. Nature. 425:737-741.
38. Ghaemmaghami, S., and T. G. Oas. 2001. Quantitative protein stability measurement in vivo. Nat. Struct. Biol. 8:879-882.
39. Ignatova, Z., and L. M. Gierasch. 2004. Monitoring protein stability and aggregation in vivo by real-time fluorescent labeling. Proc. Natl. Acad. Sci. USA. 101:523-528.
40. Batra, J., K. Xu, and H. X. Zhou. 2009. Nonadditive effects of mixed crowding on protein stability. Proteins. 77:133-138.
41. Paliy, O., S. M. Gargac, ., A. K. Dunker. 2008. Protein disorder is positively correlated with gene expression in Escherichia coli. J. Proteome Res. 7:2234-2245.