Dynamical properties of cold shock protein A from Mycobacterium tuberculosis

Biochemical and Biophysical Research Communications

Volumn 402, Issue 4, 2010, Pages 693-698

  D'Auria, Gabriella ^a,c   Esposito, Carla ^b,c   Falcigno, Lucia ^a,c   Calvanese, Luisa ^a   Iaccarino, Emanuela ^a   Ruggiero, Alessia ^b   Pedone, Carlo ^b,c   Pedone, Emilia ^c   Berisio, Rita ^c  

^a UNIVERSITY OF NAPLES FEDERICO II   (Italy)

^b Dipartimento delle Scienze Biologiche via Mezzocannone 16   (Italy)

^c CNR   (Italy)

Author keywords

Bs CspB; EMSA; High temperature MD simulations; MTB CspA; Ss DNA binding; Unfolding multiple pathways

Indexed keywords

BACTERIAL PROTEIN; COLD SHOCK PROTEIN; COLD SHOCK PROTEIN A; NUCLEIC ACID BINDING PROTEIN; OLIGONUCLEOTIDE; UNCLASSIFIED DRUG;

ARTICLE; BACILLUS SUBTILIS; CIRCULAR DICHROISM; COLD STRESS; GEL MOBILITY SHIFT ASSAY; HIGH TEMPERATURE; MOLECULAR DYNAMICS; MYCOBACTERIUM TUBERCULOSIS; NONHUMAN; NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DNA BINDING; PROTEIN FOLDING; PROTEIN FUNCTION; PROTEIN STRUCTURE; ROOM TEMPERATURE; SEQUENCE HOMOLOGY; SIMULATION; THERMOSTABILITY;

AMINO ACID SEQUENCE; BACTERIAL PROTEINS; CIRCULAR DICHROISM; MOLECULAR SEQUENCE DATA; MYCOBACTERIUM TUBERCULOSIS; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY;

BACILLUS SUBTILIS; BACTERIA (MICROORGANISMS); MYCOBACTERIUM TUBERCULOSIS;

EID: 78649486813     PISSN: 0006291X     EISSN: 10902104     Source Type: Journal    
DOI: 10.1016/j.bbrc.2010.10.086     Document Type: Article

References (35)

1. Horn G., Hofweber R., Kremer W., Kalbitzer H.R. Structure and function of bacterial cold shock proteins. Cell Mol. Life Sci. 2007, 64:1457-1470.
2. Newkirk K., Feng W., Jiang W., Tejero R., Emerson S.D., Inouye M., Montelione G.T. Solution NMR structure of the major cold shock protein (CspA) from Escherichia coli: identification of a binding epitope for DNA. Proc. Natl. Acad. Sci. USA 1994, 91:5114-5118.
3. Schindelin H., Jiang W., Inouye M., Heinemann U. Crystal structure of CspA, the major cold shock protein of Escherichia coli. Proc. Natl. Acad. Sci. USA 1994, 91:5119-5123.
4. Schindelin H., Marahiel M.A., Heinemann U. Universal nucleic acid-binding domain revealed by crystal structure of the B. subtilis major cold-shock protein. Nature 1993, 364:164-168.
5. Schnuchel A., Wiltscheck R., Czisch M., Herrler M., Willimsky G., Graumann P., Marahiel M.A., Holak T.A. Structure in solution of the major cold-shock protein from Bacillus subtilis. Nature 1993, 364:169-171.
6. Mueller U., Perl D., Schmid F.X., Heinemann U. Thermal stability and atomic-resolution crystal structure of the Bacillus caldolyticus cold shock protein. J. Mol. Biol. 2000, 297:975-988.
7. Jung A., Bamann C., Kremer W., Kalbitzer H.R., Brunner E. High-temperature solution NMR structure of TmCsp. Protein Sci. 2004, 13:342-350.
8. Kremer W., Schuler B., Harrieder S., Geyer M., Gronwald W., Welker C., Jaenicke R., Kalbitzer H.R. Solution NMR structure of the cold-shock protein from the hyperthermophilic bacterium Thermotoga maritima. Eur. J. Biochem. 2001, 268:2527-2539.
9. Reid K.L., Rodriguez H.M., Hillier B.J., Gregoret L.M. Stability and folding properties of a model beta-sheet protein, Escherichia coli CspA. Protein Sci. 1998, 7:470-479.
10. Garcia-Mira M.M., Boehringer D., Schmid F.X. The folding transition state of the cold shock protein is strongly polarized. J. Mol. Biol. 2004, 339:555-569.
11. Jacob M., Holtermann G., Perl D., Reinstein J., Schindler T., Geeves M.A., Schmid F.X. Microsecond folding of the cold shock protein measured by a pressure-jump technique. Biochemistry 1999, 38:2882-2891.
12. Perl D., Holtermann G., Schmid F.X. Role of the chain termini for the folding transition state of the cold shock protein. Biochemistry 2001, 40:15501-15511.
13. Perl D., Jacob M., Bano M., Stupak M., Antalik M., Schmid F.X. Thermodynamics of a diffusional protein folding reaction. Biophys. Chem. 2002, 96:173-190.
14. Perl D., Welker C., Schindler T., Schroder K., Marahiel M.A., Jaenicke R., Schmid F.X. Conservation of rapid two-state folding in mesophilic, thermophilic and hyperthermophilic cold shock proteins. Nat. Struct. Biol. 1998, 5:229-235.
15. Schindler T., Schmid F.X. Thermodynamic properties of an extremely rapid protein folding reaction. Biochemistry 1996, 35:16833-16842.
16. Bodenhausen G., Ruben D.J. Natural abundance nitrogen-15 NMR by enhanced heteronuclear spectroscopy. Chem. Phys. Lett. 1980, 69:185-189.
17. Marion D., Kay L.E., Sparks S.W., Torchia D.A., Bax A. Three-dimensional heteronuclear NMR of nitrogen-15 labeled proteins. J. Am. Chem. Soc. 1989, 111:1515-1517.
18. Zuiderweg E.R., Fesik S.W. Heteronuclear three-dimensional NMR spectroscopy of the inflammatory protein C5a. Biochemistry 1989, 28:2387-2391.
19. 15N Hartmann-Hahn-multiple quantum coherence and nuclear Overhauser-multiple quantum coherence spectroscopy: application to interleukin 1 beta. Biochemistry 1989, 28:6150-6156.
20. Van Der Spoel D., Lindahl E., Hess B., Groenhof G., Mark A.E., Berendsen H.J. GROMACS: fast, flexible, and free. J. Comput. Chem. 2005, 26:1701-1718.
21. Jorgensen W.L., Maxwell D.S., Tirado-Rives J. Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. J. Am. Chem. Soc. 1996, 118:11225-11236.
22. Kaminski G.A., Friesner R.A., Tirado-Rives J., Jorgensen W.L. Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptidesâ. J. Phys. Chem. B 2001, 105:6474-6487.
23. Humphrey W., Dalke A., Schulten K. VMD: visual molecular dynamics. J. Mol. Graphics 1996, 14:33-38. 27-38.
24. Chatterjee S., Jiang W., Emerson S.D., Inouye M. The backbone structure of the major cold-shock protein CS7.4 of Escherichia coli in solution includes extensive beta-sheet structure. J. Biochem. 1993, 114:663-669.
25. Hillier B.J., Rodriguez H.M., Gregoret L.M. Coupling protein stability and protein function in Escherichia coli CspA. Fold Des. 1998, 3:87-93.
26. Makhatadze G.I., Loladze V.V., Gribenko A.V., Lopez M.M. Mechanism of thermostabilization in a designed cold shock protein with optimized surface electrostatic interactions. J. Mol. Biol. 2004, 336:929-942.
27. Schindler T., Herrler M., Marahiel M.A., Schmid F.X. Extremely rapid protein folding in the absence of intermediates. Nat. Struct. Biol. 1995, 2:663-673.
28. Petrosian S.A., Makhatadze G.I. Contribution of proton linkage to the thermodynamic stability of the major cold-shock protein of Escherichia coli CspA. Protein Sci. 2000, 9:387-394.
29. Makhatadze G.I., Marahiel M.A. Effect of pH and phosphate ions on self-association properties of the major cold-shock protein from Bacillus subtilis. Protein Sci. 1994, 3:2144-2147.
30. Perl D., Schmid F.X. Electrostatic stabilization of a thermophilic cold shock protein. J. Mol. Biol. 2001, 313:343-357.
31. Hellman L.M., Fried M.G. Electrophoretic mobility shift assay (EMSA) for detecting protein-nucleic acid interactions. Nat. Protoc. 2007, 2:1849-1861.
32. Huang X., Zhou H.X. Similarity and difference in the unfolding of thermophilic and mesophilic cold shock proteins studied by molecular dynamics simulations. Biophys. J. 2006, 91:2451-2463.
33. Zhou H.X., Dong F. Electrostatic contributions to the stability of a thermophilic cold shock protein. Biophys. J. 2003, 84:2216-2222.
34. Shimizu S., Chan H.S. Temperature dependence of hydrophobic interactions: a mean force perspective, effects of water density, and nonadditivity of thermodynamic signatures. J. Chem. Phys. 2000, 113:18.
35. Daggett V. Molecular dynamics simulations of the protein unfolding/folding reaction. Acc. Chem. Res. 2002, 35:422-429.