Osmotically induced helix-coil transition in poly(glutamic acid)

Biophysical Journal

Volumn 94, Issue 11, 2008, Pages 4427-4434

  Stanley, Christopher B ^a,b   Strey, Helmut H ^b,c  

^a UNIVERSITY OF MASSACHUSETTS   (United States)

^b STONY BROOK UNIVERSITY   (United States)

^c OAK RIDGE NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MACROGOL DERIVATIVE; PROTEIN;

ARTICLE; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; OSMOTIC PRESSURE; PHASE TRANSITION; PROTEIN CONFORMATION; ULTRASTRUCTURE;

COMPUTER SIMULATION; MODELS, CHEMICAL; MODELS, MOLECULAR; OSMOTIC PRESSURE; PHASE TRANSITION; POLYETHYLENE GLYCOLS; PROTEIN CONFORMATION; PROTEINS;

EID: 44849116306     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1529/biophysj.107.122705     Document Type: Article

References (47)

1. Yancey, P. H., M. E. Clark, S. C. Hand, R. D. Bowlus, and G. N. Somero. 1982. Living with water stress: evolution of osmolyte systems. Science. 217:1214-1222.
2. Wood, J. M. 1999. Osmosensing by bacteria: signals and membrane-based sensors. Microbiol. Mol. Biol. Rev. 63:230-262.
3. Bourot, S., O. Sire, A. Trautwetter, T. Touzé, L. F. Wu, C. Blanco, and T. Bernard. 2000. Glycine betaine-assisted protein folding in a lysA mutant of Escherichia coli. J. Biol. Chem. 275:1050-1056.
4. Arakawa, T., and S. N. Timasheff. 1985. The stabilization of proteins by osmolytes. Biophys. J. 47:411-414.
5. Timasheff, S. N. 1993. The control of protein stability and association by weak interactions with water: how do solvents affect these processes? Annu. Rev. Biophys. Biomol. Struct. 22:67-97.
6. Santoro, M. M., Y. F. Liu, S. M. A. Khan, L. X. Hou, and D. W. Bolen. 1992. Increased thermal stability of proteins in the presence of naturally occurring osmolytes. Biochemistry. 31:5278-5283.
7. Wang, A. J., and D. W. Bolen. 1997. A naturally occurring protective system in urea-rich cells: mechanism of osmolyte protection of proteins against urea. Biochemistry. 36:9101-9108.
8. Baskakov, I., and D. W. Bolen. 1998. Forcing thermodynamically unfolded proteins to fold. J. Biol. Chem. 273:4831-4834.
9. Courtenay, E. S., M. W. Capp, C. F. Anderson, and M. T. Record, Jr. 2000. Vapor pressure osmometry studies of osmolyte-protein interactions: implications for the action of osmoprotectants in vivo and for the interpretation of ''osmotic stress'' experiments in vitro. Biochemistry. 39:4455-4471.
10. Harries, D., D. C. Rau, and V. A. Parsegian. 2005. Solutes probe hydration in specific association of cyclodextrin and adamantane. J. Am. Chem. Soc. 127:2184-2190.
11. Hultgren, A., and D. C. Rau. 2004. Exclusion of alcohols from spermidine-DNA assemblies: probing the physical basis of preferential hydration. Biochemistry. 43:8272-8280.
12. Sidorova, N. Y., and D. C. Rau. 2004. Differences between EcoRI nonspecific and ''star'' sequence complexes revealed by osmotic stress. Biophys. J. 87:2564-2576.
13. Sidorova, N. Y., S. Muradymov, and D. C. Rau. 2006. Differences in hydration coupled to specific and nonspecific competitive binding and to specific DNA binding of the restriction endonuclease BamHI. J. Biol. Chem. 281:35656-35666.
14. Rau, D. C. 2006. Sequestered water and binding energy are coupled in complexes of A Cro repressor with non-consensus binding sequences. J. Mol. Biol. 361:352-361.
15. Parsegian, V. A., R. P. Rand, and D. C. Rau. 1995. Macromolecules and water: probing with osmotic stress. Methods Enzymol. 259:43-94.
16. Parsegian, V. A., R. P. Rand, and D. C. Rau. 2000. Osmotic stress, crowding, preferential hydration, and binding: a comparison of perspectives. Proc. Natl. Acad. Sci. USA. 97:3987-3992.
17. Zimmerberg, J., and V. A. Parsegian. 1986. Polymer inaccessible volume changes during opening and closing of a voltage-dependent ionic channel. Nature. 323:36-39.
18. Vodyanoy, I., S. M. Bezrukov, and V. A. Parsegian. 1993. Probing alamethicin channels with water-soluble polymers: size-modulated osmotic action. Biophys. J. 65:2097-2105.
19. McGee, M. P., and H. Teuschler. 1995. Protein hydration during generation of coagulation factor Xa in aqueous phase and on phos- pholipid membranes. J. Biol. Chem. 270:15170-15174.
20. McGee, M. P., and J. Liang. 2001. Regulation of glycosaminoglycan function by osmotic potentials. Measurement of water transfer during antithrombin activation by heparin. J. Biol. Chem. 276:49275-49282.
21. Rand, R. P., N. L. Fuller, P. Butko, G. Fracis, and P. Nicholls. 1993. Measured change in protein solvation with substrate binding and turnover. Biochemistry. 32:5925-5929.
22. Reid, C., and R. P. Rand. 1997. Probing protein hydration and conformational states in solution. Biophys. J. 72:1022-1030.
23. Denisov, V. P., J. Peters, H. D. Hörlein, and B. Halle. 1996. Using buried water molecules to explore the energy landscape of proteins. Nat. Struct. Biol. 3:505-509.
24. Royer, W. E., A. Pardanani, Q. H. Gibson, E. S. Peterson, and J. M. Friedman. 1996. Ordered water molecules as key allosteric mediators in a cooperative dimeric hemoglobin. Proc. Natl. Acad. Sci. USA. 93:14526-14531.
25. Fanucci, G. E., J. Y. Lee, and D. S. Cafiso. 2003. Spectroscopic evidence that osmolytes used in crystallization buffers inhibit a conformation change in a membrane protein. Biochemistry. 42:13106-13112.
26. Kim, M., Q. Xu, G. E. Fanucci, and D. S. Cafiso. 2006. Solutes modify a conformational transition in a membrane transport protein. Biophys. J. 90:2922-2929.
27. Bhat, R., and S. N. Timasheff. 1992. Steric exclusion is the principal source of the preferential hydration of proteins in the presence of polyethylene glycols. Protein Sci. 1:1133-1143.
28. Papoian, G. A., J. Ulander, M. P. Eastwood, Z. Luthey-Schulten, and P. G. Wolynes. 2004. Water in protein structure prediction. Proc. Natl. Acad. Sci. USA. 101:3352-3357.
29. Levy, Y., and J. N. Onuchic. 2006. Water mediation in protein folding and molecular recognition. Annu. Rev. Biophys. Biomol. Struct. 35: 389-415.
30. Stanley, C. B., and H. H. Strey. 2003. Measuring osmotic pressure of poly(ethylene glycol) solutions by sedimentation equilibrium ultracen-trifugation. Macromolecules. 36:6888-6893.
31. Sanner, M. F., A. J. Olson, and J. C. Spehner. 1996. Reduced surface: an efficient way to compute molecular surfaces. Biopolymers. 38:305-320.
32. Srinivasan, R. RIBOSOME. http://www.roselab.jhu.edu/~raj/Manuals/ ribosome.html.
33. Poland, D., and H. A. Scheraga. 1970. Theory of Helix-Coil Transitions in Biopolymers. Academic Press, New York.
34. Snipp, R. L., W. G. Miller, and R. E. Nylund. 1965. Charge-induced helix-random coil transition in aqueous solution. J. Am. Chem. Soc. 87:3547-3553.
35. Shi, Z. S., C. A. Olson, G. D. Rose, R. L. Baldwin, and N. R. Kallenbach. 2002. Polyproline II structure in a sequence of seven alanine residues. Proc. Natl. Acad. Sci. USA. 99:9190-9195.
36. Ohkubo, Y. Z., and C. L. Brooks. 2003. Exploring Flory's isolated-pair hypothesis: statistical mechanics of helix-coil transitions in polyalanine and the C-peptide from RNase A. Proc. Natl. Acad. Sci. USA. 100: 13916-13921.
37. Pace, C. N., and J. M. Scholtz. 1998. A helix propensity scale based on experimental studies of peptides and proteins. Biophys. J. 75:422-427.
38. Greene, R. F., Jr., and C. N. Pace. 1974. Urea and guanidine hydrochloride denaturation of ribonuclease, lysozyme, α-chymotryp- sin, and β-lactoglobulin. J. Biol. Chem. 249:5388-5393.
39. Mello, C. C., and D. Barrick. 2003. Measuring the stability of partly folded proteins using TMAO. Protein Sci. 12:1522-1529.
40. Myers, J. K., C. N. Pace, and J. M. Scholtz. 1995. Denaturant m values and heat capacity changes: relation to changes in accessible surface areas of protein unfolding. Protein Sci. 4:2138-2148.
41. Courtenay, E. S., M. W. Capp, R. M. Saecker, and M. T. Record, Jr. 2000. Thermodynamic analysis of interactions between denaturants and protein surface exposed on unfolding: interpretation of urea and guanidinium chloride m-values and their correlation with changes in accessible surface area (ASA) using preferential interaction coefficients and the local-bulk domain model. Proteins. Suppl. 4:72-85.
42. Kuntz, I. D., and W. Kauzmann. 1974. Hydration of proteins and polypeptides. Adv. Protein Chem. 28:239-345.
43. Chalikian, T. V. 2003. Volumetric properties of proteins. Annu. Rev. Biophys. Biomol. Struct. 32:207-235.
44. Sukhishvili, S. A., and S. Granick. 2003. Simple interpretation of ionization and helix-coil stability shift when a polyelectrolyte adsorbs. Langmuir. 19:1980-1983.
45. Urry, D. W. 1997. Physical chemistry of biological free energy trans-duction as demonstrated by elastic protein-based polymers. J. Phys. Chem. B. 101:11007-11028.
46. Reiersen,H., A. R. Clarke, andA. R. Rees. 1998. Shortelastin-likepeptides exhibit the same temperature-induced structural transitions as elastin polymers: implications for protein engineering. J. Mol. Biol. 283:255-264.
47. Creighton, T. E. 1990. Protein folding. Biochem. J. 270:1-16.