Recent Applications of Kirkwood-Buff Theory to Biological Systems

Overview

Journal Cell Biochem Biophys

Specialties Biochemistry
Biophysics
Cell Biology

Date 2007 Nov 29

PMID 18043873

Citations 42

Authors

Veronica Pierce

Myungshim Kang

Mahalaxmi Aburi

Samantha Weerasinghe

Paul E Smith

Affiliations

Soon will be listed here.

Abstract

The effect of cosolvents on biomolecular equilibria has traditionally been rationalized using simple binding models. More recently, a renewed interest in the use of Kirkwood-Buff (KB) theory to analyze solution mixtures has provided new information on the effects of osmolytes and denaturants and their interactions with biomolecules. Here we review the status of KB theory as applied to biological systems. In particular, the existing models of denaturation are analyzed in terms of KB theory, and the use of KB theory to interpret computer simulation data for these systems is discussed.

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References

Tobi D, Elber R, Thirumalai D . The dominant interaction between peptide and urea is electrostatic in nature: a molecular dynamics simulation study. Biopolymers. 2003; 68(3):359-69. DOI: 10.1002/bip.10290. View

Nandi P, Robinson D . The effects of salts on the free energies of nonpolar groups in model peptides. J Am Chem Soc. 1972; 94(4):1308-15. DOI: 10.1021/ja00759a043. View

Ben-Naim A . Theory of preferential solvation of nonelectrolytes. Cell Biophys. 1988; 12:255-69. DOI: 10.1007/BF02918361. View

SCHELLMAN J, Gassner N . The enthalpy of transfer of unfolded proteins into solutions of urea and guanidinium chloride. Biophys Chem. 1996; 59(3):259-75. DOI: 10.1016/0301-4622(95)00130-1. View

Schellman J . Fifty years of solvent denaturation. Biophys Chem. 2002; 96(2-3):91-101. DOI: 10.1016/s0301-4622(02)00009-1. View

Nozaki Y, Tanford C . THE SOLUBILITY OF AMINO ACIDS AND RELATED COMPOUNDS IN AQUEOUS UREA SOLUTIONS. J Biol Chem. 1963; 238:4074-81. View

Felitsky D, Record Jr M . Application of the local-bulk partitioning and competitive binding models to interpret preferential interactions of glycine betaine and urea with protein surface. Biochemistry. 2004; 43(28):9276-88. DOI: 10.1021/bi049862t. View

Prakash V, Loucheux C, Scheufele S, Gorbunoff M, Timasheff S . Interactions of proteins with solvent components in 8 M urea. Arch Biochem Biophys. 1981; 210(2):455-64. DOI: 10.1016/0003-9861(81)90209-5. View

Dill K . Dominant forces in protein folding. Biochemistry. 1990; 29(31):7133-55. DOI: 10.1021/bi00483a001. View

10.

SCATCHARD G . Physical chemistry of protein solutions; derivation of the equations for the osmotic pressure. J Am Chem Soc. 2010; 68(11):2315-9. DOI: 10.1021/ja01215a054. View

11.

Bennion B, Daggett V . Counteraction of urea-induced protein denaturation by trimethylamine N-oxide: a chemical chaperone at atomic resolution. Proc Natl Acad Sci U S A. 2004; 101(17):6433-8. PMC: 404062. DOI: 10.1073/pnas.0308633101. View

12.

Perrett S, Zhou J . Expanding the pressure technique: insights into protein folding from combined use of pressure and chemical denaturants. Biochim Biophys Acta. 2002; 1595(1-2):210-23. DOI: 10.1016/s0167-4838(01)00345-4. View

13.

Timasheff S, Xie G . Preferential interactions of urea with lysozyme and their linkage to protein denaturation. Biophys Chem. 2003; 105(2-3):421-48. DOI: 10.1016/s0301-4622(03)00106-6. View

14.

Collins K, Washabaugh M . The Hofmeister effect and the behaviour of water at interfaces. Q Rev Biophys. 1985; 18(4):323-422. DOI: 10.1017/s0033583500005369. View

15.

SCHELLMAN J . The thermodynamics of solvent exchange. Biopolymers. 1994; 34(8):1015-26. DOI: 10.1002/bip.360340805. View

16.

Timasheff S . Water as ligand: preferential binding and exclusion of denaturants in protein unfolding. Biochemistry. 1992; 31(41):9857-64. DOI: 10.1021/bi00156a001. View

17.

Baynes B, Trout B . Rational design of solution additives for the prevention of protein aggregation. Biophys J. 2004; 87(3):1631-9. PMC: 1304568. DOI: 10.1529/biophysj.104.042473. View

18.

Caflisch A, Karplus M . Structural details of urea binding to barnase: a molecular dynamics analysis. Structure. 1999; 7(5):477-88. DOI: 10.1016/s0969-2126(99)80064-1. View

19.

Smith P . Equilibrium dialysis data and the relationships between preferential interaction parameters for biological systems in terms of Kirkwood-Buff integrals. J Phys Chem B. 2006; 110(6):2862-8. DOI: 10.1021/jp056100e. View

20.

Mountain R, Thirumalai D . Molecular dynamics simulations of end-to-end contact formation in hydrocarbon chains in water and aqueous urea solution. J Am Chem Soc. 2003; 125(7):1950-7. DOI: 10.1021/ja020496f. View