Anion Binding to the Ubiquitin Molecule

Overview

Journal Protein Sci

Specialty Biochemistry

Date 1998 Apr 16

PMID 9541401

Citations 36

Authors

G I Makhatadze

M M Lopez

J M Richardson 3rd

S T Thomas

Affiliations

Soon will be listed here.

Abstract

Effects of different salts (NaCl, MgCl2, CaCl2, GdmCl, NaBr, NaClO4, NaH2PO4, Na2SO4) on the stability of the ubiquitin molecule at pH 2.0 have been studied by differential scanning calorimetry, circular dichroism, and Tyr fluorescence spectroscopies. It is shown that all of the salts studied significantly increase the thermostability of the ubiquitin molecule, and that this stabilization can be interpreted in terms of anion binding. Estimated thermodynamic parameters of binding for Cl- show that this binding is relatively weak (Kd = 0.15 M) and is characterized by a negative enthalpy of -15 kJ/mol per site. Particularly surprising was the observed stabilizing effect of GdmCl through the entire concentration range studied (0.01-2 M), however, to a lesser extent than stabilization by NaCl. This stabilizing effect of GdmCl appears to arise from the binding of Cl- ions. Analysis of the observed changes in the stability of the ubiquitin molecule in the presence of GdmCl can be adequately described by combining the thermodynamic model of denaturant binding with Cl- binding effects.

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References

Sharp K, Friedman R, Misra V, Hecht J, Honig B . Salt effects on polyelectrolyte-ligand binding: comparison of Poisson-Boltzmann, and limiting law/counterion binding models. Biopolymers. 1995; 36(2):245-62. DOI: 10.1002/bip.360360211. View

Liu Y, Bolen D . The peptide backbone plays a dominant role in protein stabilization by naturally occurring osmolytes. Biochemistry. 1995; 34(39):12884-91. DOI: 10.1021/bi00039a051. View

Smith J, Scholtz J . Guanidine hydrochloride unfolding of peptide helices: separation of denaturant and salt effects. Biochemistry. 1996; 35(22):7292-7. DOI: 10.1021/bi960341i. View

Ledvina P, Yao N, Choudhary A, Quiocho F . Negative electrostatic surface potential of protein sites specific for anionic ligands. Proc Natl Acad Sci U S A. 1996; 93(13):6786-91. PMC: 39105. DOI: 10.1073/pnas.93.13.6786. View

Sanchez-Ruiz J . A model-independent, nonlinear extrapolation procedure for the characterization of protein folding energetics from solvent-denaturation data. Biochemistry. 1996; 35(47):14689-702. DOI: 10.1021/bi961836a. View

Dunbar J, Yennawar H, Banerjee S, Luo J, Farber G . The effect of denaturants on protein structure. Protein Sci. 1997; 6(8):1727-33. PMC: 2143764. DOI: 10.1002/pro.5560060813. View

Snape K, Tjian R, Blake C, Koshland D . Crystallographic study of the interaction of urea with lysozyme. Nature. 1974; 250(464):295-8. DOI: 10.1038/250295a0. View

Privalov P, Potekhin S . Scanning microcalorimetry in studying temperature-induced changes in proteins. Methods Enzymol. 1986; 131:4-51. DOI: 10.1016/0076-6879(86)31033-4. View

Finley D, Ozkaynak E, Varshavsky A . The yeast polyubiquitin gene is essential for resistance to high temperatures, starvation, and other stresses. Cell. 1987; 48(6):1035-46. DOI: 10.1016/0092-8674(87)90711-2. View

10.

SCHELLMAN J . Selective binding and solvent denaturation. Biopolymers. 1987; 26(4):549-59. DOI: 10.1002/bip.360260408. View

11.

Bugg C, Wilkinson K, Vierstra R, Hatfield P, Cook W . Comparison of the three-dimensional structures of human, yeast, and oat ubiquitin. J Biol Chem. 1987; 262(13):6396-9. View

12.

Weber P, Brown S, Mueller L . Sequential 1H NMR assignments and secondary structure identification of human ubiquitin. Biochemistry. 1987; 26(23):7282-90. DOI: 10.1021/bi00397a013. View

13.

Pace C, Grimsley G . Ribonuclease T1 is stabilized by cation and anion binding. Biochemistry. 1988; 27(9):3242-6. DOI: 10.1021/bi00409a018. View

14.

Presper K, Wong C, Liu L, Meadow N, Roseman S . Site-directed mutagenesis of the phosphocarrier protein. IIIGlc, a major signal-transducing protein in Escherichia coli. Proc Natl Acad Sci U S A. 1989; 86(11):4052-5. PMC: 287386. DOI: 10.1073/pnas.86.11.4052. View

15.

Goto Y, Calciano L, Fink A . Acid-induced folding of proteins. Proc Natl Acad Sci U S A. 1990; 87(2):573-7. PMC: 53307. DOI: 10.1073/pnas.87.2.573. View

16.

Arakawa T, Bhat R, Timasheff S . Why preferential hydration does not always stabilize the native structure of globular proteins. Biochemistry. 1990; 29(7):1924-31. DOI: 10.1021/bi00459a037. View

17.

Goto Y, Takahashi N, Fink A . Mechanism of acid-induced folding of proteins. Biochemistry. 1990; 29(14):3480-8. DOI: 10.1021/bi00466a009. View

18.

Studier F, Rosenberg A, Dunn J, Dubendorff J . Use of T7 RNA polymerase to direct expression of cloned genes. Methods Enzymol. 1990; 185:60-89. DOI: 10.1016/0076-6879(90)85008-c. View

19.

Kiefhaber T, Schmid F, Renner M, Hinz H, Hahn U, Quaas R . Stability of recombinant Lys25-ribonuclease T1. Biochemistry. 1990; 29(36):8250-7. DOI: 10.1021/bi00488a008. View

20.

SCHELLMAN J . A simple model for solvation in mixed solvents. Applications to the stabilization and destabilization of macromolecular structures. Biophys Chem. 1990; 37(1-3):121-40. DOI: 10.1016/0301-4622(90)88013-i. View