Anion binding to the ubiquitin molecule

Protein Science

Volumn 7, Issue 3, 1998, Pages 689-697

  Makhatadze, George I ^a   Lopez, Maria M ^a   Richardson III, John M ^a   Thomas, Susan T ^a  

^a TEXAS TECH UNIVERSITY   (United States)

Author keywords

Anion binding; Circular dichroism; Fluorescence; Scanning calorimetry; Ubiquitin

Indexed keywords

ANION; CHLORIDE ION; GUANIDINE; SODIUM CHLORIDE; UBIQUITIN;

ARTICLE; CIRCULAR DICHROISM; DIFFERENTIAL SCANNING CALORIMETRY; ENTHALPY; FLUORESCENCE SPECTROSCOPY; PRIORITY JOURNAL; PROTEIN STABILITY; THERMOSTABILITY;

EID: 0031936593     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1002/pro.5560070318     Document Type: Article

References (74)

1. Alonso DO, Dill KA. 1991. Solvent denaturation and stabilization of globular proteins. Biochemistry 30:5974-5985.
2. Arakawa T, Bhat R, Timasheff SN. 1990. Why preferential hydration does not always stabilize the native structure of globular proteins. Biochemistry 29:1924-1931.
3. Atkins PW. 1990. Physical chemistry, 4th ed. New York: W.H. Freeman and Company.
4. Breslow E, Chauchan Y, Daniel R, Tate S. 1986. Role of Met1 in ubiquitin conformation and activity. Biochem Biophys Res Commun 138:437-444.
5. Briggs MS, Roder H. 1992. Early hydrogen-bonding events in the folding reaction of ubiquitin. Proc Natl Acad Sci USA 89:2017-2021.
6. Burch TJ, Haas AL. 1994. Site-directed mutagenesis of ubiquitin. Differential roles for arginine in the interactions with ubiquitin-activating enzyme. Biochemistry 33:7300-7308.
7. Cormack B. 1992. Site-directed mutagenesis by the polymerase chain reaction. In: Ausubel FM, Brent R, Kingston RE, Moore DD, Seidman JG, Smith JA, Struhl K, eds. Short protocols in molecular biology. New York: John Wiley & Sons. pp 818-825.
8. Duffy EM, Kowalczyk PJ, Jorgensen WL. 1993. Do denaturant interact with aromatic hydrocarbons in water? J Am Chem Soc 115:9271-9275.
9. Dunbar J, Yennawar HP, Banerjee S, Luo J, Farber GK. 1997. The effect of denaturants on protein structure. Protein Sci 6:1727-1733.
10. Finley D, Ozkaynak E, Varshavsky A. 1987. The yeast polyubiquitin gene is essential for resistance to high temperatures, starvation, and other stresses. Cell 48:1035-1046.
11. Garcia-Moreno B. 1994. Estimating binding constants for site-specific interactions between monovalent ions and proteins. Methods Enzymol 240:645-667.
12. Gilson MK. 1995. Theory of electrostatic interactions in macromolecules. Curr Opin Struct Biol 5:216-223.
13. Goto Y, Calciano LJ, Fink AL. 1990. Acid-induced folding of globular proteins. Proc Natl Acad Sci USA 87:573-577.
14. Goto Y, Fink AL. 1990. Mechanism of acid-induced folding of proteins. Biochemistry 29:3480-3488.
15. Hagihara Y, Aimoto S, Fink AL, Goto Y. 1993. Guanidine hydrochloride-induced folding of proteins. J Mol Biol 231:180-184.
16. Harding MM, Williams DH, Woolfson DN. 1991. Characterization of a partially denatured state of protein by two-dimensional NMR: Reduction of hydrophobic interactions in ubiquitin. Biochemistry 30:3120-3128.
17. He JJ, Quiocho FA. 1993. Dominant role of local dipoles in stabilizing uncompensated charges on a sulfate sequestered in a periplasmic active transport protein. Protein Sci 2:1643-1647.
18. Hendsch ZS, Tidor B. 1994. Do salt bridges stabilize proteins? A continuum electrostatic analysis. Protein Sci 3:211-226.
19. Hu CQ, Sturtevant JM, Thomson JA, Erickson RE, Pace CN. 1992. Thermodynamics of ribonuclease T1 denaturation. Biochemistry 31:4876-4882.
20. Ibarra-Molero B, Sanchez-Ruiz JM. 1996. A model-independent, nonlinear extrapolation procedure for the characterization of protein folding energetics from solvent-denaturation data. Biochemistry 35:14689-14702.
21. Jenson J, Goldstein G, Breslow E. 1980. Physico-chemical properties of ubiquitin. Biochim Biopys Acta 624:378-385.
22. Khorasanizadeh S, Peters I, Butt TR, Roder H. 1993. Folding and stability of tryptophane containing mutant of ubiquitin. Biochemistry 32:7054-7063.
23. Kiefhaber T, Schmid FX, Renner M, Hinz H-J, Hahn U, Quaas R. 1990. Stability of recombinant Lys25-ribonuclease T1. Biochemistry 29:8250-8257.
24. Kim KS, Woodward C. 1993. Protein internal flexibility and global stability: Effect of urea on hydrogen exchange rates of bovine pancreatic trypsin inhibitor. Biochemistry 32:9609-9613.
25. Ledvina PS, Yao N, Choudhary A, Quiocho FA. 1996. Negative electrostatic surface potential of protein sites specific for anionic ligands. Proc Natl Acad Sci USA 93:6786-6791.
26. Lee YC, Timasheff SN. 1974. Partial specific volumes and interactions with solvent components of proteins in guanidine hydrochloride. Biochemistry 13:257-265.
27. Liu Y, Bolen DW. 1995. The peptide backbone plays a dominant role in protein stabilization by naturally occurring osmolytes. Biochemistry 34:12884-12891.
28. Lumb KJ, Dobson CM. 1992. 1H nuclear magnetic resonance studies of the interaction of urea with hen lysozyme. Origins of the conformational change induced in hen lysozyme by N-acetylglucosamine oligosaccharides. J Mol Biol 227:9-14.
29. Makhatadze GI, Privalov PL. 1992. Protein interactions with urea and guanidinium chloride. A calorimetric study. J Mol Biol 226:491-505.
30. Makhatadze GI, Clore GM, Gronenborn AM, Privalov PL. 1994. Thermodynamics of unfolding of all β-sheet protein interleukin-1β. Biochemistry 33:9327-9332.
31. Mayr LM, Schmid FX. 1993. Stabilization of a protein by guanidinium chloride. Biochemistry 32:7994-7998.
32. Oikonomakos NG, Zographos SE, Tsitsanou KE, Johnson LN, Acharya KR. 1996. Activator anion binding site in pyridoxal phosphorylase b: The binding of phosphite, phosphate, and fluorophosphate in the crystal. Protein Sci 5:2416-2428.
33. Pace CN, Grimsley GR. 1988. Ribonuclease T1 is stabilized by cation and anion binding. Biochemistry 27:3242-3246.
34. Pace CN. 1975. The stability of globular proteins. CRC Crit Rev Biochem 3:1-43.
35. Pace CN. 1986. Determination and analysis of urea and guanidine hydrochloride denaturation curves. Methods Enzymol 131:266-280.
36. Pfeil W, Privalov PL. 1976. Thermodynamic investigation of proteins. II Calorimetric study of lysozyme denaturation by guanidinium hydrochloride. Biophys Chem 4:33-30.
37. Pike AC, Acharya KR. 1994. A structural basis for the interaction of urea with lysozyme. Protein Sci 3:706-710.
38. Plaza del Pino IM, Sanchez-Ruiz JM. 1995. An osmolyte effect on the heat capacity change for protein folding. Biochemistry 34:8621-8630.
39. Potekhin S, Pfeil W. 1989. Microcalorimetric studies of conformational transitions of ferricytochrome c in acidic solution. Biophys Chem 34:55-62
40. Presper KA, Wong CY, Liu L, Meadow ND, Roseman S. 1989. Site-directed mutagenesis of the phosphocarrier protein. IIIGlc, a major signal-transducing protein in Escherichia coli. Proc Natl Acad Sci USA 86:4052-4055.
41. Privalov PL, Plotnikov VV. 1989. Three generations of scanning microcalorimeters for liquids. Thermochim Acta 139:257-277.
42. Privalov PL, Potekhin SA. 1986. Scanning microcalorimetry in studying temperature induced changes in proteins. Methods Enzymol 131:4-51.
43. Privalov PL, Ptitsyn OB, Birshtein TM. 1969. Determination of the stability of DNA double helix in an aqueous media. Biopolymers 8:559-571.
44. Quiocho FA. 1996. Atomic basis of the exquisite specificity of phosphate and sulfate transport receptors. Kidney Int 49:943-946.
45. Santoro MM, Bolen DW. 1992. A test of the linear extrapolation of unfolding free energy changes over an extended denaturant concentration range. Biochemistry 31:4901-4907.
46. Schellman JA, Gassner NC. 1996. The enthalpy of transfer of unfolded proteins into solutions of urea and guanidinium chloride. Biophys Chem 59:259-275.
47. Schellman JA. 1987. Selective binding and solvent denaturation Biopolymers 26:549-559.
48. Schellman JA. 1990. A simple model for solvation in mixed solvents. Applications to the stabilization and destabilization of macromolecular structures. Biophys Chem 37:121-140.
49. Schellman JA. 1994. The thermodynamics of solvent exchange. Biopolymers 34:1015-1026.
50. Sharp KA, Friedman RA, Misra V, Hecht J, Honig B. 1995. Salt effects on polyelectrolyte-ligand binding: Comparison of Poisson-Boltzmann, and limiting law/counterion binding models. Biopolymers 36:245-262.
51. Sharp KA. 1995. Polyelectrolyte electrostatics: salt dependence, entropic, and enthalpic contributions to free energy in the nonlinear Poisson-Boltzmann model. Biopolymers 36:227-243.
52. Sijpkes AH, van de Kleut GJ, Gill SC. 1993. Urea-diketopiperazine interactions: A model for urea induced denaturation of proteins. Biophys Chem 46:171-177.
53. Smith JS, Scholtz JM. 1996. Guanidine hydrochloride unfolding of peptide helices: Separation of denaturant and salt effects. Biochemistry 35:7292-7297.
54. Snape KW, Tijan R, Blake CCF, Koshland DE. 1974. Crystallographic study of the interaction of urea with lysozyme. Nature 250:295-298.
55. Staniforth RA, Burston SG, Smith CJ, Jackson GS, Badcoe IG, Atkinson T, Holbrook JJ, Clarke AR. 1993. The energetics and cooperativity of protein folding: A simple experimental analysis based upon the solvation of internal residues. Biochemistry 32:3842-3851.
56. Studier FW, Rosenberg AH, Dunn JJ, Dubendorf JW. 1990. Use of T7 RNA polymerase to direct expression of cloned genes. Methods Enzymol 185:60-89.
57. Swint L, Robertson AD. 1993. Thermodynamics of unfolding for turkey ovomucoid third domain: Thermal and chemical denaturation. Protein Sci 2:2037-2049.
58. Tanford C. 1968. Protein denaturation. Adv Protein Chem 23:121-282.
59. Thayer MM, Hailtwanger RC, Allured VS, Gill SC, Gill SJ. 1993. Peptide-urea interactions as observed in diketopiperazine-urea cocrystal. Biophys Chem 46:165-169.
60. Timasheff SN. 1992. Water as ligand: Preferential binding and exclusion of denaturants in protein unfolding. Biochemistry 31:9857-9864.
61. Timasheff SN. 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.
62. Timasheff SN. 1995. Solvent stabilization of protein structure. Methods Mol Biol 40:253-269.
63. Vijay-Kumar S, Bugg CE, Cook WJ. 1987a. Structure of ubiquitin refined at 1.8 Å Resolution. J Mol Biol 194:531-544.
64. Vijay-Kumar S, Buggs CE, Wilkinson KD, Vierstra RD, Hatfield PM, Cook WJ. 1987b. Comparison of the three-dimensional structures of human, yeast, and oat ubiquitin. J Biol Chem 262:6396-6399.
65. von Hippel PH, Schleich T. 1969a. Ion effects on the solution structure of biological macromolecules. Acc Chem Res 2:265-257.
66. von Hippel PH, Schleich T. 1969b. The effects of neutral salts on the structure and conformational stability of macromolecules in solution. In: Timasheff SN, Fasman GD, eds. Structure and stability of biological macromolecules. New York: Marcel Dekker Inc. pp 417-574.
67. von Hippel PH, Wong KY. 1964. Neutral salts: The generality of their effects on the stability of macromolecular conformations. Science 145:577-580.
68. Waldburger CD, Schildbach JF, Sauer RT. 1995. Are buried salt bridges important for protein stability and conformational specificity? Nat Struct Biol 2:122-128.
69. 1H NMR assignment and secondary structure identification of human ubiquitin. Biochemistry 26:7282-7290.
70. Wintrode PL, Makhatadze GI, Privalov PL. 1994. Thermodynamics of ubiquitin unfolding. Proteins 18:246-253.
71. Woolfson DN, Cooper A, Harding MM, Williams DH, Evans PA. 1993. Protein folding in the absence of the solvent ordering contribution to the hydrophobic interaction. J Mol Biol 229:502-511.
72. Yang AS, Honig B. 1992. Electrostatic effects on protein stability. Curr Opin Struct Biol 2:40-45.
73. Yao N, Ledvina PS, Choudhary A, Quiocho FA. 1996. Modulation of a salt link does not affect binding of phosphate to its specific active transport receptor. Biochemistry 35:2079-2085.
74. Yu Y, Makhatadze GI, Pace CN, Privalov PL. 1994. Energetics of ribonuclease T1 structure. Biochemistry 33:3312-3319.