A thermodynamic analysis of a family of small globular proteins: SH3 domains

Biophysical Chemistry

Volumn 77, Issue 2-3, 1999, Pages 195-208

  Filimonov, Vladimir V ^a,b   Azuaga, Ana I ^a   Viguera, Ana R ^c   Serrano, Luis ^c   Mateo, Pedro L ^a  

^a UNIVERSITY OF GRANADA   (Spain)

^b INSTITUTE OF PROTEIN RESEARCH   (Russian Federation)

^c EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

Author keywords

Folding; Scanning calorimetry; SH3 domains; Stability; Thermodynamic analysis; Urea unfolding

Indexed keywords

GLOBULAR PROTEIN; PROTEIN; UREA;

ARTICLE; CALCULATION; DENATURATION; DIFFERENTIAL SCANNING CALORIMETRY; MODEL; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN STABILITY; SIMULATION; THERMODYNAMICS;

AMINO ACID SEQUENCE; CALORIMETRY, DIFFERENTIAL SCANNING; MOLECULAR SEQUENCE DATA; PROTEIN DENATURATION; PROTEIN FOLDING; PROTEINS; PROTO-ONCOGENE PROTEINS; PROTO-ONCOGENE PROTEINS C-ABL; PROTO-ONCOGENE PROTEINS C-FYN; RIBONUCLEASES; SEQUENCE ALIGNMENT; SPECTRIN; SRC HOMOLOGY DOMAINS; THERMODYNAMICS; UREA;

EID: 0033045105     PISSN: 03014622     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0301-4622(99)00025-3     Document Type: Article

References (37)

1. Mayer B.J., Hamaguchi M., Hanafusa H. A novel viral oncogene with structural similarity to phospholipase C. Nature. 332:1988;272-275.
2. Musacchio A., Gibson T., Lehto V.P., Saraste M. SH3 - An abundant protein domain in search of a function. FEBS Lett. 307:1992;55-61.
3. Lehto V.P., Wassenius V.M., Salven P., Saraste M. Transforming and membrane proteins. Nature. 334:1988;388.
4. Pawson Y., Gish G.D. SH2 and SH3 domains: from structure to function. Cell. 71:1992;359-362.
5. Mussacchio A., Noble M.E.M., Pautit R., Wierenga R., Saraste M. Crystal structure of a Src-homology 3 (SH3) domain. Nature. 359:1992;851-855.
6. Koyama S., Yu H., Dalgarno D.C., Shin T.B., Zydowsky L.D., Schreiber S.L. Structure of the P13K SH3 domain and analysis of SH3 family. Cell. 72:1993;945-952.
7. Kohda D., Terasawa H., Ichikawa S., Ogura K., Hatanaka H., Mandiyan V., Ullrich A., Schlessinger J., Inagaki F. Solution structure and ligand-binding site of the carboxy-terminal SH3 domain GRB2. Structure. 2:1994;1029-1040.
8. Ren R., Mayer B.J., Cicchetti P., Baltimore D. Identification of a 10-aminoacid proline-rich SH3 binding site. Science. 259:1993;1157-1161.
9. Viguera A.R., Arrondo J.R.L., Musacchio A., Saraste M., Serrano L. Characterization of the interaction of natural proline-rich peptides with five different SH3 domains. Biochemistry. 33:1994;10925-10933.
10. Lim W.A., Fox R.O., Richards F.M. Stability and peptidic binding affinity of an SH3 domain from the Caenorhabiditis elegans signaling protein Sem-5. Protein Sci. 3:1994;1261-1266.
11. Pisabarro M., Ortiz A., Viguera A.R., Gago F., Serrano L. Molecular modeling of the interaction of polyproline-based peptides with the Abl-SH3 domain: rational modification of the interaction. Protein Eng. 7:1994;1455-1462.
12. Viguera A.R., Martinez J.C., Filimonov V.V., Mateo P.L., Serrano L. Thermodynamic and kinetic analysis of the SH3 domain of spectrin shows a two-state folding transition. Biochemistry. 33:1994;2142-2150.
13. Lim W.A., Richards F.M., Fox R.O. Structural determinants of peptide-binding orientation and of sequence specificity in SH3 domains. Nature. 372:1994;375-379.
14. Pace C.N. Determination and analysis of urea and guanidine hydrochloride denaturation curves. Methods Enzymol. 131:1986;266-280.
15. Matouschek A., Matthews J.M., Johnson C.M., Fersht A.R. Extrapolation to water of kinetic and equilibrium data for the unfolding of barnase in urea solutions. Protein Eng. 7:1994;1089-1095.
16. Viguera A.R., Wilmanns M., Serrano L. Different folding transition states could result in the same native structure. Nat. Struct. Biol. 3:1996;874-880.
17. Lee B.K., Richards F.M. The interpretation of protein structures: estimation of static accessibility. J. Mol. Biol. 55:1971;379-400.
18. Chothia C. The nature of the accessible and buried surfaces in proteins. J. Mol. Biol. 105:1976;1-14.
19. Myers J.K., Pace C.N., Scholtz J.M. Denaturant m values and heat capacity changes: relation to changes in accessible surface areas of protein unfolding. Prot. Sci. 4:1995;2138-2148.
20. Kellis J.T. Jr., Nyberg K., Fersht A.R. Energetics of complementary side-chain packing in a protein hydrophobic core. Biochemistry. 28:1989;4914-4922.
21. Martinez J.C., Filimonov V.V., Mateo P.L., Schreiber G., Fersht A.R. A calorimetric study of the thermal stability of barstar and its interaction with barnase. Biochemistry. 34:1995;5224-5233.
22. Privalov P.L., Tiktopulo E.I., Venyaminov S.Yu., Griko Yu.V., Makhatadze G.I., Khechinashvili N.N. Heat capacity and conformation of proteins in the denatured state. J. Mol. Biol. 205:1989;737-750.
23. Horovitz A., Matthews J.M., Fersht A.R. α-helix stability in proteins. Factors that influence stability at an internal position. J. Mol. Biol. 227:1992;560-568.
24. Plaxco K.W., Giujarro J.I., Morton C.J., Pitkeathly M., Campbell I.D., Dobson C.M. The folding kinetics and thermodynamics of the Fyn-SH3 domain. Biochemistry. 37:1998;2529-2537.
25. Spolar R.S., Livingstone J.R., Record M.T. Jr. Use of liquid hydrocarbon and amide transfer data to estimate contributions to thermodynamic functions of protein folding from the removal of nonpolar and polar surface from water. Biochemistry. 31:1992;3947-3955.
26. Murphy K.P., Freire E. Thermodynamics of structural stability and cooperative folding behavior in proteins. Adv. Protein Chem. 43:1992;313-361.
27. Makhatadze G.I., Privalov P.L. Contribution of hydration to protein folding thermodynamics. I. The enthalpy of hydration. J. Mol. Biol. 232:1993;639-659.
28. Gomez J., Freire E. Thermodynamic mapping of the inhibitor site of the aspartic protease endothiapepsin. J. Mol. Biol. 252:1995;337-350.
29. Makhatadze G.I., Privalov P.L. Energetics of protein structure. Adv. Protein Chem. 47:1995;307-425.
30. Viguera A.R., Blanco F.J., Serrano L. The order of secondary structure elements does not determine the structure of a protein but does affect its folding kinetics. J. Mol. Biol. 247:1995;670-681.
31. Johnson C., Fersht A.R. Protein stability as a function of denaturant concentration: the thermal stability of barnase in the presence of urea. Biochemistry. 34:1995;6795-6804.
32. Smith C.K., Bu Z., Anderson K.S., Sturtevant J.M., Engelman D.M., Regan L. Surface point mutations that significantly alter the structure and stability of a protein's denatured state. Protein Sci. 5:1996;2009-2019.
33. Nicholson E.M., Scholtz J.M. Conformational stability of the Escherichia coli HPr protein: test of the linear extrapolation method and a thermodynamic characterization of cold denaturation. Biochemistry. 35:1996;11369-11378.
34. Englander S.W., Mayne L., Bai Y., Sosnick T.R. Hydrogen exchange: the modern legacy of Liderstrøm-Lang. Protein Sci. 6:1997;1101-1109.
35. Bai Y., Milne J.S., Mayne L., Englander S.W. Protein stability parameters measured by hydrogen exchange. Proteins: Struct. Funct. Genet. 20:1994;4-14.
36. Pace C.N., Laurents D.V., Thomson J.A. pH dependence of the urea and guanidine hydrochloride denaturation of ribonuclease A and ribonuclease T1. Biochemistry. 29:1990;2564-2572.
37. Pace C.N., Laurents D.V., Erickson R.E. Urea denaturation of barnase: pH dependence and characterization of the unfolded state. Biochemistry. 31:1992;2728-2734.