Folding specificity induced by loop stiffness

Protein Science

Volumn 12, Issue 7, 2003, Pages 1473-1482

  Spagnolo, Laura ^a   Ventura, Salvador ^a,b   Serrano, Luis ^a  

^a EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

^b UNIVERSITAT AUTÒNOMA DE BARCELONA   (Spain)

Author keywords

Design; Hydrophobic core; Kinetics; Proteins

Indexed keywords

FODRIN;

AMINO ACID SUBSTITUTION; ARTICLE; HYDROPHOBICITY; KINETICS; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN INTERACTION; PROTEIN STABILITY; PROTEIN STRUCTURE; PROTON NUCLEAR MAGNETIC RESONANCE;

ASPARTIC ACID; CIRCULAR DICHROISM; GLOBULINS; GLYCINE; HYDROPHOBICITY; MAGNETIC RESONANCE SPECTROSCOPY; PLIABILITY; PROTEIN CONFORMATION; PROTEIN FOLDING; SPECTRIN; SRC HOMOLOGY DOMAINS; THERMODYNAMICS;

EID: 0038648562     PISSN: 09618368     EISSN: None     Source Type: Journal    
DOI: 10.1110/ps.0302603     Document Type: Article

References (27)

1. Alexandrescu, A.T., Evans, P.A., Pitkeathly, M., Baum, J., and Dobson, C.M. 1993. Structure and dynamics of the acid-denatured molten globule state of α-lactalbumin: A two-dimensional NMR study. Biochemistry 32: 1707-1718.
2. Baum, J., Dobson, C.M., Evans, P.A., and Hanley, C. 1989. Characterization of a partly folded protein by NMR methods: Studies on the molten globule state of guinea pig α-lactalbumin. Biochemistry 28: 7-13.
3. Bhattacharjya, S. and Balaram, P. 1997. Effects of organic solvents on protein structures: Observation of a structured helical core in hen egg-white lysozyme in aqueous dimethylsulfoxide. Proteins 29: 492-507.
4. Burstein, E.A., Vedenkina, N.S., and Ivkova, M.N. 1973. Fluorescence and the location of tryptophan residues in protein molecules. Photochem. Photobiol. 18: 263-279.
5. Chen, J. and Stites, W.E. 2001. Packing is a key selection factor in the evolution of protein hydrophobic cores. Biochemistry 40: 15280-15289.
6. Desjarlais, J.R. and Handel, T.M. 1995. De novo design of the hydrophobic cores of proteins. Protein Sci. 4: 2006-2018.
7. Dill, K.A. 1990. Dominant forces in protein folding. Biochemistry 29: 7133-7155.
8. Finucane, M.D. and Woolfson, D.N. 1999. Core-directed protein design. II. Rescue of a multiply mutated and destabilized variant of ubiquitin. Biochemistry 38: 11613-11623.
9. Fisinger, S., Serrano, L., and Lacroix, E. 2001. Computational estimation of specific side chain interaction energies in α helices. Protein Sci. 10: 809-818.
10. Klimov, D.K. and Thirumalai, D. 2002. Stiffness of the distal loop restricts the structural heterogeneity of the transition state ensemble in SH3 domains. J. Mol. Biol. 317: 721-737.
11. Koradi, R., Billeter, M., and Wüthrich, K. 1996. MOLMOL: A program for display and analysis of macromolecular structures. J. Mol. Graphics 14: 51-55.
12. Lopez de la Paz, M., Lacroix, E., Ramirez-Alvarado, M. and Serrano, L. 2001. Computer-aided design of β-sheet peptides. J. Mol. Biol. 312: 229-246.
13. Lumb, K.J. and Kim, P.S. 1995. A buried polar interaction imparts structural uniqueness in a designed heterodimeric coiled coil. Biochemistry 34: 8642-8648.
14. Martinez, J.C. and Serrano, L. 1999. The folding transition state between SH3 domains is conformationally restricted and evolutionarily conserved. Nat. Struct. Biol. 6: 1010-1016.
15. Martinez, J.C., Pisabarro, M.T., and Serrano, L. 1998. Obligatory steps in protein folding and the conformational diversity of the transition state. Nat. Struct. Biol. 5: 721-729.
16. Musacchio, A., Noble, M., Pauptit, R., Wierenga, R., and Saraste, M. 1992. Crystal structure of a Src-homology 3 (SH3) domain. Nature 359: 851-855.
17. Peranen, J., Rikkonen, M., Hyvonen, M., and Kaariainen, L. 1996. T7 vectors with modified T7lac promoter for expression of proteins in Escherichia coli. Anal. Biochem. 236: 371-373.
18. Ptitsyn, O.B. 1992. The molten globule state. In Protein folding (ed. T.E. Creighton), pp. 243-300. W.H. Freeman and Company, New York.
19. Semisotnov, G.V., Rodionova, N.A., Razgulyaev, O.I., Uversky, V.N., Gripas, A.F. and Gilmanshin, R.I. 1991. Study of the "molten globule" intermediate state in protein folding by a hydrophobic fluorescent probe. Biopolymers 31: 119-128.
20. Vega, M.C., Martinez, J.C., and Serrano, L. 2000. Thermodynamic and structural characterization of Asn and Ala residues in the disallowed II′ region of the Ramachandran plot. Protein Sci. 9: 2322-2328.
21. Ventura, S., Vega, M.C., Lacroix, E., Angrand, I., Spagnolo, L., and Serrano, L. 2002. Conformational strain in the hydrophobic core and its implications for protein folding and design. Nat. Struct. Biol. 9: 485-493.
22. Viguera, A.R. and Serrano, L. 2001. Bergerac-SH3: "Frustation" induced by stabilizing the folding nucleus. J. Mol. Biol. 311: 357-371.
23. Viguera, A.R., Arrondo, J.L., Musacchio, A., Saraste, M., and Serrano, L. 1994a. Characterization of the interaction of natural proline-rich peptides with five different SH3 domains. Biochemistry 33: 10925-10933.
24. Viguera, A.R., Martinez, J.C., Filimonov, V.V., Mateo, P.L., and Serrano, L. 1994b. Thermodynamic and kinetic analysis of the SH3 domain of spectrin shows a two-state folding transition. Biochemistry 33: 2142-2150.
25. Viguera, A.R., Jimenez, M.A., Rico, M., and Serrano, L. 1996. Conformational analysis of peptides corresponding to β-hairpins and a β-sheet that represent the entire sequence of the α-spectrin SH3 domain. J. Mol. Biol. 255: 507-521.
26. Walsh, S.T., Sukharev, V.I., Betz, S.F., Vekshin, N.L., and DeGrado, W.F. 2001. Hydrophobic core malleability of a de novo designed three-helix bundle protein. J. Mol. Biol. 305: 361-373.
27. Wang, C., Lascu, I., and Giartosio, A. 1998. Bovine serum fetuin is unfolded through a molten globule state. Biochemistry 37: 8457-8464.