Key residue-dominated protein folding dynamics

Biochemical and Biophysical Research Communications

Volumn 373, Issue 1, 2008, Pages 64-68

  Yao, Xin Qiu ^a,b   She, Zhen Su ^a,b,c  

^a Peking University   (China)

^b PEKING UNIVERSITY   (China)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Key residue; Order parameter; Protein folding; Side chain relaxation; Trp cage

Indexed keywords

TRANSIENT RECEPTOR POTENTIAL CHANNEL 6;

ARTICLE; KINETICS; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN FOLDING; SIMULATION;

AMINO ACID SEQUENCE; DATABASES, PROTEIN; KINETICS; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEIN FOLDING; TRYPTOPHAN;

EID: 45849116879     PISSN: 0006291X     EISSN: 10902104     Source Type: Journal    
DOI: 10.1016/j.bbrc.2008.05.179     Document Type: Article

References (17)

1. Shakhnovich E.I. Protein folding thermodynamics and dynamics: where physics, chemistry, and biology meet. Chem. Rev. 106 (2006) 1559-1588
2. Dill K.A. Theory for the folding and stability of globular proteins. Biochemistry 24 (1985) 1501-1509
3. Abkevich V.I., Gutin A.M., and Shakhnovich E.I. Specific nucleus as the transition state for protein folding: evidence from the lattice model. Biochemistry 33 (1994) 10026-10036
4. Ding F., Dokholyan N.V., Buldyrev S.V., Stanley H.E., and Shakhnovich E.I. Direct molecular dynamics observation of protein folding transition state ensemble. Biophys. J. 83 (2002) 3525-3532
5. Li H., Helling R., Tang C., and Wingreen N. Emergence of preferred structures in a simple model of protein folding. Science 273 (1996) 666-669
6. Liang J., and Dill K.A. Are proteins well-packed?. Biophys. J. 81 (2001) 751-766
7. Kussell E., Shimada J., and Shakhnovich E.I. Excluded volume in protein side-chain packing. J. Mol. Biol. 311 (2001) 183-193
8. Kussell E., Shimada J., and Shakhnovich E.I. Side-chain dynamics and protein folding. Proteins 52 (2003) 303-321
9. Wei Y., Nadler W., and Hansmann U.H. Backbone and side-chain ordering in a small protein. J. Chem. Phys. 128 (2008) 025105
10. Dill K.A. Dominant forces in protein folding. Biochemistry 29 (1990) 7133-7155
11. Neidigh J.W., Fesinmeyer R.M., and Andersen N.H. Designing a 20-residue protein. Nat. Struct. Biol. 9 (2002) 425-430
12. Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissig H., Shindyalov I.N., and Bourne P.E. The protein data bank. Nucleic Acids Res. 28 (2000) 235-242
13. Jorgensen W.L., and Tirado-Rives J. The OPLS potential functions for proteins. Energy minimizations for crystals of cyclic peptides and crambin. J. Am. Chem. Soc. 110 (1988) 1657-1666
14. Hess B., Bekker H., Berendsen H.J.C., and Fraaije J.G.E.M. LINCS: a linear constraint solver for molecular simulations. J. Comp. Chem. 18 (1997) 1463-1472
15. Ota M., Ikeguchi M., and Kidera A. Phylogeny of protein-folding trajectories reveals a unique pathway to native structure. Proc. Natl. Acad. Sci. USA 101 (2004) 17658-17663
16. Vendruscolo M., Paci E., Dobson C.M., and Karplus M. Three key residues form a critical contact network in a protein folding transition state. Nature 409 (2001) 641-645
17. Bendova-Biedermannova L., Hobza P., and Vondrasek J. Identifying stabilizing key residues in proteins using interresidue interaction energy matrix. Proteins 72 (2008) 402-413