Observation of multiple folding pathways of β-hairpin trpzip2 from independent continuous folding trajectories

Bioinformatics

Volumn 24, Issue 5, 2008, Pages 659-665

  Chen, Changjun ^a   Xiao, Yi ^a  

^a HUAZHONG UNIVERSITY OF SCIENCE AND TECHNOLOGY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BETA HAIRPIN; COMPUTER SIMULATION; HYDROPHOBICITY; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROBABILITY; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE; ROOM TEMPERATURE; STRUCTURAL BIOINFORMATICS;

AMINO ACID SEQUENCE; COMPUTER SIMULATION; HYDROGEN BONDING; MOLECULAR SEQUENCE DATA; PEPTIDES; PROTEIN CONFORMATION; PROTEIN FOLDING;

EID: 40049089464     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btn029     Document Type: Article

References (46)

1. Alexandre,M.J. et al. (2000) β-Hairpin stability and folding: molecular dynamics studies of the first β-hairpin of tendamistat. J. Mol. Biol., 296, 255-268.
2. Andrec,M. et al. (2005) Protein folding pathways from replica exchange simulations and a kinetic network model. Proc. Natl Acad. Sci. USA, 102, 6801-6806.
3. Blanco,F.J. et al. (1994) A short linear peptide that folds into a native stable β-hairpin in aqueous solution. Nat. Struct. Biol., 1, 584-590.
4. Bolhuis,P.G. (2003) Transition-path sampling of β-hairpin folding. Proc. Nat. Acad. Sci. USA, 100, 12129-12134.
5. Bryant,Z. et al. (2000) Mechanical unfolding of a β-hairpin using molecular dynamics. Biophys. J., 78, 584-589.
6. Bryngelson,J.D. et al. (1995) Funnels, pathways, and the energy landscape of protein folding-A systhesis. Proteins: Struct. Funct. Genet., 21, 167-195.
7. Chen,C. and Xiao,Y. (2006) Molecular dynamics simulations of felding processes of a β-hairpin in an implicit solvent. Phys. Biol., 3, 161-171.
8. Cochran,A.G. et al. (2001) Tryptophan zippers: Stable, monomeric β-hairpins. Proc. Natl. Acad. Sci. USA, 98, 5578-5583.
9. Cornell,W.D. et al. (1995) A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J. Am. Chem. Soc., 117, 5179-5197.
10. Ding,F. et al. (2003) Mechanism for the α-helix to β-hairpin transition. Proteins. Struct. Funct. Genet., 53, 220-228.
11. Dinner,A.R. et al. (1999) Understanding β-hairpin formation. Proc. Natl Acad. Sci. USA, 96, 9068-9073.
12. Du,D. et al. (2004) Understanding the key factors that control the rate of (β)-hairpin folding. Proc. Natl. Acad. Sci. USA, 101 15915-15920.
13. Duan,Y. et al. (2003) A point-charge force field for molecular mechanics simulations of proteins based on conderisedphase quantum mechanical calculations. J. Comput. Chem., 24, 1999-2012.
14. Fesinmeyer,R.M. et al. (2004) Enhanced hairpin stability through loop design: The case of the protein G B1 domain hairpin. J. Am. Chem. Soc., 126, 7238-7243.
15. Galzitskaya,O.V. et al. (2002) Alpha-helix and β-hairpin folding from experiment, analytical theory and molecular dynamics simulations. Curr. Protein Pept. Sci., 3, 191-200.
16. Galzitskaya,O.V. et al. (2000) β-Hairpin folds by molecular dynamics simulations. Chem. Phys. Lett., 326, 421-429.
17. Garcia,A.E. and Sanbonmatsu,K.Y. (2001) Exploring the energy landscape of a hairpin in explicit solvent. Proteins: Struct. Funct. Genet. 42, 345-354.
18. Imamural,H. and Chen,J.Z.Y. (2006) Dependence of folding dynamics and structural stability on the location of a hydrophobic pair in β-hairpin. Proteins, Struct. Funct. Genet., 63, 555-570.
19. Jorgensen,W. L. et al. (1996) Development and testing of the OPLS all-atom force field on conformational energetics and proper-ties of organic liquids. J. Am. Chem. Soc., 118, 11225-11236.
20. Kolinski,A. et al. (1999) Dynamics and thermodynamics of β-hairpin assembly: Insights from various simulation techniques, Biophys. J., 77, 2942-2952.
21. Lee,J. and Shin,S. (2001) Understanding β-hairpin formation by molecular dynamics simulations of unfolding. Biophys. J., 81 2507-2516.
22. Lee,J. et al. (2003) Folding dynamics of β-hairpins: Molecular dynamics simulations. Bull. Korean Chem. Soc., 24, 785-791.
23. Liwo,A. et al. (2005) Ab initio simulations of protein-folding pathways by molecular dynamics with the united-residue.model of polypeptide chains. Proc. Natl. Acad. Sci. USA., 102, 2362-2367.
24. Lwin,T.Z. and Luo,R (2006) Force field influences in beta-hairpin folding simulations,. Prot. Sci., 15, 2642-2655.
25. Lwin,T.Z. et al. (2006) Is Poisson-Boltzmann theory insufficient for protein folding simulations? J. Chem. Phys., 124, 34902-34907.
26. MacKerell,A.D., Jr. (1998) All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B, 102, 3586-3616.
27. Munoz,V.A.D. (2006) Folding and aggregation kinetics of a β-hairpin. Biochemistry, 45, 7023-7035.
28. Munoz,V. et al. (1997) Folding dynamics and mechanism of β-hairpin formation. Nature, 390, 196-199.
29. Mousseau,D. et al. (2004) Understanding the key factors that control the rate of β-hairpin folding. Proc. Natl Acad. Sci. USA, 101, 15915-15920.
30. Okur,A. et al. (2003) Using PC clusters to evaluate the transferability of molecular mechanics force fields for proteins, J. Comput. Chem., 24, 21-31.
31. Pande,V.S. and Rokbsar,D.S. (1999) Molecular dynamics simulations of unfolding and refolding of a β-hairpin fragment of protein G. Proc. Natl Acad. Sci. USA, 96, 9062-9067.
32. Pitera,J.W. et al. (2006) Absence of reptation in the high-temperature folding of the trpzip2 beta-hairpin peptide. J. Chem. Phys., 124, 141102.
33. Qiu,D. et al. (1997) The GB/SA continuum model for solvation. A fast analytical method for the calculation of approximate born radii. J. Phys. Chem., A., 101, 3005-3014.
34. Snow,C.D. et al. (2004) Trp zipper folding kinetics by molecular dynamics and temperature-jump spectroscopy. Proc. Natl. Acad. Sci. USA, 101, 4077-4082.
35. Soares,T.A. et al. (2005) An improved nucleic acid parameter set for the GROMOS force field. J. Comput. Chem., 26, 725-737.
36. Still,V.C. et al. (1990) Semianalytical treatment of solvation for molecular mechanics and dynamics. J. Am. Chem. Soc., 112, 6127-6129.
37. Ulmschneider,J.P. et al. (2006) Monte Carlo vs molecular dynamics for all-atom polypeptide folding simulations. J. Phys. Chem. B, 110 16733-16742.
38. Wang,J. et al. (2000) How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? J. Comput. Chem., 21, 1049-1074.
39. Wei,G. et al. (2004) Complex folding pathways in a simple β-hairpin. Proteins: Struct. Panct. Bio., 56, 464-474.
40. Yang,W.Y. et al. (2004) Heterogeneous folding of the trpzip hairpin: Full atom simulation and experiment. J. Mol. Biol., 336, 241-251.
41. Yoda,T. et al. (2004) Comparisons of force fields for proteins by generalized-ensemble simulations. Chem. Phys. Lett., 386, 460-467.
42. Zagrovic,B. et al. (2001) Hairpin folding simulations in atornistic detail using an implicit solvent model. J. Mol. Biol., 313, 151-169.
43. Zhang,J. et al. (2006) Folding mechanism of β-Hairpins studied by replica exchange molecular simulations. Proteins: Struct. Funct. Bio. 62, 672-685.
44. Zhou,R. and Berne,BT (2002) Can a continuum solvent model reproduce the free energy landscape of β-hairpjn folding in water? Proc. Natl Acad. Sci. USA, 99, 12777-12782.
45. Zhou,R. et al. (2001) Free energy landscape of a β-hairpin folding in explicit water. Proc. Natl Acad Sci. USA, 98, 14931-4936.
46. Zhou,Y. and Linhananta,A. (2002) Role of hydrophilic and hydrophobic Contacts in folding of the second β-hairpin fragment of protein G: molecular dynamics simulation studies of an all-atom model. Proteins: Struct. Funct. Genet., 47, 154-162.