Folding thermodynamics of three β-sheet peptides: A model study

Proteins: Structure, Function and Genetics

Volumn 56, Issue 1, 2004, Pages 110-116

  Irbäck, Anders ^a   Sjunnesson, Fredrik ^a  

^a LUND UNIVERSITY   (Sweden)

Author keywords

hairpin; All atom model; Monte Carlo simulation; Protein folding; Three stranded sheet

Indexed keywords

AMINO ACID; PEPTIDE; POLYPEPTIDE;

ARTICLE; BETA SHEET; COMPUTER SIMULATION; ENERGY; HYDROGEN BOND; HYDROPHOBICITY; MODEL; MONTE CARLO METHOD; PEPTIDE ANALYSIS; PRIORITY JOURNAL; PROTEIN FOLDING; TEMPERATURE DEPENDENCE; THERMODYNAMICS;

HYDROGEN BONDING; HYDROPHOBICITY; MAGNETIC RESONANCE SPECTROSCOPY; MODELS, CHEMICAL; PEPTIDES; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; TEMPERATURE; THERMODYNAMICS;

EID: 2642586516     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.20157     Document Type: Article

References (32)

1. Kortemme T, Ramírez-Alvarado M, Serrano L. Design of a 20-amino acid, three-stranded β-sheet protein. Science 1998;281:253-256.
2. López de la Paz M, Lacroix E, Ramirez-Alvarado M, Serrano L. Computer-aided design of β-sheet peptides. J Mol Biol 2001;312: 229-246.
3. de Alba E, Santaro J, Rico M, Jiménez MA. De novo design of a monomeric three-stranded antiparallel β-sheet. Protein Sci 1999; 8:854-865.
4. Bursulaya BD, Brooks CL III. Folding free energy surface of a three-stranded β-sheet protein. J Am Chem Soc 1999;121:9947-9951.
5. Colombo C, Roccatano D, Mark AE. Folding and stability of the three-stranded β-sheet peptide betanova: insights from molecular dynamics simulations. Proteins 2002;46:380-392.
6. Cavalli A, Haberthür U, Paci E, Caflisch A. Fast protein folding on downhill energy landscape. Protein Sci 2003;12:1801-1803.
7. Karanicolas J, Brooks CL III. The structural basis for biphasic kinetics in the folding of the WW domain from a formin-binding protein: lessons for protein design? Proc Natl Acad Sci USA 2003;100:3954-3959.
8. Granakaran S, Nymeyer H, Portman J, Sanbonmatsu KY, García AE. Peptide folding simulations. Curr Opin Struct Biol 2003;13: 168-174.
9. Irbäck A, Samuelsson B, Sjunnesson F, Wallin S. Thermodynamics of α- and β-structure formation in proteins. Biophys J 2003;85: 1466-1473.
10. Lockhart DJ, Kim PS. Internal Stark effect measurement of the electric field at the amino terminus of an α helix. Science 1992;257:947-951.
11. Lockhart DJ, Kim PS. Electrostatic screening of charge and dipole interactions with the helix backbone. Science 1993;260:198-202.
12. Kussell E, Shimada J, Shakhnovich EI. A structure-based method for derivation of all-atom potentials for protein folding. Proc Natl Acad Sci USA 2002;99:5343-5348.
13. Muñoz V, Thompson PA, Hofrichter J, Eaton WA. Folding dynamics and mechanism of β-hairpin formation. Nature 1997;390:196-199.
14. Branden C, Tooze J. Introduction to protein structure. New York: Garland Publishing; 1991.
15. Miyazawa S, Jernigan RL. Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density, for simulation and threading. J Mol Biol 1996;256:623-644.
16. Lyubartsev AP, Martsinovski AA, Shevkunov SV, Vorontsov-Velyaminov PN. New approach to Monte Carlo calculation of the free energy: method of expanded ensembles. J Chem Phys 1992;96: 1776-1783.
17. Marinari E, Parisi G. Simulated tempering: a new Monte Carlo scheme. Europhys Lett 1992;19:451-458.
18. Irbäck A, Potthast F. Studies of an off-lattice model for protein folding: sequence dependence and improved sampling at finite temperature. J Chem Phys 1995;103:10298-10305.
19. Hansmann UHE, Okamoto Y. New Monte Carlo algorithms for protein folding. Curr Opin Struct Biol 1999;9:177-183.
20. Lal M. Monte Carlo computer simulation of chain molecules. I. Mol Phys 1969;17:57-64.
21. Favrin G, Irbäck A, Sjunnesson F. Monte Carlo update for chain molecules: biased Gaussian steps in torsional space. J Chem Phys 2001;114:8154-8158.
22. Press WH, Flannery BP, Teukolsky SA, Vetterling WT. Numerical recipes in C: the art of scientific computing. Cambridge: Cambridge University Press; 1992.
23. Blanco FJ, Rivas G, Serrano L. A short linear peptide that folds into a native stable β-hairpin in aqueous solution. Nat Struct Biol 1994;1:584-590.
24. Roccatano D, Amadei A, Di Nola A, Berendsen HJC. A molecular dynamics study of the 41-56 β-hairpin from B1 domain of protein G. Protein Sci 1999;8:2130-2143.
25. Pande VS, Rokhsar DS. Molecular dynamics simulations of unfolding and refolding of a β-hairpin fragment from protein G. Proc Natl Acad Sci USA 1999;96:9062-9067.
26. García AE, Sanbonmatsu KY. Exploring the energy landscape of a β hairpin in explicit solvent. Proteins 2001;42:345-354.
27. Zhou R, Berne BJ, Germain R. The free energy landscape for hairpin folding in explicit water. Proc Natl Acad Sci USA 2001;98: 14931-14936.
28. Zhou R. Free energy landscape of protein folding in water: explicit vs. implicit solvent. Proteins 2003;53:148-161.
29. Dinner AR, Lazaridis T, Karplus M. Understanding β-hairpin formation. Proc Natl Acad Sci USA 1999;96:9068-9073.
30. Zagrovic B, Sorin EJ, Pande V. β-hairpin folding simulations in atomistic detail using an implicit solvent model. J Mol Biol 2001;313:151-169.
31. Favrin G, Irbäck A, Samuelsson B, Wallin S. Two-state folding over a weak free-energy barrier. Biophys J 2003;85:1457-1465.
32. Gronenborn AM, Filpula DR, Essig NZ, Achari A, Whitlow M, Wingfield PT, Clore GM. A novel, highly stable fold of the immunoglobulin-binding domain of streptococcal protein G. Science 1991;253:657-661.