Protein modeling with reduced representation: statistical potentials and protein folding mechanism
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A high resolution reduced model of proteins is used in Monte Carlo dynamics studies of the folding mechanism of a small globular protein, the B1 immunoglobulin-binding domain of streptococcal protein G. It is shown that in order to reproduce the physics of the folding transition, the united atom based model requires a set of knowledge-based potentials mimicking the short-range conformational propensities and protein-like chain stiffness, a model of directional and cooperative hydrogen bonds, and properly designed knowledge-based potentials of the long-range interactions between the side groups. The folding of the model protein is cooperative and very fast. In a single trajectory, a number of folding/unfolding cycles were observed. Typically, the folding process is initiated by assembly of a native-like structure of the C-terminal hairpin. In the next stage the rest of the four-ribbon β-sheet folds. The slowest step of this pathway is the assembly of the central helix on the scaffold of the β-sheet.
- Anfinsen CB, Scheraga HA (1975) Experimental and theoretical aspects of protein folding. Adv Protein Chem 29: 205-300.
- Blanco FJ, Serrano L (1995) Folding of protein G B1 domain studied by the conformational characterization of fragments comprising its secondary structure elements. Eur J Biochem 230: 634-649.
- Bolhuis PG (2003) Transition-path sampling of beta-hairpin folding. Proc Natl Acad Sci USA 100: 12129-12134.
- Boniecki M, Rotkiewicz P, Skolnick J, Kolinski A (2003) Protein fragment reconstruction using various modeling techniques. J Comput Aided Mol Des 17: 725-738.
- Brown S, Head-Gordon T (2004) Intermediates and the folding of proteins L and G. Protein Sci 13: 958-970.
- Dill KA, Bromberg S, Yue K, Fiebig KM, Yee DP, Thomas PD, Chan HS (1995) Principles of protein folding - A perspective from simple exact models. Protein Sci 4: 561-602.
- Finkelstein AV, Shakhnovich EI (1989) Theory of cooperative transitions in protein molecules. II. Phase diagram for a protein molecule in solution. Biopolymers 28: 1681-1694.
- Frank MK, Clore GM, Gronenborn AM (1995) Structural and dynamic characterization of the urea denatured state of the immunoglobulin binding domain of streptococcal protein G by multidimensional heteronuclear NMR spectroscopy. Protein Sci 4: 2605-2615.
- Gronenborn A, Filpula DR, Essig NZ, Achari A, Whitlow M, Wingfield PT, Clore GM (1991) A novel, highly stable fold of the immunoglobulin binding domain of streptococcal protein G. Science 253: 657-660.
- Honda S, Kobayashi N, Munekata E (2000) Thermodynamics of a beta-hairpin structure: evidence for cooperative formation of folding nucleus. J Mol Biol 295: 269-278.
- Karanicolas J, Brooks III CL (2002) The origins of asymmetry in the folding transition states of protein L and protein G. Protein Sci 11: 2351-2361.
- Klimov DK, Thirumalai D (2000) Mechanisms and kinetics of beta-hairpin formation. Proc Natl Acad Sci USA 97: 2544-2549.
- Kobayashi N, Honda S, Yoshii H, Uedaira H, Munekata E (1995) Complement assembly of two fragments of the streptococcal protein G B1 domain in aqueous solution. FEBS Lett 366: 99-103.
- Kolinski A (2004) Protein modeling and structure prediction with a reduced representation. Acta Biochim Polon 51: 349-371.
- Kolinski A, Skolnick J (1996) Lattice Models of Protein Folding, Dynamics and Thermodynamics. R.G. Landes, Austin, TX.
- Kolinski A, Skolnick J (2004) Reduced models of proteins and their applications. Polymer 45: 511-524.
- Kolinski A, Gront D, Pokarowski P, Skolnick J (2003) A simple lattice model that exhibits a protein-like cooperative all-or-none folding transition. Biopolymers 69: 399-405.
- Kolinski A, Ilkowski B, Skolnick J (1999) Dynamics and thermodynamics of β-hairpin assembly: Insight from various simulation techniques. Biophys J 77: 2942-2952.
- Kuszewski J, Clore GM, Gronenborn AM (1994) Fast folding of a prototypic polypeptide: The immunoglobin binding domain of streptococcal protein G. Protein Sci 3: 1945-1952.
- Lee MR, Tsai J, Baker D, Kollman PA (2001) Molecular dynamics in the endgame of protein structure prediction. J Mol Biol 313: 417-430.
- Ma B, Nussinov R (2003) Energy landscape and dynamics of the beta-hairpin G peptide and its isomers: Topology and sequences. Protein Sci 12: 1882-1893.
- McCallister EL, Alm E, Baker D (2000) Critical role of beta-hairpin formation in protein G folding. Nat Struct Biol 7: 669-673.
- Metropolis N, Rosenbluth AW, Rosenbluth MN, Teller AH, Teller E (1953) Equation of state calculations by fast computing machines. J Chem Phys 51: 1087-1092.
- Munoz V, Thompson PA, Hofrichter J, Eaton WA (1997) Folding dynamics and mechanism of β-hairpin formation. Nature 390: 196-197.
- Sheinerman FB, Brooks III CL (1998) Calculations on folding of segment B1 of streptococcal protein G. J Mol Biol 278: 439-456.
- Wikstrom M, Drakenberg T, Forsen S, Sjobring U, Bjorck L (1994) Three-dimensional solution structure of an immunoglobulin light chain-binding domain of protein L. Comparison with the IgG-binding domains of protein G. Biochemistry 33: 14011-14017.
- Zhou R, Berne BJ, Germain R (2001) The free energy landscape for beta hairpin folding in explicit water. Proc Natl Acad Sci USA 98: 14931-14936.
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