Modelling protein folding: the beauty and power of simplicity

Folding and Design - Tập 1 - Trang R50-R54 - 1996
Eugene I Shakhnovich1
1Eugene I Shakhnovich, Harvard University, Department of Chemistry, 12 Oxford Street, Cambridge, MA 02138, USA

Tài liệu tham khảo

Honig, 1996, Adding backbone to protein folding: why proteins are polypeptides, Folding & Design, 1, R17, 10.1016/S1359-0278(96)00005-3 Skolnick, 1991, Dynamic monte carlo simulations of a new lattice model of globular protein folding, structure and dynamics, J. Mol. Biol, 221, 499, 10.1016/0022-2836(91)80070-B Shakhnovich, 1991, Protein folding bottlenecks: a lattice monte-carlo simulation, Phys. Rev. Lett, 67, 1665, 10.1103/PhysRevLett.67.1665 Sali, 1994, How does a protein fold?, Nature, 369, 248, 10.1038/369248a0 Miller, 1992, Folding kinetics of proteins and copolymers, J. Chem. Phys, 96, 768, 10.1063/1.462462 Shakhnovich, 1994, Proteins with selected sequences fold to their unique native conformation, Phys. Rev. Lett, 72, 3907, 10.1103/PhysRevLett.72.3907 Hao, 1994, Monte-carlo simulation of a first order transition for protein folding, J. Phys. Chem, 98, 4940, 10.1021/j100069a028 Hao, 1994, Statistical thermodynamics of protein folding: sequence dependence, J. Phys. Chem, 98, 9882, 10.1021/j100090a024 Guo, 1992, Folding kinetics of proteins: a model study, J. Chem. Phys, 97, 525, 10.1063/1.463600 Abkevich, 1994, Specific nucleus as the transition state for protein folding: evidence from the lattice model, Biochemistry, 33, 10026, 10.1021/bi00199a029 Karplus, 1994, Protein folding: theoretical studies of thermodynamics and dynamics, 127 Bryngelson, 1995, Funnels, pathways, and the energy landscape of protein folding: a synthesis, Proteins, 21, 167, 10.1002/prot.340210302 Privalov, 1989, Stability of proteins. I. Small globular proteins, Annu. Rev. Biophys. Biophys. Chem, 18, 47, 10.1146/annurev.biophys.18.1.47 Goldstein, 1992, Optimal protein-folding codes from spin-glass theory, Proc. Natl. Acad. Sci. USA, 89, 4918, 10.1073/pnas.89.11.4918 Abkevich, 1995, Impact of local and non-local interactions on thermodynamics and kinetics of protein folding, J. Mol. Biol, 252, 460, 10.1006/jmbi.1995.0511 Landau, 1980 Poland, 1970 Griko, 1994, Thermodynamic puzzle of apomyoglobin unfolding, J. Mol. Biol, 235, 1318, 10.1006/jmbi.1994.1085 Shakhnovich, 1993, Engineering of stable and fast-folding sequences of model proteins, Proc. Natl. Acad. Sci. USA, 90, 7195, 10.1073/pnas.90.15.7195 Ramanathan, 1994, Statistical mechanics of proteins with “evolutionary selected” sequences, Phys. Rev. E, 50, 1303, 10.1103/PhysRevE.50.1303 Shakhnovich, 1989, Formation of unique structure in polypeptide chains. Theoretical investigation with the aid of replica approach, Biophys. Chem, 34, 187, 10.1016/0301-4622(89)80058-4 Chaffotte, 1992, Biochemistry, 31, 9694, 10.1021/bi00155a024 Davidson, 1994, Folded proteins occur frequently in libraries of random amino acid sequences, Proc. Natl. Acad. Sci. USA, 91, 2146, 10.1073/pnas.91.6.2146 Gutin, 1995, Is burst hydrophobic collapse necessary for rapid folding?, Biochemistry, 34, 3066, 10.1021/bi00009a038 Makhatadze, 1995, Energetics of protein structure, Adv. Protein Chem, 47, 307, 10.1016/S0065-3233(08)60548-3 Honig, 1995, Free energy balance in protein folding, Adv. Protein Chem, 46, 27, 10.1016/S0065-3233(08)60331-9 Kiefhaber, 1995, Kinetic of hydrogen bond breakage in the process of ribonuclease a measured by pulsed hydrogen exchange, Proc. Natl. Acad. Sci. USA, 92, 2657, 10.1073/pnas.92.7.2657 Kiefhaber, 1995, Direct NMR evidence for an intermediate preceding the rate-limiting step in the unfolding of ribonuclease A, Nature, 375, 513, 10.1038/375513a0 Shakhnovich, 1989, Theory of cooperative transitions in protein molecules. I. Why denaturation of globular protein is a first-order phase transition, Biopolymers, 28, 1667, 10.1002/bip.360281003 Matouschek, 1990, Transient folding intermediates characterized by protein engineering, Nature, 346, 440, 10.1038/346440a0 Jackson, 1993, Structure of the hydrophobic core in the transition state for folding of chymotrypsin inhibitor 2: a critical test of the protein engineering method of analysis, Biochemistry, 32, 11270, 10.1021/bi00093a002 Itzhaki, 1995, The structure of the transition state for folding of chymotrypsin inhibitor 2 analyzed by protein engineering methods: evidence for a nucleation-condensation mechanism for protein folding, J. Mol. Biol, 254, 260, 10.1006/jmbi.1995.0616 Creighton, 1992 Schildbach, 1995, Crystal structure, folding and operator binding of the hyperstable arc repressor mutant PL8, Biochemistry, 34, 1405, 10.1021/bi00004a035 Milla, 1995, P22 arc repressor: transition state properties inferred from mutational effects on the rates of protein unfolding and refolding, Biochemistry, 34, 13914, 10.1021/bi00042a024 López-Hernéndez, 1996, Structure of the transition state for folding of the 129 aa protein CheY resembles that of a smaller protein, CI-2, Folding & Design, 1, 43, 10.1016/S1359-0278(96)00011-9 Sosnick, 1996, The role of helix formation in the folding of a fully α-helical coiled-coil, Proteins, 10.1002/(SICI)1097-0134(199604)24:4<427::AID-PROT2>3.0.CO;2-B Sosnick, 1996, Molecular collapse: the rate-limiting step in two-state cytochrome C folding, Proteins, 10.1002/(SICI)1097-0134(199604)24:4<413::AID-PROT1>3.0.CO;2-F Shakhnovich, 1996, Conserved residues and the mechanism of protein folding, Nature, 379, 96, 10.1038/379096a0 Ingwall, 1968, Conformational studies of poly-L-alanine in water, Biopolymers, 6, 331, 10.1002/bip.1968.360060308 Brooks, 1988