Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential

Folding and Design - Tập 2 Số 3 - Trang 173-181 - 1997
İvet Bahar1, Ali Rana Atılgan1, Burak Erman1
1Polymer Research Center and School of Engineering, Bogazici University, TUBITAK Advanced Polymeric Materials Research Center, Bebek, 80815, Istanbul, Turkey

Tóm tắt

Từ khóa


Tài liệu tham khảo

Jernigan, 1996, Structure-derived potentials and protein simulations, Curr. Opin. Struct. Biol, 6, 195, 10.1016/S0959-440X(96)80075-3

Sippl, 1995, Knowledge-based potentials for proteins, Curr. Opin. Struct. Biol, 5, 229, 10.1016/0959-440X(95)80081-6

Srinivasan, 1995, LINUS: a hierarchic procedure to predict the fold of a protein, Proteins, 22, 81, 10.1002/prot.340220202

Yue, 1996, Folding proteins with a simple energy function and extensive conformational searching, Protein Sci, 5, 254, 10.1002/pro.5560050209

Tirion, 1996, Large amplitude elastic motions in proteins from a single-parameter atomic analysis, Phys. Rev. Lett, 77, 1905, 10.1103/PhysRevLett.77.1905

Levitt, 1983, Molecular dynamics of native protein. I. Computer simulation of trajectories, J. Mol. Biol, 168, 595, 10.1016/S0022-2836(83)80304-0

Brooks, 1983, Harmonic dynamics of proteins: normal modes and fluctuations in bovine pancreatic trypsin inhibitor, Proc. Natl Acad. Sci. USA, 80, 6571, 10.1073/pnas.80.21.6571

Levitt, 1985, Protein normal-mode dynamics: trypsin inhibitor, crambin, ribonuclease and lysozyme, J. Mol. Biol, 181, 423, 10.1016/0022-2836(85)90230-X

Horiuchi, 1991, Projection of Monte Carlo and molecular dynamics trajectories onto the normal mode axes: human lysozyme, Proteins, 10, 106, 10.1002/prot.340100204

Kidera, 1992, Normal mode refinement: crystallographic refinement of protein dynamic structure I. Theory and test by simulated diffraction data, J. Mol. Biol, 225, 457, 10.1016/0022-2836(92)90932-A

Go, 1983, Dynamics of a small globular protein in terms of low-frequency vibrational modes, Proc. Natl. Acad. Sci. USA, 80, 3696, 10.1073/pnas.80.12.3696

Case, 1994, Normal mode analysis of protein dynamics, Curr. Opin. Struct. Biol, 4, 285, 10.1016/S0959-440X(94)90321-2

Hayward, 1995, Harmonicity and anharmonicity in protein dynamics: a normal mode analysis and principal component analysis, Proteins, 23, 177, 10.1002/prot.340230207

Marques, 1995, Hinge-bending motion in citrate synthase arising from normal mode calculations, Proteins, 23, 557, 10.1002/prot.340230410

Flory, 1976, Statistical thermodynamics of random networks, Proc. R. Soc. Lond. A, 351, 351, 10.1098/rspa.1976.0146

Pearson, 1977, Scattered intensity from a chain in a rubber network, Macromolecules, 10, 696, 10.1021/ma60057a040

Kloczkowski, 1989, Chain dimensions and fluctuations in random elastomeric networks. 1. Phantom Gaussian networks in the undeformed state, Macromolecules, 22, 1423, 10.1021/ma00193a070

Eichinger, 1972, Elasticity theory. I. Distribution functions for perfect phantom networks, Macromolecules, 5, 496, 10.1021/ma60028a028

Bernstein, 1977, The protein databank: a computer-based archival file for macromolecular structures, J. Mol. Biol, 112, 535, 10.1016/S0022-2836(77)80200-3

Abola, 1987, 107

Frauenfelder, 1979, Temperature dependent X-ray diffraction as a probe of protein structural dynamics, Nature, 280, 558, 10.1038/280558a0

Ealick, 1990, Three-dimensional structure of human erythrocytic purine nucleoside phosphorylase at 3.2 Å resolution, J. Biol. Chem, 265, 1812, 10.1016/S0021-9258(19)40090-2

Kabsch, 1990, Atomic structure of the actin:DNase I complex, Nature, 347, 37, 10.1038/347037a0

Cowan, 1992, Crystal structures explain functional properties of two E. coli porins, Nature, 358, 727, 10.1038/358727a0

Rouse, 1953, A theory of the linear viscoelastic properties of dilute solutions of coiling polymers, J. Chem. Phys, 21, 1272, 10.1063/1.1699180

Eichinger, 1973, Self-avoiding random walks, circle and star graphs, and a group of singular matrices, J. Chem. Phys, 59, 5787, 10.1063/1.1679943

Frauenfelder, 1980, Structural dynamics of liganded myoglobin, Biophys. J, 53, 465, 10.1016/S0006-3495(80)84984-8

Garcia, 1992, Large-amplitude nonlinear motions in proteins, Phys. Rev. Lett, 68, 2696, 10.1103/PhysRevLett.68.2696

Noguti, 1982, Collective variable description of small amplitude conformational fluctuations in a globular protein, Nature, 296, 776, 10.1038/296776a0

Bahar, 1997, Inter-residue potentials in globular proteins and the dominance of highly specific hydrophilic interactions at close separation, J. Mol. Biol, 266, 195, 10.1006/jmbi.1996.0758

Ben-Avraham, 1995, Dynamic and elastic properties of F-actin: a normal modes analysis, Biophys. J, 68, 1231, 10.1016/S0006-3495(95)80299-7

Feller, 1968

Bahar, 1996, Coordination geometry of nonbonded residues in globular proteins, Fold. Des, 1, 357, 10.1016/S1359-0278(96)00051-X

Miyazawa, 1985, Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation, Macromolecules, 18, 534, 10.1021/ma00145a039

Sixma, 1992, Lactose binding to heat-labile enterotoxin revealed by X-ray crystallography, Nature, 355, 561, 10.1038/355561a0

Teeter, 1979, Highly ordered crystals of the plant seed protein crambin, J. Mol. Biol, 127, 219, 10.1016/0022-2836(79)90242-0

Teeter, 1984, Water structure of a hydrophobic protein at atomic resolution: pentagon rings of water molecules in crystals of crambin, Proc. Natl. Acad. Sci. USA, 81, 6014, 10.1073/pnas.81.19.6014

Wlodawer, 1987, Comparison of two highly refined structures of bovine pancreatic inhibitor, J. Mol. Biol, 193, 145, 10.1016/0022-2836(87)90633-4

Sjöberg, 1976, Thioredoxin induced by bacteriophage T4: crystallization and preliminary crystallographic data, J. Mol. Biol, 100, 415, 10.1016/S0022-2836(76)80072-1

Söderberg, 1978, Three-dimensional structure of thioredoxin induced by bacteriophage T4, Proc. Natl. Acad. Sci. USA, 75, 5827, 10.1073/pnas.75.12.5827

Stura, 1992, Crystallization of murine major histocompatibility complex class I H-2Kb with single peptides, J. Mol. Biol, 228, 975, 10.1016/0022-2836(92)90881-J

Katti, 1990, Crystal structure of thioredoxin from Escherichia coli at 1.68 Å resolution, J. Mol. Biol, 212, 167, 10.1016/0022-2836(90)90313-B

Wlodawer, 1982, The refined crystal structure of ribonuclease A at 2.0 Å resolution, J. Biol. Chem, 257, 1325, 10.1016/S0021-9258(19)68195-0

Finzel, 1985, Structure of ferricytochrome c′ from rhodospirillium molischianum at 1.67 Å resolution, J. Mol. Biol, 186, 627, 10.1016/0022-2836(85)90135-4

Weaver, 1987, Structure of bacteriophage T4 lysozyme refined at 1.7 Å resolution, J. Mol. Biol, 193, 189, 10.1016/0022-2836(87)90636-X

Matthews, 1987, Enhanced protein thermostability from site-directed mutations that decrease the entropy of unfolding, Proc. Natl. Acad. Sci. USA, 84, 6663, 10.1073/pnas.84.19.6663