Simultaneous and coupled energy optimization of homologous proteins: a new tool for structure prediction

Folding and Design - Tập 2 - Trang 247-259 - 1997
Chen Keasar1, Ron Elber2, Jeffrey Skolnick3
1Department of Physical Chemistry, Department of Biological Chemistry, Fritz Haber Research Center for Molecular Dynamics, Wolfson Center for Applied Structural Biology, Hebrew University, Givaat Ram, Jerusalem, 91904, Israel, Peptor, Limited, Kiryat Weizmann, Rehovot, 76326, Israel
2Department of Physical Chemistry, Department of Biological Chemistry, Fritz Haber Research Center for Molecular Dynamics, Wolfson Center for Applied Structural Biology, Hebrew University, Givaat Ram, Jerusalem, 91904, Israel
3Department of Molecular Biology, Scripps Research Institute, La Jolla, CA 92037, USA

Tài liệu tham khảo

Brooks, 1983, CHARM: a program for macromolecular energy minimization and dynamics calculations, J. Comput. Chem, 4, 187, 10.1002/jcc.540040211

Jorgensen, 1988, The OLPS potential function for proteins. Energy minimizations for the crystals of cyclic peptides and crambin, J. Am. Chem. Soc, 110, 1657, 10.1021/ja00214a001

Weiner, 1984, A new force field for molecular mechanical simulation of nucleic acids and proteins, J. Am. Chem. Soc, 106, 765, 10.1021/ja00315a051

Casari, 1992, Structure-derived hydrophobic potential. Hydrophobic potential derived from X-ray structures of globular proteins is able to identify native folds, J. Mol. Biol, 224, 725, 10.1016/0022-2836(92)90556-Y

Godzik, 1995, Are proteins ideal mixtures of amino acids? Analysis of energy parameter sets, Protein Sci, 4, 2107, 10.1002/pro.5560041016

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

Godzik, 1992, Simulations of the folding pathway of triose phosphate isomerase-type a/b barrel proteins, Proc. Natl Acad. Sci. USA, 89, 2629, 10.1073/pnas.89.7.2629

Covell, 1994, Lattice model simulations of polypeptide chain folding, J. Mol. Biol, 235, 1032, 10.1006/jmbi.1994.1055

Hinds, 1994, Exploring conformational space with a simple lattice model for protein structure, J. Mol. Biol, 243, 668, 10.1016/0022-2836(94)90040-X

Kolinski, 1994, Monte Carlo simulations of protein folding. I. Lattice model and interaction scheme, Proteins, 18, 338, 10.1002/prot.340180405

Bowie, 1991, A method to identify protein sequences that fold into a known three-dimensional structure, Science, 253, 164, 10.1126/science.1853201

Bryant, 1993, An empirical energy function for threading protein sequence through the folding motif, Proteins, 16, 92, 10.1002/prot.340160110

Miyazawa, 1996, Residue–residue potentials with a favorable contact pair term and an unfavorable high packing density term for simulation and threading, J. Mol. Biol, 256, 623, 10.1006/jmbi.1996.0114

Lemer, 1995, Protein structure prediction by threading methods: evaluation of current techniques, Proteins, 23, 337, 10.1002/prot.340230308

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

Kirkpatrick, 1983, Optimization by simulated annealing, Science, 220, 671, 10.1126/science.220.4598.671

Somorjai, 1991, Novel approach for computing the global minimum of proteins. 1. General concepts methods and approximations, J. Phys. Chem, 95, 4141, 10.1021/j100163a045

Piela, 1989, The multiple-minima problem in the conformational analysis of molecules. Deformation of the potential energy hypersurface by the diffusion equation method, J. Phys. Chem, 93, 3339, 10.1021/j100345a090

Ma, 1993, Approximate solution of the classical Liouville equation using gaussian phase packet dynamics: application to enhanced equilibrium averaging and global optimization, J. Chem. Phys, 99, 4024, 10.1063/1.466098

Amara, 1993, Global minimum searches using an approximate solution to the imaginary time Schrodinger equation, J. Phys. Chem, 97, 6715, 10.1021/j100127a023

Roitberg, 1991, Modeling sidechains in peptides and proteins: application of the locally enhanced sampling and the simulated annealing methods to find minimum energy conformations, J. Chem. Phys, 95, 9277, 10.1063/1.461157

Straub, 1996, Optimization techniques with applications to proteins, 137

Sander, 1991, Database of homology-derived protein structures and the structural meaning of sequence alignment, Proteins, 9, 56, 10.1002/prot.340090107

Greer, 1991, Comparative modeling of homologous proteins, Methods Enzymol, 202, 239, 10.1016/0076-6879(91)02014-Z

Maxfield, 1979, Improvements in the prediction of protein backbone topography by reduction of statistical errors, Biochemistry, 18, 697, 10.1021/bi00571a023

Niermann, 1991, Use of homologous sequences to improve protein secondary structure prediction, Methods Enzymol, 202, 45, 10.1016/0076-6879(91)02006-U

Rost, 1995, Progress of 1D protein structure prediction at last, Proteins, 23, 295, 10.1002/prot.340230304

Zvelebil, 1987, Prediction of protein secondary structure and active sites using the alignment of homologous sequences, J. Mol. Biol, 195, 957, 10.1016/0022-2836(87)90501-8

Thompson, 1996, Predicting solvent accessibility: higher accuracy using bayesian statistics and optimized residue substitution classes, Proteins, 25, 38, 10.1002/(SICI)1097-0134(199605)25:1<38::AID-PROT4>3.3.CO;2-H

Defay, 1996, Multiple sequence information for threading algorithms, J. Mol. Biol, 262, 314, 10.1006/jmbi.1996.0515

Fischer, 1996, Advances in fold recognition: directional profiles and sequence-derived predictions, Fold. Des, 1, A54

Keasar, 1995, Homology as a tool in optimization problems: structure determination of 2D heteropolymers, J. Phys. Chem, 99, 11550, 10.1021/j100029a038

Vieth, 1994, Prediction of the folding pathways and structure of the GCN4 leucine zipper, J. Mol. Biol, 237, 361, 10.1006/jmbi.1994.1239

Vieth, 1995, Prediction of quaternary structure of coiled coils. Application to mutants of the GCN4 leucine zipper, J. Mol. Biol, 251, 448, 10.1006/jmbi.1995.0447

Holm, 1992, Fast and simple Monte Carlo algorithm for sidechain optimization in proteins: application to model building by homology, Proteins, 14, 213, 10.1002/prot.340140208

Collura, 1993, Modeling of protein loops by simulated annealing, Protein Sci, 2, 1502, 10.1002/pro.5560020915

Rosenbach, 1995, Simultaneous modeling of multiple loops in proteins, Protein Sci, 4, 496, 10.1002/pro.5560040316

Zheng, 1993, Theoretical analysis of the multicopy sampling method in molecular modeling, J. Chem. Phys, 99, 8892, 10.1063/1.465557

1993

Skolnick, 1990, Simulations of the folding of a globular protein, Science, 250, 1121, 10.1126/science.250.4984.1121

Maiorov, 1995, Size-independent comparison of protein three-dimensional structures, Proteins, 22, 273, 10.1002/prot.340220308

Kabsch, 1976, Solution for best rotation to relate 2 sets of vectors, Acta Crystallogr. A, 32, 922, 10.1107/S0567739476001873

Guo, 1995, Kinetics of protein folding: nucleation mechanism time scales and pathways, Biopolymers, 36, 83, 10.1002/bip.360360108

Shakhnovich, 1991, Protein folding bottlenecks: a lattice model simulation, Phys. Rev. Lett, 67, 1665, 10.1103/PhysRevLett.67.1665

Glover, 1983, Conformational flexibility in a small globular hormone. X-ray analysis of avian pancreatic polypeptide at 0.98 Å resolution, Biopolymers, 22, 293, 10.1002/bip.360220138

Conlon, 1992, The primary structure of a PYY-related peptide from chicken intestine suggests an anomalous site of cleavage of the signal peptide in preproPYY, FEBS Lett, 313, 225, 10.1016/0014-5793(92)81196-S

Cutfield, 1987, The amino-acid sequences of sculpine islet somatostatine 28 and peptide YY, FEBS Lett, 214, 57, 10.1016/0014-5793(87)80012-1

Blomqvist, 1992, Strong evolutionary conservation of neuropeptide Y: sequences of chicken goldfish, and torpedo marmorata DNA clones, Proc. Natl Acad. Sci. USA, 89, 2350, 10.1073/pnas.89.6.2350

Yamamoto, 1986, Mosaic evolution of prepropancreatic polypeptide, J. Biol. Chem, 261, 6156, 10.1016/S0021-9258(19)84542-8

Marks, 1993, The primary structure of pancreatic polypeptide from a primitive insectivorous mammal the European hedgehog, Regul. Pept, 47, 179, 10.1016/0167-0115(93)90422-5

Tatemoto, 1982, Isolation and characterisation of peptide YY (PYY), a candidate gut hormone that inhibits pancreatic exocrine secretion, Proc. Natl Acad. Sci. USA, 79, 2514, 10.1073/pnas.79.8.2514

Sivaraja, 1994, Solution structure of a POU-specific homeodomain: 3D-NMR studies of human B-cell transcription factor OCT-2, Biochemistry, 33, 9845, 10.1021/bi00199a005

Kassis, 1986, Sequence conservation in the protein coding and intron regions of the engrailed transcription unit, EMBO J, 5, 3583, 10.1002/j.1460-2075.1986.tb04686.x

Kim, 1989, Drosophila NK-homeodomain genes, Proc. Natl Acad. Sci. USA, 86, 7716, 10.1073/pnas.86.20.7716

Scheidereit, 1988, A human lymphoid-specific transcription factor that activates immunoglobulin genes is a homoeobox protein, Nature, 336, 551, 10.1038/336551a0

Sengstag, 1987, The sequence of the Saccharomyces cerevisiae gene PHO2 code for a regulatory protein with unusual amino acid composition, Nucleic Acids Res, 15, 233, 10.1093/nar/15.1.233

Xue, 1992, Regulation of the mec-3 gene by the C. elegans homeoproteins UNC-86 and MEC-3, EMBO J, 11, 4969, 10.1002/j.1460-2075.1992.tb05604.x

Stankis, 1992, The Aa mating locus of Schizophyllum commune encodes two dissimilar multiallelic homeodomain proteins, Proc. Natl Acad. Sci. USA, 89, 7169, 10.1073/pnas.89.15.7169

Bopp, 1986, Conservation of a large protein domain in the segmentation gene paired and in functionally related genes of Drosophila, Cell, 47, 1033, 10.1016/0092-8674(86)90818-4