All in one: a highly detailed rotamer library improves both accuracy and speed in the modelling of sidechains by dead-end elimination

Folding and Design - Tập 2 - Trang 53-66 - 1997
Marc De Maeyer1, Johan Desmet2, Ignace Lasters3
1Center for Transgene Technology and Gene Therapy, Flanders Interuniversity Institute for Biotechnology, KU Leuven, Campus Gasthuisberg O&N Herestraat 49, B-3000, Leuven, Belgium e-mail:marc.demaeyermed.kuleuven.ac.be
2Interdisciplinary Research Center, KU Leuven Campus Kortrijk, B-8500, Kortrijk, Belgium
3Center for Transgene Technology and Gene Therapy, Flanders Interuniversity Institute for Biotechnology, KU Leuven, Campus Gasthuisberg O&N Herestraat 49, B-3000, Leuven, Belgium

Tài liệu tham khảo

Janin, 1978, Conformation of amino acid side-chains in proteins, J. Mol. Biol, 125, 357, 10.1016/0022-2836(78)90408-4 Bhat, 1979, An analysis of side-chain conformations in proteins, Int. J. Pept. Protein Res, 13, 170, 10.1111/j.1399-3011.1979.tb01866.x James, 1983, Structure and refinement of penicillopepsin at 1.8 Å resolution, J. Mol. Biol, 163, 299, 10.1016/0022-2836(83)90008-6 Benedetti, 1983, Statistical and energetic analysis of side-chain conformations in oligopeptides, Int. J. Pept. Protein Res, 22, 1, 10.1111/j.1399-3011.1983.tb02062.x Ponder, 1987, Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes, J. Mol. Biol, 193, 775, 10.1016/0022-2836(87)90358-5 Summers, 1987, An analysis of side-chain orientations in homologous proteins, J. Mol. Biol, 196, 157, 10.1016/0022-2836(87)90520-1 McGregor, 1987, Analysis of the relationship between side-chain conformation and secondary structure in globular proteins, J. Mol. Biol, 198, 295, 10.1016/0022-2836(87)90314-7 Šali, 1995, Modelling mutations and homologous proteins, Curr. Opin. Biotechnol, 6, 437, 10.1016/0958-1669(95)80074-3 Vásquez, 1996, Modeling side-chain conformation, Curr. Opin. Struct. Biol., 6, 217, 10.1016/S0959-440X(96)80077-7 Holm, 1991, Database algorithm for generating protein backbone and side-chain co-ordinates from a Cα trace: application to model building and detection of co-ordinate errors, J. Mol. Biol, 218, 183, 10.1016/0022-2836(91)90883-8 Holm, 1992, Fast and simple Monte Carlo algorithm for side-chain optimization in proteins: application to model building by homology, Proteins, 14, 213, 10.1002/prot.340140208 Lee, 1994, Predicting protein mutant energetics by selfconsistent ensemble optimization, J. Mol. Biol, 236, 918, 10.1006/jmbi.1994.1198 Tufféry, 1991, A new approach to the rapid determination of protein side chain conformations, J. Biomol. Struct. Dynam, 8, 1267, 10.1080/07391102.1991.10507882 Tufféry, 1993, A critical comparison of search algorithm applied to the optimization of protein side-chain conformations, J. Comput. Chem, 14, 790, 10.1002/jcc.540140705 Wilson, 1993, Modeling side-chain conformation for homologous proteins using an energy-based rotamer search, J. Mol. Biol, 229, 996, 10.1006/jmbi.1993.1100 Correa, 1990, The building of protein structures from alpha-carbon coordinates, Proteins, 7, 366, 10.1002/prot.340070408 Lee, 1991, Prediction of protein sidechain conformation by packing optimization, J. Mol. Biol, 217, 373, 10.1016/0022-2836(91)90550-P Schiffer, 1990, Prediction of homologous protein structures based on conformational searches and energetics, Proteins, 8, 30, 10.1002/prot.340080107 Eisenmenger, 1993, A method to configure protein side-chains from the main-chain trace in homology modelling, J. Mol. Biol, 231, 849, 10.1006/jmbi.1993.1331 Laughton, 1994, Prediction of protein side-chain conformations from local three-dimensional homology relationships, J. Mol. Biol, 235, 1088, 10.1006/jmbi.1994.1059 Kono, 1994, Energy minimization method using automata network for sequence and side-chain conformation prediction from given backbone geometry, Proteins, 19, 244, 10.1002/prot.340190308 Koehl, 1994, Application of a selfconsistent mean field theory to predict protein side-chains conformation and estimate their conformational entropy, J. Mol. Biol, 239, 249, 10.1006/jmbi.1994.1366 Levitt, 1992, Accurate modelling of protein conformation by automatic segment matching, J. Mol. Biol, 226, 507, 10.1016/0022-2836(92)90964-L Desmet, 1992, The dead-end elimination theorem and its use in protein sidechain positioning, Nature, 356, 539, 10.1038/356539a0 Lasters, 1993, The fuzzy-end elimination theorem: correctly implementing the side-chain placement algorithm based on the dead-end elimination theorem, Protein Eng, 6, 717, 10.1093/protein/6.7.717 Goldstein, 1994, Efficient rotamer elimination applied to protein side-chains and related spin glasses, Biophys. J, 66, 1335, 10.1016/S0006-3495(94)80923-3 Tanimura, 1994, Determinants of protein side-chain packing, Protein Sci, 3, 2358, 10.1002/pro.5560031220 Keller, 1995, Finding the global minimum: a fuzzy end elimination implementation, Protein Eng, 8, 893, 10.1093/protein/8.9.893 Lasters, 1995, Enhanced dead-end elimination in the search for the global minimum energy conformation of a collection of protein side-chains, Protein Eng, 8, 815, 10.1093/protein/8.8.815 Dahiyat, 1996, Protein design automation, Protein Sci, 5, 895, 10.1002/pro.5560050511 Desmet, 1994, 307 Schrauber, 1993, Rotamers: to be or not to be? An analysis of amino acid side-chain conformations in globular proteins, J. Mol. Biol, 230, 592, 10.1006/jmbi.1993.1172 Miller, 1987, Interior and surface of monomeric proteins, J. Mol. Biol, 196, 641, 10.1016/0022-2836(87)90038-6 Hwang, 1995, Side-chain prediction by neural networks and simulated annealing optimization, Protein Eng, 8, 363, 10.1093/protein/8.4.363 Dunbrack, 1993, Backbone-dependent rotamer library for proteins: application to side-chain prediction, J. Mol. Biol, 230, 543, 10.1006/jmbi.1993.1170 Jones, 1991, Improved methods for building protein models in electron density maps and the location of errors in these models, Acta Crystallogr. A, 47, 110, 10.1107/S0108767390010224 Zegers, 1994, Crystal structure of RNase T1 with 3′-guanylic acid and guanosine, J. Biol. Chem, 269, 127, 10.1016/S0021-9258(17)42323-4 May, 1994, Automated comparative modelling of protein structures, Curr. Opin. Biotechnol, 5, 355, 10.1016/0958-1669(94)90043-4 Wierenga, 1987, Structure determination of the glucosomal triosphosphate isomerase from Trypanosoma brucei brucei at 2.4 Å resolution, J. Mol. Biol, 198, 109, 10.1016/0022-2836(87)90461-X Richardson, 1988, Amino acid preferences for specific locations at the ends of a helices, Science, 240, 1648, 10.1126/science.3381086 IUPAC–IUB Commission on Biochemical Nomenclature, 1970, Abbreviations and symbols for the description of the conformation of polypeptide chains, J. Mol. Biol, 52, 1 Wodak, 1986, Modification of human hemoglobin by gluthadione. III Perturbations of hemoglobin conformation analyzed by computer modeling, J. Biol. Chem, 261, 14717, 10.1016/S0021-9258(18)66930-3 Bernstein, 1977, The Protein Data Bank: a computer-based archival file for macromolecular structures, J. Mol. Biol, 112, 535, 10.1016/S0022-2836(77)80200-3 Langs, 1988, Three-dimensional structure at 0.86 angstroms of the uncomplexed form of the transmembrane channel peptide gramicidin, Science, 241, 188, 10.1126/science.2455345 Hendrickson, 1981, Structure of the hydrophobic protein crambin determined directly from the anomalous scattering of sulphur, Nature, 290, 107, 10.1038/290107a0 Dauter, 1992, Refinement of rubredoxin from Desulfovibrio vulgaris at 1.0 Å with and without restraints, Acta. Crystallogr. B, 48, 42, 10.1107/S0108768191010613 Wlodawer, 1984, Structure of bovine pancreatic trypsin inhibitor. Results of joint neutron and X-ray refinement of crystal form II, . J. Mol. Biol, 180, 301, 10.1016/S0022-2836(84)80006-6 Zhao, 1992, Structure of scorpion toxin variant-3 at 1.2 Å resolution, J. Mol. Biol, 227, 239, 10.1016/0022-2836(92)90694-F Derrick, 1994, The third IgG-binding domain from streptococcal protein G. An analysis by X-ray crystallography of the structure alone and in a complex with Fab, J. Mol. Biol, 243, 906, 10.1006/jmbi.1994.1691 Matsuura, 1982, Structure of cytochrome c551 from Pseudomonas aeruginosa refined at 1.6 Å resolution and comparison of the two redox forms, J. Mol. Biol, 156, 389, 10.1016/0022-2836(82)90335-7 Lawson, 1988, Flexibility of the DNA-binding domains of trp repressor, Proteins, 3, 18, 10.1002/prot.340030103 Artymiuk, 1981, Refinement of human lysozyme at 1.5 Å resolution analysis of non-bonded and hydrogen-bond interactions, J. Mol. Biol, 152, 737, 10.1016/0022-2836(81)90125-X Zegers, 1994, The structures of RNase A complexed with 3′-CMP and d(CpA): active site conformation and conserved water molecules, Protein Sci, 3, 2322, 10.1002/pro.5560031217 Baker, 1988, Structure of azurin from Alcaligenes denitrificans refinement at 1.8 Å resolution and comparison of the two crystallographically independent molecules, J. Mol. Biol, 203, 1071, 10.1016/0022-2836(88)90129-5 Bolognesi, 1989, Aplysia limacina myoglobin. Crystallographic analysis at 1.6 Å resolution, . J. Mol. Biol, 205, 529, 10.1016/0022-2836(89)90224-6 Sacchettini, 1992, Refinement of the structure of Escherichia coli-derived rat intestinal fatty acid binding protein with bound oleate to 1.75-Å resolution. Correlation with the structures of the apoprotein and the protein with bound palmitate, J. Biol. Chem, 267, 23534, 10.1016/S0021-9258(18)35872-1 Tsunasawa, 1989, The primary structure and structural characteristics of Achromobacter lyticus protease I, a lysine-specific serine protease, . J. Biol. Chem, 264, 3832, 10.1016/S0021-9258(19)84926-8 Huber, 1974, Structure of the complex formed by bovine trypsin and bovine pancreatic trypsin inhibitor. II. Crystallographic refinement at 1.9 Å resolution, J. Mol. Biol, 89, 73, 10.1016/0022-2836(74)90163-6 Bode, 1987, The high-resolution X-ray crystal structure of the complex formed between subtilisin Carlsberg and eglin c, an elastase inhibitor from the leech Hirudo medicinalis. Structural analysis, subtilisin structure and interface geometry, Eur. J. Biochem, 166, 673, 10.1111/j.1432-1033.1987.tb13566.x Holmes, 1982, Structure of thermolysin refined at 1.6 Å resolution, J. Mol. Biol, 160, 623, 10.1016/0022-2836(82)90319-9 Morris, 1992, Stereochemical quality of protein coordinates, Proteins, 12, 345, 10.1002/prot.340120407 Alard, 1991, Detection of cavities in a set of interpenetrating spheres, J. Comp. Chem, 12, 918, 10.1002/jcc.540120803 Delhaise, 1984, Interactive computer animation of macromolecules, J. Mol. Graph, 2, 103, 10.1016/0263-7855(84)80002-8 Warshel, 1976, Theoretical studies of enzymatic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme, J. Mol. Biol, 103, 227, 10.1016/0022-2836(76)90311-9 Brooks, 1983, CHARMM: a program for macromolecular energy, minimization, and dynamics calculations, J. Comput. Chem, 4, 187, 10.1002/jcc.540040211