Структура и функционирование белков. Применение методов биоинформатики - Джон Ригден 2014
Динамика белков: от структуры к функционированию
Литература
Adcock SA, McCammon JA (2006) Molecular dynamics: survey of methods for simulating the activity of proteins. Chem Rev 106:1589-1615
Affentranger R, Tavemelli I, di lorio E (2006) A novel Hamiltonian replica exchange MD protocol to enhance protein conformational space sampling. J Chem Theory Comput 2:217-228
Amadei A, Linssen ABM, Berendsen HJC (1993) Essential dynamics of proteins. Proteins 17:412-425
Amadei A, Linssen ABM, de Groot BL, et al. (1996) An efficient method for sampling the essential subspace of proteins. J Biom Str Dyn 13:615—626
Amadei A, de Groot BL, Ceruso M-A, et al. (1999) A kinetic model for the internal motions of proteins: diffusion between multiple harmonic wells. Proteins 35:283-292
Anderson HC (1980) Molecular dynamics simulations at constant pressure and/or temperature. J Chem Phys 72:2384-2393
Anfinsen CB (1973) Principles that govern the folding of protein chains. Science 181:223—230
Austin RH, Beeson KW, Eisenstein L, et al. (1975) Dynamics of ligand binding to myoglobin. Biochemistry 14(24):5355-5373
Bahar I, Erman B, Haliloglu T, et al. (1997) Efficient characterization of collective motions and interresidue correlations in proteins by low-resolution simulations. Biochemistry 36:13512-13523
Bartels C, Karplus M (1998) Probability distributions for complex systems: Adaptive umbrella sampling of the potential energy. J Phys Chem В 102:865-880
Berendsen HJC, Postma JPM, di Nola A, et al. (1984) Molecular dynamics with coupling to an external bath. J Chem Phys 81:3684—3690
Berg BA, Celik T (1992) New approach to spin-glass simulations. Phys Rev Lett 69:2292-2295
Berg BA, Neuhaus T (1991) Multicanonical algorithms for first-order phase transitions. Phys Lett 267:249-253
Berg JM, Tymoczko JL, Stryer L (2002) Biochemistry, fifth edition. WH Freeman, New York Bond PJ, Holyoake J, Ivetac A, et al. (2007) Coarse-grained molecular dynamics simulations of membrane proteins and peptides. J Struct Biol 157:593-605
Brooks B, Karplus M (1983) Harmonic dynamics of proteins: normal modes and fluctuations in bovine pancreatic trypsin inhibitor. Proc Natl Acad Sei USA 80:6571-6575
Brooks BR, Bruccoleri RE, Olafson BD, et al. (1983) CHARMM: a program for macromolecular energy minimization and dynamics calculations. J Comp Chem 4:187-217
Burykin A, Warshel A (2003) What really prevents proton transport through aquaporin? Charge self-energy versus proton wire proposals. Biophys J 85:3696-3706
Cecchini M, Rao F, Seeber M, et al. (2004) Replica exchange molecular dynamics simulations of amyloid peptide aggregation. J Chem Phys 121:10748-10756
Chakrabarti N, Tajkhorshid E, Roux B, et al. (2004) Molecular basis of proton blockage in aquaporins. Structure 12:65-74
Chen H, Wu Y, Voth GA (2006) Origins of proton transport behavior from selectivity domain mutations of the aquaporin-1 channel. Biophys J 90:L73-L75
Cheng X, Cui G, Homak V, et al. (2005) Modified replica exchange simulation for local structure refinement. J Phys Chem В 109:8220-8230
Chodera JD, Swope WC, Pitera JW, et al. (2007) Use of the weighted histogram analysis method for the analysis of simulated and parallel tempering simulations. J Chem Theory Comput 3:26-41
Christen M, van Gunsteren WF (2006) Multigraining: an algorithm for simultaneous fine-grained and coarse-grained simulation of molecular systems. J Chem Phys 124:154106
Cook A, Fernandez E, Lindner D, et al. (2005) The structure of the nuclear export receptor csel in its cytosolic state reveals a closed conformation incompatible with caigo binding. Mol Cell 18:355-357
Currie MG Fok KF, Kato J, et al. (1992) Guanylin: an endogenous activator of intestinal guanylate cyclise. Proc Natl Acad Sci USA 89:947-951
de Groot BL, Grubmüller H (2001) Water permeation across biological membranes: Mechanism and dynamics of aquaporin-1 and GlpF. Science 294:2353-2357
de Groot BL, Amadei A, Scheek RM, et al. (1996a) An extended sampling of the configurational space of HPr from E coli. Proteins 26:314-322
de Groot BL, Amadei A, van Aalten DMF, et al. (1996b) Towards an exhaustive sampling of the configurational spaces of the two forms of the peptide hormone guanylin. J Biomol Str Dyn 13:741-751
de Groot BL, van Aalten DMF, Scheek RM, et al. (1997) Prediction of protein conformational freedom from distance constraints. Proteins 29:240-251
de Groot BL, Hayward S, van Aalten DMF, et al. (1998) Domain motions in bacteriophage T4 lysozyme: a comparison between molecular dynamics and crystallographic data. Proteins 31:116—127
de Groot BL, Vriend G, Berendsen HJC (1999) Conformational changes in the chaperonin GroEL: new insights into the allosteric mechanism. J Mol Biol 286:1241-1249
de Groot BL, Engel A, Grubmüller H (2001) A refined structure of human Aquaporin-1. FEBS Lett 504: 206-211
de Groot BL, Frigato T, Helms V, et al. (2003) The mechanism of proton exclusion in the aqua- porin-1 water channel. J Mol Biol 333:279-293
Dixon MM, Nicholson H, Shewchuk L, et al. (1992) Structure of a hinge-bending bacteriophage T4 lysozyme mutant Ile3 → Pro. J Mol Biol 227:917-933
Duda RO, Hart PE, Stork DG (2001) Pattem Classification, second edition. Wiley, New York Faber HR, Matthews BW (1990) A mutant T4 lysozyme displays five different crystal conformations. Nature 348:263-266
Frauenfelder H, Leeson DT (1998) The energy landscape in non-biological and biological molecules. Nat Struct Biol 5:757-759
Frauenfelder H, Sligar SG, Wolynes PG (1991) The energy landscapes and motions of proteins. Science 254:1598-1603
Fu D, Libson A, Miercke LJ, et al. (2000) Structure of a glycerol-conducting channel and the basis for its selectivity. Science 290: 481-486
Fukunishi H, Watanabe O, Takada S (2002) On the Hamiltonian replica exchange method for efficient sampling of biomolecular systems: application to protein structure prediction. J Chem Phys 116:9058-9067
Garcia AE (1992) Large-amplitude nonlinear motions in proteins. Phys Rev Lett 68:2696-2699
Garda AE, Onuchic JN (2003) Folding a protein in a computer: An atomic description of the fold- ing/unfolding of protein A. Proc Natl Acad Sci USA 100:13898-13903
G N, Noguti T, Nishikawa T (1983) Dynamics of a small globular protein in terms of low- frequency vibrational modes. Proc Natl Acad Sci USA 80:3696-3700
Gerstein M, Lesk AM, Chothia C (1994) Structural mechanisms for domain movements in proteins. Biochemistry 33:6739-6749
Gosh A, Rapp CS, Friesner RA (1998) Generalized Bom model based on a surface integral formulation. J Phys Chem В 102:10983-10990
Grubmüller H (1995) Predicting slow structural transitions in macromolecular systems: Conformational flooding. Phys Rev E 52:2893-2906
Hansmann UHE (1997) Effective way for determination of multicanonical weights. Phys Rev E 56:6200-6203
Hayward S, Kitao A, Go N (1995) Harmonicity and anharmonicity in protein dynamics: a normal mode analysis and principal component analysis. Proteins 23:177-186
He J, Zhang Z, Shi Y, et al. (2003) Efficiently explore the energy landscape of proteins in molecular dynamics simulations by amplifying collective motions. J Chem Phys 119:4005-4017
Hockney RW, Goel SP, Eastwood JW (1973) 10000 particle molecular dynamics model with longrange forces. Chem Phys Lett 21:589-591
Hub JS, de Groot BL (2008) Mechanism of selectivity in aquaporins and aquaglyceroporins. Proc Natl Acad Sci USA105: 1198-1203
Iba Y (2001) Extended ensemble Monte Carlo. Int J Mod Phys C 12:623-656 Пап В, Tajkhorshid E, Schulten К, et al. (2004) The mechanism of proton exclusion in aquaporin channels. Proteins 55:223-228
Jean-Charles A, Nicholls A, Sharp K, et al. (1991) Electrostatic contributions to solvation energies: comparison of free energy perturbation and continuum calculations. J Am Chem Soc 113:1454-1455
Jorgensen WL, Chandrasekhar J, Madura JD, et al. (1983) Comparison of simple potential functions for simulating liquid water. J Chem Phys 79:926-935
Jorgensen WL, Maxwell DS, Tirado-Rives J (1996) Development and testing of the OPLS all atom force field on conformational energetics and properties of organic liquids. J Am Chem Soc 118:11225-11236
Karplus M, Gao YQ (2004) Biomolecular motors: the Fl-ATPase paradigm. Curr Opin Struct Biol 14:250-259
Karplus M, Kushick JN (1981) Method for estimating the configurational entropy of macromolecules. Macromolecules 14:325-332
Kempf JQ Loria JP (2003) Protein dynamics from solution NMR theory and applications. Cell Biochem Biophys 37:187-211
Kitao A, Go- N (1999) Investigating protein dynamics in collective coordinate space. Curr Opin Struct Biol 9:143—281
Kitao A, Hirata F, Go- N (1991) The effects of solvent on the conformation and the collective motions of proteins - normal mode analysis and molecular-dynamics simulations of melittin in water and vacuum .Chem Phys 158:447-472
Kitao A, Hayward S, Go- N (1998) Energy landscape of a native protein: Jumping-among-minima model. Proteins 33:496-517
Kokubo H, Okamoto Y (2004) Prediction of membrane protein structures by replica-exchange Monte Carlo simulations: case of two helices. J Chem Phys 120:10837-10847
Kubitzki MB, de Groot BL (2007) Molecular dynamics simulations using temperature-enhanced essential dynamics replica exchange. Biophys J 92:4262-4270
Kubitzki MB, de Groot BL (2008) The atomistic mechanism of conformational transition in adenylate kinase: a TEE-REX molecular dynamics study. Structure 16:1175-1182
Kumar S, Bouzida D, Swendsen RH, et al. (1992) The weighted histogram analysis method for free-energy calculations on biomolecules. I. the method. J Comp Chem 13:1011-1021
Kumar S, Payne PW, Vasquez M (1996) Method for free-energy calculations using iterative techniques. J Comput Chem 17:1269-1275
Kuroki R, Weaver LH, Matthews BW (1993) A covalent enzyme-substrate intermediate with saccharide distortion in a mutant T4 lysozyme. Science 262:2030-2033
Levitt М, Sander С, Stern PS (1983) Normal-mode dynamics of a protein: Bovine pancreatic trypsin inhibitor. Int J Quant Chem: Quant Biol Symp 10:181-199
Levy RM, Karplus M, Kushick J, et al. (1984a) Evaluation of the configurational entropy for proteins: application to molecular dynamics of an a-helix. Macromolecules 17:1370-1374
Levy RM, Srinivasan AR, Olsen WK, et al. (1984b) Quasi-harmonic method for studying very low frequency modes in proteins. Biopolymers 23:1099-1112
Liu P, Kim B, Friesner RA, et al. (2005) Replica exchange with solute tempering: A method for sampling biological systems in explicit water. Proc Natl Acad Sci USA 102:13749-13754
Lou H, Cukier RI (2006) Molecular dynamics of apo-adenylate kinase: a distance replica exchange method for the free energy of conformational fluctuations. J Phys Chem В 110:24121-24137
Luo R, David L, Gilson ML (2002) Accelerated Poisson-Boltzmann calculations for static and dynamic systems. J Comput Chem 23:1244-1253
Lyman E, Zuckerman DM (2006) Ensemble-based convergence analysis of biomolecular trajectories. Biophys J 91:164—172
Maragakis P, Karplus M (2005) Large amplitude conformational change in proteins explored with a plastic network model: adenylate kinase. J Mol Biol 352:807-822
Marinari E, Parisi G (1992) Simulated tempering: a new Monte Carlo scheme. Europhys Lett 19:451-458
Marrink SJ, de Vries AH, Mark AE (2004) Coarse grained model for semiquantitative lipid simulations. J Phys Chem В 108:750-760
Matthews BW, Remington SJ (1974) The three dimensional structure of the lysozyme from bacteriophage T4. Proc Natl Acad Sci USA 71:4178-4182
McCammon JA, Gelin BR, Karplus M (1977) Dynamics of folded proteins. Nature 267:585-590
Mitsutake A, Sugita Y, Okamoto Y (2001) Generalized-ensemble algorithms for molecular simulations of biopolymers. Biopolymers 60:96-123
Moffat К (2003) The frontiers of time-resolved macromolecular crystallography: movies and chirped X-ray pulses. Faraday Discuss 122:65-77
Murata К, Mitsuoka К, Walz T, et al. (2000) Structural determinants of water permeation through Aquaporin-1. Nature 407: 599-605
Müller CW, Schulz GE (1992) Structure of the complex between adenylate kinase from Eschericia coli and the inhibitor Ap5A refined at 19 A resolution: a model for a catalytic transition state. J Mol Biol 224:159-177
Müller CW, Schlauderer Q Reinstein J, et al. (1996) Adenylate kinase motions during catalysis: an energetic counterweight balancing substrate binding. Structure 4:147-156
Nguyen PH, Mu Y, Stock G (2005) Structure and energy landscape of a photoswitchable peptide: a replica exchange molecular dynamics study. Proteins 60:485-494
Nose S (1984) A unified formulation of the constant temperature molecular dynamics method. J Chem Phys 81:511-519
Pitera JW, Swope W (2003) Understanding folding and design: replica-exchange simulations of “Trp-cage” miniproteins. Proc Natl Acad Sci USA 100:7587-7592
Rao F, Caflisch A (2003) Replica exchange molecular dynamics simulations of reversible folding. J Chem Phys 119:4035-4042
Romo TD, Clarage JB, Sorensen DC, et al. (1995) Automatic identification of discrete substates in proteins: singular value decomposition analysis of time-averaged crystallographic refinements. Proteins 22:311-321
Schotte F, Lim M, Jackson TA, et al. (2003) Watching a protein as it functions with 150 ps timeresolved X-ray crystallography. Science 300:1944-1947
Seeliger D, Haas J, de Groot BL (2007) Geometry-based sampling of conformational transitions in proteins. Structure 15:1482-1492
Seibert MM, Patriksson A, Hess B, et al. (2005) Reproducible polypeptide folding and structure prediction using molecular dynamics simulations. J Mol Biol 354:173-183
Shapiro YE, Meirovitch E (2006) Activation energy of catalysis-related domain motion in E coli adenylate kinase. J Phys Chem В 110:11519-11524
Shapiro YE, Kahana E, Tugarinov V, et al. (2002) Domain flexibility in ligand-free and inhibitor bound Eschericia coli adenylate kinase based on a mode-coupling analysis of 15N spin relaxation. Biochemistry 41:6271—6281
Smith GR, Bruce AD (1996) Multicanonical Monte Carlo study of solid-solid phase coexistence in a model colloid. Phys Rev E 53:6530-6543
Snow С, Qi G Hayward S (2007) Essential dynamics sampling study of adenylate kinase: comparison to citrate synthase and implication for the hinge and shear mechanisms of domain motion. Proteins 67:325-337
Still WC, Tempczyk A, Hawley RC, et al. (1990) Semianalytical treatment of solvation for molecular mechanics and dynamics. J Am Chem Soc 112:6127-6129 Sugita Y, Okamoto Y (1999) Replica-exchange molecular dynamics method for protein folding. Chem Phys Lett 314:141-151
Sugita Y, Kitao A, Okamoto Y (2000) Multidimensional replica-exchange method for free-energy calculations. J Chem Phys 113:6042-6051
Suhre K, Sanejouand YH (2004a) ElNemo: a normal mode web-server for protein movement analysis and the generation of templates for molecular replacement. Nucl Acids Res 32:610-614
Suhre K, Sanejouand YH (2004b) On the potential of normal mode analysis for solving difficult molecular replacement problems. Act Cryst D 60:796-799
Sui H, Han B-G, Lee JK, et al. (2001) Structural basis of water-specific transport through the AQP1 water channel. Nature 414: 872-878
Tai К (2004) Conformational sampling for the impatient. Biophys Chem 107:213-220
Tajkhorshid E, Nollert P, Jensen M0, et al. (2002) Control of the selectivity of the aquaporin water channel family by global orientational tuning. Science 296: 525-530
Teeter MM, Case DA (1990) Harmonic and quasi harmonic descriptions of crambin. J Phys Chem 94:8091-8097
Temiz NA, Meirovitch E, Bahar I (2004) Eschericia coli adenylate kinase dynamics: comparison of elastic network model modes with mode-coupling 15N-NMR relaxation data. Proteins 57:468-480
Tirion MM (1996) Large amplitude elastic motions in proteins from a single-parameter atomic analysis. Phys Rev Lett 77:186-195
Tugarinov V, Shapiro YE, Liang Z, et al. (2002) A novel view of domain flexibility in E coli adenylate kinase based on structural mode-coupling 15N NMR spin relaxation. J Mol Biol 315:155-170
Van Aalten DMF, Amadei A, Vriend G, et al. (1995a) The essential dynamics of thermolysin - confirmation of hinge-bending motion and comparison of simulations in vacuum and water. Prot Eng 8:1129-1136
Van Aalten DMF, Findlay JBC, Amadei A, et al. (1995b) Essential dynamics of the cellular retinol binding protein - evidence for ligand induced conformational changes. Prot Eng 8:1129-1136
Van Gunsteren WF, Berendsen HJC (1987) Groningen Molecular Simulation (GROMOS) Library Manual. Biomos, Groningen
Van Gunsteren WF, Berendsen HJC (1990) Computer-simulation of molecular-dynamics - methodology, applications, and perspectives in chemistry. Angew Chem Int Edit Engl 29:992-1023
Warshel A, Kato M, Pisliakov AV (2007) Polarizable force fields: history test cases and prospects. J Chem Theory Comput 3:2034-2045
Weiner SJ, Kollman PA, Nguyen DT, et al. (1986) An all atom force field for simulations of proteins and nucleic acids. J Comp Chem 7:230-252
Weiss S (1999) Fluorescence spectroscopy of single biomolecules. Science 283:1676-1683
Whitford PC, Miyashita O, Levy Y, et al. (2007) Conformational transitions of adenylate kinase: switching by cracking. J Mol Biol 366:1661-1671
Xu Z, Horwich AL, Sigler PB (1997) The crystal structure of the asymmetric Gro-EL-GroES- (ADP)7 chaperonin complex. Nature 388:741-750
Zachariae U, Grubmuller H (2006) A highly strained nuclear conformation of the exportin Cselp revealed by molecular dynamics simulations. Structure 14:1469-1478
Zhang X-J, Wozniak JA, Matthews BW (1995) Protein flexibility and adaptability seen in 25 crystal forms of T4 lysozyme. J Mol Biol 250:527-552
Zhang Z, Shi Y, Liu H (2003) Molecular dynamics simulations of peptides, and proteins with amplified collective motions. Biophys J 84:3583-3593
Zheng W, Brooks BR (2005) Probing the local dynamics of nucleotide-binding pocket coupled to the global dynamics: myosin versus kinesin. Biophys J 89(1): 167-178
Zheng W, Doniach S (2003) A comparative study of motor-protein motions by using a simple elastic-network model. Proc Natl Acad Sci USA 100(23): 13253-13258
Zhou R Berne BJ, Germain R (2001) The free energy landscape for ß-hairpin folding in explicit water. Proc Natl Acad Sci USA 98:14931-14936