From Protein Structure to Function with Bioinformatics.pdf

9 Protein Dynamics: From Structure to Function 245Bartels C, Karplus M (1998) Probability distributions for complex systems: Adaptive umbrellasampling of the potential energy. J Phys Chem B 102:865–880Berendsen HJC, Postma JPM, di Nola A, et al. (1984) Molecular dynamics with coupling to anexternal bath. J Chem Phys 81:3684–3690Berg BA, Celik T (1992) New approach to spin-glass simulations. Phys Rev Lett 69:2292–2295Berg BA, Neuhaus T (1991) Multicanonical algorithms for first-order phase transitions. Phys Lett267:249–253Berg JM, Tymoczko JL, Stryer L (2002) Biochemistry, fifth edition. WH Freeman, New YorkBond PJ, Holyoake J, Ivetac A, et al. (2007) Coarse-grained molecular dynamics simulations ofmembrane proteins and peptides. J Struct Biol 157:593–605Brooks B, Karplus M (1983) Harmonic dynamics of proteins: normal modes and fluctuations inbovine pancreatic trypsin inhibitor. Proc Natl Acad Sci USA 80:6571–6575Brooks BR, Bruccoleri RE, Olafson BD, et al. (1983) CHARMM: a program for macromolecularenergy minimization and dynamics calculations. J Comp Chem 4:187–217Burykin A, Warshel A (2003) What really prevents proton transport through aquaporin? Chargeself-energy versus proton wire proposals. Biophys J 85:3696–3706Cecchini M, Rao F, Seeber M, et al. (2004) Replica exchange molecular dynamics simulations ofamyloid peptide aggregation. J Chem Phys 121:10748–10756Chakrabarti N, Tajkhorshid E, Roux B, et al. (2004) Molecular basis of proton blockage inaquaporins. Structure 12:65–74Chen H, Wu Y, Voth GA (2006) Origins of proton transport behavior from selectivity domainmutations of the aquaporin-1 channel. Biophys J 90:L73–L75Cheng X, Cui G, Hornak V, et al. (2005) Modified replica exchange simulation for local structurerefinement. J Phys Chem B 109:8220–8230Chodera JD, Swope WC, Pitera JW, et al. (2007) Use of the weighted histogram analysis methodfor the analysis of simulated and parallel tempering simulations. J Chem Theory Comput3:26–41Christen M, van Gunsteren WF (2006) Multigraining: an algorithm for simultaneous fine-grainedand coarse-grained simulation of molecular systems. J Chem Phys 124:154106Cook A, Fernandez E, Lindner D, et al. (2005) The structure of the nuclear export receptor cse1in its cytosolic state reveals a closed conformation incompatible with cargo binding. Mol Cell18:355–357Currie MG, Fok KF, Kato J, et al. (1992) Guanylin: an endogenous activator of intestinal guanylatecyclise. Proc Natl Acad Sci USA 89:947–951de Groot BL, Grubmüller H (2001) Water permeation across biological membranes: Mechanismand dynamics of aquaporin-1 and GlpF. Science 294:2353–2357de Groot BL, Amadei A, Scheek RM, et al. (1996a) An extended sampling of the configurationalspace of HPr from E coli. Proteins 26:314–322de Groot BL, Amadei A, van Aalten DMF, et al. (1996b) Towards an exhaustive sampling of theconfigurational spaces of the two forms of the peptide hormone guanylin. J Biomol Str Dyn13:741–751de Groot BL, van Aalten DMF, Scheek RM, et al. (1997) Prediction of protein conformationalfreedom from distance constraints. Proteins 29:240–251de Groot BL, Hayward S, van Aalten DMF, et al. (1998) Domain motions in bacteriophage T4lysozyme: a comparison between molecular dynamics and crystallographic data. Proteins31:116–127de Groot BL, Vriend G, Berendsen HJC (1999) Conformational changes in the chaperoninGroEL: new insights into the allosteric mechanism. J Mol Biol 286:1241–1249de Groot BL, Engel A, Grubmüller H (2001) A refined structure of human Aquaporin-1. FEBSLett 504: 206–211de Groot BL, Frigato T, Helms V, et al. (2003) The mechanism of proton exclusion in theaquaporin-1 water channel. J Mol Biol 333:279–293Dixon MM, Nicholson H, Shewchuk L, et al. (1992) Structure of a hinge-bending bacteriophageT4 lysozyme mutant Ile3 → Pro. J Mol Biol 227:917–933