Evaluating Molecular Mechanical Potentials for Helical Peptides and Proteins 英文参考文献.docVIP

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Evaluating Molecular Mechanical Potentials for Helical Peptides and Proteins 英文参考文献.doc

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Evaluating Molecular Mechanical Potentials for Helical Peptides and Proteins 英文参考文献

EvaluatingMolecularMechanicalPotentialsforHelical PeptidesandProteins ErikJ.Thompson1,AllisonJ.DePaul2,SaravS.Patel2,EricJ.Sorin2* 1Department of Chemical Engineering, California State University Long Beach, Long Beach, California, United States of America, 2Department of Chemistry Biochemistry,CaliforniaStateUniversityLongBeach,LongBeach,California,UnitedStatesofAmerica Abstract MultiplevariantsoftheAMBERall-atomforcefieldwerequantitativelyevaluatedwithrespecttotheirabilitytoaccurately characterize helix-coil equilibria in explicit solvent simulations. Using a global distributed computing network, absolute conformational convergence was achieved for large ensembles of the capped A21 and Fs helical peptides. Further assessment of these AMBER variants was conducted via simulations of a flexible 164-residue five-helix-bundle protein, apolipophorin-III, on the 100ns timescale. Of the contemporary potentials that had not been assessed previously, the AMBER-99SBforcefieldshowedsignificanthelix-destabilizingtendencies,withbetabridgeformationoccurringinhelical peptides, and unfolding of apolipophorin-III occurring on the tens of nanoseconds timescale. The AMBER-03 force field, whileshowingadequatehelicalpropensitiesforbothpeptidesandstabilizingapolipophorin-III,(i)predictsanunexpected + decrease in helicity with ALARARG substitution, (ii) lacks experimentally observed 310 helical content, and (iii) deviates stronglyfromaverageapolipophorin-IIINMRstructuralproperties.AsisobservedforAMBER-99SB,AMBER-03significantly overweighsthecontributionofextendedandpolyprolinebackboneconfigurationstotheconformationalequilibrium.In contrast, the AMBER-99w force field, which was previously shown to best reproduce experimental measurements of the helix-coiltransitioninmodelhelicalpeptides,adequatelystabilizesapolipophorin-IIIandyieldsbothanaveragegyration radiusandpolarsolventexposedsurfaceareathatareinexcellentagreementwiththeNMRensemble. Citation:ThompsonEJ,DePaulAJ,PatelSS,SorinEJ(201