Effects of Macromolecular Crowding on Protein Conformational Changes 英文参考文献.docVIP

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Effects of Macromolecular Crowding on Protein Conformational Changes 英文参考文献.doc

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Effects of Macromolecular Crowding on Protein Conformational Changes 英文参考文献

EffectsofMacromolecularCrowdingonProtein ConformationalChanges HaoDong,SanboQin,Huan-XiangZhou* DepartmentofPhysicsandInstituteofMolecularBiophysics,FloridaStateUniversity,Tallahassee,Florida,UnitedStatesofAmerica Abstract Many protein functions can be directly linked to conformational changes. Inside cells, the equilibria and transition rates between different conformations may be affected by macromolecular crowding. We have recently developed a new approachformodelingcrowdingeffects,whichenablesanatomisticrepresentationof‘‘test’’proteins.Herethisapproachis appliedtostudyhowcrowdingaffectstheequilibriaandtransitionratesbetweenopenandclosedconformationsofseven proteins:yeastproteindisulfideisomerase(yPDI),adenylatekinase(AdK),orotidinephosphatedecarboxylase(ODCase),Trp repressor (TrpR), hemoglobin, DNA b-glucosyltransferase, and Ap4A hydrolase. For each protein, molecular dynamics simulationsoftheopenandclosedstatesareseparatelyrun.Representativeopenandclosedconformationsarethenused tocalculatethecrowding-inducedchangesinchemicalpotentialforthetwostates.Thedifferenceinchemical-potential changebetweenthetwostatesfinallypredictstheeffectsofcrowdingonthepopulationratioofthetwostates.Crowding isfoundtoreducetheopenpopulationtovariousextents.Inthepresenceofcrowderswitha15A? radiusandoccupying 35%ofvolume,theopen-to-closedpopulationratiosofyPDI,AdK,ODCaseandTrpRarereducedby79%,78%,62%and 55%,respectively.Thereductionsfortheremainingthreeproteinsare20–44%.Asexpected,thefourproteinsexperiencing the stronger crowding effects are those with larger conformational changes between open and closed states (e.g., as measured by the change in radius of gyration). Larger proteins also tend to experience stronger crowding effects than smaller ones[e.g., comparing yPDI(480 residues) andTrpR(98 residues)].The potentials ofmeanforce along theopen- closedreactioncoordinateofapoandligand-boundODCasearealteredbycrowding,suggestingthattransitionratesare alsoaffected.Thesequantita