Perturbation-Response Scanning Reveals Ligand Entry-Exit Mechanisms of Ferric Binding Protein 英文参考文献.docVIP

Perturbation-Response Scanning Reveals Ligand Entry-Exit Mechanisms ofFerric Binding Protein CananAtilgan*,AliRanaAtilgan FacultyofEngineeringandNaturalSciences,SabanciUniversity,Istanbul,Turkey Abstract We study apo and holo forms of the bacterial ferric binding protein (FBP) which exhibits the so-called ferric transport dilemma:ituptakesironfromthehostwithremarkableaffinity,yetreleasesitwitheaseinthecytoplasmforsubsequent use.Theobservationsfitthe‘‘conformationalselection’’modelwherebytheexistenceofaweaklypopulated,higherenergy conformation that is stabilized in the presence of the ligand is proposed. We introduce a new tool that we term perturbation-response scanning (PRS) for the analysis of remote control strategies utilized. The approach relies on the systematic use of computational perturbation/response techniques based on linear response theory, by sequentially applying directed forces on single-residues along the chain and recording the resulting relative changes in the residue coordinates.Wefurtherobtainclosed-formexpressionsforthemagnitudeandthedirectionalityoftheresponse.UsingPRS, westudytheligandreleasemechanismsofFBPandsupportthefindingsbymoleculardynamicssimulations.Wefindthat theresidue-by-residuedisplacementsbetweentheapoandtheholoforms,asdeterminedfromtheX-raystructures,are faithfully reproduced by perturbations applied on the majority of the residues of the apo form. However, once the stabilizingligand(Fe)isintegratedtothesysteminholoFBP,perturbingonlyafewselectresiduessuccessfullyreproduces theexperimentaldisplacements.Thus,ironuptakebyFBPisafavoredprocessinthefluctuatingenvironmentoftheprotein, whereas iron release is controlled by mechanisms including chelation and allostery. The directional analysis that we implementinthePRSmethodologyimplicatesthelattermechanismbyleadingtoafewdistant,charged,andexposedloop residues.Uponperturbingthese,irrespectiveofthedirectionoftheoperatingforces,wefindthatthecapresiduesinvolved inironreleasearemadetooperate