農学部研究紹介_英語版_2024_2025

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Free energy calculation and sampling conformational ensemble for protein folding and protein-ligand bindingSearching new ligand-binding site from database based on similarity of local 3D structureDeveloping coarse-grained model of biomolecule to study effects of post-translational modification (e.g. phosphorylation) on intermolecular interactionBDMoleculeーStructure ー•theoretical models•dynamics, flexibility•solvationMolecular simulationstructure-activity relationship Understandingligand-binding mechanismActivityComputationalーFunction ー•binding partner•active conformation•affinity, kinetics …StructuralBiologyDatabase analysisNew knowledge ofBindingprocessmodification?signaling?32Biotechnology DivisionLaboratory of FunctionalMolecular DesignKojiUMEZAWAAssistantProfessor,Ph.D.Bioinformatics,Biophysics, Molecular Dynamics Simulation, Molecular Modeling, Computational Structural BiologyMoleculehasalotofpossibleconformationsatroomtemperature.Thereshouldbeabiologicallyactiveconformation.Theactiveconformationisinterestingandprovidesakeytointerpretthebiologicalfunction.However,itisdifficulttocharacterizethatconformation.Then,wehaveusedmoleculardynamicssimulationanddatabaseanalysistofigureouttherelationshipofmolecularconformationanddynamicswiththebiologicalactivitysuchasproteinfolding,ligandrecognition,post-translationalmodificationeffects,andligand-association/dissociationcontrol.Ourcurrenttopicsdescribedbelowhavebeenstudied.Relationship between structural information and Cfunction has been explored computationally.In silico study・Molecular modeling・ProgramingWe have developed molecular modeling and programing to study ligand-binding mechanism.