Jimin Wang, PhD
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Research Scientist in Molecular Biophysics and Biochemistry
Biography
Dr. Wang completed his BS in Chemistry at Peking University in China in June, 1982, his PhD in Chemistry and Biochemistry at UC, San Diego in June, 1988. Following a brief post-doctoral training at UC, San Diego, Dr. Wang moved to Yale University in September, 1991, to work with Professor T. A. Steitz. He has been at Yale University since then.
Jimin is skilled in developing new methods for quantitative analysis of experimental charge density maps and electrostatic potential maps. He is knowledgeable in analysis of molecular dynamics trajectories and other large-scale structural analysis, and many software packages for publication quality illustrations. He has published over 150 peer-reviewed scientific papers. He is knowledgeable in many aspects of Biology, Chemistry, Physics, and their interfaces.
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Molecular Biophysics and Biochemistry
Research ScientistPrimary
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Education & Training
- PhD
- University of California, San Diego (1988)
Research
Research at a Glance
Yale Co-Authors
Frequent collaborators of Jimin Wang's published research.
Publications Timeline
A big-picture view of Jimin Wang's research output by year.
Victor Batista
Gary Brudvig
Elias Lolis, PhD
Joan Steitz, PhD
Christian Schlieker, PhD
Peter Moore, PhD
170Publications
11,312Citations
Publications
2024
Mutation-induced shift of the photosystem II active site reveals insight into conserved water channels
Flesher D, Liu J, Wang J, Gisriel C, Yang K, Batista V, Debus R, Brudvig G. Mutation-induced shift of the photosystem II active site reveals insight into conserved water channels. Journal Of Biological Chemistry 2024, 300: 107475. PMID: 38879008, DOI: 10.1016/j.jbc.2024.107475.Peer-Reviewed Original ResearchAltmetricConceptsOxygen-evolving complexPhotosystem II active sitePhotosystem IIJahn-Teller distortionPhotosystem II complexD1-Asp170Jahn-TellerResolution cryo-EM structureMutation-induced structural changesCryo-EM structureMagnetic propertiesD1 subunitActive siteOxygenic photosynthesisMutagenesis studiesLight-driven water oxidationSpectroscopic propertiesStructural basisSpectroscopic dataAmino acidsWater oxidation mechanismPhotosystemMutationsMutation-induced shiftWater oxidationOccupancy Analysis of Water Molecules inside Channels within 25 Å Radius of the Oxygen-Evolving Center of Photosystem II in Molecular Dynamics Simulations
Kaur D, Reiss K, Wang J, Batista V, Brudvig G, Gunner M. Occupancy Analysis of Water Molecules inside Channels within 25 Å Radius of the Oxygen-Evolving Center of Photosystem II in Molecular Dynamics Simulations. The Journal Of Physical Chemistry B 2024, 128: 2236-2248. PMID: 38377592, DOI: 10.1021/acs.jpcb.3c05367.Peer-Reviewed Original ResearchCitationsAltmetricConceptsOxygen-evolving centerWater moleculesPhotosystem IIPositions of water moleculesAnalysis of water moleculesCatalyze water oxidationHydrogen bond networkOccupancy of water moleculesMolecular dynamics simulationsD1-D61Electron density mapsMolecular dynamics analysisProton transferWater oxidationCrystallographic dataIce latticeMD simulationsMolecular dynamicsStructural transitionDynamics simulationsSubstrate waterOxygen-evolvingRoom temperatureProtein residuesMolecules
2023
Computing the Relative Affinity of Chlorophylls a and b to Light-Harvesting Complex II
Ranepura G, Mao J, Vermaas J, Wang J, Gisriel C, Wei R, Ortiz-Soto J, Uddin R, Amin M, Brudvig G, Gunner M. Computing the Relative Affinity of Chlorophylls a and b to Light-Harvesting Complex II. The Journal Of Physical Chemistry B 2023, 127: 10974-10986. PMID: 38097367, DOI: 10.1021/acs.jpcb.3c06273.Peer-Reviewed Original ResearchAltmetricBridging the Coordination Chemistry of Small Compounds and Metalloproteins Using Machine Learning
Kapuścińska K, Dukała Z, Doha M, Ansari E, Wang J, Brudvig G, Brooks B, Amin M. Bridging the Coordination Chemistry of Small Compounds and Metalloproteins Using Machine Learning. Journal Of Chemical Information And Modeling 2023, 64: 2586-2593. PMID: 38054243, DOI: 10.1021/acs.jcim.3c01564.Peer-Reviewed Original ResearchCitationsAltmetricConceptsOxidation stateMetal ionsActive siteCambridge Crystallographic Data CentreMetal oxidation stateElectron transfer reactionsStandard reduction potentialLower oxidation statesX-ray crystallographyCoordination chemistryCryogenic electron microscopyMetal clustersTransfer reactionsReaction mechanismReduction potentialXFEL crystallographyMetalloproteinsAppropriate experimental conditionsSmall moleculesCrystallographySmall compoundsSpecific reactionElectron microscopyRemarkable efficiencyMetalsSubstrate-independent activation pathways of the CRISPR-Cas9 HNH nuclease
Wang J, Maschietto F, Qiu T, Arantes P, Skeens E, Palermo G, Lisi G, Batista V. Substrate-independent activation pathways of the CRISPR-Cas9 HNH nuclease. Biophysical Journal 2023, 122: 4635-4644. PMID: 37936350, PMCID: PMC10754686, DOI: 10.1016/j.bpj.2023.11.005.Peer-Reviewed Original ResearchAltmetricMeSH Keywords and ConceptsConceptsHNH domainHNH nucleaseHigh fidelity enzymesInduced-fit mechanismActivation pathwayActive stateMolecular dynamics trajectoriesCognate substratesConformation 2Conformational selectionObligate stepAla mutantBackbone amidesΑ-helixSide chainsSingle LysEssential roleNucleasePathwayDynamics trajectoriesResiduesConformationMutantsInterconversion pathwaysCRISPRA quantitative assessment of (bacterio)chlorophyll assignments in the cryo-EM structure of the Chloracidobacterium thermophilum reaction center
Gisriel C, Flesher D, Long Z, Liu J, Wang J, Bryant D, Batista V, Brudvig G. A quantitative assessment of (bacterio)chlorophyll assignments in the cryo-EM structure of the Chloracidobacterium thermophilum reaction center. Photosynthesis Research 2023, 1-10. PMID: 37749456, DOI: 10.1007/s11120-023-01047-5.Peer-Reviewed Original ResearchAltmetricConceptsCryo-EM mapsCryogenic electron microscopy structureReaction centersHydrogen bond donorCryo-EM structureElectron microscopy structureReaction center complexBond donorPhotosynthetic organismsMicroscopy structureProtein complexesElectron transferMolecular structureFunctional insightsStructural biologyLight harvestingProtein environmentChemical environmentExperimental cryo-EM mapsDownstream investigationsCenter complexPrimary pigmentEnergy transferStructural dataAcetyl moietyValproate-coenzyme A conjugate blocks opening of receptor binding domains in the spike trimer of SARS-CoV-2 through an allosteric mechanism
Maschietto F, Qiu T, Wang J, Shi Y, Allen B, Lisi G, Lolis E, Batista V. Valproate-coenzyme A conjugate blocks opening of receptor binding domains in the spike trimer of SARS-CoV-2 through an allosteric mechanism. Computational And Structural Biotechnology Journal 2023, 21: 1066-1076. PMID: 36688026, PMCID: PMC9841741, DOI: 10.1016/j.csbj.2023.01.014.Peer-Reviewed Original ResearchCitationsAltmetricTwisting and swiveling domain motions in Cas9 to recognize target DNA duplexes, make double-strand breaks, and release cleaved duplexes
Wang J, Arantes P, Ahsan M, Sinha S, Kyro G, Maschietto F, Allen B, Skeens E, Lisi G, Batista V, Palermo G. Twisting and swiveling domain motions in Cas9 to recognize target DNA duplexes, make double-strand breaks, and release cleaved duplexes. Frontiers In Molecular Biosciences 2023, 9: 1072733. PMID: 36699705, PMCID: PMC9868570, DOI: 10.3389/fmolb.2022.1072733.Peer-Reviewed Original ResearchCitationsAltmetric
2022
Identification and mechanistic basis of non-ACE2 blocking neutralizing antibodies from COVID-19 patients with deep RNA sequencing and molecular dynamics simulations
Fredericks A, East K, Shi Y, Liu J, Maschietto F, Ayala A, Cioffi W, Cohen M, Fairbrother W, Lefort C, Nau G, Levy M, Wang J, Batista V, Lisi G, Monaghan S. Identification and mechanistic basis of non-ACE2 blocking neutralizing antibodies from COVID-19 patients with deep RNA sequencing and molecular dynamics simulations. Frontiers In Molecular Biosciences 2022, 9: 1080964. PMID: 36589229, PMCID: PMC9800910, DOI: 10.3389/fmolb.2022.1080964.Peer-Reviewed Original ResearchCitationsAltmetricConceptsCOVID-19 patientsSARS-CoV-2Severe acute respiratory syndrome coronavirus 2Acute respiratory syndrome coronavirus 2Respiratory syndrome coronavirus 2Spike proteinSevere COVID-19Intensive care unitSyndrome coronavirus 2RNA sequencingCertain immune responsesCOVID-19 infectionSARS-CoV-2 spike proteinEffectiveness of treatmentDeep RNA sequencingICU admissionCare unitSingle centerCoronavirus 2Peripheral bloodMultiple time pointsClinical dataImmune responseEarly infection timesSpecific NAbsTranslocation pause of remdesivir-containing primer/template RNA duplex within SARS-CoV-2’s RNA polymerase complexes
Shi Y, Wang J, Batista V. Translocation pause of remdesivir-containing primer/template RNA duplex within SARS-CoV-2’s RNA polymerase complexes. Frontiers In Molecular Biosciences 2022, 9: 999291. PMID: 36387272, PMCID: PMC9640752, DOI: 10.3389/fmolb.2022.999291.Peer-Reviewed Original ResearchCitationsAltmetric
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