HUANG, Xuhui - University of Wisconsin-Madison

个人简介

EDUCATION 2006 Ph.D. in Chemical Physics, Columbia University (Thesis advisor: B. J.Berne) 2001 B.S. in Chemical Physics, University of Science and Technology of China (USTC) PROFESSIONAL EXPERIENCE Sept 2021- Present Hirschfelder Chair in Theoretical Chemistry, Department of Chemistry, University of Wisconsin-Madison July 2019-Aug 2021 Professor, Department of Chemistry, The Hong Kong University of Science and Technology July 2017-June 2019 Padma Harilela Associate Professor of Science, Department of Chemistry, The Hong Kong University of Science and Technology July 2017- Aug 2021 Associate Professor & Professor (Joint appointment), Department of Chemical and Biological Engineering, The Hong Kong University of Science and Technology Jan 2015-July 2017 Associate Professor, Department of Chemistry, The Hong Kong University of Science and Technology Oct 2011-July 2017 Assistant & Associate Professor (Joint appointment), Division of Biomedical Engineering, The Hong Kong University of Science and Technology Jan 2010- Dec 2014 Assistant Professor, Department of Chemistry, The Hong Kong University of Science and Technology Sep 2008-Dec 2009 Research Associate, Department of Bioengineering, Stanford University Aug 2006-Aug 2008 Simbios Distinguished Postdoctoral Scholar, Stanford University (Advisor: M. Levitt, Nobel Laureate in Chemistry 2013 , and V. S. Pande )

研究领域

Our research is in the area of Theoretical Chemistry and Molecular Biophysics. The operation of biological molecules is a highly dynamic process that relies on numerous functional conformational changes. We are interested in elucidating the dynamics of these conformational changes by developing new methods based on statistical mechanics that can bridge the gap between experiments and atomistic molecular dynamics (MD) simulations. We believe that tight integration of analytical theories with modern computer simulations and machine learning techniques can lead to breakthroughs in many aspects of theoretical chemistry. We also believe that establishing links between molecular mechanisms of bio-systems and their cellular and genome-wide behaviors is key to understanding many fundamental biological processes. To fulfill our vision, our group is currently working on the following directions: Methodological advances of the Markov State Models (MSMs) and Generalized Master Equation for bimolecular dynamics. Elucidation of functional conformational changes of RNA Polymerases. Elucidation of dynamics for molecular recognition and self-assembly. Development of new Integral Equation Theories for solvation. Development of deep learning based algorithms for to predict novel inhibitors against desired protein targets. Elucidation of structural ensemble from heterogeneity Cryo-EM datasets.

近期论文

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Unarta, I.S., Cao, S., Kubo, S., Wang, W., Cheung, P.P.H., Gao, X., Takada, S., Huang, X.* “Role of Bacterial RNA Polymerase Gate Opening Dynamics in DNA Loading and Antibiotics Inhibition Elucidated by quasi-Markov State Model”, Proc. Nat. Acad. Sci. U.S.A., 118(17), e2024324118, (2021) Li, C., Liu, Z., Goonetilleke, E.C., Huang, X.* “Temperature-dependent Kinetic Pathways of Heterogeneous Ice Nucleation Competing between Classical and Non-classical Nucleation”, Nature Communications, 12, 4954, (2021) Konovalov, K.A., Unarta, I.S., Cao, S., Goonetilleke1, E.C., Huang, X.*, “Markov state models to study the functional dynamics of proteins in the wake of machine learning”, J. Am. Chem. Soc. Au, Published On-line, (2021), DOI:10.1021/jacsau.1c00254 Xu, X., Zhang, L.*, Chu, J.T.S., Wang, Y., Chin, A.W.H., Chong, T.H., Dai, Z., Poon, L.L.M., Cheung P.P.H.*, Huang, X.* “A Novel Mechanism of Enhanced Transcription Activity and Fidelity for Influenza A Viral RNA-dependent RNA Polymerase”, Nucleic Acids Res., 49(15), 8796-8810, (2021) Oh, J., Shin, J., Unarta, I.S., Wang, W., Feldman, A.W., Karadeema, R.J., Xu, L., Chong, J., Krishnamurthy, R., Huang, X., Romesberg, F.E., Wang, D., “Transcriptional processing of an unnatural base pair by eukaryotic RNA polymerase II”, Nature Chemical Biology, 17, 906–914, (2021) Yuan, C., Wang, Goonetilleke, E.C., Unarta, I.S., Huang, X.*, “Incorporation Efficiency and Inhibition Mechanism of 2’-Substituted Nucleotide Analogs against SARS-CoV-2 RNA-dependent RNA polymerase”, Phys. Chem. Chem. Phys., 23, 20117 – 20128, (2021) Konovalov, K.A., Wang, W., Wang, G., Goonetilleke, E.C., Gao, X., Wang, D., Huang, X.*, “Comprehensive mechanism for 5-carboxylcytosine induced transcriptional pausing revealed by Markov state models”, J. Biol. Chem., 296, 100735, (2021) Wang, Y., Yuan, C., Xu, X., Chong, T.H., Zhang, L., Cheung P.P.H.*, Huang, X.* “The mechanism of action of T-705 as a unique delayed chain terminator on influenza viral polymerase transcription”, Biophysical Chemistry,277, 106652, (2021) Liu, Z., Li, C., Goonetilleke, E.C., Cui, Y., Huang, X.* “Role of Surface Templating on Ice Nucleation Efficiency on a Silver Iodide Surface”, J. Phys. Chem. C, 125 (34), 18857-18865, (2021) Unarta, I.S., Xu, J., Shang, Y., Cheung, H.P., Zhu, R., Chen, X., Cao, S., Cheung, P.P.H., Bierer, D., Zhang, M.*, Huang, X.*, Li, X.* “Entropy of Stapled Peptide Inhibitors in Free State is the Major Contributor to the Improvement of Binding Affinity”, RSC Chem. Biol., 2, 1274-1284, (2021) Quinn, T., Steussy, C.N.; Haines, B.E., Lei, J.; Wang, W.; Sheong, F. K., Cynthia V.S., Huang, X., Norrby, P., Helquist, P., Wiest, O. “Microsecond Timescale Simulations at the Transition State of PmHMGR Predict Remote Allosteric Residues”, Chemical Science, 12, 6413-6418, (2021) Wang, X., Unarta, I.C., Cheung P.P.H., Huang, X.* “Elucidating Molecular Mechanisms of Functional Conformational Changes of Proteins via Markov State Models”, Curr. Opin. Struct. Biol, 67, 69-77, (2021) Zhang, L.*, Zhang, D., Yuan, C., Wang, X., Li, Y., Jia, X., Gao, X., Yen, H.-L., Cheung, P.*, Huang, X.*, “Role of 1′-Ribose Cyano Substitution for Remdesivir to Effectively Inhibit both Nucleotide Addition and Proofreading in SARS-CoV-2 Viral RNA Replication”, Phys. Chem. Chem. Phys., 23, 5852-5863, (2021), bioRxiv Peng, S., Wang, X., Zhang L.*, He, S., Zhao, X.S, Huang, X.*, Chen, C.* “Target search and recognition mechanisms of glycosylase AlkD revealed by scanning FRET-FCS and Markov State Models”, Proc. Nat. Acad. Sci. U.S.A., 117 (36), 21889-21895, (2020) Cao, S., Montoya-Castillo, Andres., Wang, W., Markland, T.*, Huang, X.*, “On the Advantages of Exploiting Memory in Markov State Models for Biomolecular Dynamics”, J. Chem. Phys.,153, 014105, (2020) Cheung, P., Jiang, B., Booth, G.T., Chong, T.H., Unartar, I.C., Wang, Y., Suarez, G.D., Wang, J.*, Lis, J.T.*, Huang, X.*, “Identifying Transcription Error-Enriched Genomic Loci Using Nuclear Run-On Circular-Sequencing Coupled with Background Error Modeling”, J. Mol. Biol., 432(13), 3933-3949, (2020) Choy, K., Wong, A., Kaewpreedee, P., Sia, S., Chen, D., Hui, K., Chu, D., Chan, M., Cheung, P., Huang, X., Peiris, M., Yen, H-L, “Remdesivir, lopinavir, emetine, and homoharringtonine inhibit SARS-CoV-2 replication in vitro”, Antiviral Research, 178: 104786, (2020) Pan, C., Liu, C., Peng, J., Ren, P.*, Huang, X.*, “Three-site and Five-site Fixed-charge Water Models Compatible with AMOEBA Force Field”, J. Comput. Chem., 41:1034–1044, (2020) Lam, J.H., Li, Y., Zhu, L., Umarov, R., Jiang, H., Heliou, A., Sheong, F.K., Liu, T., Long, Y., Li, Y., Fang, L., Altman, R., Chen, W., Huang, X.*, Gao, X.*, “A deep learning framework to predict binding preference of RNA constituents on protein surface”, Nature Communications, 10, 4941, (2019)