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Yingjie Wang, Ph.D. - Publications

Affiliations: 
2014 Chemical Physics University of Minnesota, Twin Cities, Minneapolis, MN 
Area:
Chemical Biology; Chemical Physics; Computational Chemistry; Physical Chemistry; Organic Chemistry
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31 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Yao W, Li Y, Ma D, Hou X, Wang H, Tang X, Cheng D, Zhang H, Du C, Pan H, Li C, Lin H, Sun M, Ding Q, Wang Y, et al. Evolution of SARS-CoV-2 Spikes shapes their binding affinities to animal ACE2 orthologs. Microbiology Spectrum. e0267623. PMID 37943512 DOI: 10.1128/spectrum.02676-23  0.421
2023 Olivieri C, Wang Y, Walker C, Subrahmanian MV, Ha KN, Bernlohr DA, Gao J, Camilloni C, Vendruscolo M, Taylor SS, Veglia G. The αC-β4 loop controls the allosteric cooperativity between nucleotide and substrate in the catalytic subunit of protein kinase A. Biorxiv : the Preprint Server For Biology. PMID 37745542 DOI: 10.1101/2023.09.12.557419  0.492
2023 Ruan M, Li H, Zhang Y, Zhao R, Zhang J, Wang Y, Gao J, Wang Z, Wang Y, Sun D, Ding W, Weng Y. Cryo-EM structures of LHCII in photo-active and photo-protecting states reveal allosteric regulation of light harvesting and excess energy dissipation. Nature Plants. PMID 37653340 DOI: 10.1038/s41477-023-01500-2  0.484
2023 Ju M, Chen Z, Zhu H, Cai R, Lin Z, Chen Y, Wang Y, Gao J, Long X, Yang S. Fe(III) Docking-Activated Sites in Layered Birnessite for Efficient Water Oxidation. Journal of the American Chemical Society. 145: 11215-11226. PMID 37173623 DOI: 10.1021/jacs.3c01181  0.426
2022 Hou X, Gao J, Wang Y. Epistatic Variations in the Omicron Receptor Binding Domain Can Enhance Host Recognition: An Assessment and Prediction. The Journal of Physical Chemistry Letters. 13: 8808-8815. PMID 36106917 DOI: 10.1021/acs.jpclett.2c02209  0.468
2021 Zhou S, Wang Y, Gao J. Solvation Induction of Free Energy Barriers of Decarboxylation Reactions in Aqueous Solution from Dual-Level QM/MM Simulations. Jacs Au. 1: 233-244. PMID 34467287 DOI: 10.1021/jacsau.0c00110  0.472
2021 Walker C, Wang Y, Olivieri C, V S M, Gao J, Bernlohr DA, Calebiro D, Taylor SS, Veglia G. Is disrupted nucleotide-substrate cooperativity a common trait for Cushing's syndrome driving mutations of protein kinase A? Journal of Molecular Biology. 167123. PMID 34224748 DOI: 10.1016/j.jmb.2021.167123  0.464
2021 Walker C, Wang Y, Olivieri C, V S M, Gao J, Bernlohr DA, Calebiro D, Taylor SS, Veglia G. Is disrupted nucleotide-substrate cooperativity a common trait for Cushing's syndrome driving mutations of protein kinase A? Journal of Molecular Biology. 167123. PMID 34224748 DOI: 10.1016/j.jmb.2021.167123  0.464
2021 Wang Y, Veglia G, Zhong D, Gao J. Activation mechanism of cryptochrome through an allosteric switch. Science Advances. 7. PMID 34144991 DOI: 10.1126/sciadv.abg3815  0.477
2021 Wang Y, Veglia G, Zhong D, Gao J. Activation mechanism of cryptochrome through an allosteric switch. Science Advances. 7. PMID 34144991 DOI: 10.1126/sciadv.abg3815  0.477
2020 Li H, Wang Y, Ye M, Li S, Li D, Ren H, Wang M, Du L, Li H, Veglia G, Gao J, Weng Y. Dynamical and allosteric regulation of photoprotection in light harvesting complex II. Science China. Chemistry. 63: 1121-1133. PMID 33163014 DOI: 10.1007/S11426-020-9771-2  0.524
2020 Tang J, Wang Y, Zhou H, Ye Y, Talukdar M, Fu Z, Liu Z, Li J, Neculai D, Gao J, Huang H. Sunitinib inhibits RNase L by destabilizing its active dimer conformation. The Biochemical Journal. PMID 32830849 DOI: 10.1042/BCJ20200260  0.43
2020 Yang D, Zhu W, Wang Y, Tan F, Ma Z, Gao J, Lin X. Selection of mutant µplasmin for amyloid-β cleavage in vivo. Scientific Reports. 10: 12117. PMID 32694536 DOI: 10.1038/S41598-020-69079-8  0.408
2020 Wang Y, Liu M, Gao J. Enhanced receptor binding of SARS-CoV-2 through networks of hydrogen-bonding and hydrophobic interactions. Proceedings of the National Academy of Sciences of the United States of America. PMID 32503918 DOI: 10.1073/Pnas.2008209117  0.534
2020 Olivieri C, Wang Y, Li GC, Subrahmanian MV, Kim J, Stultz BR, Neibergall M, Porcelli F, Muretta JM, T Thomas DD, Gao J, Blumenthal DK, Taylor SS, Veglia G. Multi-state recognition pathway of the intrinsically disordered protein kinase inhibitor by protein kinase A. Elife. 9. PMID 32338601 DOI: 10.7554/Elife.55607  0.533
2020 Olivieri C, Wang Y, Li GC, S MV, Kim J, Stultz BR, Neibergall M, Porcelli F, Muretta JM, Thomas DD, Gao J, Blumenthal DK, Taylor SS, Veglia G. Author response: Multi-state recognition pathway of the intrinsically disordered protein kinase inhibitor by protein kinase A Elife. DOI: 10.7554/Elife.55607.Sa2  0.494
2019 Walker C, Wang Y, Olivieri C, Karamafrooz A, Casby J, Bathon K, Calebiro D, Gao J, Bernlohr DA, Taylor SS, Veglia G. Cushing's syndrome driver mutation disrupts protein kinase A allosteric network, altering both regulation and substrate specificity. Science Advances. 5: eaaw9298. PMID 31489371 DOI: 10.1126/Sciadv.Aaw9298  0.534
2019 Wang Y, V S M, Kim J, Li G, Ahuja LG, Aoto P, Taylor SS, Veglia G. Globally correlated conformational entropy underlies positive and negative cooperativity in a kinase's enzymatic cycle. Nature Communications. 10: 799. PMID 30778078 DOI: 10.1038/S41467-019-08655-7  0.332
2018 Tomasini MD, Wang Y, Karamafrooz A, Li G, Beuming T, Gao J, Taylor SS, Veglia G, Simon SM. Conformational Landscape of the PRKACA-DNAJB1 Chimeric Kinase, the Driver for Fibrolamellar Hepatocellular Carcinoma. Scientific Reports. 8: 720. PMID 29335433 DOI: 10.1038/S41598-017-18956-W  0.531
2018 Wang Y, Kim J, Olivieri C, Gao J, Veglia G. Inactivation Mechanism of Protein Kinase a Revealed by Markov Model Biophysical Journal. 114: 190a. DOI: 10.1016/J.Bpj.2017.11.1062  0.514
2017 Wang Y, Camilloni C, Kim J, Vendruscolo M, Gao J, Veglia G. Characterization of Protein Kinase a Free Energy Landscape by NMR-Restrained Metadynamics Biophysical Journal. 112: 50a. DOI: 10.1016/J.Bpj.2016.11.310  0.567
2016 Wang Y, Cembran A, Gao J, Veglia G, Taylor SS, Simon SM. Molecular Dynamics Simulation and Markov State Model Reveal Irregular Metastable Conformation and Allostery In DNAJB-PKAc Biophysical Journal. 110: 51a-52a. DOI: 10.1016/J.Bpj.2015.11.343  0.543
2015 Wang Y, Gao J. Projected hybrid orbitals: a general QM/MM method. The Journal of Physical Chemistry. B. 119: 1213-24. PMID 25317748 DOI: 10.1021/Jp507983U  0.485
2014 Liu M, Wang Y, Chen Y, Field MJ, Gao J. QM/MM through the 1990s: The First Twenty Years of Method Development and Applications. Israel Journal of Chemistry. 54: 1250-1263. PMID 29386687 DOI: 10.1002/Ijch.201400036  0.5
2014 Gao J, Truhlar DG, Wang Y, Mazack MJ, Löffler P, Provorse MR, Rehak P. Explicit polarization: a quantum mechanical framework for developing next generation force fields. Accounts of Chemical Research. 47: 2837-45. PMID 25098651 DOI: 10.1021/Ar5002186  0.663
2013 Isegawa M, Fiedler L, Leverentz HR, Wang Y, Nachimuthu S, Gao J, Truhlar DG. Polarized Molecular Orbital Model Chemistry 3. The PMO Method Extended to Organic Chemistry. Journal of Chemical Theory and Computation. 9: 33-45. PMID 23704835 DOI: 10.1021/Ct300509D  0.721
2012 Wang Y, Sosa CP, Cembran A, Truhlar DG, Gao J. Multilevel X-Pol: a fragment-based method with mixed quantum mechanical representations of different fragments. The Journal of Physical Chemistry. B. 116: 6781-8. PMID 22428657 DOI: 10.1021/Jp212399G  0.54
2012 Gao J, Wang Y. Communication: variational many-body expansion: accounting for exchange repulsion, charge delocalization, and dispersion in the fragment-based explicit polarization method. The Journal of Chemical Physics. 136: 071101. PMID 22360228 DOI: 10.1063/1.3688232  0.564
2010 Cembran A, Bao P, Wang Y, Song L, Truhlar DG, Gao J. On the Interfragment Exchange in the X-Pol Method. Journal of Chemical Theory and Computation. 6: 2469-2476. PMID 20730021 DOI: 10.1021/Ct100268P  0.655
2009 Yang W, Qian Z, Miao Q, Wang Y, Bi S. Density functional theory study of the aluminium(III) hydrolysis in aqueous solution. Physical Chemistry Chemical Physics : Pccp. 11: 2396-401. PMID 19325971 DOI: 10.1039/B819484J  0.326
2009 Qian Z, Feng H, Zhang Z, Yang W, Wang M, Wang Y, Bi S. Theoretical exploration of the water exchange mechanism of the polyoxocation GaO4Al12(OH)24(H2O)127+ in aqueous solution Geochimica Et Cosmochimica Acta. 73: 1588-1596. DOI: 10.1016/J.Gca.2008.12.017  0.318
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