Publications

• Hasse T and Huang Y-mM* (2024) Multiple Parameter Replica Exchange Gaussian Accelerated Molecular Dynamics for Enhanced Sampling and Free Energy Calculation of Biomolecular Systems. J. Chem. Theory Comput. 20:6485

• Hasse T, Mantei E, Shahoei R, Pawnikar S, Wang J, Miao Y, and Huang Y-mM* (2024) Mechanistic insights into ligand dissociation from the SARS-CoV-2 spike glycoprotein. PLoS Compt. Bio. 7: e1011955

• Xu Y, Xiong B, Huang Y-mM, Xu J, Yan He, and Lu Z (2024) Exploring Additives Beyond Phthalates: Release from Plastic Mulching Films, Biodegradation and Occurrence in Agricultural Soils. Sci. Total Environ. 918: 170763.

• Hasse T, Zhang Z, and Huang Y-mM* (2023) Molecular dynamics study reveals key disruptors of MEIG1-PACRG interaction. Proteins: Struc. Func. Bioinfo. 91: 437

• Thepsuwan P, Bhattacharya A, Song Z, Hippleheuser S, Feng S, Wei X, Das NK, Sierra M, Wei J, Fang D, Huang Y-mM, Zhang K, Shah YM, and Sun S* (2023) Hepatic SEL1L-HRD1 ER-associated degradation regulates systemic iron homeostasis via ceruloplasmin. Proc. Natl. Acad. Sci. 120: e2212644120

• Shahoei R, Pangeni S, Sanders MA, Zhang H, Mladenovic-Lucas L, Roush WR, Halvorsen G, Kelly, CV, Granneman, JG, and Huang Y-mM* (2022) Molecular modeling of ABHD5 structure and ligand recognition. Front. Mol. Biosci. 9: 935375

• Ellson CD, Rica IG, Kim JS, Huang Y-mM, Lim D, Mitra T, Hsu AL, Wei EX, Barrett CD, Otterbein LE, Hauser CJ, Wahl M, Delbruck H, Heinemann U, Oschkinat H, Chang CEA, and Yaffe MB* (2022) An integrated pharmacological, structural, and genetic analysis of extracellular versus intracellular ROS production in neutrophils. J. Mol. Bio. 434: 167533

• Huang Y-mM* (2021) Multi-scale computational investigation of ligand association pathways: Case of p38 MAP kinase and its inhibitors. Biophys. J. 120: 3881 (Cover Highlight: Ligand Binding Pathways to the p38 Kinase)

• Zhan T, Cui S, Liu X, Zhang C, Huang Y-mM*, and Zhuang S* (2021) Enhanced disrupting effect of benzophenone-1 chlorination byproducts to androgen receptor: Cell-based assays and Gaussian accelerated molecular dynamics simulations. Chem. Res. Toxicol. 34: 1140

• Wang J#, Arantes PR#, Bhattarai A, Hsu RV, Pawnikar S, Huang Y-mM, Palermo G*, and Miao Y* (2021) Gaussian accelerated molecular dynamics (GaMD): Principals and applications. WIREs Comp. Mol. Sci. e1521

• Qiu M, Hu A, Huang Y-mM, Zhao Y, He Y, Xu J, and Lu Z* (2020) Elucidating degradation mechanisms of florfrnicol in soil by stable-isotope assisted nontarget screening. J. Hazard Mater. 403: 123974

• Huang Y-mM*, Munguia J, Miao Y, Nizet V, and McCammon JA (2019) Docking simulation and antibiotic discovery targeting the MlaC protein in Gram-negative bacteria. Chem. Biol. Drug Des. 93: 647

• Miao Y*, Huang Y-mM*, Walker RC, McCammon JA, and Chang C-eA (2018) Ligand binding pathways and conformational transitions of the HIV protease. Biochemistry 57: 1533

• Huang Y-mM*, McCammon JA, and Miao Y (2018) Replica exchange Gaussian accelerated molecular dynamics: Improved enhanced sampling and free energy calculation. J. Chem. Theory Comput. 14: 1853

• Huang Y-mM*, Huber GA, Wang N, Minteer SD, and McCammon JA (2018) Brownian dynamic study of an enzyme metabolon in the TCA cycle: Substrate kinetics and channeling. Protein Sci. 27: 463

•  Huang Y-mM, Raymundo MAV, Chen W, and Chang C-eA* (2017) Mechanism of the association pathways for a pair of fast and slow binding ligands of HIV-1 protease. Biochemistry 56: 1311

• Zhang CH, Brown MQ, van de Ven W, Zhang ZM, Wu B, Young MC, Synek L, Borchardt D, Harrison R, Pan SQ, Luo N, Huang Y-mM, Ghang YJ, Ung N, Li RX, Isley J, Morikis D, Song JK, Guo W, Hooley RJ, Chang C-eA, Yang ZB, Zarsky V, Muday GK, Hicks GR, and Raikhel NV* (2016) Endosidin2 targets conserved exocyst complex subunit EXO70 to inhibit exocytosis. Proc. Natl. Acad. Sci. U. S. A. 113: E41

• You WL, Huang Y-mM, Kizhake S, Natarajan A, and Chang C-eA* (2016) Characterization of promiscuous binding of phosphor ligands to breast-cancer-gene 1 (BRCA1) c-terminal (BRCT): Molecular dynamics, free energy, entropy and inhibitor design. PLoS Comput. Biol. 12: e1005057

• Huang Y-mM, You WL, Caulkins BG, Dunn MF, Mueller LJ and, Chang C-eA* (2016) Protonation states and catalysis: Molecular dynamics studies of intermediates in tryptophan synthase. Protein Sci. 25: 166

• Huang Y-mM*, Miao YL, Munguia J, Lin L, Nizet V, and McCammon JA (2016) Molecular dynamic study of MlaC protein in Gram-negative bacteria: conformational flexibility, solvent effect and protein-phospholipid binding. Protein Sci. 25: 1430

• Hilario E, Caulkins BG, Huang Y-mM, You W, Chang C-eA, Mueller LJ, Dunn MF, and Fan L* (2016) Visualizing the tunnel in tryptophan synthase with crystallography: Insights into a selective filter for accommodating indole and rejecting water. Biochimica Et Biophysica Acta-Proteins and Proteomics 1864: 268

• Chang C-eA*, Huang Y-mM, Mueller LJ, and You W (2016) Investigation of structural dynamics of enzymes and protonation states of substrates using computational tools. Catalysts 6: 82 (review)

• Huang Y-mM*, Huber G, and McCammon JA (2015) Electrostatic steering enhances the rate of cAMP binding to phosphodiesterase: Brownian dynamics modeling. Protein Sci. 24: 1884

• Zeng S, Huang Y-mM, Chang C-eA, and Zhong W* (2014) Protein binding for detection of small changes on a nanoparticle surface. Analyst 139: 1364

• Huang Y-mM, Kang M, and Chang C-eA* (2014) Switches of hydrogen bonds during ligand-protein association processes determine binding kinetics. J. Mol. Recognit. 27: 537

• Huang Y-mM* and Chang C-eA* (2014) Achieving peptide binding specificity and promiscuity by loops: Case of the forkhead-associated domain. PLoS ONE 9: e98291

• Caulkins BG, Bastin B, Yang C, Neubauer TJ, Young RP, Hilario E, Huang Y-mM, Chang C-eA, Fan L, Dunn MF, Marsella MJ, and Mueller LJ* (2014) Protonation states of the tryptophan synthase internal aldimine active site from solid-state NMR spectroscopy: Direct observation of the protonated schiff base linkage to pyridoxal-5 '-phosphate. J. Am. Chem. Soc. 136: 12824

• Huang Y-mM#, Kang M#, and Chang C-eA* (2012) Mechanistic insights into phosphopeptide-BRCT domain association: Preorganization, flexibility, and phosphate recognition. J. Phys. Chem. B 116: 10247

• Huang Y-mM, Chen W, Potter MJ, and Chang C-eA* (2012) Insights from free-energy calculations: Protein conformational equilibrium, driving forces, and ligand-binding modes. Biophys. J. 103: 342

• Huang Y-mM and Chang C-eA* (2011) Mechanism of phosphoThreonine/Serine recognition and specificity for modular domains from all-atom molecular dynamics. BMC Biophys. 4: 12