Lawrence Livermore National Laboratory
My research focuses on the Cytochrome P450 (CYP) enzyme superfamily. I use molecular dynamics computer simulations to explore three stages of CYP catalysis: the binding process, the chemical reactions involved, and the release of product. CYPs catalyze the oxidation of xenobiotic compounds, e.g., drugs, and thus play an important role in drug metabolism. CYPs rely on the heme-cofactor for their catalytic activity. Classes of CYPs exhibit different substrate selectivities and product regioselectivities even though the classes share a nearly identical heme complex. Understanding the CYP catalysis mechanism can help predict unwanted drug adverse effects in the early stage of drug discovery.
- Yang, Y., Wong, S. E., Lightstone, F. C. (2014), Understanding a Substrate’s Product Regioselectivity in a Family of Enzymes: A Case Study of Acetaminophen Binding in Cytochrome P450s. PLoS ONE, 9(2): e87058.
- Yang, Y., Wong, S. E., Lightstone, F. C. (2013), Approaches to efficiently estimate solvation and explicit water energetics in ligand binding: the use of WaterMap. Expert Opin. Drug Discovery, 8, 277-287.
- Yang, Y., Wang, B., Ucisik, M. N., Cui, G., Fierke, C. A., Merz, K. M. (2012), Insights into the Mechanistic Dichotomy of the Protein Farnesyltransferase Peptide Substrates CVIM and CVLS. J. Am. Chem. Soc., 134, 820-823.
- Yang, Y., Miao, Y., Wang, B., Cui, G., A., Merz, K. M. (2012), Catalytic mechanism of aromatic prenylation by NphB. Biochemistry 51, 2606-2618.
- Yang, Y., Chakravorty, D. K., and Merz, K. M. (2010) Finding a needle in the haystack: Computational modeling of Mg2+ binding in the active site of protein farnesyltransferase, Biochemistry 49, 9658-9666.
- Peters, M. B., Yang, Y., Wang, B., Fusti-Molnar, L., Weaver, M. N., and Merz, K. M. (2010) Structural survey of zinc-containing proteins and development of the zinc amber force field (ZAFF), J. Chem. Theory Comput. 6, 2935-2947.
- Weaver, M. N., Yang, Y. and Merz, K. M. (2009) Assessment of the ccsd and ccsd(t) coupled-cluster methods in calculating heats of formation for Zn complexes, J. Phys. Chem. A. 113, 10081-10088.
- Yang, Y., Weaver, M. N., and Merz, K. M. (2009) Assessment of the "6-31+g**+lanl2dz" Mixed basis set coupled with density functional theory methods and the effective core potential: Prediction of heats of formation and ionization potentials for first-row-transition-metal complexes, J. Phys. Chem. A. 113, 9843-9851
- Yang, Y., Zhang, D., Wu, L. Z., Chen, B., Zhang, L. P., and Tung, C. H. (2004) Photosensitized oxidative deprotection of oximes to their corresponding carbonyl compounds by platinum(ii) terpyridyl acetylide complex, J. Org. Chem. 69, 4788-4791.