Ph.D., Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA
My research focuses on application and development of computational approaches to understand biological structure and function. One of our research directions is to investigate catalytic mechanisms and specificity/promiscuity of enzymes and inhibitor binding processes by use of state-of-the art computational approaches. We are interested in understanding the origin of high catalytic efficiency and selectivity/promiscuity of enzyme-catalyzed reactions. These studies would, in addition to being of fundamental scientific importance, also improve the basis for designing inhibitors, efficient drugs and enzyme mimics. We use molecular dynamics (MD) simulations, free energy calculations, mixed quantum mechanical/molecular mechanical (QM/MM) methods and some other computational approaches to address questions in this research area. Several enzyme systems are currently under investigations in our laboratory. Another direction of our research is to integrate structural information (such as 3-dimensional protein models) with other datasets for understanding the enzymatic and regulatory pathways required for Crassulacean Acid Metabolism (CAM) of plants, which provides an excellent opportunity to engineer enhanced photosynthetic performance and water use efficiency (WUE) into bioenergy crops. We also study structural and dynamic features of proteins and try to understand the forces that that stabilize proteins.
Xie, M., Muchero, W., Bryan, A. C., Yee, K.,… , Guo, H.,… Tuskan, G. A. (2018). A 5-Enolpyruvylshikimate 3-Phosphate Synthase Functions as a Transcriptional Repressor in Populus.. Plant Cell, 30(7), 1645-1660. doi:10.1105/tpc.18.00168
Yue, Y., Ma, Y., Qian, P., & Guo, H. (2018). Catalytic Mechanism of the Ubiquitin-Like NEDD8 Transfer in RING E3-E2 similar to NEDD8-Target Complex from QM/MM Free Energy Simulations. Journal of Chemical Information and Modeling, 58(2), 422-429. doi:10.1021/acs.jcim.7b00662
Guo, H. -B., Ma, Y., Tuskan, G. A., Yang, X., & Guo, H. (2018). Classification of Complete Proteomes of Different Organisms and Protein Sets Based on Their Protein Distributions in Terms of Some Key Attributes of Proteins. International Journal of Genomics, 12 pages. doi:10.1155/2018/9784161
Yang, X., Hu, R., Yin, H., Jenkins, J., Shu, S., Tang, H., . . ., Guo, H., . . ., Tuskan, G. A. (2017). The Kalanchoe genome provides insights into convergent evolution and building blocks of crassulacean acid metabolism. Nature Communications, 8, 15 pages. doi:10.1038/s41467-017-01491-7
Qian, P., Guo, H., Wang, L., & Guo, H. (2017). QM/MM Investigation of Substrate and Product Specificities of Suv4-20h2: How Does This Enzyme Generate Dimethylated H4K20 from Monomethylated Substrate?. Journal of Chemical Theory and Computation, 13(6), 2977-2986. doi:10.1021/acs.jctc.7b00069
Ming, R., VanBuren, R., Wai, C. M., Tang, H., Schatz, M. C., Bowers, J. E., . . .Yu, Q. (2015). The pineapple genome and the evolution of CAM photosynthesis. Nature Genetics, 47(12), 1435-1442. doi:10.1038/ng.3435