My current research efforts focus on utilizing computational and bioinformatics methods to generate and analyze three-dimensional structures of protein molecules, and to gain insight into protein sequence, structure and function relationships. Leveraging and combining a broad range of techniques enables us to tackle biological problems in multiple dimensions.

There are several research areas I'm interested in. First is the development of new tools to aid in the quantitative description of the protein 3D structures currently available in databases. One impact of such analyses is to allow for a more detailed understanding of protein conformation change resulting from changes in external conditions, e.g. upon ligand binding. Individual residues of a protein molecule are generally believed to contribute to its functions unevenly. Correlation of the observed structural change to its sequence may help to determine their functional roles.

A second research area of interest is the construction of protein and protein-complex models designed to help elucidate biological mechanisms. Determination of the spatial arrangement of protein molecules in cells is an eminent challenge in the post-genomic era. An active project currently ongoing in this area is to model three-dimensional structures of chemoreceptor-CheR complexes through collaboration with experimentalists. Bacterial chemoreceptors detect environmental changes and relate them to conditions inside the cells through reverse methylation by the methyltransferse, CheR, and the methylesterase, CheB. However, it is unknown how the methylation occurs at the atomic level. We're trying to address this question through computational modeling.

In addition, I am also interested in protein sequence analysis and molecular dynamics simulations of covalently modified DNA molecules.

‡ Undergraduate Student
* Graduate Student

W. Lai, L. Huang, P. Ho, Z. Li, D. Montefiori and C.-H. Chen, 2008, "Small Molecules Target HIV-1 V3 Loop with Broad Anti-HIV-1 Entry Activity", Antimicrobial Agents and Chemotherapy 52, 128-136.

V. Pabuwal* and Z. Li, 2008, "Network Pattern of Residue Packing in Helical Membrane Proteins and Its Application in Membrane Protein Structure Prediction", Protein Eng. Des. Sel., 21, 55-64.

U.K. Muppirala and Z. Li, 2006, "A Simple Approach for Protein Structure Discrimination Based on the Network Pattern of Conserved Hydrophobic Residues", Protein Eng. Des. Sel., 19, 265-275.

M. Dong, Z. Li, D.I. Pinon, T.P. Lybrand and L.J. Miller, 2004, "Spatial Approximation between the Amino Terminus of a Peptide Agonist and the Top of the Sixth Transmembrane Segment of the Secretin Receptor", J. Biological Chem., 279, 2894-2903.

M. Dong, Z. Li, M. Zang, D.I. Pinon, T.P. Lybrand and L.J. Miller, 2003, "Spatial Approximation between Two Residues in the Mid-region of Secretin and the Amino Terminus of its Receptor. Incorporation of Seven Sets of Such Constraints into a Three-Dimensional Model of the Agonist-Bound Secretin Receptor", J. Biological Chem., 278, 48300-48312.

Z. Li, L. Huang, P. Dande, B. gold and M.P. Stone, 2002, "Structure of a Tethered Cationic 3-Aminopropyl Chain Incorporated into an Oligodeoxynucleotide: Evidence for 3'-Orientation in the Major Groove Accompanied by DNA Bending" J. Am. Chem. Soc., 124, 8553-8560.