Zhijun Li, PhD
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Zhijun Li
Research Assistant Professor of Biochemistry
Assistant Professor, Bioinformatics
PhD, Biophysical Chemistry
Vanderbilt University, 2000
Bioinformatics
Biochemistry
Computational Chemistry
Physical Chemistry
(215) 596-7539; STC 219
z.li@usp.edu
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Research Interests
- Bioinformatics
- Computational Chemistry
- Molecular Modeling
Research Summary
My current research efforts focus on utilizing and developing 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. I’m also interested in exploring their application in molecular modeling, drug design and protein function annotation. 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 novel tools to aid in the quantitative description of the protein 3D structures currently available in databases. This will help uncover the underlying principles governing the packing of membrane and soluble protein structures. Membrane proteins account for 20-30% of human genome; yet their structures represent <1% in the PDB database. Revealing the packing principles in membrane proteins will facilitate the development of the computational tools for their structure prediction.
A second research area of interest is the construction of protein and protein-complex models designed to help elucidate biological mechanisms through non-classic protein structure modeling. 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.
The third area of interest is to apply computational and bioinformatics tools for computer-aided drug design. Computer-aided drug design tools facilitate the discovery of new ligands targeting specific proteins in cells. A collaborative project has been initiated to develop small molecule inhibitors of human complement factors.
Recent or Representative Publications
‡ Undergraduate Student
* Graduate Student
J. Gao and Z. Li, 2009, “Conserved Network Property of Homologous Structures at Twilight Zone Provides an Intrinsic Measure for Model Assessment.” Protein Eng. Des. Sel. Submitted.
U. K. Muppirala, S. Desensi, T. P. Lybrand, G. L. Hazelbauer and Z. Li, 2009, “Molecular Modeling of Flexible Arm-Mediated Interactions between a Bacterial Chemoreceptor and its Modification Enzyme” Protein Science, Submitted.
J. Gao and Z. Li, 2009, “Comparing Four Different Approaches for the Determination of Inter-Residue Interactions Provides Insight for the Structure Prediction of Helical Membrane Proteins.” Biopolymers In press.
J. Gao and Z. Li, 2009, “Conserved Network Properties of helical Membrane Protein Structures and Its Implication for Improving Membrane Protein Homology Modeling at the Twilight Zone” J. Computer-Aided Mol. Des. In press.
V. Pabuwal and Z. Li, 2009, “Comparative analysis of the packing topology of structurally important residues in helical membrane and soluble proteins” Protein Eng. Des. Sel. 22, 67-73.
J. Gao and Z. Li, 2008, “Inter-residue interactions in protein structures exhibit power-law behavior” Biopolymers 89, 1174-1178.
J. F. Galan, J. Gao, V. Pabuwal, P. J. Meek and Z. Li, 2008, “Application of network theory in understanding and predicting protein structure and function” Current Proteomics 5(3), 181-190.
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.