Beckman Institute, University of Illinois at Urbana-Champaign
405 N. Mathews Ave, Urbana, IL 61801
Home Department: Department of Biochemistry
Office Address: Room 3017, Beckman Institute.
Email Address: firstname.lastname@example.org
Ph.D., Biophysics and Computational Biology, 2014. University of Illinois at Urbana-Champaign.
M.S., Biochemistry and Molecular Biology, 2008. Beijing Normal University, China.
B.S., Chemistry, 2004. Beijing Normal University, China.
- I am interested in studying the relationships among sequence, structure, dynamics and function of specific protein family, using computational approaches.
My major research interest is in the application of molecular dynamics simulation to study the molecular mechanism underlying protein structure and dynamics.
- Molecular mechanism of membrane transporters Living cells rely on the continuous exchange of diverse molecular species, e.g., nutrients, precursors, and reaction products, across the cellular membrane for their proper function. Membrane transporters are proteins that serve as active gatekeepers closely regulating the traffic of these species across the membrane. Structurally, the traverse between main functional states of transporters rely on a complex set of rearrangements between their structural elements, in conjunction with the coordinated movements of the transported species, rendering the dynamics of the transporters highly functional relevant. Due to the dynamic nature of membrane transporters, I employ all-atom molecular dynamics (MD) simulations to study many critical aspects of the transport mechanism. Currently we are developing and employing new enhanced sampling approaches to study the large scale conformational change during the state transitions in transporters, and to quantitatively characterize the thermodynamical properties of membrane transport.
- Cell adhesion mechanics Adherens junctions contribute significantly to animal development and tissue homeostasis, and its defects leads to various human pathologies, including cancers. Adherens junction relies on the coupling between cell adhesion and actin cytoskeleton, which is mediated by the cadherin-catenin-F-actin complex. However, many critical aspects of adherens junctions and their core constituents are not understood yet. I am now employing all-atom MD simulations, especially steered MD simulations, to study the molecular mechanism of two essential components, alpha-catenin and cadherin, to elucidate the activation mechanism of alpha-catenin, and dimerization process of cadherins.
J. Li, P.-C. Wen, M. Moradi, and E. Tajkhorshid (2015) Computational Characterization of Structural Dynamics Underlying Function in Active Membrane Transporters Current Opinion in Structural Biology, 31: 96-105.
G. Enkavi, J. Li, P.-C. Wen, S. Thangapandian, M. Moradi, T. Jiang, W. Han, and E. Tajkhorshid (2014) A Microscopic View of the Mechanisms of Active Transport Across the Cellular Membrane. Annual Reports in Computational Chemistry, 10:77-125.
J. Li, G. Enkavi, P.-C. Wen, S. A. Shaikh, and E. Tajkhorshid (2013) Transient Formation of Water-conducting States in Membrane Transporters. Proceedings of the National Academy of Sciences USA, 110: 7696-7701. PMCID: PMC3651479
S. A. Shaikh, J. Li, G. Enkavi, P.-C. Wen, Z. Huang, and E. Tajkhorshid (2013) Visualizing Functional Motions of Membrane Transporters with Molecular Dynamics Simulations. Biochemistry (Current Topic), 52: 569-587. PMCID: PMC3560430
G. Enkavi, J. Li, P. Mahinthichaichan, P.-C. Wen, Z. Huang, S. A. Shaikh, and E. Tajkhorshid (2013) Simulation Studies of the Mechanism of Membrane Transporters. Methods in Molecular Biology, 924: 361-405.
J. Li and E. Tajkhorshid (2012) A Gate-Free Pathway for Substrate Release from the Inward-Facing State of the Na+-Galactose Transporter. Biochimica et Biophysica Acta (BBA) - Biomembranes, 1818: 263-271. NIHMSID: 329267
Y.-D. Feng, J. Li, W. Zhou, Z. Jia and Q. Wei (2012) Identification of the Critical Structural Determinants of the EF-hand Domain Arrangements in Calcium Binding Proteins. Biochimica et Biophysica Acta (BBA) - Protein and Proteomics, 1824: 608-619.
Z. Huang, S. A. Shaikh, P.-C. Wen, G. Enkavi, J. Li, and E. Tajkhorshid (2011) Membrane Transporters - Molecular Machines Coupling Cellular Energy to Vectorial Transport Across the Membrane. Molecular Machines , World Scientific.
Q. Chen, W. Wu, J. Li and Q. Wei (2010) The Polarity of the Amino Acid Residue 118 of Calcineurin B is Closely Linked to Calcineurin Enzyme Activity. IUBMB Life, 62: 561-567.
J. Li and E. Tajkhorshid (2009) Ion-releasing State of A Secondary Membrane Transporter. Biophysical Journal, 97: L29-L31.
J. Li, Z. Jia, W. Zhou, and Q. Wei (2009) Calcineurin Regulatory Subunit B is a Unique Calcium Sensor that Regulates Calcineurin in Both Calcium-dependent and Calcium-independent Manner. Proteins: Structure, Function, and Bioinformatics, 77: 612-623.
G. Yin, Y. Li, J. Li, J. Li, W. Du, Q. Wei, and W. Fang (2008) Solution 1H NMR Study of the Active Site Structure for the Double Mutant H64Q/V68F Cyanide Complex from Mouse Neuroglobin. Biophysical Chemistry, 136: 115-123.