Computational biophysics and bioinformatics play significant roles in understanding biological processes in various biology systems and provide new tools to investigate human diseases. Our research has been focused on developing computational programs and packages as well as applying them to model biological systems which are important to human health. One of the most important and challenging biological systems we are interested in is the molecular motor. We are also quite interested in many other biologically important systems such as viral capsid assembly.
Dr. Lin Li, Assistant Professor
Graduate students: Chitra Karki, Yuejiao Xian
Undergraduate students: Jazmin Paz, Alan Lopez Hernandez, Ianellie Munguia, Brenda Juarez
- Virual capsid assembly: Virual capsids are assembled by capsomer periodically. In order to reveal the mechanisms of the virus capsids assembly pathway, we simulate the process of the virus capsid assembly by using several numerical approaches. We are aiming at two goals: 1. Exploring the possible binding modes between two capsomers; 2. Revealing how the single capsomer binds to existing capsid segment during the capsid assembly.
- Molecular motors: Molecular motors (such as kinesin and dynein) transport cargos along microtubules in the cell. Dysfunction of molecular motors leads to many serious diseases. Several computational approaches are developed and applied to study the molecular motors at different levels. Our simulations demonstrate that the long-range electrostatic interaction plays several essential roles during dynein’s motion. The electrostatic forces control dynein’s binding position and orientation in each step. The electrostatic binding affinity is also a key factor to determine dynein’s velocity and run length.
- Software development: In order to understand the fundamentals and mechanisms of biological processes, proper tools are highly demanded. We develop novel computational software and packages to model and simulate biological systems. These tools are developed to study protein-protein interactions, electrostatic force calculations, large scale simulations, etc.
- Yuejiao Xian, Chitra Karki, Sebastian Silva, Lin Li*, Chuan Xiao*. The Roles of Electrostatic Interactions in Capsid Assembly Mechanisms of Giant Viruses. International journal of molecular sciences. 2019 Jan;20(8):1876.
- Lin Li, Arghya Chakravorty, and Emil Alexov. "DelPhiForce, a tool for electrostatic force calculations: Applications to macromolecular binding." Journal of computational chemistry9 (2017): 584-593.
- Lin Li, Joshua Alper, and Emil Alexov. "Cytoplasmic dynein binding, run length, and velocity are guided by long-range electrostatic interactions." Scientific reports6 (2016): 31523.
- Lin Li, Chuan Li, Zhe Zhang, Emil Alexov. On the dielectric “constant” of proteins: smooth dielectric function for macromolecular modeling and its implementation in DelPhi. Journal of chemical theory and computation, 9(4) (2013) 2126-2136.