Motor proteins are the essential agents of movement in living organisms. They convert the chemical energy present in ATP into mechanical energy and play crucial roles in the essential biological functions such as cell division, cellular transport and muscle contraction etc.. Understanding the mechanisms of the motor proteins transport will not only improve our understanding of how biological systems function but will also help us in finding new materials and fighting diseases, e.g., through designing new and more efficient drugs. Currently, our group are interested in three typical classes of motor proteins: kinesin, dynein and myosin (See figure below).

The dynamics of motor proteins structure and conformation changes typically involve reactions that occur in a large range of time and length scales. We are developing multi-scale and coarse-grained computational methods to study these processes. For example, approaches at various levels of details are integrated together to study the chemomechanical coupling mechanism of motor proteins, such as kinesin and dynein. A couple of methods that we developed slow down the protein motion in the fast degrees of freedom (e.g., vibration of chemical bonds) without changing the thermodynamics. The slow motions such as large conformational changes are at the same time accelerated. These methods are being applied in molecular dynamic simulations to study the detailed chemical reaction and energy transduction mechanism, to understand biochemical experiments. Brownian dynamic simulations using coarse-grained potential energy surfaces are being performed to study the mechanical properties of kinesin and dynein, such as their response to the variation of substrate concentrations and external force. Combining these studies, we expect to provide a detailed understanding on how these proteins function as efficient motors in living cells. The goal of this research is to investigate the chemical and mechanical processes involved in the function of a protein motor over the large range of time scales and build a bridge between the events separated by several orders of magnitude in time. As a result, we expect to obtain a picture that is detailed enough that important chemical catalytic domain and energy transduction pathway can be identified and is also general enough to provide understanding on how different motors respond to their environment, such as the external load. For this purpose, research is being carried out in the following directions: (1) master equation simulations (2) coarse-grained normal mode analysis, and (3) accelerated molecular dynamic simulations. Remarkable results for both dynein and kinesin have been achieved by our group recently, please find the details in our publications page.