Molecular dynamics simulation on the interaction between domain I of gK and extracellular domain IV of UL20
Konstantin G. Kousoulas, Ph.D.
Louisiana State University, School of Veterinary Medicine, Department of Pathobiological Science
Ebrahim Khosravi, Ph.D.
Southern University and A&M College, Department of Computer Science
Pilot Project (October 1, 2011 – April 30, 2012)
In this project, we will utilize computational tools to simulate a biomedical research question: how does the domain I of herpes simplex virus type 1(HSV-1) glycoprotein K (gK) and the extracellular domain IV of UL20 interact. We aim to obtain a stable structure of the domain I and first segment membrane part of HSV-1 gK and the extracellular domain IV of UL20 using computational approaches, which are currently available as stand-alone software and our groupâ€™s specific analysis tools. We will optimize and derive the best combination of currently available algorithms that can arrive at an optimum stable structure faster. We will then analyze the final stable structure that would be helpful in explain the experimental data and even predict the possible properties that is hard to perform with current experiment equipments. We would expect that an efficient and accurate potential database established after the implementation of this proposed project. The research is expected to facilitate a better understanding of the interaction of gK and UL20p and thereafter drug design to combat herpes virus infections.
This research has two specific aims: specific aim 1 will focus on model setup and HPC simulation of the domain I of herpes simplex virus type 1 gK and the extracellular domain IV of UL20 through computational methods. Specific aim 2 will focus on analyzing the domain I gK homologs, delineate conserved and divergent structural features, and the gK/membraneinteraction properties. A graduate student will be involved in this research.