Insights into Protein Structure Prediction and Design, using Biomolecular Simulations
Department of Chemical Engineering, Texas A&M University
Computational methods, including molecular dynamics (MD) simulations and free energy calculations, are increasingly becoming powerful tools in the fields of protein structure prediction and de novo protein design. Despite the continuous advancement of experimental methods, computational tools have proved to be of utmost importance to fill crucial “gaps”, obtain information that is not accessible from experiments, and lead to the discovery of novel biomaterials and therapeutics. The first part of the seminar will focus on the use of MD simulations and free energy calculations to investigate the formation of self-assembled peptide structures, aiming at providing impetus for the fabrication of novel biomaterials with promising biomedical or technological applications. The second part of the seminar will demonstrate the power of computational methods in the derivation of complex biomolecular structures, and more specifically the first, highly-accurate, atomic-detail structures of an HIV-1 gp120 V3 loop in complex with chemokine receptors CXCR4 and CCR5.