Emil Alexov, Ph.D.
Computational Biophysics and Bioinformatics, Department of Physics, Clemson University

Title: Multi-scale modeling of kinesin motion along microtubule utilizing DelPhi     Poisson-Boltzmann solver

Abstract: Electrostatics plays major role in molecular biology because practically all atoms carry partial charge while being situated at Angstroms distances. Many biological phenomena involve the binding of proteins to a large object. Because the electrostatic forces that guide binding act over large distances, truncating the size of the system to facilitate computational modeling frequently yields inaccurate results. Here we report a multiscale approach that implements a computational focusing method that permits computation of large systems without truncating the electrostatic potential and achieves the high resolution required for modeling macromolecular interactions, all while keeping the computational time reasonable. We tested our approach on the motility of various kinesin motor domains. We found that electrostatics help guide kinesins as they walk: N-kinesins towards the plus-end, and C-kinesins towards the minus-end of microtubules. Our methodology enables computation in similar, large systems including protein binding to DNA, viruses, and membranes. Lab webpage: http://compbio.clemson.edu