AMMCS-2013 Semi-Plenary Talk

Role of dipolar interactions in protein folding

Silvina Matysiak, University of Maryland

Abstract: The role of dipole interactions in protein folding A generic coarse-grained (CG) protein model will be presented to characterize the driving forces behind protein folding. The change in orientation of the atoms in the coarse-grained unit is captured by the addition of Drude oscillators inside each polar coarse-grained bead. The addition of dummy sites inside the polar beads introduces structural polarization into the coarse-grained model.

Realistic alpha/beta content is achieved de novo without any biases in the force-field toward a particular secondary structure. The dipoles created by the Drude oscillators interact with each other and drive the protein models to fold into unique structures depending on the amino acid patterning and presence of capping residues. In this talk, we will show the role of dipole-dipole and dipole-charge interactions in shaping the secondary and tertiary structure of proteins. In particular, we will focus on the folding of beta-hairpins and single helices and in helix bundles and multiple beta-sheet strands. In the folded ensemble, dipoles along a helix are found aligned parallel and stabilized by the presence of charged capping residues. On the other hand, beta-sheets exhibit antiparallel neighboring dipoles.

Dr. Silvina Matysiak is an assistant professor in the Fischell Department of Bioengineering at the University of Maryland College Park. She received her B.S. in Chemical Engineering from the Instituto Tecnológico de Buenos Aires in 2001 and her PhD in Chemistry from Rice University in 2007. Before joining Maryland, she was a postdoctoral fellow at the University of Texas at Austin.

Matysiak's primary area of interest is the characterization of protein dynamics and function at the molecular level. Her work includes using computer simulations to study the mechanism of protein folding and misfolding associated with neurodegenerative diseases, development of multiscale simulation approaches to bridge different time- and length-scales and how solvent organization affects cooperative transitions in biomolecular systems.