Event
Bioengineering Seminar Series: Silvina Matysiak
Friday, December 6, 2013
9:00 a.m.-10:00 a.m.
Pepco Room, Jeong H. Kim Engineering Building
Yu Chen
yuchen@umd.edu
Multiscale Modeling of Biomolecular Systems.
Silvina Matysiak
Assistant Professor
Fischell Department of Bioengineering
University of Maryland
Protein motion spans 16 orders of magnitude (fs to s), from fast vibrations to highly cooperative transitions. In the first part of my talk I will describe our recently developed generic coarse-grained protein model 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, thus effectively introducing structural polarization into the model.
Realistic α/ß 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. I will present the role of dipole-dipole and dipole-charge interactions in shaping the secondary and tertiary structure of proteins. In particular, I will focus on the folding of ß-hairpins and single helices and in helix bundles and multiple ß-sheet strands.
Characterizing how sequence patterning affects protein stability and conformational preferences in extreme thermodynamic conditions (cold temperatures or high pressures) is of extreme importance to understand how proteins function in extreme environments. In the second part of my talk, I will present results from a heteropolymer model that exhibits a T,P dependence similar to biological proteins. At non-physiological conditions the weakening of hydrophobic interactions facilitates the population of non-native, compact conformations stabilized by polar interactions. A molecular explanation on how stable protein conformations can be switched according to the environment will be presented.
Finally in the last part of my talk, I will present my group efforts into the formulation of a multiscale simulation technique that can join, in a single simulation, two-levels of molecular resolutions, all-atom and coarse-grained thus enabling to bridge fast and slow molecular motions. Results obtained from this multiscale technique will be presented for liquid water.
