Bulletin of the American Physical Society
Joint Fall 2010 Meeting of the Texas Sections of the APS, AAPT, Zone 13 of SPS and the National Society of Hispanic Physicists
Volume 55, Number 11
Thursday–Saturday, October 21–23, 2010; San Antonio, Texas
Session FI1: Opening Remarks and Invited Session I |
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Chair: M. Yacaman, University of Texas at San Antonio Room: University Center III Ballroom I, 1st floor |
Friday, October 22, 2010 8:15AM - 8:30AM |
FI1.00001: OPENING REMARKS Invited Speaker: |
Friday, October 22, 2010 8:30AM - 9:06AM |
FI1.00002: Towards a Model of Cold Denaturation of Proteins Invited Speaker: Proteins/enzymes can undergo \textit{cold denaturation} or cold deactivation. In the active or natured state, a protein exists in a unique folded/ordered state. In the deactivated (denatured) state, a protein unfolds and exists in a disordered expanded state. This protein folding/unfolding or order/disorder transition can be triggered by a temperature change. What seems paradoxical is that the active (ordered) state can be induced by heating, or equivalently, the disordered inactive state can be induced by cooling. This is equivalent to an Ising spin model passing from a disordered array of spins to an ordered array by increasing temperature! Hydrogels and their corresponding polyelectrolyte chains behave similarly, i.e., the swollen disordered state can be induced by cooling while the more ordered collapsed or globular state is induced by heating (an entropically driven phase transition). In a living cell at the physiological temperature of 37 C, activation and deactivation of proteins is triggered by local environmental changes in pH, salinity, etc. The important physics is that the denaturation temperature can be moved up or down relative to 37 C by these stimuli. Moving the transition temperature up can destabilize the active protein while moving it down leads to stabilization. An analytical polymer model will be described that exhibits cold denaturation behavior. [Preview Abstract] |
Friday, October 22, 2010 9:06AM - 9:42AM |
FI1.00003: Milestoning: A rigorous coarse graining method for simulating properties of biological molecules Invited Speaker: Milestoning is a method for calculating kinetics and thermodynamics of long time processes typically not accessible for straightforward Molecular Dynamics (MD) simulation. In the Milestoning approach, the system of interest is partitioned into cells by dividing hypersurfaces (Milestones) and transitions are computed between nearby hypersurfaces. Kinetics and thermodynamics are derived from the statistics of these local transitions. We describe an extension to the original Milestoning that we called Directional Milestoning. It avoids the use of a reaction coordinate, provides exact first hitting distribution at the interfaces, and supports sufficiently long relaxation time between the interfaces for better accuracy. I will describe the adjusted theory and algorithm, and will present results on a model system alanine dipeptide and for the folding of the helical peptide WAAAH. Interestingly the kinetic of folding of WAAAH shows significant co-operativity and is close to an all or none transition. The calculations are consistent with experimental measurements of kinetic, thermodynamic, and structure of this peptide. [Preview Abstract] |
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