Bulletin of the American Physical Society
APS March Meeting 2011
Volume 56, Number 1
Monday–Friday, March 21–25, 2011; Dallas, Texas
Session D6: Physics of Proteins I: Unifying Principles and Concepts |
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Sponsoring Units: DBP DPOLY DCMP Chair: Robert Austin, Princeton University Room: Ballroom C2 |
Monday, March 21, 2011 2:30PM - 3:06PM |
D6.00001: Protein Dynamics Invited Speaker: Proteins combine properties of solids, liquids, and glasses. Schr\"{o}dinger anticipated the main features of biomolecules long ago by stating that they had to be solid-like, but able to assume many different conformations. Indeed proteins can assume a gigantic number of conformational substates with the same primary sequence but different conformations. The different substates are described as craters in a very-high-dimensional energy landscape. The energy landscape is organized in a hierarchy of tiers, craters within craters within craters. Protein motions are pictured as transition between substates - jumps from crater to crater. Initially we assumed that these jumps were controlled by internal barriers between substates, but experiments have shown that nature selected a different approach. Proteins are surrounded by one to two layers of water and are embedded in a bulk solvent. Structural motions of the protein are controlled by the alpha fluctuations in the solvent surrounding the protein. Some internal motions most likely involving side chains are controlled electrostatically by beta fluctuations in the hydration shell. The dynamics of proteins is consequently dominated by the environment (H. Frauenfelder et al. PNAS 106, 5129 (2009). One can speculate that this organization permits exchange of information among biomolecules. The energy landscape is not just organized into two tiers, alpha and beta, but cryogenic experiments have revealed more tiers and protein more properties similar to that of glasses. While proteins function at ambient temperatures, cryogenic studies are necessary to understand the physics relevant for biology. [Preview Abstract] |
Monday, March 21, 2011 3:06PM - 3:42PM |
D6.00002: Engineering electron tunneling in natural and artificial proteins Invited Speaker: Experimental investigation of oxidoreductases has revealed their naturally selected electron tunneling engineering that underlies oxidative and reductive catalysis. This engineering is relatively simple, which allows us to design artificial oxidoreductases from scratch, without the unnecessary complexity found in natural proteins. We have constructed a simple, four $\alpha$-helix protein bundle protein framework that can be manipulated to support a range of cofactor and substrate binding, and redox and light driven actions. For example, by controlling water access and mobility, this framework can support hemoglobin-like oxygen transport without anything resembling a globin fold. The same framework provides a clear path to artificial proteins designed to catalyze single or multi electron tunneling coupled to chemistry. [Preview Abstract] |
Monday, March 21, 2011 3:42PM - 4:18PM |
D6.00003: The Physical Mechanism of Proton Transfer in Proteins Invited Speaker: Proteins are able to perform an enormous variety of functions, while using only a limited number of underlying processes. One of these is proton transfer. The physical mechanism of proton transfer has been extensively studied, using a variety of experimental and computational methods. However, it remains unclear what determines the direction and rate of proton transfer reactions in proteins. We have developed and applied a new approach to this long-standing problem by integrating structural dissection, energy landscape, first principle calculation (quantum theory), and molecular dynamics simulation. Our proof of concept study reveals key structural elements that control the direction and rate of proton transfer in proteins. The results are of predictive power and can be generally applied to different proteins. [Preview Abstract] |
Monday, March 21, 2011 4:18PM - 4:54PM |
D6.00004: Frustration and the Functional and Folding Landscape of Proteins Invited Speaker: The energy landscape for folding is funnel-like and largely correlates topology directly with energetics. Thus many of the ``excited states'' important for function are ensembles of structures in which entropy balances partial unfolding energy costs. I will discuss such spectra for cytochrome c. Another way of achieving low free energy excitations is via frustration which entails deviations from the simple funnel landscapes responsible for setting the overall protein shape. I will discuss interesting examples of the consequences of frustration for binding, allostery and for membrane protein systems. [Preview Abstract] |
Monday, March 21, 2011 4:54PM - 5:30PM |
D6.00005: Dynamics and mechanism of water-protein interactions Invited Speaker: Water-protein interactions are essential to biology and such interactions are not static but dynamic in nature. With femtosecond spectroscopy and site-directed mutagenesis, we have systematically investigated protein surface hydration dynamics and the actual time scales of their fluctuations. These new results are significant to understanding the physics of protein dynamics at the most fundamental level. [Preview Abstract] |
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