Bulletin of the American Physical Society
APS March Meeting 2015
Volume 60, Number 1
Monday–Friday, March 2–6, 2015; San Antonio, Texas
Session F46: Invited Session: DBIO Award Symposium |
Hide Abstracts |
Sponsoring Units: DBIO Chair: Wolfgang Losert, University of Maryland Room: 217A |
Tuesday, March 3, 2015 8:00AM - 8:36AM |
F46.00001: Max Delbruck Prize in Biological Physics Award Lecture Invited Speaker: Stanislas Leibler . [Preview Abstract] |
Tuesday, March 3, 2015 8:36AM - 9:12AM |
F46.00002: Using evolutionary sequence variation to make inferences about protein structure and function Invited Speaker: Lucy Colwell The evolutionary trajectory of a protein through sequence space is constrained by its function. Collections of sequence homologs record the outcomes of millions of evolutionary experiments in which the protein evolves according to these constraints. The explosive growth in the number of available protein sequences raises the possibility of using the natural variation present in homologous protein sequences to infer these constraints and thus identify residues that control different protein phenotypes. Because in many cases phenotypic changes are controlled by more than one amino acid, the mutations that separate one phenotype from another may not be independent, requiring us to understand the correlation structure of the data. To address this we build a maximum entropy probability model for the protein sequence. The parameters of the inferred model are constrained by the statistics of a large sequence alignment. Pairs of sequence positions with the strongest interactions accurately predict contacts in protein tertiary structure, enabling all atom structural models to be constructed. We describe development of a theoretical inference framework that enables the relationship between the amount of available input data and the reliability of structural predictions to be better understood. [Preview Abstract] |
Tuesday, March 3, 2015 9:12AM - 9:48AM |
F46.00003: Dynamics of living matter: can we ``see'' collective motions in proteins? Invited Speaker: Doeke Hekstra Proteins are ideal model systems for quantitative study of the interplay of physical and evolutionary forces. Collective, anharmonic motions of amino acid residues within proteins are thought to be central to their function, and to explain, in large part, the complex dependence of protein function on its constituent parts. Currently, the experimental characterization of such motions poses a major stumbling block on the way to a physical understanding of protein function and evolution. We are addressing this problem in two ways. First, alternate conformations of protein residues can often be distinguished in the electron density estimated from room-temperature X-ray crystallography. The dense packing of residues in the folded protein requires that such conformational variations must propagate through networks of amino acids to preclude local steric clashes. Fraser and colleagues\footnote{Van den Bedem, H., Bhabha, G., Yang, K., Wright, P. E. {\&} Fraser, J. S., \textit{Nat. Methods} \textbf{10,} 896--902 (2013).} showed that such steric conflicts can be used to extract contact networks of residues collectively switching conformation. We ask if these networks are conserved over homologous sequences and connected to the functional reaction coordinate, both of which would demonstrate their fundamental importance. I will describe initial results for the family of PDZ domains: small ligand-binding proteins for which a network of energetically and conformationally coupled residues controlling ligand affinity has been demonstrated previously by a range of methods. Second, the analysis of collective motions in proteins, by nearly any means, is indirect: nothing is seen moving. To directly induce and ``see'' motions on a range of time scales, we developed a new approach based on (a) electric field pulses to induce motions within a protein crystal and (b) time-resolved crystallography to observe these motions. Since proteins generically have a heterogeneous, modifiable charge distribution, this method could provide a powerful, general way of probing the collective motions, and excited states, of proteins in kinetic and atomic detail. I will present initial experiments showing the method is feasible. Taken together, these experiments begin to provide a basis for the development of a physical theory of proteins consistent with their function and adaptation -- the source of their survival throughout the evolutionary process. [Preview Abstract] |
Tuesday, March 3, 2015 9:48AM - 10:24AM |
F46.00004: Heredity in Evolution \& Evolution of Heredity Invited Speaker: Olivier Rivoire The inheritance of characteristics induced by the environment has often been opposed to the theory of evolution by natural selection. However, although evolution by natural selection requires new heritable traits to be produced and transmitted, it does not prescribe, {\it per se}, the mechanisms by which this is operated. The mechanisms of inheritance are not, however, unconstrained, because they are themselves subject to natural selection. We introduce a schematic, analytically solvable mathematical model to compare the adaptive value of different schemes of inheritance. Our model allows for variations to be inherited, randomly produced, or environmentally induced, and, irrespectively, to be either transmitted or not during reproduction. The adaptation of the different schemes for processing variations is quantified for a range of fluctuating environments, following an approach that links quantitative genetics with stochastic control theory. [Preview Abstract] |
Tuesday, March 3, 2015 10:24AM - 11:00AM |
F46.00005: Associative memory through self-assembly Invited Speaker: Zorana Zeravcic Self-assembly has recently emerged as a powerful technique for synthesizing structures on the nano- and micro-scale. The basis of this development is the use of biopolymers, like DNA, to design specific interactions between multiple species of components, allowing the spontaneous assembly of complex structures. Here we address a fundamental limitation of the existing approaches to self-assembly: Namely, every target structure must have its own dedicated set of components, which are programmed to assemble only that very structure. In contrast, in biological systems, the same set of components can assemble many different complexes. Inspired by this, we extend the self-assembly framework to mixtures of shared components capable of assembling distinct structures at will. [Preview Abstract] |
Follow Us |
Engage
Become an APS Member |
My APS
Renew Membership |
Information for |
About APSThe American Physical Society (APS) is a non-profit membership organization working to advance the knowledge of physics. |
© 2024 American Physical Society
| All rights reserved | Terms of Use
| Contact Us
Headquarters
1 Physics Ellipse, College Park, MD 20740-3844
(301) 209-3200
Editorial Office
100 Motor Pkwy, Suite 110, Hauppauge, NY 11788
(631) 591-4000
Office of Public Affairs
529 14th St NW, Suite 1050, Washington, D.C. 20045-2001
(202) 662-8700