Bulletin of the American Physical Society
2007 APS March Meeting
Volume 52, Number 1
Monday–Friday, March 5–9, 2007; Denver, Colorado
Session B26: Focus Session: Protein Folding: Theory and Simulations II |
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Sponsoring Units: DCP DBP Chair: Jose Onuchic, University of California, San Diego Room: Colorado Convention Center 205 |
Monday, March 5, 2007 11:15AM - 11:51AM |
B26.00001: Invited Speaker: |
Monday, March 5, 2007 11:51AM - 12:27PM |
B26.00002: Protein folding and dynamics from simulations of coarse protein models. Invited Speaker: The dynamics and folding transitions of proteins are studied by computer simulations of coarse-grained models. The simulations are related to experimental studies of the unfolding of proteins under mechanical force, and the effects of mutations on the folding rates using phi-value analysis. Coarse protein models have also been useful in studies of slow conformational transitions. Applications to the helix-to-sheet transition of an arc repressor mutant, and the open-to-closed transition of the calmodulin C-terminal domain indicate that local unfolding events can contribute significantly to the slow dynamics of these proteins. [Preview Abstract] |
Monday, March 5, 2007 12:27PM - 1:03PM |
B26.00003: Invited Speaker: |
Monday, March 5, 2007 1:03PM - 1:15PM |
B26.00004: The folding of an ``average'' beta trefoil protein. Shachi Gosavi, Pat Jennings, Jose Onuchic The beta-trefoil fold is characterized by twelve beta strands folded into three similar beta-beta-beta-loop-beta (trefoil) units. The overall fold has pseudo-threefold symmetry and consists of a six stranded-barrel, capped by a triangular hairpin triplet. The loops connecting the beta-strands vary in length and structure. It is these loops that give the fold its varied binding capability and the binding sites lie in different parts of the fold. The beta-trefoil proteins have little sequence similarity (sometimes less than 17{\%}) and bind a range of molecules, including other proteins, DNA, membranes and carbohydrates. Protein folding experiments have been performed on four of the beta trefoils, namely, interleukin-1 (IL1B), acidic and basic fibroblast growth factors (FGF-1 and FGF-2) and hisactophilin (HIS). These experiments indicate that the proteins fold by different routes. Folding simulations of the proteins identify the possible folding routes and also show that the shapes of the barriers are different for the different proteins. In this work, we design a model protein which contains only the core fold elements of the beta-trefoil fold. We compare the folding of this ``average'' protein to the folding of His, FGF and IL1B and make some connections with function. [Preview Abstract] |
Monday, March 5, 2007 1:15PM - 1:27PM |
B26.00005: Life in a Crowd: Macromolecular Crowding and Confinement Effects on Protein Interactions in Living Systems Margaret Cheung Biological polymers carry out their functions in living systems where the environment is very concentrated or crowded by macromolecules. Physically, the composition of a cell is more than ``a sack of water''; its consistency is closer to Jell-O. Experiments suggests that, because of this macromolecular crowding effect that confines polymeric dynamics, the kinetics and thermodynamics of protein folding and the association rate constants of protein-protein interactions in a cell (in vivo) are very different from that ina diluted test tube (in vitro). In order to quantitatively understand macromolecular crowding and confinement effects on protein dynamics, we used coarse-grained models that physically captured interactions between crowders and a protein. The folding rates of a model protein nonmonotonically increased with the volume fraction of the crowders. At lower volume fractions, depletion-induced attractions from crowders could be mapped according to the spherical confinement model. A result of spherical confinement was the destabilization of denatured states by disallowing extended configurations that were longer than the pore size. However, at higher volume fractions, conformational fluctuations of a protein were susceptible to the shape of the confining condition. Thus, an approximation of the spherical confinement to mimic crowding effects was no longer effective. [Preview Abstract] |
Monday, March 5, 2007 1:27PM - 1:39PM |
B26.00006: 2D IR Spectroscopy of Ubiquitin Unfolding Dynamics Ziad Ganim, Hoi Sung Chung, Andrei Tokmakoff The unfolding dynamics of ubiquitin have been studied using a combination of amide I 2D IR spectroscopy and spectral calculations drawing on structures from molecular dynamics simulations. Equilibrium temperature-dependent 2D IR spectra and transient 2D IR spectra following a nanosecond temperature jump are used to follow the unfolding of ubiquitin's $\beta$-sheet. The equilibrium 2D IR spectra show two features that arise from delocalized $\beta$-sheet vibrations of which differ by whether C=O oscillators vibrate parallel or perpendicular to its strands. Spectral changes in the transient difference spectrum start with an abrupt blue shift of the perpendicular diagonal region, which corresponds to the disruption of hydrogen bonds between water and solvent-exposed peptide groups. This change is followed over $\mu$s to ms time scales by a blue shift of the perpendicular region and disappearance of a cross peak, which reflect the gradual unfolding of the $\beta$-sheet of the protein. The experiments are compared with 2D IR spectra calculated from molecular dynamics trajectories of ubiquitin unfolding using a structure-based model for protein amide I spectroscopy. [Preview Abstract] |
Monday, March 5, 2007 1:39PM - 1:51PM |
B26.00007: Generalization of distance to higher dimensional objects, and applications to biopolymer folding Steven Plotkin The measurement of distance between two objects is generalized to the case where the objects are no longer points but are one-dimensional (strings) or many-dimensional (differential manifolds). Applications to biopolymer folding will be discussed. [Preview Abstract] |
Monday, March 5, 2007 1:51PM - 2:03PM |
B26.00008: Collapse transition for self-avoiding random walks with hydrophobic interaction on a 2 dimensional lattice Mathieu Gaudreault, Jorge Vinals We study the collapse transition of a protein model with an explicit coarse-grained model of solvent hydrophobicity using Monte Carlo simulation. The protein is modelled as self- avoiding random walk with nearest neighbour interaction on a two dimensional lattice by using the pivot algorithm. Without the solvent, universal quantities of the chain around the transition temperature are well known. Hydrophobicity is modelled through a lattice of solvent molecules in which each molecule can have q states, depending of an orientation variable. Only one state is energetically favoured, when two neighbouring solvent molecules are both in the same state of orientation. The monomers are placed in interstitial position of the solvent lattice, and are only allowed to occupy sites surrounded by solvent cells of the same orientation. The potential of mean force between two interstitial solute molecules is calculated, showing that the strength of attraction increases by increasing the free energy of H-bond formation while its range decreases. We also show that the temperature of the collapse transition is shifted in the presence of solvent, while the universal quantities of the protein transition are conserved. [Preview Abstract] |
Monday, March 5, 2007 2:03PM - 2:15PM |
B26.00009: ABSTRACT WITHDRAWN |
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