Bulletin of the American Physical Society
2007 APS March Meeting
Volume 52, Number 1
Monday–Friday, March 5–9, 2007; Denver, Colorado
Session P35: Focus Session: Protein Motin Vibrations to Conformational Changes |
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Sponsoring Units: DBP DCP Chair: Aihua Xie, Oklahoma State University Room: Colorado Convention Center 405 |
Wednesday, March 7, 2007 11:15AM - 11:27AM |
P35.00001: Dose and exposure requirements for the protein x-ray serial crystallography. Dmitri Starodub We have proposed spraying proteins (aligned by a laser) across a synchrotron beam to solve proteins which cannot be crystallized.$^{1}$ A single-file stream of ice-jacketed proteins is considered. We compute diffraction patterns for the GroEL at the incident x-ray flux predicted for a new coherent scattering beamline at the Advanced Photon Source. Using iterative phasing of the data, we determine the relationship between the count rate at a reconstructed pixel (or 3D voxel) of a given size in the real-space charge-density map and number N of proteins in the 10-$\mu $m 2 kV x-ray beam at any instant. A modulation transfer function estimates resolution for various exposure times. With the incident flux of 10$^{6}$ photons/s\textbf{/}nm$^{2}$ and N=10, over 5,000 counts/s are distributed over the entire diffraction pattern, which is sufficient for a nm resolution with 200 s exposure. We compare the results of this numerical lensless imaging experiment with a simple theoretical treatment of image formation in the dark and bright field phase contrast. Supported by ARO, NSF and co-workers.$^{1}$ $^{1}$J. Chem Phys. 123, 244304 . [Preview Abstract] |
Wednesday, March 7, 2007 11:27AM - 11:39AM |
P35.00002: Impact of solvent pH on buried charge formation and protein quake of photoactive yellow protein Aihua Xie, Sandip Kaledhonkar, Lorand Kelemen, Wouter D. Hoff, Anupama Thubagere Embedding a charge group inside a protein in a low dielectric environment is energetically unfavorable. Therefore, most charged groups are solvent exposed. We have developed a hypothesis that a new buried charge transiently formed in a non-polar environment serves as an electrostatic epicenter that drives protein quake (protein conformational changes). Here we report an experimental study on the effects of solvent pH on the protonation states of buried ionizable groups, and their correlation with protein quakes. Time-resolved Fourier transfer infrared (FTIR) difference absorbance spectroscopy is the major experimental technique for simultaneous detection of the proton transfer event (to generate a new buried charge) and the protein quake event. The results are expected to provide insight into the impact of solvent pH on protein structural dynamics in general. [Preview Abstract] |
Wednesday, March 7, 2007 11:39AM - 11:51AM |
P35.00003: ABSTRACT HAS BEEN MOVED TO D26.00011 |
Wednesday, March 7, 2007 11:51AM - 12:03PM |
P35.00004: Conformational dependence of a protein kinase phosphate transfer reaction Montiago LaBute, Graeme Henkelman, Chang-Shung Tung, Paul Fenimore, Ben McMahon Atomic motions and energetics for a phosphate transfer reaction catalyzed by the cAMP-dependent protein kinase have been calculated using plane-wave density functional theory, starting from structures of proteins crystallized in both the reactant conformation (RC) and the transition-state conformation (TC). In TC, we calculate that the reactants and products are nearly isoenergetic with a 20-kJ/mol barrier, whereas phosphate transfer is unfavorable by 120 kJ/mol in the RC, with an even higher barrier. Our results demonstrate that the phosphate transfer reaction occurs rapidly and reversibly in a particular conformation of the protein, and that the reaction can be gated by changes of a few tenths of an angstrom in the catalytic site [1]. [1] G.H. Henkelman, M.X. LaBute, C.-S. Tung, P.W. Fenimore, B.H. McMahon, Proc. Natl. Acad. Sci. USA vol. 102, no. 43:15347-15351 (2005). [Preview Abstract] |
Wednesday, March 7, 2007 12:03PM - 12:15PM |
P35.00005: Interaction of Receptors and GTPase-Activating Proteins in a G Protein Signaling Module Marc Turcotte, Wei Tang, Elliott M. Ross We have developed a model of the interactions of proteins involved in G protein signaling using steady-state data from reconstituted vesicles. The model includes receptor, G protein (G), GTPase activating protein (GAP), GTP and GDP. Implementation is done using coupled ordinary differential equations. We performed a global fit to the model parameters against enzymologic and nucleotide-binding data using simulated annealing constrained by thermodynamics. Validation was done using Monte Carlo data. Fit parameters uncertainties were obtained via multiple repeats of stochastic searches. We studied fit parameter correlations near a solution by local thermal sampling of the cost manifold. The best fit parameters agree with values derived from dynamic data not used in our fit. We used our model to study signaling in familiar regimes and to predict new, testable behaviors in others. Signal output is a complex function of the inputs: receptor and GAP at physiologic and experimental concentrations of GTP and GDP. We studied the shape of the activation surface. Its complexity derives from stoichiometric relationships among protein concentrations. Our model predicts signaling pathways and dynamical response in G protein modules. [Preview Abstract] |
Wednesday, March 7, 2007 12:15PM - 12:27PM |
P35.00006: Fast motion of the surface alcohol molecules deduced from sum-frequency vibrational spectroscopy Jaeho Sung, Doseok Kim Sum-frequency generation (SFG) vibrational spectroscopy was used to investigate the surface of the homolog series of alcohols from methanol to octanol. It was found that SFG signal strengths from the terminal methyl group of short-chain alcohols cannot be explained by assuming the surface molecules were fixed in time. Introduction of the rotational motion with time scale comparable to the dephasing time of the vibrational mode of the terminal methyl group ($\sim $0.7 picosecond) was able to explain the reduction of the SFG signal by motional averaging effect. This timescale of motion increased with the increase in the molecule size and bulk viscosity. Our result also suggests that surface alcohol molecules move faster as compared to the same molecules in the bulk liquid. [Preview Abstract] |
Wednesday, March 7, 2007 12:27PM - 12:39PM |
P35.00007: Effect of molecular vibrations on charge transfer in polypeptide chains Nikolai Sergueev, Alexander Demkov We present first principles framework suitable for analyzing and understanding the effect of molecular vibrations on charge transfer in polypeptide chains. Our approach is based on density functional theory and Keldysh nonequilibrium Green's function formalism. This method allows us to treat both electrons and molecular vibrations (phonons) on equal footing in a self-consistent manner. The salient feature of our technique is that we consider the vibration of the whole polypeptide bridge. We present a numerical results for a charge transfer through alanine polypeptide chains of the various length and show that the electron tunneling is greatly affected when the interaction between electrons and molecular vibrations is taken into account. We also present a vibrational spectroscopy analysis and identify those vibrational modes of the alanine polypeptides involved into the inelastic charge transfer. [Preview Abstract] |
Wednesday, March 7, 2007 12:39PM - 12:51PM |
P35.00008: No Long-Lived Coherent Oscillations in Proteins at Room Temperature Robert Austin, Michael White A recent PRL (PRL 95, 253601 (2005)) suggested that proteins could have very narrow holes (Hz wide) burnt into their electronic spectra at 300K, and suggested that ``snail-paced'' light group velocity light could result. We will show that the authors mistook conformational diffusion phase shifts for narrow lines and show that there are no narrow long-lived holes in a protein spectra at 300 K nor is there any snail-paced light. [Preview Abstract] |
Wednesday, March 7, 2007 12:51PM - 1:03PM |
P35.00009: Slow light with bacteriorhodopsin solutions Chandra Yelleswarapu, Francisco Aranda, Reji Philip, Rao Devulapalli Slow light in gases and solids has been studied in recent years. Various applications are possible depending on the modulation frequency and the amount of delay that can be induced in the traveling wave. Recently we demonstrated ultra slow light in the biological photo-membrane bacteriorhodopsin (bR) polymer film at room temperature [Phy. Rev. Lett., \textbf{95}, 2536011, 2005]. By exploiting the photoisomerization property of bR for coherent population oscillation, the group velocity is controlled from about 0.1 mm/sec to the speed of light. But as bR is embedded in a polymer matrix, the isomerization rates are slow and hence limited to low modulation frequencies. On the other hand bacteriorhodopsin solution can be used for obtaining slow light at higher modulation frequencies. Studies in solution also offer the advantage of changing the optical density at ease resulting in longer pulse delays. Detailed results on slow light where the delay is varied with modulation frequency, optical density and all-optical control with a blue laser beam will be presented. [Preview Abstract] |
Wednesday, March 7, 2007 1:03PM - 1:15PM |
P35.00010: Physical basis for membrane-charge selectivity of cationic antimicrobial peptides Bae-Yeun Ha, Sattar Taheri-Araghi Antimicrobial peptides are known to selectively disrupt (highly-charged) microbial membranes by asymmetrical incorporation into the outer layers. We present a physical basis for membrane-charge selectivity of cationic antimicrobial peptides. In particular, we provide a clear picture of how peptide charge, Q, influences the asymmetrical insertion -- one salient feature is the existence of an optimal peptide charge, at which selective insertion is optimized. Our results suggest that large Q is required for antimicrobial selectivity, consistent with experiments. [Preview Abstract] |
Wednesday, March 7, 2007 1:15PM - 1:51PM |
P35.00011: Investigating Potential Surfaces with QM/MM Methods Invited Speaker: Geometry optimization of large QM/MM systems is not trivial, especially when transition states or higher order saddle points are desired. The optimization can be carried out with a macro/micro scheme, which alternates (internal coordinate) geometry steps in the QM region with full (cartesian) minimizations of the MM region. This significantly reduces the number of QM calculations, and avoids bottlenecks associated with coordinate transformation and Hessian manipulation. This standard macro/micro scheme, however, suffers from numerical instability and compromised convergence behavior. This affects particularly the optimization of transition states, which is therefore not often successful. To address these problems we present extensions to the macro/micro scheme, which have been implemented in the ONIOM framework for hybrid methods. In the standard scheme, the QM and MM regions are coupled only through first order terms. We now include second order coupling using analytical MM contributions, employing linear scaling methods. We show how this improves convergence and allows for the optimization and characterization of saddle points in very large systems. We demonstrate our methods using various examples, such as the hydrogen peroxide reduction by Selenoprotein Glutathione Peroxidase, proton transfer in H-Y zeolite, and thermal isomerization of retinal in Bacteriorhodopsin. [Preview Abstract] |
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