Bulletin of the American Physical Society
2005 APS March Meeting
Monday–Friday, March 21–25, 2005; Los Angeles, CA
Session N34: Dynamics in Condensed Phase II |
Hide Abstracts |
Sponsoring Units: DCP Chair: Everett Lipman, University of California-Santa Barbara Room: LACC 511A |
Wednesday, March 23, 2005 8:00AM - 8:36AM |
N34.00001: Multiple probes of heterogeneous protein kinetics Invited Speaker: Transition state theories break down for very fast folding proteins, where substantial populations exist along the reaction coordinate on a nanosecond to microsecond timescale. For such proteins, different spectroscopic probes yield different dynamics, i.e. there is no well-defined rate coefficient or set of rate coefficients. I will discuss fast relaxation experiments for several such proteins, as well as modeling by Langevin dynamics and molecular dynamics simulations, which now connect with experiment on the 0.1-10 microsecond time scale. [Preview Abstract] |
Wednesday, March 23, 2005 8:36AM - 8:48AM |
N34.00002: Picosecond Studies of Enzyme Mechanism in B12 Dependent Glutamase Mutase Roseanne Sension Adenosylcobalamin-dependent (coenzyme B12, AdoCbl) enzymes catalyze a variety of chemically difficult reactions that proceed by mechanisms involving organic radicals. Radicals are initially generated by homolysis of the cobalt-carbon bond to generate an adenosyl radical and a cob(II)alamin radical. In the present study time-resolved spectroscopic measurements spanning the time range from 10 fs to 10 ns are used to investigate the kinetics of homolysis and recombination for adenosylcobalamin bound in the active site of glutamate mutase. These are the first such direct measurements on an adenosylcobalamin dependent enzyme. A short-lived intermediate is formed prior to formation of the cob(II)alamin radical. This intermediate was not observed upon photolysis of adenosylcobalamin in free solution. The intrinsic rate constant for geminate recombination for adenosylcobalamin bound to glutamate mutase is only slightly smaller than the rate constant measured in free solution, suggesting the protein does not greatly perturb the stability of the cobalt-carbon bond upon binding the coenzyme. [Preview Abstract] |
Wednesday, March 23, 2005 8:48AM - 9:24AM |
N34.00003: Nonequilibrium fluctuations of a single biomolecule Invited Speaker: In recent years it has been realized that equilibrium information is subtly encoded in the fluctuations experienced by a system that is driven away from equilibrium. The key to decoding this information is a simple statistical reweighting procedure involving the external work performed in driving the system out of equilibrium. I will discuss the theoretical background of these results, as well as their applicability to the analysis of single- biomolecule pulling experiments, and to the numerical estimation of free energy differences. [Preview Abstract] |
Wednesday, March 23, 2005 9:24AM - 9:36AM |
N34.00004: Photoinduced vibrational coherence transfer in molecular aggregates D. S. Kilin, O. V. Prezhdo, Yu. V. Pereverzev, V. Nagarajan, W. W. Parson At short times faster than the time of dephasing a strong photoinduced excitation in an electron-phonon molecular structure induces evolution of the vibrational subsystem that depends on the electronic evolution. The equilibrium position and oscillation frequency of the mean nuclear coordinate depend on which electronic state keeps the major part of the population. This effect is described theoretically at a simple analytic level by applying the quantized Hamiltonian dynamics (QHD) formalism [J. Chem. Phys. {\bf 120} 11209 (2004)] to the electronic and vibrational degrees of freedom of a model molecular aggregate, as motivated by recent experimental data in a bacteriochlorophyll aggregate [J. Phys. Chem. B {\bf 103} 2297 (1999)]. The ultrafast pump-probe signal is considered. The vibronic wavepacket driven by electronic energy transfer sequentially visits different excited states. The probe signal oscillates with the nuclear configuration at the frequency that is modulated depending on the curvature of the current potential energy surface. This modulation of the frequency of the probe signal known as coherence transfer is described within simple analytic and numerical models by the QHD method that can be easily extended to many degrees of freedom. [Preview Abstract] |
Wednesday, March 23, 2005 9:36AM - 10:12AM |
N34.00005: New 2D IR techniques for studying the structures and dynamics of biomolecules Invited Speaker: Two-dimensional infrared spectroscopy is proving to be a powerful technique for studying biomolecular structures and their rapid dynamics. We report investigations into the equilibrium structures of a series of DNA oligomers using 2D IR spectroscopy, where we have found vibrational modes that are delocalized over stacked bases and coupled to adjacent strands through hydrogen bonded basepairs. We also report new advances in time-resolved pulse sequences optimized for extracting vibrational dynamics and the coupling between vibrational modes of biomolecules. [Preview Abstract] |
Wednesday, March 23, 2005 10:12AM - 10:24AM |
N34.00006: Two-dimensional infrared spectroscopy of the thermal unfolding of proteins Andrei Tokmakoff, Hoi Sung Chung, Munira Khalil, Adam Smith, Ziad Ganim Steady-state and transient conformational changes upon the thermal unfolding of ubiquitin were investigated with femtosecond infrared spectroscopy of the amide I vibrations. Equilibrium temperature-dependent 2D IR spectroscopy reveals the unfolding of the $\beta $-sheet of ubiquitin through the loss of cross peaks formed between transitions arising from vibrations of the $\beta $-sheet. Transient unfolding following a nanosecond temperature jump is monitored with vibrational echo spectroscopy, a projection of the 2D IR spectrum. While the equilibrium study follows a simple two-state unfolding, the transient experiments observe complex relaxation behavior that differs for various spectral components and spans time scales from nanoseconds to milliseconds. By modeling the amide I vibrations of ubiquitin, this observation is explained as unfolding of the less stable strands \textit{III-V} of the $\beta $-sheet prior to unfolding of the hairpin that forms part of the hydrophobic core. [Preview Abstract] |
Wednesday, March 23, 2005 10:24AM - 10:36AM |
N34.00007: Response of Biomolecules to Ultrafast Laser Pulses Roland Allen, Robert Murawski, Petra Sauer, Yusheug Dou, Traian Dumitrica, John R.H. Xie Using two complementary techniques -- semiclassical electron-radiation-ion dynamics (SERID) and time- dependent density functional theory (TDDFT) -- we are studying the response of various biologically relevant molecules to femtosecond-scale laser pulses. Our simulations provide microscopic information on mechanisms for photoisomerization [1] and other molecular transformations [2] and on spectroscopic identification of pathogens with schemes like FAST CARS [3]. The coupled dynamics of electrons and nuclei is determined by solving the time-dependent Schr\"{o}dinger equation and using Ehrenfest's theorem, with a 30 attosecond time step. Results will be shown for molecules including stilbene, benzene, and dipicloninc acid. [1] Y. Dou and R. E. Allen, Chemical Physics Letters 378, 323 (2003).2] B. Torralva and R. E. Allen, Journal of Modern Optics 49, 593 - 625 (2002).3] M. O. Scully et al., Proc. Nat. Acad. Sci. 99, 10994 (2002). [Preview Abstract] |
Wednesday, March 23, 2005 10:36AM - 10:48AM |
N34.00008: Thermal Fluctuations and Charge-Transfer Dynamics in 2-Aminopurine-Labeled DNA John Jean We present results from picosecond fluorescence experiments and hybrid TDDFT/molecular dynamics simulations that examine the roles of rapid fluctuations in base-stacking interactions on both charge transfer and electronic energy transfer dynamics in single-stranded DNA trimers containing a central 2AP. Direct excitation of the 2AP $\pi -\pi $* state shows that in these highly flexible systems, the 2AP$\to $X charge transfer process occurs on timescales ranging from $<$50 ps to several ns. The dependence of the fluorescence decays on temperature and viscosity suggest that those trimers that are optimally stacked undergo rapid CT leading to a nonequilibrium ``hole'' in the conformational distribution. Diffusion of bases back into a stacked conformation plays a critical role in determining the long-time decays. Energy transfer (A$\to $2AP) in these systems occurs on the timescale of $\sim $1 picosecond. The energy transfer efficiency shows little dependence on solution viscosity over the range of 1-15 cP, suggesting that the large amplitude structural fluctuations that are important in the CT dynamics are ``frozen out'' on the EET timescale. These results are supported by TDDFT/MD simulations of the dynamic electronic coupling between 2AP and its flanking bases. Using a modified Forster approach, which incorporates the full multipole-multipole coupling between bases, we examine the sensitivity of the EET rates to conformational fluctuations and compute the ensemble-averaged (steady-state) transfer efficiency. [Preview Abstract] |
Wednesday, March 23, 2005 10:48AM - 11:00AM |
N34.00009: Effect of electrostatic interactions on DNA melting observed using microcantilevers Sibani Biswal, Henryk Birecki, Alison Chaiken, Arun Majumdar Mechanical detection for biochemical reactions through the use of microcantilevers is an emerging technique that can be used to measure the biophysical properties of macromolecules.$^{1}$ By optically monitoring the bending of micocantilevers, we can measure the surface stress exerted on the cantilever as a DNA complex undergoes melting. With the microcantilevers, we are able to explore the stability of DNA under a variety of solution conditions. Differences in the lengths and intermolecular interactions between single and double stranded DNA are highlighted by variations in cantilever deflection. Additional parameters such as long-range electrostatic interactions between nucleic acids and ions affect the surface stress on a cantilever. Higher monovalent ion concentrations screen this interaction which results in higher stability of DNA. In our study, we evaluate the stability of short linear DNA complexes from 10-20 nucleotides at varying salt concentrations. We show that this technique is a useful probe of DNA melting dynamics, which allows us to better understand the stability of DNA complexes. Reference: \begin{enumerate} \item Wu, et al. ``Origin of Nanomechanical Cantilever Motion Generated from Biomolecular Interactions,'' Proc. National Acad. Science, Vol. 98, pp. 1560-1564 (2001). \end{enumerate} [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