Bulletin of the American Physical Society
2005 APS March Meeting
Monday–Friday, March 21–25, 2005; Los Angeles, CA
Session L34: Dynamics in Condensed Phase I |
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Sponsoring Units: DCP Chair: Haw Yang, UC-Berkeley Room: LACC 511A |
Tuesday, March 22, 2005 2:30PM - 3:06PM |
L34.00001: Refinement and Application of Single Molecule Resonance Energy Transfer Invited Speaker: Single molecule fluorescence measurement of resonance energy transfer (RET) is revealing a new level of detailed information about biomolecular systems that exhibit conformational change. This technique has been particularly successful when applied to processes that involve large, binary intramolecular movements, for example rearrangement of enzymes and the folding of two-state proteins. Despite many advances in the application of single molecule RET, most researchers are still reluctant to convert measured energy transfer efficiencies to distances. A number of experiments inspired by Stryer and Haugland's 1967 ``spectroscopic ruler'' paper have been carried out at the single molecule level using DNA and polyproline, but the results are not nearly so clear as they were in that original work. I will discuss progress that has been made toward understanding the results of these experiments and the deviations they show from F\"orster's theory. [Preview Abstract] |
Tuesday, March 22, 2005 3:06PM - 3:18PM |
L34.00002: In vitro translation study using single molecule fluorescence resonance energy transfer Tae-Hee Lee, Scott Blanchard, Joseph Puglisi, Steven Chu Single molecule fluorescence resonance energy transfer (FRET) reveals the mechanism of tRNA selection by ribosome. In biological protein synthesis, or translation, a ribosome selects correct tRNAs according to the genetic code written on an mRNA with an unusually low error frequency (1/10,000). Single molecule study showed that a correct tRNA has slightly stronger interaction with the mRNA than an incorrect tRNA, resulting in tighter binding to the ribosome. Results further suggest that a small difference in the initial tRNA-mRNA interaction induces a significant difference in the fluctuation of the system to proceed to the next step. Only correct tRNA-mRNA interaction often leads the system to the correct pathway to the next step with a high energy barrier, i.e. GTP hydrolysis. Such induction process overcoming a high energy barrier is found to be critical in explaining the abnormally low translation error. [Preview Abstract] |
Tuesday, March 22, 2005 3:18PM - 3:30PM |
L34.00003: First-principles study of the excited-state properties of Tryptophan in water Je-Luen Li, J.B. Neaton, Paul Tangney, Ned S. Wingreen, Roberto Car, Steven G. Louie Tryptophan (Trp) is an optically-active amino acid that is highly sensitive to its local environment and responsible for much of the UV fluorescence in proteins. The spectral properties of Trp are primarily associated with the two low-lying excited states, $^1\rm L_a$ and $^1\rm L_b$, of its indole side chain. These states possess strong dipole moments and give rise to a complex excited-state relaxation dynamics in polar solvents like water. Here we apply first-principles calculations to examine the impact of the surrounding solution on the indole excited states responsible for UV fluorescence. Results of excited-state calculations of molecular indole using the GW-Bethe Salpeter equation (GW-BSE) formalism will be presented and compared with existing quantum-chemical calculations. Results of ground- and excited-state molecular dynamics simulations will also be presented. [Preview Abstract] |
Tuesday, March 22, 2005 3:30PM - 4:06PM |
L34.00004: Single-Molecule Studies of Enzymatic Structure-Function Dynamics Invited Speaker: Many biological macromolecules rely on some form of conformational flexibility to perform their designated tasks. This flexibility can be a factor in such important effects as cooperativity and allostery, or in providing the basis for entropic control. The structural origins and functional manifestations of enzymatic flexibility, however, are still poorly understood. F\"{o}rster Resonance Energy Transfer (FRET) mediated measurements of intra-molecular distance in single molecules can help to bridge this gap. In this way, the 3D structural motions of individual AKe molecules were projected on the 1D coordinate, $q$, defined by the placement of FRET probes. Here, we report the application of single-molecule time-resolved FRET to measuring the conformational fluctuation of adenylate kinase from \textit{E. coli} (AKe) under reactive conditions. The velocity-position time traces on the $\left( {\dot {q},q} \right)$ configuration space were acquired from single AKe molecules. Information about reaction dynamics was extracted photon-by-photon using the recently developed maximum-information and change-point methods. The structure-function dynamics will be discussed from the perspective of such configuration-space trajectories. [Preview Abstract] |
Tuesday, March 22, 2005 4:06PM - 4:18PM |
L34.00005: Onsets of Anharmonicity in Protein Dynamics Alexei Sokolov, Joon Ho Roh, Joseph Curtis Dynamics of protein lysozyme at various hydration levels is studied using neutron scattering spectroscopy and molecular dynamic simulations. Two onsets of anharmonicity are observed in the temperature variations of the mean-squared displacements of atoms $<$x$^{2}>$. One at $T\sim $100K appears in all samples regardless of hydration level. Based on analysis of experimental and simulations data, we ascribe the onset primarily to methyl group rotation. The second, the well-known dynamical transition at $T\sim $200--230K, is only observed at a hydration level $h$ greater than $\sim $0.2 and is ascribed to the activation of an additional relaxation process. We demonstrate that its variation with hydration correlates well with variation of catalytic activity suggesting that the relaxation process is directly related to the activation of modes required for protein function. Microscopic nature of this relaxation process is discussed. [Preview Abstract] |
Tuesday, March 22, 2005 4:18PM - 4:30PM |
L34.00006: Power-Law Dynamics in DNA Mark Berg, Daniele Andreatta, Sobhan Sen, Catherine Murphy, J. Louis Perez-Lustres, Sergey Kovalenko, Nikolas Ernsting, Robert Coleman Measurements of solvation dynamics in the interior of DNA have been extended to cover a six decade time range from 40 fs to 40 ns. The solvation dynamics are reported by the Stokes shift of a coumarin group that is covalently bound within an oligonucleotide in place of a native base pair. Results from three techniques: time-correlated single photon counting, fluorescence up-conversion and transient absorption; are combined to cover the entire time range. Over this range, the dynamics follow a simple power law with a small exponent of 0.15. If the coumarin group is placed near the end of the oligonucleotide, a process with a 10 ps time constant occurs, in addition to the power-law dynamics. The power-law dynamics change if the counterion changes, and they change in a manner that correlates with the hydrodynamic radius of the counterion. Results on single-stranded DNA and on a DNA:protein complex are also reported. These experiments provide a variety of unexplained results that provide a challenge to the theory of DNA dynamics on fast time scales. [Preview Abstract] |
Tuesday, March 22, 2005 4:30PM - 5:06PM |
L34.00007: Invited Speaker: |
Tuesday, March 22, 2005 5:06PM - 5:18PM |
L34.00008: Polymer translocation through a nanopore studied by Langevin dynamics Lei Guo, Erik Luijten Polymer translocation through a nanopore has gained considerable attention in recent years, due to its potential application in DNA-sequencing. The design of a corresponding device requires a full understanding of the translocation dynamics. The scaling of polymer translocation time $\tau$ with polymer chain length $N$ is an important measure of the underlying dynamics. A recent experiment\footnote{A. J. Storm \emph{et al.}, arXiv q-bio/0404041 (2004).} has uncovered a scaling behavior $\tau \propto N^{1.26}$ that differs from the linear law observed in other experiments. To explain this newly-observed scaling behavior, we have employed Langevin dynamics simulations. Using a bead--spring model for the polymer chain and a membrane composed of one layer of hard-sphere particles, we have studied a wide range of chain lengths $20 \leq N \leq640$, for different friction coefficients $\xi$. A crossover scaling behavior was found for $\tau$, which is controlled by both $N$ and $\xi$. We explain the measured scaling behavior from the chain conformations and instantaneous translocation velocities. [Preview Abstract] |
Tuesday, March 22, 2005 5:18PM - 5:30PM |
L34.00009: Rotational motions in the dynamics of proteins and biological macromolecules Florence J. Lin By changing its shape while conserving angular momentum, a polyatomic molecule can return to its initial shape with a different orientation (as a ``falling cat'' or a diver can do). Examples where this phenomenon has been observed include the dynamics of protein molecules and the dynamics of a rotary molecular motor. Computational biophysicists have observed the overall rotation of a protein molecule at zero total angular momentum due to the molecule's flexibility. A counter-rotary motion has been observed in the rotary ${\rm F}_o$ motor of ATP synthase. Using geometric mechanics, the net angle of overall rotation is described in terms of coordinates. The net angle of overall rotation is the sum of a dynamic phase and a geometric phase; the latter is also described in terms of a gauge potential. This is an extension of a result for smaller polyatomic systems, where the geometric phase contribution is also described explicitly in terms of moments of inertia and, alternatively, molecular rotational constants. Potential applications of this result include computational molecular dynamics studies. [Preview Abstract] |
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