Bulletin of the American Physical Society
2005 APS March Meeting
Monday–Friday, March 21–25, 2005; Los Angeles, CA
Session V21: Localized Dynamical States |
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Sponsoring Units: DBP Chair: Bernard Gerstman, Florida International University Room: LACC 409A |
Thursday, March 24, 2005 11:15AM - 11:51AM |
V21.00001: Protein structure determination via EPR of endogenous and introduced electron spins Invited Speaker: Electron Paramagnetic Resonance (EPR) probes the environment of unpaired electron spins. Short range structural information (within 10 {\AA}ngstr\"{o}ms) can be obtained by determining the identity, number and location of nuclei coupled to the electron spin(s). EPR-based experiments designed to achieve these measurements include continuous wave (CW) EPR, 1-dimensional pulsed techniques (Electron Spin Echo Envelope Modulation or ESEEM), 2-dimensional pulsed techniques (Hyperfine Sublevel Correlation or HYSCORE), double resonance spectroscopy (Electron Nuclear Double Resonance or ENDOR), and High Frequency EPR (HFEPR). These experiments are typically performed on ``endogenous'' electrons spins localized on metal ions, substrate radicals or amino acid radicals in or near enzyme active sites. Long range structural information (10--50 {\AA}ngstr\"{o}ms) can be obtained by measuring the dipolar interaction between two or more electron spins using CW and pulsed (Double Electron-Electron Resonance or DEER) techniques. The electron spins for these measurements are typically ``introduced'' into the system under study using site directed spin labeling (SDSL). This technique expands the applicability of EPR to macromolecules that do not contain an endogenous electron spin, and allows long range structure determination in large molecular weight samples without the requirement of single crystals. Examples of all of these EPR-based techniques will be presented as applied to a variety of protein systems, including Prostaglandin H Synthase, PI 3-Kinase, Prion protein and models, and ribonucleotide reductase. [Preview Abstract] |
Thursday, March 24, 2005 11:51AM - 12:03PM |
V21.00002: Coherent Pumping of Vibrational States within Proteins Robert Austin, Aihua Xie, Lex van der Meer, Britta Redlich, Marlan Scully, Per-Anker Lingard, Hans Frauenfelder We show that there exist narrow spectral states within the amide I band of proteins which have dephasing times on the order of 10 picoseconds. We also show that these states can be pumped coherently by the Rabi mechanism if the pump pulse has a linewidth less than the anharmonic shift between the first and second excited states of the cabonyl anharmonic oscillator. The spectral region of these narrow states lies on the short wavelength region of the amide I band, suggesting that these long coherence states originate from buried amino acids which are not in contact with the hydration shell of the protein. [Preview Abstract] |
Thursday, March 24, 2005 12:03PM - 12:15PM |
V21.00003: Developing a Vibrational Spectral Maker for Probing the Hydrogen Bonding Status of Buried Asp and Glu Residues Aihua Xie, Beining Nie, Jerrod Stutzman Hydrogen bonding is a fundamental element in protein structure and function. Breaking a single hydrogen bond may impair the stability of a protein. We report an infrared vibrational spectral marker for probing the hydrogen bond number for buried, protonated Asp or Glu residues in proteins. Ab initio computational studies were performed on hydrogen bonding interactions of a COOH group with a variety of side chain model compounds of polar and charged amino acids in vacuum using density function theory. In addition, we show an approximate linear correlation between the C=O stretching frequency and the hydrogen-bond strength. We propose that a two-dimensional infrared spectroscopy, C=O stretching vs. O-H stretching, may be employed to identify the specific type of hydrogen bonding interaction. This vibrational spectral marker for hydrogen bonding interaction is expected to enhance the power of time-resolved Fourier transform infrared spectroscopy for structural characterization of functionally important intermediates of proteins. [Preview Abstract] |
Thursday, March 24, 2005 12:15PM - 12:27PM |
V21.00004: Interprotein electron transfer through aqueous pathways Jianping Lin, Ilya Balabin, David Beratan Water contributes to tunneling mediation pathways as well as to reorganization energy in biological electron transfer. We examine the distance dependence of the inter-protein electron transfer through water at protein-protein interfaces by combining molecular dynamics (MD) and extended-H\"{u}ckel analysis of cytochrome b5 self-exchange. Rather than describe the ET rate decay with a single exponential parameter, we employ explicit electronic structure calculations and find three distinct tunneling mediation regimes: a conventional protein-mediated regime at protein-protein contact, a ``structured water'' regime with soft distance dependence for small protein-protein gaps, and a bulk water regime with a rapidly decaying coupling at larger distance. Water density calculations also specify these three regimes. We calculate the bimolecular electron rate of cytochrome b$_{5}$ self-exchange system using Brownian dynamics with the multi-exponential decay electron transfer model built from these three regimes and the results are comparable with the experimental results within a factor of 5. [Preview Abstract] |
Thursday, March 24, 2005 12:27PM - 1:03PM |
V21.00005: Resonance effects indicate radical pair mechanism for avian magnetic compass Invited Speaker: Migratory birds possess a physiological magnetic compass that helps them to find north during their migratory flights, but the mechanism underlying this ability is not understood. In vitro experiments show that two types of mechanisms are in principle capable of detecting earth-strength magnetic fields in biological systems: the use of biological magnetic materials such as magnetite crystals, or magnetically sensitive chemical reactions. We have recently demonstrated that oscillating magnetic fields can provide a viable diagnostic test to identify the existence of a radical-pair mechanism as they will not affect the properties of magnetite-based sensors, but disrupt a radical-pair based mechanism through resonance effects. European robins, a species of migratory birds, were disoriented in a magnetic orientation test when a very weak (100 nT) oscillating field of 1.3 or 7 MHz was added to the geomagnetic field. Moreover, the effect of the oscillating field depended on the alignment of oscillating field with the geomagnetic field and showed an intensity dependence consistent with theoretical expectations from the radical pair mechanism, thereby providing evidence for the existence of a radical-pair mechanism in birds. We will discuss future avenues of research towards identifying not only the mechanism, but also the chemical nature of the receptors underlying magnetoreception, and in particular the photoreceptor chryptochrome, an emerging candidate for the long sought after magnetoreceptor. [Preview Abstract] |
Thursday, March 24, 2005 1:03PM - 1:15PM |
V21.00006: Inelastic Tunneling Spectroscopy Through a Macromolecule K.\O. Rasmussen, Jian-Xin Zhu, A.V. Balatsky, A.R. Bishop We propose inelastic electron tunneling spectroscopy scanning tunneling microscopy (IETS-STM) as a means of exciting and observing localized modes in a macromolecule. As a demonstration, inelastic tunneling features of the density of states are calculated for a nonlinear elastic Morse chain. We typically investigate the role of vibration modes from the anharmonic potential in the tunneling spectrum. The general formalism we have developed for the IETS is applicable to other nonlinear extended objects, such as DNA on a substrate. [Preview Abstract] |
Thursday, March 24, 2005 1:15PM - 1:27PM |
V21.00007: Single molecule FRET to resolve conformational fluctuations in proteins Keith Weninger, Brandon Choi, David Murray, Steve Story Proteins fold into complex shapes that are intimately linked to their function. High-resolution techniques are capable of determining static images of these structures with atomic detail, but biological function and regulation is achieved through dynamic changes in protein conformation. Single molecule fluorescence techniques have a unique capability to detect transient molecular conformations. The power of the single molecule approach arises because it avoids the averaging over molecules and over time that are inherent in ensemble measurements. We report application of single molecule fluorescence resonance energy transfer (smFRET) to tSNARE to directly observe a conformational transition that is postulated to have an auto-regulatory function. We present a series of measurements using mutants of the proteins as well as homologues of different species in order to gain a molecular level understanding of these transitions. The techniques demonstrated here are directly applicable to investigations of conformational dynamics in other protein based macro-molecular machines. [Preview Abstract] |
Thursday, March 24, 2005 1:27PM - 1:39PM |
V21.00008: Inhibiting CDK2: A Study with First Principles and Classical Methods Lucy Heady, Marivi Fernandez-Serra, Lucio Colombi Ciacchi, Emilio Artacho, Mike Payne Cyclin-dependent kinases (CDKs) are a group of proteins responsible for controlling entry to different phases of the cell cycle, and are therefore promising targets for the treatment of cancerous tumours. Using DFT we have calculated the binding energy of a number of different inhibitors to the ATP binding pocket of CDK2. Data for these calculations were taken from X- ray crystal structures. The binding energies calculated predict the correct rank order of the inhibitors considered and correlate well with the available experimental values of binding affinity with the exception of the inhibitor SU9516. This suggests that the crystal structure is not showing all of the direct interactions. Dynamical effects in the binding pocket have been investigated in a series of classical molecular dynamics simulations. During the simulation of CDK2 bound to SU9516, a major structural change occurs bringing the inhibitor into close contact with a polar lysine residue. This missing interaction accounts for the discrepancy in the binding energy. It also explains the observed greater potency of SU9516 for CDK2 over CDK4, as in CDK4 this polar lysine is not present. [Preview Abstract] |
Thursday, March 24, 2005 1:39PM - 1:51PM |
V21.00009: Calculation of the optical response of biomolecules using TDDFT Argyrios Tsolakidis, Efthimios Kaxiras We present calculations of the optical response of various biomolecules, using time-dependent density functional theory (TDDFT). These calculations are performed in real time within the adiabatic approximation with a basis of local orbitals. First we study the DNA bases and base-pairs both in their normal and tautomeric forms in the gas phase. Our results for the individual bases are in good agreement with experiment and computationally more demanding calculations of chemical accuracy. The optical response of base pairs indicates that the differences between normal and tautomeric forms in certain cases are significant enough to provide a means of identification. The second part of our work deals with the effect of hydration on the absorption spectrum of the aromatic amino acids Tryptophan, Phenylalanine and Tyrosine. We discuss the changes that occur with the inclusion of several water molecules and compare with experiment and other theoretical calculations. [Preview Abstract] |
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