Bulletin of the American Physical Society
2009 APS March Meeting
Volume 54, Number 1
Monday–Friday, March 16–20, 2009; Pittsburgh, Pennsylvania
Session L37: Focus Session: Spectroscopic Probes of Biomolecular Structure and Function III |
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Sponsoring Units: DCP Chair: David Pratt, University of Pittsburgh Room: 409 |
Tuesday, March 17, 2009 2:30PM - 3:06PM |
L37.00001: UV Resonance Raman Discovery of Gibbs Free Energy Landscape for Protein Alpha Helix Folding Invited Speaker: We developed a powerful method to follow the evolution of secondary structure in the amide peptide bonds of peptides and proteins. UV Raman excitation into these $\sim $200 nm electronic transitions results in the enhancement of the amide vibrations of the peptide backbone. In our most recent studies we reassigned the amide III region and found a particular band (the amide III$_{3}$ band) which reports selectively on the Ramachandran $\Psi $ angle and the state of peptide bond hydrogen bonding. We demonstrate that this band is Raman scattered independently by each peptide bond with insignificant coupling between peptide bonds. We also show that isotope editing of a peptide bond (by replacing the C$_{\alpha }$- H with C$_{\alpha }$- D) allows us to determine the frequency of an individual peptide bond within a peptide or protein which gives us its $\Psi $ angle. Consideration of the Boltzmann equilibria allows us to determine the $\Psi $ angle energy landscape which connects secondary structure conformations. The $\Psi $ angle coordinate is the most important reaction coordinate required to enable the understanding of the mechanism(s) of protein folding. [Preview Abstract] |
Tuesday, March 17, 2009 3:06PM - 3:42PM |
L37.00002: IR/UV laser spectroscopy of secondary structures in isolated peptide chains: an original insight onto the non-covalent interactions that shape proteins Invited Speaker: Protein shape and flexibility is governed by non-covalent interactions that need to be accurately described by molecular structure simulations. However, the computational methods adapted for large molecules like proteins have difficulties to reproduce precisely these non-covalent interactions and cannot reach the level of structural details required to address many biological relevant issues. Special efforts are currently done to document these interactions by carrying out experiments on simple model systems\footnote{J.-P. Schermann, Spectroscopy and modeling of biomolecular building blocks. (Elsevier, 2007).} in order to help the development of reliable DFT-D calculations\footnote{P. Jurecka, J. Cerny, P. Hobza, and D. R. Salahub, J. Comput. Chem. \textbf{28} (2), 555 (2007); S. Grimme, J. Comput. Chem. \textbf{27} (15), 1787 (2006).} and polarisable force fields explorations.\footnote{N. Gresh, G. A. Cisneros, T. A. Darden, and J. P. Piquemal, Journal of Chemical Theory and Computation \textbf{3} (6), 1960 (2007).} The selectivity of the IR/UV double resonance spectroscopy of gas phase isolated peptides (less than 10 residues) laser desorbed and cooled in a molecular beam enables us to discriminate the spectral signature of the several H-bonds shaping the molecular conformation. This can be carried out for each conformation detected in the molecular beam, providing a precise IR fingerprint of the intramolecular \textbf{hydrogen bond network} of these molecules\footnote{W. Chin, F. Piuzzi, I. Dimicoli, and M. Mons, Phys. Chem. Chem. Phys. \textbf{8}, 1 (2006); W. Chin, M. Mons, J.-P. Dognon, F. Piuzzi, B. Tardivel, and I. Dimicoli, Phys. Chem. Chem. Phys. \textbf{6}, 2700 (2004); E. Gloaguen, F. Pagliarulo, V. Brenner, W. Chin, F. Piuzzi, B. Tardivel, and M. Mons, PCCP \textbf{9}, 4491 (2007).}$^{\mbox{ and references therein}}$ These IR frequencies are directly compared to the calculated frequencies of selected conformations of the isolated molecule for assignment purpose. Once the experimentally observed conformations are known, the accuracy and the predictability of several computational methods can then be assessed through their ability to provide structures for each conformation that are both geometrically and energetically in accordance with the experimental results. In addition to H-bonds, other weaker non-covalent interactions such as NH-$\pi $, $\pi -\pi $ or $\pi $-CH$_{3}$ are also at play in these systems. They can indeed impact the H-bond network in a measurable way, which makes the investigation of these computationally challenging weak forces also accessible to this powerful experimental technique. [Preview Abstract] |
Tuesday, March 17, 2009 3:42PM - 3:54PM |
L37.00003: Inhibition of urinary calculi -- a spectroscopic study Felicia Manciu, Jayesh Govani, William Durrer, Layra Reza, Luis Pinales We present multi-technique spectroscopic investigations by Raman, infrared absorption, X-ray photoelectron spectroscopy (XPS), and photoluminescence on the effects of the herb \textit{Rotula Aquatica Lour (RAL)} on the growth of synthetically prepared Mg-based calculi of similar composition to common urinary calculi. Three samples were prepared; one MgPO$_{4}$-based standard and two others, separately incorporating 1 wt.{\%}~and 2 wt.{\%} \textit{RAL} herbal extract. Raman and infrared data show a newberyite structure for the crystals without and with inhibitor. XPS revealed the unexpected presence of Zn and a significant increase in Mg in the samples with \textit{RAL} inhibitor. The presence of metallic Zn may contribute to the inhibition process by initiating rapid stone formation. XPS and Raman results also suggest another mechanism of inhibition by revealing evidence for Mg-O bonding between the plant extract and the phosphate units of urinary calculus. Similarity between our photoluminescence measurements and those of \textit{in vivo} \textit{chlorophyll a} provides additional evidence of Mg-related inhibition. [Preview Abstract] |
Tuesday, March 17, 2009 3:54PM - 4:06PM |
L37.00004: Application of a Newly Built Chirped-Pulse Fourier Transform Microwave (CP-FTMW) Spectrometer to Study Biomolecules in the Gas Phase Ryan Bird, David Pratt, Justin Neill, Brooks Pate Chirped-pulse Fourier Transform Microwave (CP-FTMW) spectroscopy is an exciting new technique that makes possible the recording of the complete microwave spectrum of a gas phase sample using a single 1 $\mu$s pulse.\footnote[2]{G.~G.~Brown et al. \textit{J.~Mol.~Spectrosc.} \textbf{238}, 200-212 (2006).} In this report, we will describe the recent introduction of a laser ablation nozzle for the study of small biomolecules using this technique. Potential applications to samples such as nucleic acid base pairs and small polypeptides will also be described. [Preview Abstract] |
Tuesday, March 17, 2009 4:06PM - 4:18PM |
L37.00005: Optical Conformational Transition Pathways of DsRed, Elucidated by Polarization-Modulated Fourier Imaging Correlation Spectroscopy Andrew Marcus, Eric Senning, Geoffrey Lott, Michael Fink This work presents a novel `phase-selective' approach to fluorescence fluctuation spectroscopy that simultaneously determines the joint probability distributions and two-dimensional spectral densities of protein conformational transitions, and nanometer center-of-mass displacements. Fourier imaging correlation spectroscopy (FICS) combines polarization- and intensity-modulated photo-excitation with phase-sensitive signal detection to monitor the collective coordinate fluctuations from a large population of fluorescent molecules (N $\sim $ 106). FICS is based on the principle that fluctuations of partially averaged molecular coordinates can be monitored through variations of an optical signal phase. Experiments are performed on DsRed, a tetrameric complex of fluorescent protein subunits, derived from a reef-building coral. Thermally induced conformational transitions of the DsRed complex lead to fluctuations in the optical dipolar coupling between adjacent chromophore sites. An analysis of polarization-resolved FICS fluctuation data, in terms of two-dimensional spectra and joint probability distributions, provides detailed information about cooperative `transition pathways' between distinct dipole-coupled DsRed conformations. [Preview Abstract] |
Tuesday, March 17, 2009 4:18PM - 4:30PM |
L37.00006: Insights on the Structural Details of Endonuclease EcoRI-DNA Complexes by Electron Spin Resonance Jessica Sarver Pulsed electron spin resonance (ESR) was used to probe the binding specificity of EcoRI, a restriction endonuclease. Using site-directed spin labeling, a nitroxide side chain was incorporated into the protein, enabling the use of ESR to study structural details of EcoRI. Distance measurements were performed on EcoRI mutants when bound to varying sequences of DNA using the Double Electron-Electron Resonance experiment. These distances demonstrated that the average structure in the arm regions of EcoRI, thought to play a major role in binding specificity, is the same when the protein binds to different sequences of DNA. Also, it was determined that the arms exhibit higher flexibility when bound to sequences other than the specific sequence due to the larger distance distributions acquired from these spin labeled complexes. Molecular dynamics (MD) simulations were performed on the spin-label-modified specific EcoRI-DNA crystal structure to model the average nitroxide orientation. The distance distributions from MD were found to be narrower than experiment, indicating the need for a more rigorous sampling of the nitroxide conformers in silico. [Preview Abstract] |
Tuesday, March 17, 2009 4:30PM - 4:42PM |
L37.00007: 1D and 2D-IR spectroscopy of blended polymer-porphyrin thin films Aaron Massari, Audrey Eigner, Patrick Konold One and two-dimensional IR spectroscopies are used to study the static and dynamic environments that form when ruthenium(II)tetraphenylporphyrin carbonyl is blended with regioregular poly(3-hexylthiophene). The 1D-IR spectra of the Ru-bound CO symmetric stretch indicate the development of several inhomogeneously broadened microenvironments as the concentration of porphyrin is increased. Transmission electron microscopy is used to characterize the blended films, which show evidence of phase-segregation. By correlating the degree of separation with the relative proportions of each component of the 1D-IR spectrum, we identify the IR spectra corresponding to the free and aggregated porphyrin-CO stretches. 2D-IR vibrational echo spectroscopy is then used to measure the ultrafast dynamics that are present in the polymer and porphyrin phases. [Preview Abstract] |
Tuesday, March 17, 2009 4:42PM - 4:54PM |
L37.00008: Microtubule-associated-protein (MAP) Tau Regulates the Number of Protofilaments in Microtubules: A Synchrotron X-ray Scattering Study Myung Chul Choi, Uri Raviv, Herbert Miller, Michelle Gaylord, Erkan Kiris, Donovan Ventimiglia, Daniel Needleman, Mahn Won Kim, Leslie Wilson, Stuart Feinstein, Cyrus Safinya Microtubules (MTs), 25 nm protein nanotubes, are a major filamentous element of the cytoskeleton involved in intracellular trafficking and cell division. MAP tau regulates tubulin assembly and MT stability. Dysfunction of tau has been correlated with numerous neurodegenerative diseases. We describe our recent findings about the effects of six naturally occurring central nervous system (CNS) tau isoforms on the assembly structure of taxol-stabilized MTs, using synchrotron small angle x-ray scattering (SAXS). Most significantly, we found that tau, at low binding density, regulates the distribution of protofilament numbers in MTs. DOE DE-FG02-06ER46314, NSF DMR-0803103, NIHI RO1-NS35010 and NS13560. [Preview Abstract] |
Tuesday, March 17, 2009 4:54PM - 5:06PM |
L37.00009: ESR distance measures show that Cu$^{2+}$ coordinates to Histidine 114 in the EcoRI-DNA complex Zhongyu Yang Metal coordination of EcoRI is intimately connected to its function of cleaving viral DNA. In order to gain insight into this process pulsed ESR distance measurement methodology was extended to the case of copper-copper and copper-nitroxide in proteins. This talk will discuss the first results on Cu$^{2+}$-Cu$^{2+}$ and Cu$^{2+}$-nitroxide distances measured in proteins by pulsed ESR. A triangulation procedure that involved the measurement of several long range distances (2-4 nm) demonstrates that copper ions bind to histidines 114 in EcoRI. The combination of ESR distance measurement and molecular dynamics simulations show distinct differences in the coordination of Cu$^{2+}$ versus the natural cofactor Mg$^{2+}$. This difference translates into the differences in roles of the metal ions - Mg$^{2+}$ catalyzes cleavage while Cu$^{2+}$ binding without cleavage of DNA. [Preview Abstract] |
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