Bulletin of the American Physical Society
2009 APS March Meeting
Volume 54, Number 1
Monday–Friday, March 16–20, 2009; Pittsburgh, Pennsylvania
Session J37: Focus Session: Spectroscopic Probes of Biomolecular Structure and Function II |
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Sponsoring Units: DCP Chair: Angela Gronenborn, University of Pittsburgh Room: 409 |
Tuesday, March 17, 2009 11:15AM - 11:51AM |
J37.00001: Structures of Amyloid Fibrils and Protein Folding Intermediates: New Insights from Solid State NMR Invited Speaker: I will present recent results from two projects: (1) We are using a combination of solid state NMR techniques and electron microscopy techniques to develop full molecular models for amyloid fibrils formed by the beta-amyloid peptide of Alzheimer's disease and by other peptides and proteins. Amyloid fibrils are often polymorphic, so that the detailed molecular structure depends on growth conditions or other factors. I will describe two structural models for beta-amyloid fibrils with two distinct morphologies. I will also describe efforts to determine which fibril structure develops in the brains of Alzheimer's disease patients, and solid state NMR methods that contribute to our amyloid studies; (2) Structural properties of unfolded or partially folded states of proteins are not well understood. In principle, solid state NMR measurements on freeze-trapped samples can reveal site-specific, quantitative aspects of protein structures in unfolded states. I will describe experiments on thermodynamically unfolded states (i.e., denatured states) and on transient states that are trapped by freezing on the microsecond time scale. Both types of experiments reveal structural properties that are unanticipated and could not be detected by more conventional protein folding measurements. [Preview Abstract] |
Tuesday, March 17, 2009 11:51AM - 12:27PM |
J37.00002: Two-Dimensional Infrared Probes of Peptide Conformations: the 3$_{10}$-Helical Secondary Structure Invited Speaker: The 3$_{10}$-helix is a secondary structure that has important biological functions and has been proposed as a picosecond intermediate in the folding of $\alpha $-helices. Two-dimensional infrared (2D IR) spectroscopy with its high structural sensitivity and time resolution is a powerful approach for investigating the structure and dynamics of peptides and proteins. In this talk, we will describe how we are using 2D IR and isotope labeling to study 3$_{10}$-helical oligopeptides that are rich in C$^{\alpha }$-methylated amino acids. These peptides are attractive models for developing and refining experimental and theoretical approaches to peptide conformational analysis. By manipulating networks of vibrational modes using judicious choices of laser polarizations and pulse ordering, we demonstrate that 2D IR can provide diagnostic cross-peak patterns for distinguishing different helical structures and probe the onset of 3$_{10}$-helical secondary structure. Using a series of peptides with $^{13}$C=$^{18}$O and $^{15}$N isotope labels, we observe cross-peak signature that reveals vibrational couplings between amide-I and amide-II modes across a 3$_{10}$-helical hydrogen bond. The results provide a direct evidence for local helical structure formation. Experimental spectra are compared to simulations based on nonlinear response theory, vibrational eigenstates and couplings derived from DFT-optimized structures, and trajectories from molecular dynamics simulations. [Preview Abstract] |
Tuesday, March 17, 2009 12:27PM - 1:03PM |
J37.00003: Earle K. Plyler Prize Talk: Using High Resolution Electronic Spectroscopy to Probe Reactive Chemical Intermediates Invited Speaker: Gas phase chemical reactions, such as occur in atmospheric chemistry, combustion, plasma processing, etc. are of great importance to our economy and society. These reactions are typically very complex involving up to 1000's of elementary steps with a corresponding number of reactive chemical intermediates. Spectrospic diagnostics, based upon well analyzed and well understood spectra of the intermediates, are crucial for monitoring such reactions and unraveling their mechanisms. These spectral analyses often benefit from the guidance provided by quantum chemical calculations and conversely the molecular parameters, experimentally determined from the spectra, serve as ``gold standards'' for benchmarking such calculations. Such standards are especially valuable for reactive intermediates whose electronic or geometric structure is particularly complex because of electron-spin interactions, Jahn-Teller effects or other vibronic interactions, hindered internal motions, large molecular size and weight, etc. The organic alkoxy, RO$\cdot$, and peroxy, RO$_2\cdot$, (R=alkyl group) free radicals are excellent examples of such species. The talk will focus on our recent characterization of these radicals via their ``high-resolution,'' mostly rotationally resolved, electronic spectra utilizing the techniques of laser induced fluorescence, stimulated emission pumping, and cavity ringdown spectroscopy. Selected spectra, their analysis, and the molecular information resulting therefrom will be discussed. [Preview Abstract] |
Tuesday, March 17, 2009 1:03PM - 1:15PM |
J37.00004: Solvent induced fluctuations and the collective librational dynamics of myoglobin, hemoglobin, and lysozyme studied with infrared spectroscopy Kristina Woods We will discuss the use of (THz and Mid-) infrared spectroscopy to investigate the dynamics of several globular proteins under varying hydration and temperature conditions. Analysis of the experimental spectra has revealed that the amount of solvent in the hydration shell has a strong influence on the amplitude and the rate of relaxation associated with the low frequency protein conformational fluctuations and also the arrangement of hydrogen bonds in the protein secondary structure. At at a hydration level $>$ 0.2 we identify modes in the secondary structure of all of the proteins investigated that suggest extra mobility in the protein structure that is not present at low hydration. We will discuss how greater insight into the origin and nature of these detected solvent induced fluctuations may be important for developing a better understanding about energy localization and its relationship with biological function. [Preview Abstract] |
Tuesday, March 17, 2009 1:15PM - 1:27PM |
J37.00005: Label-Free Determination of Protein Binding in Aqueous Solution using Overlayer Enhanced Attenuated Total Reflectance Fourier Transform Infrared Spectroscopy (OE-ATR-FTIR) Travis Ruthenburg, Tolulope Aweda, Simon Park, Claude Meares, Donald Land Protein binding/affinity studies are often performed using Surface Plasmon Resonance techniques that don't produce much spectral information. Measurement of protein binding affinity using FTIR is traditionally performed using high protein concentration or deuterated solvent. By immobilizing a protein near the surface of a gold-coated germanium internal reflection element interactions can be measured between an immobilized protein and free proteins or small molecules in aqueous solution. By monitoring the on and off rates of these interactions, the dissociation constant for the system can be determined. The dissociation constant for the molecule Yttrium-DOTA binding to the antibody 2D12.5 system was determined to be 100nM. Results will also be presented from our measurements of Bovine Serum Albumin (BSA) binding to anti-BSA. [Preview Abstract] |
Tuesday, March 17, 2009 1:27PM - 1:39PM |
J37.00006: Solute-protein interactions: Variations in correlation times and spin label mobility. Mandy Blackburn, Luis Galiano, Angelo Veloro, Gail Fanucci Using EPR, NMR and fluorescence spectroscopy, the effects of several viscogen monomers (sucrose, glycerol, and ethylene glycol) and macromolecular crowding polymers (Ficoll400 and various size polyethylene glycols (PEG)) on the mobility of spin labels at aqueous exposed sites in the flap of HIV-1 protease, the correlation time of this protein, as well as conformation of the hair pin flaps were investigated. Results show that, as expected, protein correlation time is more strongly altered by the small viscogens compared to the macromolecular crowders. On the other hand, EPR line shapes reveal that the chemistry (ie hydrophobicity) and not the size of the solutes correlates to changes seen in the spectra. The conformations of the $\beta $-hair pin flaps in HIV-1 protease were unchanged by any of solutes as determined by pulsed EPR distance measurements. Thus, indicating that specific solute interactions with the surface of the protein are responsible for the changes observed in the EPR spin label spectra. [Preview Abstract] |
Tuesday, March 17, 2009 1:39PM - 1:51PM |
J37.00007: On The Electronic Properties of Photoacids In The Gas Phase. Electric Dipole Moments of \textit{CIS}- and \textit{TRANS}-2-Naphthol Adam Fleisher, Philip Morgan, David Pratt The permanent electric dipole moments ($\mu )$ of two conformers of 2-naphthol (2HN) in their ground and electronically excited states have been experimentally determined by Stark-effect measurements in a molecular beam. Upon UV excitation, little change in the magnitudes of $\mu $ is observed, but the orientation of the dipole moment within each conformer shifts significantly, indicating photon-induced rearrangements in electronic distributions. \textit{cis}-2HN has $\Delta \mu $ = +0.17 D and $\Delta $\textit{$\theta $}$_{a}$ = -28\r{ } and \textit{trans}-2HN has $\Delta \mu $ = +0.05 D and $\Delta $\textit{$\theta $}$_{a}$ = +28\r{ } (\textit{trans}-2HN). The $\Delta $\textit{$\theta $}$_{a}$ values for the two conformers differ in sign. The small changes in the magnitudes of the dipole moments suggest that the isolated molecules do not undergo large charge separations upon excitation. Our study, void of solvent perturbations, is of importance to the larger community currently describing aromatic biomolecule and ``super'' photoacid behavior \textit{via} theoretical modeling and condensed phase solvatochromism. [Preview Abstract] |
Tuesday, March 17, 2009 1:51PM - 2:03PM |
J37.00008: Threading of Binuclear Ruthenium Complex Through DNA Bases Thayaparan Paramanathan, Fredrik Westerlund, Micah McCauley, Per Lincoln, Ioulia Rouzina, Mark Williams Due to steric constraints the dumb-bell shaped binuclear ruthenium complex can only intercalate DNA by threading, which requires local melting of the DNA to occur. By mechanically manipulating a single DNA molecule held with optical tweezers, we lower the barrier to threading compared to bulk experiments. Stretching single DNA molecules with different drug concentrations and holding a constant force allows the binding to reach equilibrium. We can obtain the equilibrium fractional ligand binding and length of DNA at saturation. Fitting these results yields quantitative measurements of the binding thermodynamics and kinetics. In addition, we obtain the minimum binding site size, which may be determined by either electrostatic repulsion or steric constraints. [Preview Abstract] |
Tuesday, March 17, 2009 2:03PM - 2:15PM |
J37.00009: Raman Spectral Signatures as Conformational Probes of Biomolecules Ilana Bar, Amir Golan, Nitzan Mayorkas, Salman Rosenwaks A first application of ionization-loss stimulated Raman spectroscopy (ILSRS) monitoring the spectral features of four conformers of a gas phase neurotransmitter (2-phenylethylamine) is reported. The Raman spectra of the conformers show bands that uniquely identify the conformational structure of the molecule and are well matched by density functional theory calculations. The measurement of spectral signatures by ILSRS in an extended spectral range, with a relatively convenient laser source, is extremely important, allowing enhanced accessibility to intra- and inter-molecular forces, which are significant in biological structure and activity. [Preview Abstract] |
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