Bulletin of the American Physical Society
2006 APS March Meeting
Monday–Friday, March 13–17, 2006; Baltimore, MD
Session G13: Focus Session: Spectroscopy of Biomolecules from Isolated Molecules to Cell Environment IV |
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Sponsoring Units: DCP DBP Chair: Tobias Baumgart, University of Pennsylvania Room: Baltimore Convention Center 305 |
Tuesday, March 14, 2006 8:00AM - 8:36AM |
G13.00001: Laser spectroscopy probes of biomolecular conformation: Valley-to-valley searches for molecular-scale mountain passes Invited Speaker: This talk will describe recent studies of the spectroscopy and conformational isomerization dynamics of isolated gas-phase biomolecules with several flexible coordinates. These studies employ conformation-specific excitation and detection, taking advantage of the unique infrared and ultraviolet signatures of the individual conformations when cooled in a supersonic expansion. The examples given will include recent studies of the bichromophore 3-(4-hydroxyphenyl)-N-benzyl-propionamide (HNBPA) and of the `double-chain' molecule O-(acetamidoethyl)-$N$-acetyltyramine (OANAT). \newline \newline In collaboration with Jasper Clarkson, Esteban Baquero, Virgil Shubert, Tracy LeGreve and William James, Dept. of Chemistry, Purdue University. [Preview Abstract] |
Tuesday, March 14, 2006 8:36AM - 9:12AM |
G13.00002: Ultrafast dynamic exchange of hydrogen bonds Invited Speaker: Measurements of H-bond dynamics in solutions aim to obtain energetics and equilibrium dynamics of making and breaking these bonds. Two dimensional IR with fs pulses can follow both the vibrational kinetics associated with H-bonds and the dynamic effects of exchange on vibrational coherence. The principles are analogous to those from 2D-NMR chemical exchange but the 2D IR measures dynamics on the fs to ps time scales and exchange is coupled to ultrafast spectral diffusion. Therefore distinctive types of reactions can be accessed by 2D IR. Results will be presented for CN vibrators in liquid methanol and carbonyl and NH groups of peptides in water and methanol. In all examples the solute modes act as probes of the dynamics of the surrounding liquid structures. As a consequence the exchange coupling between different vibrators that results in energy transport along the chains of peptides is also seen. This research was supported by NSF-CHE, NIH-GM and by an NIH Resource Grant all to RMH. [Preview Abstract] |
Tuesday, March 14, 2006 9:12AM - 9:24AM |
G13.00003: PS Dynamics and Dephasing Times of Internal Amino Acids in Proteins Robert Austin, Aihua Xie, Britta Redlich, Lex van der Meer We present results on very narrow linewidth (2 cm$^{-1}$), high peak flux (1 $\mu$J in a 50 $\mu$ spot) pump/probe and photon echo experiments on the amide I band of proteins. Using the continuous tuning capability of the FELIX FEL we scan across the amide I band with these narrow, high intensity pulses searching for signs of energy trapping in the inner core of a protein, and seach for correlations between trapped states and long dephasing times of the trapped states. [Preview Abstract] |
Tuesday, March 14, 2006 9:24AM - 9:36AM |
G13.00004: Probing the conformation of DNA by time-resolved fluorescence Anita Jones, Robert Neely, Eleanor Bonnist, David Dryden, Dalia Daujotyte, Saulius Grazulis, Saulius Klimasauskas, Thomas Lenz, Elmar Weinhold The fluorescent adenine analogue, 2-aminopurine (AP), is a widely used probe of DNA structure and dynamics. We have investigated the time-resolved fluorescence of AP-labelled duplexes in single crystals, in solution and in frozen matrices, to elucidate the influence of interbase interaction and base dynamics on the photophysics of AP. DNA undergoes conformational change in response to interaction with agents such as enzymes and drugs. Base flipping, induced by DNA methyltransferase enzymes, is a remarkable example of conformational distortion; the target nucleotide is rotated around the phosphate backbone, out of the duplex and into the enzyme active site. We will report the first time-resolved fluorescence measurements of single crystals of AP-labelled DNA duplexes complexed with methyltransferase enzymes (M.HhaI and M.TaqI). Correlation of these results with studies on the analogous solution-phase systems shows that the fluorescence response of AP is a definitive indicator of the base flipping mechanism. Moreover, the AP decay parameters provide detailed information on the nature of the interaction between enzyme and duplex. [Preview Abstract] |
Tuesday, March 14, 2006 9:36AM - 9:48AM |
G13.00005: Conformational Structure Determination of Biomolecules in the Gas Phase using Broadband Fourier Transform Microwave Spectroscopy Brooks Pate, Gordon Brown, Brian Dian, Kevin Douglass, David Pratt, Leonardo Alvarez We have recently developed a true broadband Fourier transform microwave (FTMW) spectrometer that obtains the rotational spectrum in the 7.5 -- 18.5 GHz range with 50 kHz resolution for each individual valve pulse in a molecular beam spectrometer. The ability to observe an 11 GHz broad rotational spectrum for each valve pulse is particularly useful for experiments where the molecular beam source conditions require optimization and in cases where the biological sample decomposes over a time scale of a few minutes. The high resolution of the measurement makes it possible to unravel the conformational complexity of gas phase biomolecules. Conformational assignments of the pure rotational spectrum of p-methoxyphenethylamine (MPEA) will be presented to illustrate the capabilities of the spectrometer. The spectrometer can also be employed in laser-FTMW double-resonance experiments where the conformational assignments in the pure rotational spectrum are used to automatically assign absorption features in either vibrational or electronic spectra. [Preview Abstract] |
Tuesday, March 14, 2006 9:48AM - 10:24AM |
G13.00006: Probing secondary structures of peptide chains using gas phase laser spectroscopy Invited Speaker: A bottom-up approach involving conformer-specific IR studies of short peptide sequences enables us to map the intramolecular interactions that shape the peptide backbone, in particular those H-bonds that are responsible for stability and formation of secondary structures in proteins, like turns or helices. The combination of laser-desorption of solid samples coupled to the efficient cooling in a supersonic expansion makes it possible to isolate in the gas phase the lowest conformations of the energy landscape of small flexible biomolecules. The low temperature achieved enables spectroscopists to record UV spectra in which the contribution of each conformer populated can be distinguished and the corresponding conformation identified using IR/UV double resonance spectroscopy. Data collected are directly comparable to the best quantum chemistry calculations on these species and therefore constitute a severe test for the theoretical methods used. It will be shown how investigation of sequences with an increasing number of building blocks permits to deduce the robust structural trends of a peptide backbone: i) local conformational preference of the backbone in one-residue chains, ii) in capped dipeptides, the competition between a succession of local conformational preferences and overall folded structures, in which a different type of H-bonding scheme, involving distant H-bonding sites along the backbone, takes place: in particular beta-turns, the secondary structure responsible for chain reversals, and finally iii) evidence for the spontaneous helical folding (short 3-10 helix) of three-residue chains will be presented, illustrating the relative weakness of the H-bonding in these molecular assemblies. [Preview Abstract] |
Tuesday, March 14, 2006 10:24AM - 10:36AM |
G13.00007: Permanent Electric Dipole Moments of Four Tryptamine Conformers in the Gas Phase. A New Diagnostic of Structure and Dynamics. David Pratt, Tri V. Nguyen Rotationally resolved electronic spectroscopy in the gas phase, in the absence and presence of an applied electric field, has been used to determine the charge distribution of a cross section of the energy landscape of tryptamine (TRA). We report the magnitude and direction of the permanent electric dipole moments of the four TRA conformers GPyout, GPyup, GPhup and Antiup in their S$_{0}$ and S$_{1}$ electronic states.~Each dipole moment is unique, providing a powerful new tool for conformational analysis of biomolecules in the gas phase.~A comparison of the results for the different conformers of TRA reveals that the position and orientation of the ethylamine side chain plays a major role in determining both the permanent and induced electric dipole moments of the different species in both electronic states [Preview Abstract] |
Tuesday, March 14, 2006 10:36AM - 10:48AM |
G13.00008: Thermodynamics of Membrane Proteins: Kinetics Dipti Sharma, Atin Mandel, Jose Arguello, Germano Iannacchione An AC-Calorimetric study of membrane proteins was performed at various scan rates in order to probe the energetics and dynamics of the unfolding mechanism. Two thermophilic (Archaeoglobus Fulgidus: AfCopA and AfCopA+ATP) and one mesophilic (E. Coli: EcCopA) membrane proteins were studied at scan rates of 5 and 30 K/hr. Clear signatures of the protein unfolding were found whose character was dependent on the presence of ligands and scan rate. The slower scan rate data reveal a much broader temperature range of unfolding with evidence of a two stage unfolding process. Comparison between the two scan rates indicates that the kinetics of the first unfolding process is complex while the second primary feature represents the stability limit of that particular protein. [Preview Abstract] |
Tuesday, March 14, 2006 10:48AM - 11:00AM |
G13.00009: Conformational Isomerism in 1-Heptanal Jonathan M. Fisher, Li-Hong Xu, R.D. Suemran, Brooks Pate, Kevin Douglass The rotational spectrum of 1-heptanal has been recorded over the 10 GHz to 22 GHz region using a pulsed-molecular-beam, Fourier transform microwave spectrometer. The spectrum has been analyzed using the jb95 spectral analysis program. The spectra of thirteen conformational isomers have been identified and assigned in the rich soup of observed transitions. Transitions of these isomers have relative intensities that are well above the intensity level of the onset of $^{13}$C isotopomers, which are a factor of 100 down in intensity. In addition to the above 13 isomers, two additional spectra were identified and assigned that belong to dimers that consist of 1-heptanal and one water molecule. In order to map the observed spectra to conformational geometries, high-level \textit{ab initio} calculations have been carried out. All fifteen observed conformers have been associated with \textit{ab initio} determined structure configurations. In general, the agreement in rotational constants and dipole intensity pattern between the \textit{ab initio} results and the experimentally observed spectra is quite good. [Preview Abstract] |
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