Bulletin of the American Physical Society
2009 APS March Meeting
Volume 54, Number 1
Monday–Friday, March 16–20, 2009; Pittsburgh, Pennsylvania
Session H37: Focus Session: Spectroscopic Probes of Biomolecular Structure and Function I |
Hide Abstracts |
Sponsoring Units: DCP Chair: Sunil Saxena, University of Pittsburgh Room: 409 |
Tuesday, March 17, 2009 8:00AM - 8:36AM |
H37.00001: Structure and dynamics in B12 enzyme catalysis revealed by electron paramagnetic resonance spectroscopy Invited Speaker: Challenges to the understanding of how protein structure and dynamics contribute to catalysis in enzymes, and the use of time-resolved electron paramagnetic resonance (EPR) spectroscopic techniques to address the challenges, are examined in the context of the coenzyme B12-dependent enzyme, ethanolamine ammonia-lyase (EAL), from \textit{Salmonella typhimurium}. EAL conducts the homolytic cleavage of the coenzyme cobalt-carbon bond, intraprotein radical migration (5-6 {\AA}), and hydrogen atom transfers, which enable the core radical-mediated rearrangement reaction. Thermodynamic and activation parameters are measured in two experimental systems, which were developed to isolate sub-sequences from the multi-step catalytic cycle, as follows: ($1)$ A dimethylsulfoxide (DMSO)/water cryosolvent system is used to prepare the kinetically-arrested enzyme/coenzyme/substrate ternary complex in fluid solution at 230 K.[1] Temperature-step initiated cobalt-carbon bond cleavage and radical pair separation to form the Co(II)-substrate radical pair are monitored by using time-resolved, full-spectrum EPR spectroscopy (234$\le T\le $250 K).[1] ($2)$ The Co(II)-substrate radical pair is cryotrapped in frozen aqueous solution at $T<$150 K, and then promoted to react by a temperature step. The reaction of the substrate radical along the native pathway to form the diamagnetic bound products is monitored by using time-resolved, full-spectrum EPR spectroscopy (187$\le T\le $217 K).[2] High temporal resolution is achieved, because the reactions are dramatically slowed at the low temperatures, relative to the initiation and spectrum acquistion times. The results are combined with high resolution structures of the reactant centers, obtained by pulsed-EPR spectroscopies,[3] and the protein, obtained by structural proteomics[4] and EPR and electron spin echo envelope modulation (ESEEM) in combination with site directed mutagenesis,[5] to approach a molecular level description of protein contributions to catalysis in EAL. \\[4pt] [1] Wang, M. {\&} Warncke, K. \textit{J. Am. Chem. Soc.} \textbf{2008}, $130$, 4846. \\[0pt] [2] Chen, Z. and Warncke, K. \textit{Biophys. J. }\textbf{2008}, $95$ (December) \\[0pt] [3] Canfield, J. M. and Warncke, K. \textit{J. Phys. Chem. B }\textbf{2002}, $106$, 8831. \\[0pt] [4] Sun, L. and Warncke, K. \textit{Proteins} \textbf{2006}, $64$, 308. \\[0pt] [5] Sun, L., Groover, O., Canfield, J. M., and Warncke, K. \textit{Biochemistry} \textbf{2008}, $47$, 5523. [Preview Abstract] |
Tuesday, March 17, 2009 8:36AM - 9:12AM |
H37.00002: Time-resolved X-ray scattering of proteins in solution: a new method for probing biomolecular structure and function Invited Speaker: X-ray scattering patterns from proteins in solution exhibit a radial intensity distribution that is sensitive to protein size, shape, and structure. When acquired in a time-resolved fashion, these `fingerprints' unveil conformational changes that occur as a protein executes its designed function. We recently developed the infrastructure required to record X-ray scattering snapshots with $\sim $100-ps time resolution on the BioCARS beamline at the Advanced Photon Source in Argonne, IL. This methodology was used to probe structural changes in hemoglobin after photodissociating a bound ligand. Remarkably, the scattering fingerprint exhibited changes at the earliest times resolved, evidently corresponding to small amplitude tertiary structure changes. On longer time scales, the allosteric quaternary structure transition was resolved. These scattering fingerprints provide robust constraints for structural models of intermediates and their dynamics, which are crucial to develop a detailed understanding of biophysical processes. [Preview Abstract] |
Tuesday, March 17, 2009 9:12AM - 9:48AM |
H37.00003: Ultrafast Photodynamics in Diverse DNA Structures from A-tracts to Z-DNA Invited Speaker: The vulnerability of the genome to UV photodamage has sustained interest in excited electronic states in DNA for over 50 years. Progress in understanding the nature and dynamics of electronic excitations in DNA has accelerated rapidly thanks in part to ultrafast spectroscopy. Most excitations in single DNA bases decay nonradiatively in hundreds of femtoseconds. Surprisingly, much longer-lived excited states are observed in femtosecond pump-probe experiments on single- and double-stranded DNAs. Localized charge transfer states are prominent in runs of adenine bases (A tracts). DNA is polymorphic and can adopt a range of structures beyond the iconic B-form double helix. The effect of helix conformation on excited-state dynamics has been studied in a double-stranded oligonucleotide that can be switched between B- and Z-forms. Experiments on G quadruplex structures and on $i$-motif DNA reveal that these forms have significantly slower relaxation than B-DNA. By altering $\pi -\pi $ stacking and hydrogen bonding, structure profoundly affects the complex photoprocesses observed in DNA. [Preview Abstract] |
Tuesday, March 17, 2009 9:48AM - 10:00AM |
H37.00004: Charge Transfer States of Aqueous B-DNA at Energies Above the Bright $^1\pi\pi^\ast$ Exciton States Adrian Lange, John Herbert Charge transfer states have been proposed to explain experimentally observed long-lived excited state dynamics in aqueous DNA oligomers\footnote{Crespo-Hern\'andez,~C.~E.;\ \ Cohen,~B.;Kohler,~B. \textit{Nature} \textbf{2005}, \textsl{436}, 1141.}. Due to the large number of atoms, tractably describing such excited states in DNA systems with \textit{ab initio} theory is limited to TD-DFT. However, standard TD-DFT exchange-correlation functionals significantly underestimate CT excitation energies owing to incorrect asymptotic behavior. To circumvent this error, we instead apply recently developed and optimized long-range corrected TD-DFT functionals to better assess the low lying CT and exciton states of DNA oligomers. We show that long-range corrected TD-DFT yields results comparable to correlated wave function models, placing CT states of aqueous B-DNA at energies above the optically bright $^1\pi\pi^\ast$ exciton states, contrary to TD-DFT results which find CT states below the exciton states. [Preview Abstract] |
Tuesday, March 17, 2009 10:00AM - 10:12AM |
H37.00005: Low frequency dynamics of Cytochrome c Karunakaran Venugopal, Paul Champion Femtosecond coherence spectroscopy is used to investigate the low frequency dynamics of cytochrome c (cyt c). There is good agreement between the higher frequency oscillatory components of the coherence spectra and the low frequency Raman spectra. A mode near $\sim $40 cm$^{-1}$ is a universal feature of heme systems and has been assigned to doming motions that are strongly enhanced upon ligand photolysis [1]. A dominant heme ruffling mode near $\sim $60 cm$^{-1}$ [2] appears in ferric cyt c for excitation in the region 425-432nm, to the red of the Soret maximum (408nm). This, along with a phase jump of $\sim \pi $ in this region, suggests the ruffling mode is coupled to a charge transfer (CT) band underlying the Soret band [3] and that it is a potentially important electron transfer reaction coordinate. [1] F. Gruia, M. Kubo, X. Ye, P. M. Champion, \textit{Biophys. J}., \textbf{2008}, $94$, 2252. [2] M. Kubo, F. Gruia, A. Benabbas, A. Barabanschikov, W. R. Montfort, E. M. Maes, P. M. Champion, \textit{J. Am. Chem. Soc.,} \textbf{2008}, $130$, 9800. [3] K. T. Schomacker, P. M. Champion, \textit{J. Chem. Phys.,} \textbf{1986}, $84$, 5314. [Preview Abstract] |
Tuesday, March 17, 2009 10:12AM - 10:24AM |
H37.00006: Ultrafast Dynamics of Leu-Enkephalin in Water and Membranes Soohwan Sul, Yuan Feng, Uyen Le, Nien-Hui Ge Ultrafast two-dimensional infrared (2D IR) spectroscopy has been applied to investigate the peptide-membrane interaction and conformational distribution of Leu-enkephalin (Lenk) in bilayer membranes. We compare the results from linear and 2D IR experiments on p-cresol in water, Lenk in water, and Lenk in membranes, focusing on the ring stretching mode of the Tyr side chain. Frequency-frequency correlation functions obtained from a series of waiting-time-dependent 2D IR spectra reveal a fast decaying component with a $\sim $ 1 ps time constant that is common for all three systems. This spectral diffusion component is attributed to hydrogen-bond making-breaking dynamics of the Tyr side chain. Unlike p-cresol in water, both Lenk systems exhibit substantial spectral inhomogeneity that does not decay within the 4 ps window. The observed hydrogen-bond dynamics suggests that the Tyr side chain of Lenk in membranes is located at the water-abundant region at the water-membrane interface. The experimental results are compared with those from MD simulations and DFT calculations. [Preview Abstract] |
Tuesday, March 17, 2009 10:24AM - 10:36AM |
H37.00007: Flap Conformations in HIV-1 Protease are Altered by Mutations Gail Fanucci, Mandy Blackburn, Angelo Veloro, Luis Galiano, Ding Fangu, Carlos Simmerling HIV-1 protease (PR) is an enzyme that is a major drug target in the treatment of AIDS. Although the structure and function of HIV-1 PR have been studied for over 20 years, questions remain regarding the conformations and dynamics of the \textit{$\beta $}-hairpin turns (flaps) that cover the active site cavity. Distance measurements with pulsed EPR spectroscopy of spin labeled constructs of HIV-1 PR have been used to characterize the flap conformations in the apo and inhibitor bound states. From the most probably distances and the breadth of the distance distribution profiles from analysis of the EPR data, insights regarding the flap conformations and flexibility are gained. The EPR results clearly show how drug pressure selected mutations alter the average conformation of the flaps and the degree of opening of the flaps. Molecular dynamics simulations successfully regenerate the experimentally determined distance distribution profiles, and more importantly, provide structural models for full interpretation of the EPR results. By combining experiment and theory to understand the role that altered flap flexibility/conformations play in the mechanism of drug resistance, key insights are gained toward the rational development of new inhibitors of this important enzyme. [Preview Abstract] |
Tuesday, March 17, 2009 10:36AM - 10:48AM |
H37.00008: An Investigation of Ionic Binding to Fatty Acid Monolayers by Broad-bandwidth Sum Frequency Generation Vibrational Spectroscopy Cheng Tang, Heather Allen Model study of ionic binding of fatty acid monolayer is a good proxy towards understanding the fundamental chemistry in biological processes. In this study, we used broad-bandwidth sum frequency generation (BBSFG) vibrational spectroscopy to investigate the ionic binding event that leads to deprotonation of the fatty acid head groups. Palmitic acid (C15C00H) exists as monolayer on aqueous surfaces, and on aqueous alkali and alkaline solutions surfaces. Surface vibrational stretching modes of palmitic acid from 1400 cm$^{-1}$ to 3700 cm$^{-1}$ were observed (COO$^{-}$, C=O, C-H, and O-H). Palmitic acid is mostly protonated at the aqueous surface at neutral pH ($\sim $6). However, various degrees of deprotonation are initiated by introduction of different cations in the salt solutions albeit at neutral pH. [Preview Abstract] |
Tuesday, March 17, 2009 10:48AM - 11:00AM |
H37.00009: Using Rotationally Resolved Electronic Spectroscopy to Probe Chiral Molecules in the Gas Phase Justin Young, Leonardo Alvarez-Valtierra, David Pratt It is well established that biological processes involving chiral molecules can show a preference of one enantiomer relative to the other. Reported here are high resolution spectroscopy experiments that allow one to distinguish one diastereomer from another, and thereby establish if the structural requirments for diastereoism are present. [Preview Abstract] |
Follow Us |
Engage
Become an APS Member |
My APS
Renew Membership |
Information for |
About APSThe American Physical Society (APS) is a non-profit membership organization working to advance the knowledge of physics. |
© 2024 American Physical Society
| All rights reserved | Terms of Use
| Contact Us
Headquarters
1 Physics Ellipse, College Park, MD 20740-3844
(301) 209-3200
Editorial Office
100 Motor Pkwy, Suite 110, Hauppauge, NY 11788
(631) 591-4000
Office of Public Affairs
529 14th St NW, Suite 1050, Washington, D.C. 20045-2001
(202) 662-8700