Bulletin of the American Physical Society
2006 APS March Meeting
Monday–Friday, March 13–17, 2006; Baltimore, MD
Session A13: Focus Session: Spectroscopy of Biomolecules from Isolated Molecules to Cell Environment I |
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Sponsoring Units: DCP DBP Chair: David Pratt, University of Pittsburgh Room: Baltimore Convention Center 305 |
Monday, March 13, 2006 8:00AM - 8:36AM |
A13.00001: Watching proteins function with picosecond X-ray crystallography and molecular dynamics simulations. Invited Speaker: Time-resolved electron density maps of myoglobin, a ligand-binding heme protein, have been stitched together into movies that unveil with $<$ 2-{\AA} spatial resolution and 150-ps time-resolution the correlated protein motions that accompany and/or mediate ligand migration within the hydrophobic interior of a protein. A joint analysis of all-atom molecular dynamics (MD) calculations and picosecond time-resolved X-ray structures provides single-molecule insights into mechanisms of protein function. Ensemble-averaged MD simulations of the L29F mutant of myoglobin following ligand dissociation reproduce the direction, amplitude, and timescales of crystallographically-determined structural changes. This close agreement with experiments at comparable resolution in space and time validates the individual MD trajectories, which identify and structurally characterize a conformational switch that directs dissociated ligands to one of two nearby protein cavities. This unique combination of simulation and experiment unveils functional protein motions and illustrates at an atomic level relationships among protein structure, dynamics, and function. \newline \newline In collaboration with Friedrich Schotte and Gerhard Hummer, NIH. [Preview Abstract] |
Monday, March 13, 2006 8:36AM - 8:48AM |
A13.00002: Raman spectra of normal and cancerous mouse mammary gland tissue using near infrared excitation energy Vaman Naik, G.K. Serhatkulu, H. Dai, N. Shukla, R. Weber, J.S. Thakur, D.C. Freeman, A.K. Pandya, G.W. Auner, R. Naik, R.F. Miller, A. Cao, M.D. Klein, R. Rabah Raman spectra of normal mammary gland tissues, malignant mammary gland tumors, and lymph nodes have been recorded using fresh tissue from mice. Tumors were induced in mice by subcutaneously injecting 4T1 BALB/c mammary tumor (a highly malignant) cell line. The Raman spectra were collected using the same tissues that were examined by histopathology for determining the cancerous/normal state of the tissue. Differences in various peak intensities, peak shifts and peak ratios were analyzed to determine the Raman spectral features that differentiate mammary gland tumors from non-tumorous tissue. Tissues that were confirmed by pathology as cancerous (tumors) show several distinctive features in the Raman spectra compared to the spectra of the normal tissues. For example, the cancerous tissues show Raman peaks at 621, 642, 1004, 1032, 1175 and 1208 cm$^{-1 }$that are assignable to amino acids containing aromatic side-chains such as phenylalanine, tryptophan and tyrosine. Further, the cancerous tissues show a greatly reduced level of phospholipids compared to the normal tissues. The Raman spectral regions that are sensitive to pathologic alteration in the tissue will be discussed. [Preview Abstract] |
Monday, March 13, 2006 8:48AM - 9:00AM |
A13.00003: Probing the $\beta $-hairpin local structure by FTIR, 2D IR and ab initio calculations Jianping Wang, Jianxin Chen, Robin M. Hochstrasser Small peptides form vibrational exciton systems that can be examined by means of recently developed two-dimensional infrared (2D IR) correlation techniques. We used these methods to examine a 12-residue $\beta $-hairpin (trpzip2) and its two $^{13}$C-isotopomers in the 6-$\mu $m region. Different frequency shifts are seen when $^{13}$C=$^{16}$O substitution is in the terminal or turn region of the hairpin. The difference is believed to be due to the localization of the amide-I modes, which is supported by molecular dynamics simulations. In addition, $^{13}$C-substitution perturbs the amide-I vibrational exciton band, providing a spectroscopic probe for peptide local conformation. Peptide global and local structural information were derived from the diagonal and the cross peaks of the 2D IR correlation spectra. The measured intermode vibration coupling constants were compared with those predicted by ab initio DFT computations and transition charge coupling calculations. [Preview Abstract] |
Monday, March 13, 2006 9:00AM - 9:12AM |
A13.00004: Spectral Signatures of 3$_{10}$- and $\alpha $-Helices Revealed by Two-Dimensional Infrared Spectroscopy Nien-Hui Ge, Hiroaki Maekawa, Claudio Toniolo, Quirinus Broxterman Femtosecond two-dimensional infrared (2D IR) spectroscopy is applied to the amide I modes of the homo-octapeptide $Z$-[L-($\alpha $Me)Val]$_{8}$-O$t$Bu in CDCl$_{3}$, TFE and HFIP solutions to acquire 2D spectral signatures that distinguish between 3$_{10}$- and $\alpha $-helix structures. Suppression of diagonal peaks by controlling polarizations of IR pulses clearly reveals cross-peak patterns that are crucial for structural determination. A doublet feature is observed when the peptide forms a 3$_{10}$-helix in CDCl$_{3}$ and TFE, and when it is at the initial stage of 3$_{10}$- to $\alpha $-helix transition in HFIP. In contrast, the 2D IR spectrum shows a multiple peak pattern after the peptide has become an $\alpha $-helix in HFIP. This is the first report on the experimental 2D IR signature of a 3$_{10}$-helical peptide. These results for a model octapeptide demonstrate the powerful capability of 2D IR spectroscopy to discriminate between different helical structures. [Preview Abstract] |
Monday, March 13, 2006 9:12AM - 9:24AM |
A13.00005: Terahertz Absorption and Circular Dichroism Spectroscopy of Solvated Biopolymers Jing Xu, Kevin Plaxco, S. James Allen Biopolymers are expected to exhibit broad spectral features in the terahertz frequency range, corresponding to their functionally relevant, global and sub-global collective vibrational modes with $\sim $ picosecond timescale. Recent advances in terahertz technology have stimulated researchers to employ terahertz absorption spectroscopy to directly probe these postulated collective modes. However, these pioneering studies have been limited to dry and, at best, moist samples. Successful isolation of low frequency vibrational activities of solvated biopolymers in their natural water environment has remained elusive, due to the overwhelming attenuation of the terahertz radiation by water. Here we have developed a terahertz absorption and circular dichroism spectrometer suitable for studying biopolymers in biologically relevant water solutions. We have precisely isolated, for the first time, the terahertz absorption of solvated prototypical proteins, Bovine Serum Albumin and Lysozyme, and made important direct comparison to the existing molecular dynamic simulations and normal mode calculations. We have also successfully demonstrated the magnetic circular dichroism in semiconductors, and placed upper bounds on the terahertz circular dichroism signatures of prototypical proteins in water solution. [Preview Abstract] |
Monday, March 13, 2006 9:24AM - 10:00AM |
A13.00006: Intermediate couplings: NMR at the solids-liquids interface Invited Speaker: Anisotropic interactions like dipolar couplings and chemical shift anisotropy have long offered solid-state NMR spectroscopists valuable structural information. Recently, solution-state NMR structural studies have begun to exploit residual dipolar couplings of biological molecules in weakly anisotropic solutions. These residual couplings are about 0.1\% of the coupling magnitudes observed in the solid state, allowing simple, high-resolution NMR spectra to be retained. In this work, we examine the membrane-associated opioid, leucine enkephalin (lenk), in which the ordering is ten times larger than that for residual dipolar coupling experiments, requiring a combination of solution-state and solid-state NMR techniques. We adapted conventional solid-state NMR techniques like adiabatic cross- polarization and REDOR for use with such a system, and measured small amide bond dipolar couplings in order to determine the orientation of the amide bonds (and therefore the peptide) with respect to the membrane surface. However, the couplings measured indicate large structural rearrangements on the surface and contradict the published structures obtained by NOESY constraints, a reminder that such methods are of limited use in the presence of large-scale dynamics. [Preview Abstract] |
Monday, March 13, 2006 10:00AM - 10:12AM |
A13.00007: Time correlation functions in Light Harvesting Complexes embedded in Glassy Hosts Felipe Caycedo, Ferney Rodriguez Using a Monte Carlo Wave function approach we describe the dynamics and correlation functions of light harvesting complexes (LH2) embedded in glassy hosts interacting with a classical light field. Using a dipolar interaction, we investigate the general features of coherence and (anti) bunching on a multiple-molecular system subject to cw excitation light. Spectral difusion due to environmental perturbations, produces distinct features on the fluorescent intensity and statistical properties of light emitted by the chromophores. We demonstrate how it is possible to quantify the number of chromophores involved in emission through the second-order correlation function $g^{(2)}(\tau)$ at small $\tau$ values. By changing properly the incident field, it is possible modulate the bunching or antibunching features. Finally we compare $g^{(2)}(\tau)$ for different environment conditions. [Preview Abstract] |
Monday, March 13, 2006 10:12AM - 10:24AM |
A13.00008: Conformational Dynamics of the Receptor Protein Galactose/Glucose Binding Protein Troy Messina, David Talaga We have performed time-correlated single photon counting (TCSPC) anisotropy and Stokes Shift measurements on bulk solutions of galactose/glucose binding protein. Site-directed mutagenesis was used to provide a single cysteine amino acid near the sugar-binding center of the protein (glutamine 26 to cysteine -- Q26C). The cysteine was covalently labeled with the environmentally-sensitive fluorophore acrylodan, and a long-lived ruthenium complex was covalently attached to the N-terminus to provide a fluorescent reference. The TCSPC data were analyzed using global convolute-and-compare fitting routines over the entire glucose titration and temperature range to provide minimal reduced chi-squared values and the highest time resolution possible. Using a standard ligand-binding model, the resulting distributions show that the closed (ligand-bound) conformation exists even at zero glucose concentration. At $20^{\circ}$C, the relative abundance of this conformation is as high as 40\%. The temperature dependence of this conformational study will be discussed and related to the ligand-binding free energy surface. [Preview Abstract] |
Monday, March 13, 2006 10:24AM - 10:36AM |
A13.00009: Quantifying Energy, Entropy and Free-Energy in Protein Folding Funnels Bernard Gerstman, Prem Chapagain The folding of proteins is a self-organizing process in which a long chain heteropolymer in a disorganized configuration spontaneously changes its shape to a highly organized structure. Several different forces work together to organize the structure while random thermal motion tends to cause disorganization. In order for folding to occur in a biologically relevant time, the Levinthal Paradox shows that folding cannot occur by a process that samples all of configuration space by randomly jumping from one microstate to another. Instead, folding pathways allow the organizing forces to incrementally direct the chain to ever-shrinking regions of configuration space in a funneling process. In order to understand how these self-organizing forces direct folding, we have quantified the narrowing of the folding funnel for a model two helix bundle. We have calculated the dependence of entropy and free-energy as a function of average energy by determining the statistical mechanical canonical probability for the chain to occupy each possible configuration as a function of average energy. [Preview Abstract] |
Monday, March 13, 2006 10:36AM - 10:48AM |
A13.00010: Landscape model of protein-DNA search: coupling of folding and sliding. Michael Slutsky, Mehran Kardar, Leonid Mirny In search for its specific site on genomic DNA, a DNA-binding protein needs to sample 10$^{6}$-10$^{9}$ other sites. Classical model of this process suggests that sliding along DNA provides an efficient mechanism for sampling sites. This model however disregards the sequence-specific energy of binding and flexibility of the protein. Recent NMR studies suggest that a protein searching for its site is partially unfolded, while folding on the cognate site. Can conformational flexibility of the protein-DNA complex help it to sample sites fast and then strongly bind its cognate site? Here we study how a protein finds its site on DNA by modeling protein sliding as diffusion in the sequence-specific free energy landscape. The landscape has two dimensions: one corresponds to motion along DNA, the other is a reaction coordinate of protein's conformational transition. Our simulations demonstrate that low-energy sites can trigger folding transition in the protein, making it fold preferentially on cognate-like sites. This mechanism provides kinetic pre-selection of sites, allowing a protein to search fast and strongly bind its cognate site. Importantly our study connects microscopic time of the conformational transition (10$^{-5}$-10$^{-3}$s) to the macroscopic time of promoter binding (10$^{1}$-10$^{3}$s). Comparison with recent experimental studies of LacI conformational dynamics suggests that coupling between protein flexibility and sequence-specific binding is necessary for rapid regulation of gene expression. [Preview Abstract] |
Monday, March 13, 2006 10:48AM - 11:00AM |
A13.00011: Modelling Ultra-fast folding proteins Kingshuk Ghosh, S. Banu Ozkan, Ken Dill Ultrafast-folding proteins are interesting because of their complex temperature dependent rates (including negative activation barriers). We develop a simple mesoscopic model that represents protein folding as a funnel through multiple routes. We have compared the model to experiments on several ultra-fast folding proteins. The model predicts the observed temperature dependences of folding and unfolding relaxation. Our model allows us to calculate the number of routes a molecule takes as it folds. We show that number of folding routes correlates with the folding time and also with the relative contact order: faster folders have more folding routes. Our model suggests a hard speed limit of 50 ns, when every protein folds via its own private route, and this corresponds to the folding time of an alpha helix. The model also computes folding time distributions which will be of interest for single molecule experiments. [Preview Abstract] |
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