Bulletin of the American Physical Society
2006 APS March Meeting
Monday–Friday, March 13–17, 2006; Baltimore, MD
Session B13: Focus Session: Spectroscopy of Biomolecules from Isolated Molecules to Cell Environment II |
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Sponsoring Units: DCP DBP Chair: Philip Anfinrud, National Institutes of Health Room: Baltimore Convention Center 305 |
Monday, March 13, 2006 11:15AM - 11:51AM |
B13.00001: Structure and Interactions of Isolated Biomolecular Building Blocks. Invited Speaker: We investigate biomolecular building blocks and their clusters with each other and with water on a single molecular level. The motivation is the need to distinguish between intrinsic molecular properties and those that result from the biological environment. This is achieved by a combination of laser desorption and jet cooling, applied to aromatic amino acids, small peptides containing those, nucleobases and nucleosides. This approach is coupled with a number of laser spectroscopic techniques, including resonant multi-photon ionization, spectral hole burning and infra-red ion-dip spectroscopy. We will discuss examples illustrating how information can be obtained on spatial structure of individual biomolecules, including peptide conformations and details of DNA base-pairing. [Preview Abstract] |
Monday, March 13, 2006 11:51AM - 12:27PM |
B13.00002: TBA Invited Speaker: \\ [Preview Abstract] |
Monday, March 13, 2006 12:27PM - 12:39PM |
B13.00003: Folding an infinitely long polypeptide into a helical conformation Joel Ireta, Matthias Scheffler The potential-energy surface and harmonic vibrational analysis of an infinitely long polypeptide are studied using density- functional theory in the Perdew, Burke, and Ernzerhof approximation to the exchange-correlation functional. We find that the $\pi$-helix, $\alpha$-helix, and $3_{10}$-helix are stable respect to the fully extended structure (FES) at 0 K, both in right- and left-handed conformations. Accounting for the temperature effects it is found that the left-handed helices are energetically degenerated respect to FES and the right-handed helices slightly more stable than FES, at room temperature. The minimum-energy pathway along the potential- energy surface shows that the barrier to fold a FES into a left- handed helix is at least three times larger than the barrier to fold it into a right-handed helix. This suggests that the very low occurrence of left-handed helices in protein structures is due to both thermodynamic and kinetic effects. [Preview Abstract] |
Monday, March 13, 2006 12:39PM - 12:51PM |
B13.00004: The Effect of Terminal Truncation on the Folding Dynamics of Coiled-coil GCN4-p1 Michelle Bunagan, Lidia Cristian, William DeGrado, Feng Gai Structural perturbation by terminal truncation has been used extensively in protein folding studies because it yields valuable information that could be used to dissect the folding mechanism of the protein of interest. Herein, we studied the folding dynamics of a truncated variant of a cross-linked GCN4-p1 coiled-coil using the technique of laser-induced temperature-jump (T-jump) in conjunction with infrared spectroscopy. While the full-length GCN4-p1 exhibits first-order kinetics in stopped-flow CD and fluorescence folding experiments, a recent T-jump study has shown that one or two folding intermediates may exist at the native side of the major folding barrier. However, the current truncated variant of GCN4-p1 not only shows first order folding kinetics, but also exhibits ultrafast folding behaviors, suggesting that there are no detectable intermediates populated on its folding pathway. Therefore, these results have interesting implications for the understanding of the folding mechanism of coiled-coil structures. [Preview Abstract] |
Monday, March 13, 2006 12:51PM - 1:03PM |
B13.00005: Fast Events in Protein Folding following Ultrarapid Mixing Lisa Lapidus, Kimberly Cooper, Emily Tubmann, David Hertzog, Juan Santiago, Olgica Bakajin A continuous flow microfluidic mixer fabricated out of fused silica was used to study microsecond time scales of protein folding by monitoring natural tryptophan fluorescence. This mixer uses hydrodynamic focusing and diffusion to lower the concentration of the initial denaturant, inducing the protein to fold. The mixing time can be as fast as 8 $\mu $s and allows access to times that are inaccessible in conventional mixers. Using a confocal microscope we observe the UV fluorescence spectrum from naturally occurring tryptophans in 3 well-studied proteins, cytochrome c, apomyoglobin and lysozyme, as a function of time after rapid mixing. Single value decomposition of the time dependent spectra reveal two separate processes: 1) a spectral shift which occurs within the mixing time and 2) a fluorescence decay occurring between 100 and 300 microseconds. We attribute the first process to hydrophobic collapse and the second process the formation of the first tertiary contacts. While the slower rate obviously depends on the details of the folding trajectory of each protein, we note that all three measured rates anti-correlate well with the fraction of secondary structure formed. This work demonstrates that hydrophobic collapse is much faster than had been estimated with slower mixing methods and is in good agreement with measured rates of intramolecular diffusion in unstructured peptides. [Preview Abstract] |
Monday, March 13, 2006 1:03PM - 1:15PM |
B13.00006: Fast diffusive folding dynamics of Tryptophan Zipper peptides Stephen Hagen Simple synthetic peptides that fold into elemental structures like $\alpha $-helices and $\beta $-hairpins serve as useful model systems for experimental and computational studies of protein folding dynamics. The folding of the Tryptophan Zippers, for example, represents an interesting case of nearly barrier-less folding. These short (12-16 residue) peptides designed by Cochran et al. (2001) fold into stable, well-defined $\beta $-hairpins on time scales of just a few microseconds. Our laser temperature-jump fluorescence spectroscopy shows that the ``TrpZip'' molecules encounter little internal friction and almost no enthalpic barrier as they proceed from the unfolded to the folded state: Favorable solvent conditions reduce the entropic barrier as well, until the folding dynamics become complex and diffusive, and different experimental probes see the system as folding on rather different time scales. We will present experimental signatures of these complex dynamics, discuss the role of internal polymer friction in TrpZip folding, and briefly consider suitable approaches for modeling the free energy surface that controls such a folding reaction. [Preview Abstract] |
Monday, March 13, 2006 1:15PM - 1:51PM |
B13.00007: Sugars in the gas phase Invited Speaker: The functional importance of carbohydrates in biological processes, particularly those involving specific molecular recognition is immense. Characterizing the three-dimensional structures of carbohydrates and glycoconjugates and their interactions with other molecules, particularly the ubiquitous solvent, water, are key starting points on the road towards the understanding of these processes. A new strategy, combining electronic and vibrational spectroscopy of mass-selected carbohydrate molecules and their hydrated complexes, conducted under molecular beam conditions, with ab initio computation is being exploited to characterize carbohydrate conformations and hydrated structures, the hydrogen-bonded networks they support (or which support them) and the specificity of their interactions with other molecules. The spectral features of monosaccharide residues can be used to refine the assignment of larger, oligosaccharide structures - a supplementary `building-block' approach to the study of complex structures based upon an `alphabet' of established IR spectral signatures of different conformations of the monosaccharide units - when their spectroscopic patterns are retained. When their patterns are altered the changes may be understood by analyzing the modification of the hydrogen-bonded networks, eg., the retention (or disruption) of the secondary structural motifs generated by intra-residue hydrogen-bonding. Feedback from the increasing body of experimental data will also help to inform and guide future theoretical conformational searches. [Preview Abstract] |
Monday, March 13, 2006 1:51PM - 2:03PM |
B13.00008: 2D IR measurements of the coupling in transmembrane helix dimers Chong Fang, Lidia Cristian, Alessandro Senes, William Degrado, Robin Hochstrasser Ultrafast 2D IR photon echo spectroscopy has been adapted to the study of transmembrane helix dimers. Residues Gly-79 on each of the two helical strands of Glycophorin A (GpA) dimers in sodium dodecyl sulfate (SDS) micelles were isotopically selected. The 2D IR spectra reveal the tertiary interaction between the helices. The waiting time dependence of the echo informs on the conformational dynamics of different regions of the GpA dimer. Both the $^{13}$C and $^{13}$C=$^{18}$O labeled homodimers showed elongated diagonal peaks in the 2D IR correlation spectra. The cross peaks in the heterodimer spectrum indicated an off-diagonal anharmonicity of $\sim $3.8 cm$^{-1}$. This anharmonicity is caused by through-space interactions between amide units on different strands. The angle between the two Gly-79 amide-I transition dipoles was estimated to be $\sim $35\r{ } from the polarization of the 2D IR signal in the cross-peak region. The method also identifies residues that are exposed to water. [Preview Abstract] |
Monday, March 13, 2006 2:03PM - 2:15PM |
B13.00009: Solvent and Peptide Conformational Fluctuations Revealed with Two-Dimensional Infrared Spectroscopy Ziad Ganim, Andrei Tokmakoff Two-dimensional nonlinear infrared spectroscopy (2D-IR) is emerging as a new biophysical tool that offers the sensitivity to protein secondary structure and fast time resolution of linear Fourier transform infrared spectroscopy (FT-IR), but with the added ability to separate overlapping contributions and reveal vibrational couplings. Amide I nonlinear spectroscopy has been used to probe the thermal stability of proteins and peptides and reveal a detailed picture of how the beta-sheet of ubiquitin unfolds from nanoseconds to milliseconds. We show that the standard techniques that are sufficient in calculating FT-IR spectra from a static structure fail to reproduce observed 2D-IR lineshapes. By combining DFT parameterized semi-empirical models and structure trajectories from molecular dynamics simulations, we obtain good agreement with experimental FT-IR and 2D-IR spectra of trpzip2, a model beta-hairpin. We then demonstrate how hydrogen bonding, conformational variation, and their fluctuations are each manifested in 2D-IR spectra. This methodology provides a means of calculating FT-IR and 2D-IR spectra directly from any atomistic molecular dynamics simulation - allowing richer data analysis and a means of validating mechanistic predictions from simulations. [Preview Abstract] |
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