Bulletin of the American Physical Society
APS March Meeting 2015
Volume 60, Number 1
Monday–Friday, March 2–6, 2015; San Antonio, Texas
Session G48: Focus Session: Physics of Proteins II |
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Sponsoring Units: DBIO Chair: Katherine Niessen, State University of New York, Buffalo Room: 217C |
Tuesday, March 3, 2015 11:15AM - 11:27AM |
G48.00001: Probing the conformational changes of proteins in liquid water by dielectric terahertz spectroscopy Ali Charkhesht, Deepu George, Nguyen Vinh Proteins solvated in their biological milieu are expected to exhibit strong absorption in the terahertz range that contain information on their global and sub-global collective vibrational modes (conformational dynamics) and global dynamical correlations among solvent water molecules and proteins. Measurements in this region, however, are challenging due to the strong absorption of water and often severe interference artifacts. In response, we have developed a highly sensitive dielectric terahertz frequency-domain system and a terahertz-time domain system for probing the collective dynamics in aqueous solution. Using these techniques we explore the complex dielectric response from 5 GHz up to 3 THz that directly probes such questions as the hydration level around proteins and the large scale vibrational modes of biological polymers. We make a direct comparison to the existing molecular dynamic simulations and normal mode calculations and investigate the dependence of the terahertz frequency dynamics on protein concentration. Our measurements shed light on the macromolecular motions in a biologically relevant water environment. [Preview Abstract] |
Tuesday, March 3, 2015 11:27AM - 11:39AM |
G48.00002: Nature of Light-Harvesting-System Excited States Prepared by Thermal Light Juan David Botero, Paul Brumer, Leonardo Pachon The nature of excited states produced by incoherent natural thermal light is analyzed in the context of light-harvesting system. In the absence of proteomic environments or solvents, it is shown that natural thermal light generates extremely long-lasting coherent dynamics in photosynthetic light-harvesting systems provided by the super-Ohmic character of the radiation, the lack of pure dephasing dynamics and the small energy gap between donors and acceptors. Although this unexpectected result has the potential of changing the entire direction of the discussion on the nature of excitonic states prepared by sunlight, when the environment is considered, the extremely long-lasting coherences induced by incoherent light are removed and stationary coherences are established in the photosynthetic light-harvesting system. [Preview Abstract] |
Tuesday, March 3, 2015 11:39AM - 11:51AM |
G48.00003: The Hydrophobic Solvation Energies of Molecular-Scale Cavities Depend on the Detailed Structure of the Molecular Surface Robert Harris, B. Montgomery Pettitt Both the energy ($\Delta G_{\mathrm{vdw}}$) of inserting an uncharged molecular cavity into solution by turning on the Lennard-Jones interactions between the solute and solvent and the energy ($\Delta G_{\mathrm{rep}}$) of inserting a nearly hard cavity into solution have often been assumed to increase linearly with the solvent-accessible surface area ($A$), in analogy with the energy of forming macroscopic cavities in solution. Because these energies are assumed to increase with $A$, they have often been assumed to drive protein collapse during folding. However we have shown that for molecular-scale cavities neither of these energies are simple linear functions of $A$. Additionally, for both alanine and glycine peptides we have shown that $\Delta G_{\mathrm{vdw}}$ decreases with $A$, implying that $\Delta G_{\mathrm{vdw}}$ opposes folding for these systems. We also show that assuming that $\Delta G_{\mathrm{rep}}$ is linear in $A$ for large molecules but linear in the solvent-accessible volume ($V$) for small molecules is inconsistent with our findings. Any theory that can accurately predict $\Delta G_{\mathrm{vdw}}$ or $\Delta G_{\mathrm{rep}}$ will have to consider the details of the molecular shape rather than relying on coarse measures, such as $A$ and $V$. [Preview Abstract] |
Tuesday, March 3, 2015 11:51AM - 12:27PM |
G48.00004: Novel Photodynamics in Phytochrome {\&} Cyanobacteriochrome Photosensory Proteins Invited Speaker: Delmar Larsen The photodynamics of recently characterized phytochrome and cyanobacteriochrome photoreceptors are discussed. Phytochromes are red/far-red photosensory proteins that utilize the photoisomerization of a linear tetrapyrrole (bilin) chromophore to detect the red to far-red light ratio. Cyanobacteriochromes (CBCRs) are distantly related cyanobacterial photosensors with homologous bilin-binding GAF domains, but exhibit greater spectral diversity. The excited-state mechanisms underlying the initial photoisomerization in the forward reactions of the cyanobacterial photoreceptor Cph1 from \textit{Synechocystis}, the RcaE CBCR from \textit{Fremyella diplosiphon}, and Npr6012g4 CBCR from \textit{Nostoc punctiforme} were contrasted via multipulse pump-dump-probe transient spectroscopy. A rich excited-state dynamics are resolved involving a complex interplay of excited-state proton transfer, photoisomerization, multilayered inhomogeneity, and reactive intermediates, and Le Chatelier redistribution. NpR6012g4 exhibits a high quantum yield for its forward photoreaction (40{\%}) that was ascribed to the activity of hidden, productive ground-state intermediates via a ``second chance initiation dynamics'' (SCID) mechanism. [Preview Abstract] |
Tuesday, March 3, 2015 12:27PM - 12:39PM |
G48.00005: Pushing single molecule techniques to microsecond resolution proves that T4 Lysozyme is a Brownian ratchet Maxim V. Akhterov, Yongki Choi, Tivoli J. Olsen, Patrick C. Sims, Mariam Iftikhar, O. Tolga Gul, Brad L. Corso, Gregory A. Weiss, Philip G. Collins Single-molecule techniques can monitor conformational dynamics of proteins, but such methods usually lack the resolution to directly observe conformational pathways or intermediate conformational states. We have recently described a single-molecule electronic technique that breaks this barrier. Using a 1 MHz-bandwidth carbon nanotube transistor, the transition pathways between open and closed conformations of T4 lysozyme have been recorded with a microsecond resolution. We directly resolve a smooth, continuous transition with an average duration of 37 microseconds. Unexpectedly, the mechanical closing and re-opening of the enzyme have identical distributions of transition durations, and the motion is independent of the enzyme catalyzing the substrate. These results illustrate the principle of microscopic reversibility applied to a Brownian ratchet, with lysozyme tracing a single pathway for closing and the reverse pathway for enzyme opening, regardless of its instantaneous catalytic productivity. [Preview Abstract] |
Tuesday, March 3, 2015 12:39PM - 12:51PM |
G48.00006: Detection Enhancement of Protein Structural Vibrations: Measurements and Calculations Katherine Niessen, Mengyang Xu, Edward Snell, Vivian Cody, James Pace, Marius Schmidt, Andrea Markelz Narrow band intramolecular protein vibrations have been successfully measured using crystal anisotropy THz microscopy (CATM), a near-field technique, on protein crystals [1]. To address the question of how these motions are related to protein function we developed a variation of this technique to rapidly measure a variety of protein crystals. The variation anisotropy measurement consists of introducing a wire-grid polarizer in the THz path and rotating the polarizer between measurements, instead of the sample. While the resulting anisotropic spectra confirm reproducibility and protein specific nature of the response the signal is not directly related to the absorption spectra and in fact shows more structure than CATM. This is due to the polarization sensitivity of the electro-optical detection crystal and the changing THz polarization direction and amplitude at the detector [2]. This combination leads to an enhancement of specific resonances and increased sensitivity to rotation of the THz polarization from the sample itself. Preliminary calculations suggest that the technique is sensitive to the birefringence associated with anisotropic absorbance. The results and significance of these measurements on protein and sucrose crystals and the calculated expected response will be discussed. 1. Acbas, G., et al. (2014). Nat Commun 5. 2. Planken, P.C.M., et al. (2001). J. Opt. Soc. Am. B. 18(3). [Preview Abstract] |
Tuesday, March 3, 2015 12:51PM - 1:03PM |
G48.00007: Microtubule Severing Stymied by Free Tubulin Jennifer Ross, Megan Bailey Proper organization of the microtubule cytoskeletal network is required to perform many necessary cellular functions including mitosis, cell development, and cell motility. Network organization is achieved through filament remodeling by microtubule-associated proteins (MAPs) that control microtubule dynamics. MAPs that stabilize are relatively well understood, while less is known about destabilizing MAPs, such as severing enzymes. Katanin, the first-discovered microtubule-severing enzyme, is a AAA$+$ enzyme that oligomerizes into hexamers and uses ATP hydrolysis to sever microtubules. Using quantitative fluorescence imaging on reconstituted microtubule severing assays in vitro we investigate how katanin can regulate microtubule dynamics. Interestingly, we find microtubule dynamics inhibits katanin severing activity; dynamic microtubules are not severed. Using systematic experiments introducing free tubulin into the assays we find that free tubulin can compete for microtubule filaments for the katanin proteins. Our work indicates that katanin could function best on stabile microtubules or stabile regions of microtubules in cells in regions where free tubulin is sequesters, low, or depleted. [Preview Abstract] |
Tuesday, March 3, 2015 1:03PM - 1:39PM |
G48.00008: Stereoelectronic Determinants of Color Vision: Engineering Protein Mimics of Pigmented Rhodopsins and Designing New Protein Fusion Tags Invited Speaker: Babak Borhan The field of protein engineering has undergone phenomenal growth from its inception approximately 20 years ago. A wide variety of topics have been addressed, including the construction of new protein folds, the introduction of metal binding sites that are both structural and catalytic, the development of novel enzymatic activity and the creation and optimization of new ligand binding sites. However, left behind has been the issue of protein/chromophore interactions. Protein-chromophore interactions are a central component of a wide variety of critical biological processes such as color vision and photosynthesis. To understand the fundamental elements that contribute to spectral tuning of a chromophore inside the protein cavity, we redesigned small cyctosolic human proteins to fully encapsulate all-trans-retinal and form a covalent bond as a protonated Schiff base. These systems, using rational mutagenesis, have led to restructuring of the electrostatic environment within the binding pocket of the host protein, enabling the regulation of the absorption maximum of the pigment over 200 nm. So far our work has shown that the manipulation of the electrostatic potential projected by the protein onto the chromophore has a powerful effect on the absorption properties of the ligand. We have parlayed these results towards developing new protein fusion tags and pH responsive protein dyes. [Preview Abstract] |
Tuesday, March 3, 2015 1:39PM - 1:51PM |
G48.00009: Obtaining structural information of small proteins using solid-state nanopores and high-bandwidth measurements David Niedzwiecki, Christopher Lanci, Jeffery Saven, Marija Drndic The use of biological nanopores sensors to characterize proteins has proved a fruitful field of study. Solid-state nanopores hold several advantages over their biological counterparts, including the ability to tune pore diameter and their robustness to external conditions. Despite these advantages, the use of solid-state nanopores for protein analysis has proved difficult due to rapid translocation times of proteins and poor signal-to-noise of small peptides. Recently, improvements in high-bandwidth acquisition and in signal-to-noise have made the study of small peptides using solid-state nanopores feasible. Here we report on the detection and characterization of peptides as small as 33 amino-acids in length using sub-10 nm thin silicon nitride nanopores, giving high signal levels, combined with high-bandwidth electronics. In addition we show differentiation between monomers and dimer forms of the GCN-4 p1 leucine zipper, a coil-coil structure, and compare this with the unstructured 33-mer. The differentiation between these two forms demonstrates the possibility of extracting useful structural information from short peptide structures using modern solid-state nanopore systems. [Preview Abstract] |
Tuesday, March 3, 2015 1:51PM - 2:03PM |
G48.00010: Determination of Kinetic Isotope Effects in Yeast Alcohol Dehydrogenase Using Transition Path Sampling Matthew Varga, Steven Schwartz The experimental determination of kinetic isotope effects in enzymatic systems can be a difficult, time-consuming, and expensive process. In this study, we use the Chandler-Bolhius method for the determination of reaction rates within transition path sampling (rTPS) to determine the primary kinetic isotope effect in yeast alcohol dehydrogenase (YADH). In this study, normal mode centroid molecular dynamics (CMD) was applied to the transferring hydride/deuteride in order to correctly incorporate quantum effects into the molecular simulations. Though previous studies have used rTPS to calculate reaction rate constants in various model and real systems, it has not been applied to a system as large as YADH. Due to the fact that particle transfer is not wholly indicative of the chemical step, this method cannot be used to determine reaction rate constants in YADH. However, it is possible to determine the transition rate constant of the particle transfer, and the kinetic isotope effect of that step. This method provides a set of tools to determine kinetic isotope effects with the atomistic detail of molecular simulations. [Preview Abstract] |
Tuesday, March 3, 2015 2:03PM - 2:15PM |
G48.00011: ABSTRACT WITHDRAWN |
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