Bulletin of the American Physical Society
76th Annual Meeting of the Southeastern Section of APS
Volume 54, Number 16
Wednesday–Saturday, November 11–14, 2009; Atlanta, Georgia
Session NC: Experimental Biophysics II |
Hide Abstracts |
Chair: Jennifer Curtis, Georgia Institute of Technology Room: Paris |
Saturday, November 14, 2009 8:30AM - 8:42AM |
NC.00001: Relative Orientation of Imidazole Ligands in Cu(II) Model and Abeta peptides Complexes revealed by ESEEM Spectroscopy Jessica Hernandez, Li Sun, Kurt Warncke Alzheimer's Disease (AD) is associated with the aggregation and fibrillization of the beta-amyloid protein (Abeta). The coordination of Cu(II) by peptide histidine imidazole sidechains is proposed to play an important role in determining the fibrillization ``switch'' [$1$]. We have developed techniques of X-band electron spin echo envelope modulation (ESEEM) spectroscopy to determine the molecular structure of the Cu(II)-histidine imidazole coordination in cryotrapped soluble and fibrillar forms of Abeta peptides, in order to gain insight into the factors that govern fibrillization. Focusing on the ESEEM double quantum harmonic feature, we use our hybrid optimization-based OPTESIM simulation software [$2$] to determine the mutual orientation of the imidazole rings in Cu(II)--bis-imidazole complexes that include \textit{cis}- versus \textit{trans}- coordination. The technique has been applied to Abeta(13-21) peptide to reveal the Cu(II) coordination mode in fibrils. [1] Dong , J., et al., \textit{Proc. Natl. Acad. Sci.,} 2007, \underline {\textit{104}}, 13313. [2] Sun, L., et al., \textit{J. Magn. Reson.} 2009, \underline {\textit{200}}, 21 [Preview Abstract] |
Saturday, November 14, 2009 8:42AM - 8:54AM |
NC.00002: Dynamics of DNA Mismatch Repair Julie Coats, Yuyen Lin, Ivan Rasnik DNA mismatch repair protects the genome from spontaneous mutations by recognizing errors, excising damage, and re-synthesizing DNA in a pathway that is highly conserved. Mismatch recognition is accomplished by the MutS family of proteins which are weak ATPases that bind specifically to damaged DNA, but the specific molecular mechanisms by which these proteins recognize damage and initiate excision are not known. Previous structural investigations have implied that protein-induced conformational changes are central to mismatch recognition. Because damage detection is a highly dynamic process in which conformational changes of the protein-DNA complexes occur on a time scale of a few seconds, it is difficult to obtain meaningful kinetic information with traditional ensemble techniques. In this work, we use single molecule fluorescence resonance energy transfer (smFRET) to study the conformational dynamics of fluorescently labeled DNA substrates in the presence of the mismatch repair protein MutS from \textit{E. coli} and its human homolog MSH2/MSH6. Our studies allow us to obtain quantitative kinetic information about the rates of binding and dissociation and to determine the conformational states for each protein-DNA complex. [Preview Abstract] |
Saturday, November 14, 2009 8:54AM - 9:06AM |
NC.00003: Lifetime Resolved Fluorescence Fluctuation Spectroscopy Peng Guo, Keith Berland Fluorescence correlation spectroscopy (FCS) has been widely used investigate molecular dynamics and interactions in biological systems. FCS typically resolves the component species of a sample either through differences in diffusion coefficient or molecular brightness. Diffusion based assays currently have a major limitation which requires that the diffusion coefficients of component species in a sample must be substantially different in order to be resolved. This criterion is not met in many important cases, such as when molecules of similar molecular weight bind to each other. This limitation can be overcome, and resolution of FCS measurements enhanced, by combining FCS measurements with measurements of fluorescence lifetimes. By using of global analysis on simultaneously acquired FCS and lifetime data we show that we can dramatically enhance resolution in FCS measurements, and accurately resolve the concentration and diffusion coefficients of multiple sample components even when their diffusion coefficients are identical provided there is a difference in the lifetime of the component species. We show examples of this technique using both simulations and experiments. It is expected that this method will be of significance for binding assays studying molecular interactions. [Preview Abstract] |
Saturday, November 14, 2009 9:06AM - 9:18AM |
NC.00004: Calculated and Experimental Vibrational Properties of P700 and the Iron Sulfur Cluster in Photosystem I Hari Lamichhane, Gary Hastings Density functional theory (DFT) based vibrational frequency calculations of Fe$_{4}$S$_{4}$(SR)$_{4}^{n-}$ clusters show that the intense iron-sulfur stretching modes lie in the frequency region between 300-400 cm$^{-1}$. Among them the iron-sulfur ligand (Fe-S$^{t})$ stretching modes are more intense and $\sim $ 30 cm$^{-1}$ lower in frequency than the iron-sulfur body (Fe-S$^{b})$ stretching modes. Calculations in tetrahydrofuran (THF) show that all these iron-sulfur stretching modes of vibration downshift by $\sim $ 20 cm$^{-1}$ upon reduction of the molecule. On the other hand, we have not observed any intense bands from chlorophyll a in the frequency region 400 to 320 cm$^{-1}$ from the calculations. In an attempt to detect modes associated with iron sulfur clusters in PS I we have obtained light induced (P700$^{+ }$- P700) FTIR difference spectra for PSI particles from $S. 6803$ in the far infrared region. We observe difference bands at many frequencies in the 600-300 cm$^{-1}$ region. Based on our calculations and literature values we claim that the negative bands at 388 cm$^{-1}$ and 353 cm$^{-1}$ in the (P700$^{+ }$- P700) FTIR difference spectra be assigned to Fe-S$^{b }$and Fe-S$^{t}$ stretching modes of the ground state of the iron-sulfur cluster F$_{B}$. [Preview Abstract] |
Saturday, November 14, 2009 9:18AM - 9:30AM |
NC.00005: FTIR Difference Spectroscopy for the Study of Photosystem I A$_{1 }$Acceper Nan Zhao, Gary Hastings Photosystem I (PS I) is a protein complex which carries out light-induced charge separation in oxygenic photosynthesis. Phylloquinone acts as the secondary electron acceptor in PS I. The A$_{1}$accepter is of interest because it has the lowest reduction potential of any quinone found in nature. In \textit{Men}B mutant PS I particles from \textit{Synechocystis} sp. 6803, a plastoquinone-9 molecule occupies the A$_{1}$ binding site instead of phylloquinone. Using \textit{men}B PS I particles, it has been shown that it is possible to replace plastoquinone-9 in the A$_{1}$ site with phylloquinone. To probe the molecular properties of phylloquinone and its environment in both the neutral and reduced state, we have used time-resolved step-scan FTIR difference spectroscopy (TRSS FTIR DS) to supply dynamic structural information concerning the electron-transfer cofactor. We have produced time-resolved A$_{1}^{-}$/A$_{1}$ FTIR DS using \textit{men}B mutant PS I particles in which phylloquinone has been reintroduced into the A$_{1}$ binding site. We also have obtained time-resolved A$_{1}^{-}$/A$_{1}$ FTIR difference spectra for \textit{men}B PS I particles that are globally $^{13}$C labeled where $^{12}$C labeled phylloquinone was incorporated into the A$_{1}$ binding site. By incorporating $^{12}$C labeled phylloquinone into $^{13}$C labeled PS I, we are able to identify carbonyl (C=O)-sensitive bands of A$_{1}^{-}$ and A$_{1}$. [Preview Abstract] |
Saturday, November 14, 2009 9:30AM - 9:42AM |
NC.00006: ABSTRACT WITHDRAWN |
Saturday, November 14, 2009 9:42AM - 9:54AM |
NC.00007: Modifying P700, An Important Chlorophyll Species Involved In Solar Energy Conversion in Plants and Bacteria Gary Hastings, Sreeja Parameswaran P700 is the primary electron donor of photosystem I. It is an asymmetric chlorophyll $a$' (P$_{A})$/ chlorophyll $a $(P$_{B})$ heterodimer. This asymmetry is a result hydrogen-bonding with predominantly three amino acids and a water molecule near P$_{A}$. P$_{B}$ is not involved in hydrogen bonding. In an attempt to decrease this level of assymmetry, and introduce hydrogen bonds to P$_{B}$, we have changed 1, 2 or all 3 of the amino acids near P$_{B}$ with the corresponding amino acids on P$_{A}$. To investigate mutation induced alteration of pigment-protein interactions we have obtained (P700$^{+}$-P700) FTIR difference spectra for PS I particles from wild type and all three mutants. Upon mutation, many FTIR difference bands are altered, and some of the changes are difficult to rationalize using the accepted set of assignments for bands in (P700$^{+}$-P700) FTIR difference spectra. To model aspects of the experimental FTIR difference spectra, density functional theory based vibrational frequency calculations of chlorophyll-$a$ in the presence of solvents and H-bond interactions were undertaken. Our calculations show that mutation induced mode intensity and frequency shifts are difficult to predict \textit{a priori}. However, via calculation many of the puzzling mutation induced alteration of bands in (P700$^{+}$-P700) FTIR difference spectra can be understood. [Preview Abstract] |
Saturday, November 14, 2009 9:54AM - 10:06AM |
NC.00008: Magnetic Image Force for Biophysical Force Measurements Di Deng, Patrick Yang, Benjamin Yellen, Randall Erb Current methods for measuring biomolecular interactions such as atomic force microscopy (AFM), biomembrane force probe (BFP), and optical tweezing (OT) have various logistical limitations. Most importantly, these methods can study only one molecule at a time, which greatly limits the ability to observe the ensemble mechanical properties. We investigated a new highly parallel molecular force spectroscopy approach in which up to thousands of bonds can be studied simultaneously. This new method utilizes the concept of ``image forces'' arising in suspension of nonmagnetic beads, which is purely repulsive and tunable with the applied field. We have shown that it is possible to directly measure the rupture force between the bead and substrate which is mediated through ideally single Biotin-Streptavidin (B-S) bonds. We have measured for the first time the rupture force for single B-S bonds at the lowest ever force loading rates ($<$1fN/s). Rupture force vs. loading rate diagrams for B-S bonds will be discussed. [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