Bulletin of the American Physical Society
2006 APS March Meeting
Monday–Friday, March 13–17, 2006; Baltimore, MD
Session G29: Focus Session: Physical and Engineering Constraints on the Function of Biological Systems |
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Sponsoring Units: DBP Chair: Partha Mitra, Cold Spring Harbor Laboratory Room: Baltimore Convention Center 326 |
Tuesday, March 14, 2006 8:00AM - 8:36AM |
G29.00001: A Framework for Globular Proteins Invited Speaker: Due to their remarkable chemical specificity and diversity, globular proteins play a crucial role in the network of molecular interactions of life. Over the past several decades, much experimental data has been accumulated on proteins, but the overarching principles that govern the general features of proteins remain largely unknown. Here, a novel framework for understanding many key attributes of globular proteins is presented. This framework suggests that the characteristics of globular proteins that make them well-suited for biological function are the emergent properties of a unique phase of matter. Implications of this picture include the provision of a fixed backdrop for molecular evolution and natural selection and design restrictions on molecular machinery. The work described here was carried out in collaboration with Jayanth Banavar and Amos Maritan. [Preview Abstract] |
Tuesday, March 14, 2006 8:36AM - 8:48AM |
G29.00002: Chiral Heterorecognition of Organic Molecules and Inorganic Surfaces Thomas Greber, Richard Schillinger, Joachim Wider, Zeliko Sljivancanin, Bjork Hammer Atomic kinks on surfaces are chiral and may thus be used to distinguish left-handed from right-handed molecules. Two distinct non-mirror-symmetric conformations of D- and L-cysteine were found after adsorption on Au(17~11~9)$^S$. This demonstrates chiral heterorecognition, i.e. enantioselectivity of $S$-kinks on vicinal Au(111). The structures as determined by angle scanned X-ray photoelectron diffraction (XPD) agree well with those from density functional theory (DFT) calculations. The calculations predict adsorption energies of $\approx$2~eV where D-cysteine binds 140~meV stronger than L-cysteine. The classical three point contact model for molecular recognition fails to explain these findings. [Preview Abstract] |
Tuesday, March 14, 2006 8:48AM - 9:00AM |
G29.00003: Nucleotide Mutation and Amino Acid Evolution Jose Parra, Bernard Gerstman We have found a set of nucleotide coupling propensities (ncp) that best reproduces the currently observed probability distribution of amino acids found in protein data banks. These ncp represent the biochemical potentials that produce different probabilities for different mutations within a sequence of nucleotides. We have allowed these ncp to act on a random sequence of nucleotides whose codons initially produce a random arrangement of amino acid residues. Interestingly, though the mutating action of the ncp on the chain of nucleotides results in the correct evolution of the probability of appearance of each individual amino acid towards the present distribution, there is however no evolutionary trend in major global characteristics of the amino acid distribution. We present results that show that properties of amino acids that are considered important for protein structure do not evolve on average, such as: hydrophobic/hydrophilic, size, aromatic/non-aromatic, aliphatic/non-aliphatic, helical-preference/beta-strand. [Preview Abstract] |
Tuesday, March 14, 2006 9:00AM - 9:12AM |
G29.00004: Quantitative modeling and data analysis of SELEX experiments Marko Djordjevic, Anirvan M. Sengupta SELEX (Systematic Evolution of Ligands by Exponential Enrichment) is an experimental procedure that allows extracting, from an initially random pool of DNA, those oligomers with high affinity for a given DNA-binding protein. We address what is a suitable experimental and computational procedure to infer parameters of transcription factor-DNA interaction from SELEX experiments. To answer this, we use a biophysical model of transcription factor-DNA interactions to quantitatively model SELEX. We show that a standard procedure is unsuitable for obtaining accurate interaction parameters. However, we theoretically show that a modified experiment in which chemical potential is fixed through different rounds of the experiment allows robust generation of an appropriate data set. Based on our quantitative model, we propose a novel bioinformatic method of data analysis for such modified experiment and apply it to extract the interaction parameters for a mammalian transcription factor CTF/NFI. From a practical point of view, our method results in a significantly improved false positive/false negative trade-off, as compared to both the standard information theory based method and a widely used empirically formulated procedure. This work will appear in Physical Biology. This work was supported by NIH grant GM67794. Final parts of this work were supported by NSF under Agreement No. 0112050 and NSF grant MCB-0418891. [Preview Abstract] |
Tuesday, March 14, 2006 9:12AM - 9:24AM |
G29.00005: Low Temperature IPD AgO Bacterial Static / Bactericidal Coatings for Various Medical Applications Daniel Storey Low temperature Ionic Plasma Deposition (IPD) has been successfully used to deposit silver and silver oxide large area ($>$ 18,000 in2/hour) thin films on several types of wound care products, catheters, implantables, and surgical tools. The IPD process has been proven to be able to provide predictable infection control for short term bacterial-stasis implantable devices, to long term ($>$ 60 day) bacterial toxicity. Silver and silver oxide has been deposited on substrates including PTFE, polypropylene, PVC, 440 stainless steel, Al2O3, and Ti6Al4V to name a few. [Preview Abstract] |
Tuesday, March 14, 2006 9:24AM - 9:36AM |
G29.00006: Energy Dependence of Cancer Cell Irradiation Rachel Black A proof-of-principle experiment was done to investigate the energy damage of beta particles on cancer cells. This study is the first of its kind that spans into the MeV range. This research seeks to provide information on the possibility of mono-energetic Brachytherapy sources, reaction mechanisms of cancer cell death and cancer genome identification. It is expected that different cancer types will respond to different energies. Protein expressions from the irradiation of breast cancer cells were identified via a 2D diagram (pH versus mass) showing a strong energy dependence. Preliminary results will be presented and discussed. [Preview Abstract] |
Tuesday, March 14, 2006 9:36AM - 9:48AM |
G29.00007: Calibration Of A System For Energy Dependence Study Of Cancer Cell Irradiation Ariano Munden Calibration of individual electron energies and dose distribution exiting a dipole magnet perpendicular at the dispersive plane was performed using a collimated scintillating fiber based detector. The dipole was constructed from two 5.08x5.08x2.54 cm$^{3}$ permanent magnets separated by a distance of 2 cm and having a maximum filed of about 5 kG. A 1 cm diameter collimated electron beam exiting a $^{90}$Sr/Y radioactive with a 25 $\mu $Ci activity and a 2.28 MeV maximum energy was placed at the entrance face of the magnet. Mapping of the magnetic field was done using a Hall probe with an accuracy of about 2 G. The electron detector consisted of blue shifted scintillating fibers with thicknesses of 1 mm. The setup provides an energy resolution of about 10{\%}. This system will be used to study the differential response of cancer cell irradiation to selected energies. We will present results and discussed the results obtained from this work. [Preview Abstract] |
Tuesday, March 14, 2006 9:48AM - 10:24AM |
G29.00008: Invited Speaker: |
Tuesday, March 14, 2006 10:24AM - 10:36AM |
G29.00009: Radiation Damage From Mono-energetic Electrons Up to 200 keV On Biological Systems Yuriy Prilepskiy The electron gun of the CEBAF machine at Jefferson lab (Newport News, VA) is capable of delivering electrons with energies up to 200 keV with a resolution of about 10$^{-5}$. This 1.5 GHz beam permits to generate cellular radiation damage within minutes. We have performed irradiation of cancer cells with different energies and different currents to investigate their biological responses. This study will permit to address the physical processes involved in the RBE and LET at a level that supersedes current data listed in the literature by orders of magnitude. We will discuss the experimental setup and results of the first stage of data collected with this novel system. This research is part of a global program to provide detailed information for the understanding of radiation based cancer treatments. [Preview Abstract] |
Tuesday, March 14, 2006 10:36AM - 10:48AM |
G29.00010: The cost of linearization Danielle Morel, William B Levy Information processing in the brain is metabolically expensive and energy usage by the different components of the nervous system is not well understood. In a continuing effort to explore the costs and constraints of information processing at the single neuron level, dendritic processes are being studied. More specifically, the role of various ion channel conductances is explored in terms of integrating dendritic excitatory synaptic input. Biophysical simulations of dendritic behavior show that the complexity of voltage-dependent, non-linear dendritic conductances can produce simplicity in the form of linear synaptic integration. Over increasing levels of synaptic activity, it is shown that two types of voltage-dependent conductances produce linearization over a limited range. This range is determined by the parameters defining the ion channel and the 'passive' properties of the dendrite. A persistent sodium and a transient A-type potassium channel were considered at steady-state transmembrane potentials in the vicinity of and hyperpolarized to the threshold for action potential initiation. The persistent sodium is seen to amplify and linearize the synaptic input over a short range of low synaptic activity. In contrast, the A-type potassium channel has a broader linearization range but tends to operate at higher levels of synaptic bombardment. Given equivalent 'passive' dendritic properties, the persistent sodium is found to be less costly than the A-type potassium in linearizing synaptic input. [Preview Abstract] |
Tuesday, March 14, 2006 10:48AM - 11:00AM |
G29.00011: Fast noniterative biexponential fluorescence lifetime imaging in the investigation of phagocyting neutrophyls Raluca Aura Niesner The cofactors NADH and NADPH [NAD(P)H] belong to the principal endogenous indicators of the cellular metabolism. Since the metabolic activity of cells is given by the ratio between the concentrations of free and protein-bound NAD(P)H, the development of techniques which measure the modifications to this ratio is particularly significant. The biexponential fluorescence lifetime imaging (FLIM) is employed to discriminate between the free and the protein-bound NAD(P)H without any previous calibration. Thus a high-resolution map of the cellular metabolism, i.e. an image of the contribution of the protein-bound NAD(P)H to the cumulative NAD(P)H signal, is obtained. This method is applied in the investigation of neutrophyls phagocyting the spores of Aspergillus Fumigatus. Particularly the activation of the NADPH oxidase is studied. Since an important aspect in biological applications is to monitor the dynamics of the relevant processes, rapid techniques, e.g. fast biexponential FLIM, are needed. We implement for the first time in FLIM a noniterative method originally developed by Prony and verified it in biexponential time-domain FLIM experiments on homogenous mixtures and on different types of cells. [Preview Abstract] |
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