AUTHOR: Lauren Cooper
TITLE: Flow through flexible beams inspired by the endothelial glycocalyx
Lauren Cooper, Daniel Fovargue and Laura Miller,
University of North Carolina at Chapel Hill
ABSTRACT: In the ongoing quest to understand and develop treatments for hypertension, there has been a shift in research away from only treating risk factors in light of the mere 20-30% reduction in the condition seen from this approach. The current interest is centered on strengthening the protective traits of the vessel walls in hopes of inhibiting high blood pressure. Key to interpreting the vessel walls’ protective functions is in understanding the interaction it has with the blood flowing through it. This poster focuses on providing insight into the aforementioned interaction by numerically examining the shear stress experienced by the blood vessel at the endothelial surface layer (ESL). The ESL coats the endothelial cells in the lining of the vessel wall and is of interest to the biological community mainly due to its function as a mechanosensor, converting mechanical stress to chemical reactions as occurs in the expansion of blood vessels during exercise. In this poster the shear stress distributions along the ESL layer in the Reynolds number regime of a rat capillary are examined by utilizing the Immersed Boundary Method. The ESL is modeled by individual fibers allowed to stretch and bend in response to the blood flows and the vessel wall is kept mainly stiff. This poster will also present shear stress compared to the density of the fibers and the length of the fibers since the actual geometry of the ESL is still under debate.
AUTHOR: Xiang-qiang Chu
TITLE: Proteins Remain Soft at Lower Temperatures under Pressure
Xiang-qiang Chu, Antonio Faraone, Chansoo Kim, Emiliano Fratini, Piero
Juscelino B. Leao and Sow-Hsin Chen
ABSTRACT: The low temperature behavior of proteins under high pressure is not as extensively investigated as that at ambient pressure. Recently, we study the dynamics of a hydrated protein under moderately high pressures at low temperatures using quasi-elastic neutron scattering method. We show that when applying pressure to the protein-water system, the dynamics of the protein hydration water does not slow down, but becomes faster instead. The degree of “softness” of the protein, which is intimately related to the enzymatic activity of the protein, shows the same trend as its hydration water as a function of temperature at different pressures. These two results taken together suggest that at lower temperatures, the protein remains soft and active under pressure.
AUTHOR: Roy Dar
TITLE: Gene Expression Correlation Spectroscopy of Transcriptional Bursting in the Integrated HIV Promoter"
R. D. Dar [1,2], A. Singh , B. Razooky , D. K. Karig , J. F. Cooke , C. D. Cox [4,5], L. S. Weinberger [6,7], and M. L. Simpson [1,3]
Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Tennessee 37831, Departments of Physics and Astronomy , Materials Science , and Civil and Environmental Engineering , and the Center for Environmental Biotechnology , University of Tennessee, Knoxville, Tennessee 37996,  Department of Chemistry and Biochemistry, and  Whitaker Institute for Biomedical Engineering, University of California San Diego, La Jolla, CA 92093
ABSTRACT: We have developed a technique which exploits a probative use of biological noise in the in vivo characterization of genetic circuit architectures and elucidation of their structure-function relationships. We demonstrate its novelty by characterizing integrations of the long terminal repeat (LTR) promoter of HIV across colonies of Human cells (Immune T cells). Our analysis enables a quantitative characterization of transcriptional bursting expression dynamics in individual living cells.
We observe higher gene expression noise magnitude in cells with higher basal expression levels which by theory suggests expression in short intense transcriptional bursts. Although still under investigation, these dynamics may possibly suggest that the highly expressed HIV promoter integrations fall within stress response gene architectures which have also been reported to be transcriptionaly bursty. Finally, these modeling insights may play an important role in viral entrance and exit from latency within cells.
AUTHOR: Mitchel Doktycz
TITLE: Experimental and Computational Challenges in the Development of Cell Mimics
ABSTRACT: The cell is an engineering marvel that is capable of efficiently transducing energy, information, and materials to meet its needs. This capacity results from confined chemical reaction systems that are capable of controllably exchanging chemical reagents and signals with their environment. Emulating these natural structures offers the potential to realize some of their abilities in robust synthetic devices. To this end, synthetic cell mimics are being constructed using advanced nanofabrication techniques. The resulting devices are being integrated with biochemical reaction systems that sense and respond to their local environment. Results related to the fabrication and testing of these biologically inspired cell mimics will be presented.
AUTHOR: Jon Erickson, Discovery Chemistry & Research Technology, Lilly Research Laboratories, Indianapolis IN 46285
TITLE: Challenges of Ligand Binding Mode Prediction for use in Drug Design
ABSTRACT: Structure-based design (SBDD) is a key strategy in drug discovery and optimization. A key component of SBDD process is the ability to predict the binding mode of a ligand to the target receptor. As such, the accuracy of binding mode prediction can be critical to the success of a SBDD effort. Molecular docking methods in combination with X-ray crystallography are typically the main avenue to predict binding modes in SBDD efforts. This talk will frame the importance of accurate docking through an example of an SBDD effort on BACE. This will be followed by a discussion of the results of some studies on molecular docking accuracy and potential strategies for improvement.
AUTHOR: Bashar Hamza
TITLE: Top-Down Approach to the Fabrication of a GaN-based PhC Biosensor
B. M. Hamza, H. Yalamanchili, H. Andagana, X. Cao, L. A. Hornak, J. Dawson, D. Korakakis
Lane Department of Computer Science and Electrical Engineering, West Virginia University, Morgantown, WV, U.S.A
Combining optics and microfluidics to create a portable optofluidic photonic crystal (PhC) biosensor is a novel idea with promising applications in the fields of counter-terrorism, agricultural sciences, and health sciences. GaN is being targeted as the photonic crystal slab material for two main reasons: its transparency in the visible spectral range, within which the excitation and emission wavelengths of the commercial fluorescent-labeling dyes fall, and its intrinsic thermal stability which provides an increased flexibility of operating in different environments. Optical modeling efforts indicate a 25-fold enhancement of the fluorescent emission in this portable fluorescent-based PhC biosensor. Presented here are fabrication processes of a gallium nitride (GaN)-based PhC biosensor with a resonance-enhanced fluorescence detection mechanism that shows potential for meeting the single molecule detection requirements of the aforementioned application areas. A top-down approach, in which the fabricated GaN wafer was grown on sapphire, was followed to produce our photonic crystal structures. Initially, photolithography and Inductively Coupled Plasma (ICP) etching was used to produce an integrated waveguide structure in GaN. PhC patterns were then fabricated using electron beam lithography and then ICP etched to produce the GaN-based PhC structures where metal or SiO2 acted as a mask. Scanning electron microscopy (SEM) images will be presented at each point in the study. Theoretical results using MIT Photonic Bands (MPB) software as well as initial optical testing of our GaN-based PhC will be discussed.
AUTHORS: R. L. Hettich(1), A. L. Russell(1), N. C. VerBerkmoes(1), M. Shah(1), Claire Fraser-Liggett(2), J. K. Jansson(3)
TITLE: An Integrated Experimental / Bioinformatic Approach for Characterizing the Molecular Activities of the Human Gut Microbiome*
ABSTRACT: The human gastrointestinal tract is a complex ecosystem containing a delicate balance of human and microbial cells involved in an intricate symbiotic relationship. In general, the microbial constituency helps maintain a healthy environment and aids in the efficient digestion. However, environmental and/or genetic factors may result in an altered bacterial composition that manifests in a diseased condition, such as Crohn’s disease. The recent availability of genomic-based molecular technologies such as whole community genome sequencing and whole community proteomics have provided unique capabilities of profiling the compositions and activities of this microbiome without having to cultivate its membership. We are utilizing a non-targeted, mass spectrometry-based proteomics approach to identify the microbial proteins in fecal samples from human female identical twins. Proteome samples were analyzed with technical duplicates via a multidimensional LC tandem mass spectrometric approach on a hybrid linear ion trap-Orbitrap. The proteome measurements identified ~ 1000 -1400 proteins for each sample and replicate. Amongst the microbial genomes, Bacteroides thetaiotaomicron, Bifidobacterium longum, Bacteroides fragilis and Bifidobacterium adolescentis were the most highly identified species, as expected since these are known to be among the most abundant bacteria in the human gut. Interestingly, the majority of the microbial proteins that were identified were classified into COG categories for translation, energy generation, and carbohydrate metabolism. The latter category is especially interesting in that it reveals one of the synergistic relationships between humans and microbes in this ecosystem. Surprisingly, a number of innate human immunity proteins were also observed, suggesting a level of human regulation of microbial abundance. A number of abundant unknown proteins were also identified. The results of this study demonstrate that it is possible to obtain high quality, extensive protein identifications by screening translated metagenome sequence data collected from completely different individuals
* Research support provided by NIH-HMP Demonstration Program. Oak Ridge National Laboratory is managed by UT-Battelle, LLC, for the U.S. Department of Energy under Contract No. DE-AC05-00OR22725.
AUTHORS: Jeremy Jay
TITLE: The Ontological Discovery Environment : Integrating gene-centered data across diverse experiments
Jeremy J Jay (1), Vivek Philip (2), Zuopan Li (1), Yun Zhang (1), Roumyana Kirova (3),
Michael A Langston (1), Erich J Baker (4), Elissa J Chesler (3)
1 Computer Science Department, University of Tennessee, Knoxville, TN
2 Genome Science and Technology, University of Tennessee & Oak Ridge
National Laboratory, Oak Ridge, TN
3 BioSciences Division, Oak Ridge National Laboratory, Oak Ridge, TN
4 Computer Science Department, Baylor University, Waco, TX
ABSTRACT: The Ontological Discovery Environment (ODE) is a web-based resource located at www.ontologicaldiscovery.org. It facilitates discrete data integration across species, tissue and experimental platform. Sets can be stored, retrieved, and shared publicly or privately, and compared across the over 7,000 data sets now available. Many tools are online to assist in comparison across multiple diverse data sets. These tools include Hypergeometric tests, Jaccard similarity, Clustering, and Phenome Maps as derived from bi-partite graph analyses. Recent enhancements of the Phenome Map tool provide tests to measure the significance of observed gene overlap in multiple data sets, along with visualization and interaction.
AUTHOR: Wen Jiang and Xiaopeng Zhao
TITLE: A Novel Control Protocol for Regulating Pore Radius in Electroporation
Mechanical, Aerospace and Biomedical Engineering Department University of Tennessee Knoxville, TN 37996-2030
ABSTRACT: Electroporation, which has wide applications in biology and medicine, is a technique in which electric pulses are used to create transient and nonselective pores in cells membranes to deliver chemical or biologically active molecules into cells. To ensure proper uptake of drug molecules and to avoid possible injury to cells, it is essential to control the radii of the pores and the time duration for which the pores remain open. Conventional open-loop implementation of electroporation has two limitations: One is the resulted pore radii cannot be known beforehand, and the other is a range of pore radii is physically unstable for a given external voltage and thus cannot be achieved in practical operations. To overcome these problems, we design a novel control strategy to stabilize the originally unstable solutions. The control protocol consists of two steps. First, we construct the nullcline of the pore-growth dynamics utilizing a quasi-static loading process. Then, a feedback control input is computed based on the nullcline for the desired pore radius. The present control is a global method utilizing global dynamical properties of the nonlinear system. Moreover, this model-independent protocol does not require detailed knowledge about the governing equations of the system, making it easy to be implemented in experiments. Extensive numerical simulations based on realistic models of electroporation demonstrate the robustness and effectiveness of the control protocol. This control protocol may enhance the application of electroporation and may lead to new applications of the technique.
AUTHOR: Vadzim Karpusenko
TITLE: Secondary structure prediction of alanine-based proteins via Landau free energy calculations
Vadzim Karpusenka, Volodymyr Babin, Christopher Roland and Celeste Sagui
North Carolina State University
ABSTRACT: We performed a computational study of short alanine-based and monomer peptides using host-guest technique. The free energy distribution as a function of the hydrogen bonds number, the handedness and radius of gyration have been calculated using the recently introduced Adaptively Biased Molecular Dynamics (ABMD) method, combined with parallel temperature replica exchange and post-processing Umbrella Correction. The free energy surfaces are in agreement with empirical evidence of preferred secondary structures for the peptides.
AUTHOR: Nicholas LaRacuente
TITLE: Real-time Autocorrelation with Desktop Graphics Cards for Fluorescence Correlation Spectroscopy"
Nicholas LaRacuente and Carl Grossman
ABSTRACT: We aim to develop fast, real-time autocorrelation software using the parallel capabilities of stream processors for use in measuring the diffusion constants of chemicals embedded in lipid vesicle layers. Recent developments in hardware and software have made several APIs and languages available for general computing tasks using the cheaply available stream processors of desktop graphics hardware. These are more suited to emulating the specialized hardware of expensive autocorrelator cards than traditional CPU-based software approaches. We will use this software to perform fluorescence correlation spectroscopy, in our case demanding autocorrelation in the millisecond time range. Combining this with other techniques, we intend to develop a low-cost, generally applicable method for measuring the diffusion of chemicals in lipid membranes.
AUTHOR: Tian Li
TITLE: A Novel Potential Gating Mechanism in the Arabidopsis NIP7;1 Boric Acid Transporter
Tian Li (1), Jerome Baudry (1,2), and Dan Roberts (1,2)
1. Graduate School of Genome Science and Technology, UT-ORNL
2.Department of Biochemistry and Cellular and Molecular Biology, UT
ABSTRACT: Functional analysis shows that there are two subfamilies of aquaporin: aquaporin which transport water specifically, and the aquaglyceroporins which can facilitate conduct of glycerol, urea, and other small molecules in addition to water. Structure analysis indicate that all the aquaporin adopt ‘hourglass’ conformation with 6 transmembrane alpha-helices linked by 5 loops. There are two constraints: two highly conserved domains with ‘NPA motifs’ are located on loop B and loop E and a tetrad of amino acid residues that contains aromatic residues and a conserved Arginine referred as Ar/R region. AtNIP7;1 belongs to the second subgroup of plant nodrolin-26 like intrinsic protein with AtNIP5;1 and AtNIP6;1. The functions of AtNIP5;1 and AtNIP6;1 have already been elucidated that both of them can conduct boric acid in order to transport boron to the shoot tissue. Previous work been done on AtNIP7;1 indicates that AtNIP7;1 doesn't transport water or glycerol. Boric acid uptake assay didn’t show apparent boric acid conductivity in AtNIP7;1. Homology modeling on AtNIP7;1 provides an idea that the Y81 probably is the key residue blocking the hole by observation of up and down conformation of Y81, and mutation of Y81 to C facilitates boric acid transportation by boric acid uptake assay. Molecular dynamics simulation shows another residue---R220, which belongs to Ar/R region, adopts two conformations: up and down which could interact with Y81 by hydrogen bond. These two residues Y81 and R220 could be the very candidates involving in the gating mechanism of AtNIP7;1.
AUTHOR: Karl Martini
TITLE: Thermodynamics and Electrostatics of the Eye Lens Protein GammaB"
KM Martini, D Hollenbeck, A Harkin, DS. Ross, A Langner and GM Thurston
Department of Physics, Chemistry, and School of Mathematics at Rochester Institute of Technology
ABSTRACT: Thermodynamics and Electrostatics of the Eye Lens Protein GammaB Crystallin Cataracts are one of the leading causes of blindness in the world. In order to better understand the liquid-liquid phase transition of the cytoplasm of eye lens cells, one cause of cataract, we are studying the electrostatic contribution to interactions between bovine eye lens gammaB crystallin proteins. Experimentally, this protein shows strong dependence of liquid-liquid phase separation and liquid structure on both pH and ionic strength. Gamma crystallin phase diagrams are also known to be sensitive to orientation-dependent protein interactions, as well as to cataractogenic mutations that alter electrostatic properties. We are constructing computer simulations of gammaB electrostatics that are designed to incorporate the complications of ionic screening of charge interactions, the dynamic response of protonatable groups on a protein to the local electrostatic potential, a phenomenon known as charge regulation, and orientation-dependent interactions of the protein. We aim to construct a grand canonical distribution treatment of charge regulation-mediated protein interactions. Towards this goal, a finite difference method using a rectangular grid is employed to solve the linearized Poisson-Boltzmann equation in the region exterior to proteins together with Poisson’s equation interior to the protein, so as to estimate the needed dependence of the free energy of charging for both isolated and neighboring proteins. We compare our results with experimental findings for aqueous solutions of bovine gammaB crystallin.
AUTHOR: Adrianne Norris
TITLE: The Aminoglycoside Acetyltransferase-(3)-IIIb: Kinetic and Thermodynamic Insight Into an Antibiotic Resistance Protein
Adrianne L. Norris* and Engin H. Serpersu* **
*Department of Biochemistry, Cellular and Molecular Biology
**The Graduate School of Genome Science and Technology, Oak Ridge National Laboratory
The University of Tennessee, Knoxville
ABSTRACT: The aminoglycoside acetyltransferase (3)-IIIb (AAC), targets the deoxystreptamine ring that is common to all aminoglycoside antibiotics and modifies a large number of aminoglycosides. Kinetic studies have revealed that Km values fall within a small micro-molar range for aminoglycosides of varying size and structure. However, based on kcat/Km values, neomycins are more favored than kanamycins. Kinetic studies also yielded activation energies of 11.6 and 9.6 kcal/mol for the modification of kanamycin A and neomycin B, respectively. Isothermal titration calorimetry (ITC) experiments revealed that binding of aminoglycosides to AAC occurs with favorable enthalpy (∆H<0) and unfavorable entropy (∆S<0). The formation of ternary complexes is enthalpically more favored while entropically more disfavored compared to the formation of the respective binary complexes. Furthermore, a two-way synergistic effect has been observed for antibiotic and coenzyme binding. These results represent the first thermodynamic/kinetic characterization of an aminoglycoside-modifying enzyme that modifies the 2-deoxystreptamine ring of aminoglycosides.
AUTHOR: Letitia Olson
TITLE: Transit peptide-Toc protein interactions revealed through chemical cross-linking
Letitia N. Olson 1,2 L. Evan Reddick 1,2 Barry D. Bruce 2
1 Contributed Equally to this Poster, 2 Department of Biochemistry, Cellular and Molecular Biology, Univ. Tennessee, Knoxville TN 37996
ABSTRACT: The majority of chloroplasts proteins are nuclear encoded necessitating a targeting and import mechanism for this organelle. These Chloroplast bound proteins are translated as high molecular weight precursor proteins in the cytosol and contain an N-terminal targeting sequence known as the transit peptide (tp). The tp is recognized by membrane bound GTPases comprising the Translocon of the Outer Chloroplast membrane (TOC complex). While limited information is known about the separate pieces of this puzzle, the molecular details of the interaction between the transit peptide and the Toc complex are not well defined; however, it is known that there are two related GTPase import receptors, Toc34 and Toc159 that directly bind to and interact with the transit peptide. To probe these interactions, we have developed a chemical cross-linking approach to investigate the dynamics of hetero and homodimerization of the Toc components as well as tp binding. We have selected the optimum length of homobifunctional thiol specific cross-linkers to permit maximum efficiency in cross-linking. This assay uses thiol based cross-linking to determine the site of interaction between Toc159, Toc34, and tp by utilizing a series of single cysteine mutants of the transit peptide of the small subunit of Rubisco, as well as a single cysteine mutation of Toc159G. By crosslinking in the presence/absence of nucleotides and tp, we can determine the oligomeric status of the translocon in vitro. The tp cysteine variants were created in a cysteine-free mutant transit peptide (C58Y) to produce a series of double mutants each containing a single cysteine. We have designed, mutated, expressed, and purified 7 different peptides where the single cysteine is placed approximately every 8 amino acids. By iodinating the single tyrosine on the tp we can follow the crosslinking and map the interaction domain. Using this approach we probed the transit peptide region that is proximal to the cysteine residue associated with psToc34, and 159G; transit peptide titration revealed a lower Kd for Toc34 than for Toc159. Also it was found that GTP-bound Toc34 has a higher affinity for tp than Toc159, which is not activated by the nucleotide state. Turn residue mutations of tp no longer stimulate the hydrolysis of Toc34, and do not stimulate the dimer to momomer transition that is observed with wild type tp. Through our experimentation, we hope to be able to map the recognition elements of tp in order to better understand the function of this essential element of chloroplast protein translocation.
Funding for this research was provided by a National Science Foundation Cell Biology grant to B.D.B, a Science Alliance grant and Sigma Xi contribution to L.E.R. and an NIH PEER training grant has recently been awarded to L.N.O.
AUTHOR: Jennifer Pascal
TITLE: Optimal Separation Times of Biomolecules in an Electrical Field Flow Fractionation (EFFF) separator: Effect of electroosmotic flow
Jennifer A. Pascal 1, Mario A. Oyanader 1,2, and Pedro E. Arce 1
1 Department of Chemical Engineering, Tennessee Technological University, Cookeville, TN
2 Engineering Department, Universidad Arturo Prat, Iquique, Chile
ABSTRACT: Electrokinetic methods are used a wide variety of applications related to separations, environmental remediation, and drug delivery, to name a few. Separation of biomacromolecules for pharmaceutical processes is a multi-million dollar effort where even the smallest increase in the separation efficiency has a very healthy economical impact on the process or application. Antibiotics, proteins, and DNA are some key examples of biomacromolecules where new techniques and approaches for separation and or characterization are required. In this presentation, the authors will discuss a model that can be applied to an EFFF separation device to determine the effect of electroosmotic flow on the separation efficiency. In particular, optimal times of separation will be computed and parametrically analyzed for a wide range of values. Principles of electrokinetic hydrodynamics (EKHD) allow for the connection to the convective-diffusive transport with the aid of the spatial averaging approach. Results of the research effort will predict the effects of electroosmosis on the optimal separation times to design and or optimize an EFFF separation device where electroosmotic flow could play a role.
AUTHOR: Tatiana Perevozchikova1, Christopher Stanley2, Helen P. McWilliams-Koeppen1, and Valerie Berthelier1 1Graduate School of Medicine, University of Tennessee Medical Center, Knoxville, TN 37920 2Neutron Scattering Science Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831
TITLE: Influence of Polyglutamine Repeat Length on the Structure of Amyloid Fibril Formation Studied by Time Resolved Small Angle Neutron Scattering
ABSTRACT: Amyloid aggregates are filamentous fibrils that form as a result of self-assembly of numerous polypeptides. The formation of the aggregates has been found to be directly associated with diverse neurodegenerative disorders, including Alzheimer’s, Parkinson’s and Huntington’s (HD) diseases. Mutant Huntingtin peptide (Htt), which is linked to Huntington’s disease (HD), contains an abnormally long stretch of polyglutamine (polyGln) repeats that leads to the formation of fibrils with stable, -sheet rich structures. Here we conduct a comparative analysis on the differences between aggregation pathway of native and mutant Htt peptide, containing 22 and 42 glutamine residues, respectively. We are using time-resolved small angle neutron scattering (SANS) to probe the aggregates formed by these peptides. SANS is a very useful technique for following structural changes of particles in a solution. From the time-resolved SANS data we obtain the radius of gyration and mass per length of the forming aggregates as the kinetic reactions ensure. We are also able to observe the internal structure of the mature fibrils from both normal and pathological peptides. This research is providing new insights into the pathway of polyGln aggregation and should assist in determining the factor of glutamine length on the structure of Htt amyloid fibrils.
AUTHOR: Mahmoud PourArsalan
TITLE: Organ Dose and Organ Dose Equivalent Rate Calculations from October, 2003 Solar Energetic Particle (SEP) Event using Earth-Moon-Mars Radiation Environment Module (EMMREM)
M. PourArsalan 1; L.W. Townsend 1; N.A. Schwadron 2; M.A. Dayeh 3; M. Desai,3; K. Kozarev 2
1 Department of Nuclear Engineering, University of Tennessee;
2 Department of Astronomy, Boston University;
3 Southwest Research Institute.
ABSTRACT: The central objective of the Earth-Moon-Mars Radiation Environment Module (EMMREM) is to develop a numerical model for completely characterizing the time-dependent radiation environment in the Earth-Moon-Mars and Interplanetary space environments. The Module includes a 3D energetic particle transport model (EPREM), and utilizes a version of the space radiation transport code (BRYNTRN) developed at NASA Langley Research Center. With the initial setup of the Earth-Moon-Mars Radiation Environment Module (EMMREM) framework in place, we are turning to performing realistic simulations with observations from October, 2003 Solar Energetic Particle (SEP) event for module testing and as an example of the module capabilities. In this work we present and discuss the Earth-Moon-Mars Radiation Environment Module (EMMREM) predictions for the organ dose rate, organ dose equivalent rate for skin and BFO in space, throughout the event, for various aluminum and water shield thicknesses. These results will permit time-dependent estimates of organ exposures for human crews in deep space.
AUTHOR: John Richards
TITLE: A real time neutron imaging system to resolve large unit cell crystal structure (~1,000,000 atoms) for istruments using TOF neutron diffraction techniques at the new Spallation Neutron Source (SNS), USA.
J.D.Richards, R.G.Cooper, C.Donahue, and T.Visscher
ABSTRACT: Detector systems for proposed (macromolecular diffractomer) MANDI instrument at the SNS are being developed to meet challenges for investigating structures of ever more complicated proteins. While X-rays have traditionally been used to probe protein structure, many further experimental challenges require neutron diffractometry. The world's most intense pulsed neutron facility is now available at the SNS. High resolution real time (stamp) neutron imagers are proposed for the MANDI instrument. These are built on newer technologies also developed at the SNS. This poster discusses the experimental challenges faced to deliver the highest resolution posible to better enable input for experiment and computation used to elucidate protein structure.
AUTHOR: Kevin Segall
TITLE: STATIC LIGHT SCATTERING STUDIES OF THE MOLECULAR WEIGHT AND SECOND VIRIAL COEFFICIENT OF EYE LENS ALPHA CRYSTALLIN"
Kevin Segall, Rochester Institute of Technology
ABSTRACTThe electrostatic properties of eye lens proteins are important in determining their high concentration light scattering and phase separation, relevant to cataract disease. We are using static light scattering to measure the molecular weight and second virial coefficient of the largest, most prevalent eye lens protein, alpha crystallin, as functions of pH and ionic strength, in order to investigate the consequences of varying both protein charge and charge screening in solution. Alpha crystallin is a large, somewhat polydisperse globular protein that comprises numerous subunits, each approximately 20,000 grams per mole (20kDa). Measurements of the intensity of the scattered light, at low protein concentrations, give direct information about the molecular weight and interactions of particles in solution. Upon varying the pH from 6 to 7.4 we find that alpha crystallin has an approximately stable molecular weight of around 750 kDa, in good agreement with literature values, but also varies about 100kDa from this average as a function of pH. Changing the ionic strength had a comparatively small effect on the molecular weight. Alpha crystallin second virial coefficients, in units normalized by particle volume, were found to be between 5 and 18, depending on pH and ionic strength. These values are consistent with interactions that are on average more repulsive than those of hard spheres, which have a corresponding normalized second virial coefficient of 4. In the stated pH range, we find that lowering the ionic strength increases alpha crystallin second virial coefficients, corresponding to increasingly repulsive interprotein interactions. Near neutral pH, well away from the alpha crystallin isoelectric point and at high ionic strength, the second virial coefficient indicates progressively more attractive interactions, as the pH is lowered towards the isoelectric pH. However, a more complicated dependence of second virial coefficients on pH occurs closer to the isoelectric pH.
AUTHOR: Megan Scoppa
TITLE: Molecular Modeling of the ATP-synthase Motor F0 Subunit and Proton Translocation
Megan Scoppa and Margaret Cheung,
University of Houston, Physics Dept
ABSTRACT: According to the National Institute of Health (2007), 57 million Americans were suffering from symptoms related to impaired glucose diseases, such as diabetes. The metabolism's power house, the Adenoise-Triphosphate (ATP) synthase motor, holds the clues to help treat these and other similar conditions. The ATP motor is divided into two parts, the F1 and F0 subunits. The F0 subunit is located inside the mitochondria's inner membrane, which has resulted in the inability of an accurate all-atom NMR to be experimentally found.My research involves using steered molecular dynamics simulations, from which it is possible to show a stochastic model of this F0 subunit along with the ability to follow a proton from the periplasm through the motor, to be used as a chemical energy fuel from Hydrogen-Bonding to create torque for the subunit, and finally out through the cytoplasm.
AUTHOR: Jyothirmai Simhadri
TITLE: EFFECT OF MATERIAL MORPHOLOGY ON ELECTROKINETIC-BASED SEPARATION OF BIO-MOLECULES: A COMPUTATIONAL-BASED APPROACH"
Jyothirmai J. Simhadri, Pedro Arce, Mario Oyanader & Holly Stretz
Tennessee Technological University, Cookeville, TN 38505
ABSTRACT: Electrophoresis in polymer hydrogels with nanometer-scale pore structure is widely used for the separation and purification of biological macromolecules. In gel-electrophoresis, the internal morphology of the gel also plays an important role in improving the separation. Tuning the nanometer-scale pore structure of the gel either by templating or by adding nanoparticles to improve separations has been the current area of focus in our research group. Moreover, analysis of the effects of the nature of the pore alignment, pore length and diameters on the transport of macromolecules is an important aspect to be studied either analytically or computationally as shown by previous efforts (Trinh et al, 1999; Hidalgo et. al, 2007). In this research, we propose to computationally analyze different pore models (associated with gel materials) and study the effect of geometry on the transport properties in this anisotropic-like media. Results will illustrate, for example, the role of pore-scale in conjunction with electrical fields and identify potentially usual architectures for an optimal separation.
References: 1. Trinh, S., B.R. Locke and P.E. Arce, “Convective and Electroconvective Transport in Non-Uniform Channels with Application to Macromolecular Separations,” Separation and Purification Technology, 15, 255 (1999). 2. Hidalgo, R., M. A. Oyanader (*), and P. E. Arce, “Dispersive Mixing Effect Caused by Combined Effect of Channel Morphology and Electrophoretic Mobility in Poiseuille Flows.” AIChE Annual Meeting, Salt Lake City, 2007. (*) Speaker.
AUTHOR: Jeremy C. Smith, Director: Center for Molecular Biophysics, Oak Ridge National Laboratory.
Prospects for Biology with Next-Generation Neutron Scattering and High-Performance Computer Simulation.
ABSTRACT: The ramping up of the Spallation Neutron Source and the National Leadership Computing Facility Jaguar XT4 at ORNL brings new opportunities for fundamental advances in our understanding of biomolecular structure, dynamics and function. To illustrate the potential recent results will be presented combining neutron scattering with computer simulation to bring about qualitatively new insight into binding phenomena, protein:protein interactions and protein folding. The mechanism of energy transduction in a light-driven proton pump protein is described. Computational approaches to understanding molecular machines are outlined. Finally, we describe a strategy for optimal utilization of petascale supercomputing in biomolecular research, and the types of problems that might then be within reach.
AUTHOR: Adam Sullivan
TITLE: Long-term Behaviors of Infectious Disease Transmission Dynamics
Adam M. Sullivan and Xiaopeng Zhao
University of Tennessee, Knoxville MABE
ABSTRACT: Infectious diseases are caused by parasites including viruses, bacteria, protozoans, helminthes, and arthropods. Infectious diseases are an important mortality factor in populations of mammals and birds. Outbreaks of infectious diseases in human society may cause several social and economic consequences. In this work, we develop a predator-prey type model to describe the transmission dynamics of directly transmittable diseases. The goal of this work is to investigate long term influences of infectious diseases to the host population. Detailed bifurcation analysis reveals that the result of a disease depends on a critical parameter, which is a function of several important factors, namely: the transmission rate from one host to the next; the degree to which the disease induces mortality; the extent to which the host acquires immunity; and the carrying capacity for the host population. When the parameter is less than a threshold, the diseases will naturally die out whereas when the parameter is larger than the threshold, the disease will regulate the host population and a portion of the population will remain infected. When the parameter is further increased, transients of the disease may demonstrate damped oscillations. As a result, the system may exhibit a phenomenon, known as stochastic resonance. Specifically, when the transmission rate is subject to randomness, the interaction between the demographic stochasticity and the propensity to damped oscillations may lead to cyclic patterns in the long-term dynamics. The analysis and simulation may lead to remarkable insights on understanding the mechanisms of infectious diseases and thus provide guidelines in disease control.
AUTHOR: Tran, Nhiem
TITLE: "Increased osteoblast density in the present of calcium phosphate coated magnetic nanoparticles"
Nhiem Tran1, Rajesh Pareta2, Thomas Webster2
1 Department of Physics, Brown University
2 Division of Engineering, Brown University, Providence, RI 02912.
ABSTRACT: Magnetic nanoparticles have been used widely as drug delivery materials in recent years. The present research goal is to treat bone diseases (such as osteoporosis and infection) by using surface modified magnetic nanoparticles. Magnetite (Fe3O4) and maghemite (Fe2O3) were synthesized and coated with calcium phosphate (CaP) using wet chemical method. The resulting nanoparticles were treated hydrothermally to change the crystalline properties of CaP. Nanoparticles were characterized via transmission electron microscopy (TEM) and vibrating sample magnetometry (VSM). TEM was also used to study the uptake of nanoparticles into osteoblasts (OB) and bacteria. OB proliferation experiments were conducted after 1, 3 and 5 days in the presence of the various iron oxide nanoparticles alone and CaP coated iron oxide magnetic nanoparticles. OB proliferation experiments were also conducted after 1, 3 and 5 days in the presence of various concentrations of CaP coated nanoparticles to examine a possible concentration dependent trend on OB density. Staph epidermidis were incubated with different doses of Fe3O4 to determine the effect of these nanoparticles on bacteria activity. Results of this in vitro study demonstrated greater OB functions and inhibited bacteria functions in the presence of select magnetic nanoparticles. In summary, the results of this study showed that magnetic nanoparticles should be further studied for various orthopedic applications.
AUTHOR: Phong Tran
TITLE: Cell-Cell Interaction on Titanium Surfaces
Phong A. Tran, Love Sarin, Robert H. Hurt and Thomas J. Webster
ABSTRACT: Two common causes leading to bone implant failure are: an insufficient bonding between the implant and the surrounding bone as well as infection. Patients with implant failure often undergo revision surgery which are costly and painful. Moreover, for patients who receive orthopedic implants after cancerous tissue is removed, it would be beneficial to implant an anti-cancer material that can impede the return of cancerous tissue growth that may develop from cancer cells not removed during surgery. Therefore, in this study we create a coating material that can: (i) promote healthy, normal bone growth and (ii) impede cancer growth. For that, conventional orthopedic implant materials (such as titanium (Ti), stainless steel and ultra high molecular weight polyethylene) were coated with selenium (Se) nanoclusters. Different coating densities were achieved by varying Se concentration in the reaction mixture. For the first time, Se nanocluster coatings formed on all materials mentioned were shown to enhance healthy osteoblast (bone-forming cell) and inhibit cancerous osteoblast proliferation in either separate-culture experiments or co-culture experiments. Interestingly, the results from co-culture experiments indicated some interaction between cancer cells and healthy cells that affect growth of both kinds of cells. Mathematical models will be used to simulate the growth of two cell types and determine the interaction factor.
AUTHOR: Edward N. Trifonov
TITLE: The Thrill of Linking Polymer Statistics and Sequence Space with Protein Structure and Function.
ABSTRACT: As every discipline protein science went through many discoveries each time opening new perspectives and closing some paths. Two developments of last decade are especially devastating being very fundamental and simple, impossible to ignore. As the result, the whole course of protein science has to be changed. These are discovery of structural modules of proteins - closed loops of standard size, 25-30 amino acid residues (1, 2), and the break-through into protein sequence space that turned out to consist of isolated networks each representing individual protein module type (3, 4).
The closed loops come from flexibility properties of protein chain. They are demanded to be there by polymer statistics. Only they appear in proteins much more often than in random chains. Apparently, the earliest proteins were of that elementary size and structure. Surely, the folding of both elementary loops and their linear combinations falls out from the astronomic time range suggested by Levinthal paradox.
The formatted sequence space is made of over 100 million 20 residue long natural sequence fragments. Closely related fragments (nodes) connect pair-wise, forming long walks and convoluted networks. Spectacularly, while the fragments from the same network are functionally and structurally the same, their sequences may differ as much as not to have a single matching residue.
The strategy of protein structure/function/sequence research turns now inside-out: one has to catch up and study first the constituent modules rather than whole proteins.
1. Berezovsky, I. N., Grosberg, A. Y., Trifonov, E. N., Closed loops of nearly standard size: common basic element of protein structure. FEBS Letters 466, 283-286 (2000)
2. Trifonov, E. N., Berezovsky, I. N., Evolutionary aspects of protein structure and folding, Curr. Opinion Struct. Biol. 13, 110-114 (2003)
3. Frenkel, Z. M., Trifonov, E. N., Walking through protein sequence space. J Theor Biol 244, 77-80 (2007)
4. Trifonov, E. N., Frenkel, Z. M., Evolution of protein modularity, Curr Opinion Struct Biol 19, 335-340 (2009)
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AUTHOR: Wu, Lingzhi
TITLE: Deciphering interactions of the aminoglycoside phosphotransferase(3′)-IIIa with its ligands
Lingzhi Wu and Engin Serpersu
University of Tennessee, Knoxville
ABSTRACT: The thermodynamic characterization of interactions of APH with its ligands are done by determining dissociation constants of enzyme–substrate complexes. Metal binding studies showed that three divalent cations bind to the apo-enzyme with low affinity. The presence of nucleotide promotes three additional divalent cations with much higher affinity. The presence of metal ions, with or without aminoglycoside, shows only a small effect on binding affinity of the nucleotide to APH. The presence of metal–nucleotide, increases the binding affinity of aminoglycosides to APH. Replacement of magnesium with manganese lowered the catalytic rates significantly while affecting the substrate selectivity of APH such that the aminoglycosides with 2′-NH2 become better substrates than those with 2′-OH.
AUTHOR: Zhenli Xu
TITLE: Optimal Integral Expressions for Effective Born Radii
Zhenli Xu, Wei Cai, and Andrij Baumketner
University of North Carolina at Charlotte, Charlotte, NC 28223, USA
ABSTRACT: Fast and accurate calculation of solvation energies has become an essential task in molecular dynamic and Monte Carlo simulations of biomolecules in aqueous environments. The generalized Born theory is one of the most successful macroscopic approaches for electrostatic interactions, which approximately reproduces the result from Poisson or Poisson-Boltzmann equation models through a semi-analytical pairwise summation. The goal of this Poster is to derive better approximations for effective Born radii in the generalized Born model of molecular solvation by analyzing the Kirkwood-series solution of the Poisson equation for a spherical solute. The main focus is on solutes under non-conducting boundaries, where the solute dielectric constant and solvent dielectric constant lead to a non-vanishing ratio $Δ$. A series approximation is developed for the Born radius, in which a dominant leading term is corrected by terms of the order of $O(Δ)$. The series is further approximated by an expansion of volume integrals over the solute domain. Optimal combinations of integrals are then proposed, based on computational cost and accuracy criteria. The combinations are tested on solute molecules with non-spherical geometry including a prolate spheroidal model and a protein molecule. For finite values of $Δ$, the proposed formulas are seen to work better than the models developed previously. The relative accuracy of integral expressions is seen to vary among spherical and non-spherical solutes.