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Differential accessibility of a rotavirus VP6 epitope in trimers comprising type I, II, or III channels as revealed by binding of a human rotavirus VP6-specific antibody.
Aiyegbo MS, Eli IM, Spiller BW, Williams DR, Kim R, Lee DE, Liu T, Li S, Stewart PL, Crowe JE
(2014) J Virol 88: 469-76
MeSH Terms: Amino Acid Sequence, Antibodies, Viral, Antigens, Viral, Base Sequence, Binding Sites, Antibody, Biopolymers, Capsid Proteins, Cryoelectron Microscopy, DNA Primers, Epitopes, Mass Spectrometry, Molecular Sequence Data
Show Abstract · Added March 7, 2014
Previous human antibody studies have shown that the human VH1-46 antibody variable gene segment encodes much of the naturally occurring human B cell response to rotavirus and is directed to virus protein 6 (VP6). It is currently unknown why some of the VH1-46-encoded human VP6 monoclonal antibodies inhibit viral transcription while others do not. In part, there are affinity differences between antibodies that likely affect inhibitory activity, but we also hypothesize that there are differing modes of binding to VP6 that affect the ability to block the transcriptional pore on double-layered particles. Here, we used a hybrid method approach for antibody epitope mapping, including single-particle cryo-electron microscopy (cryo-EM) and enhanced amide hydrogen-deuterium exchange mass spectrometry (DXMS) to determine the location and mode of binding of a VH1-46-encoded antibody, RV6-25. The structure of the RV6-25 antibody-double-layered particle (DLP) complex indicated a very complex binding pattern that revealed subtle differences in accessibility of the VP6 epitope depending on its position in the type I, II, or III channels. These subtle variations in the presentation or accessibility of the RV VP6 capsid layer led to position-specific differences in occupancy for binding of the RV6-25 antibody. The studies also showed that the location of binding of the noninhibitory antibody RV6-25 on the apical surface of RV VP6 head domain does not obstruct the transcription pore upon antibody binding, in contrast to binding of an inhibitory antibody, RV6-26, deeper in the transcriptional pore.
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12 MeSH Terms
Contributions of chemical and diffusive exchange to T1ρ dispersion.
Cobb JG, Xie J, Gore JC
(2013) Magn Reson Med 69: 1357-66
MeSH Terms: Algorithms, Artifacts, Biopolymers, Diffusion Magnetic Resonance Imaging, Image Enhancement, Image Interpretation, Computer-Assisted, Magnetic Resonance Spectroscopy, Reproducibility of Results, Sensitivity and Specificity
Show Abstract · Added March 7, 2014
Variations in local magnetic susceptibility may induce magnetic field gradients that affect the signals acquired for MR imaging. Under appropriate diffusion conditions, such fields produce effects similar to slow chemical exchange. These effects may also be found in combination with other chemical exchange processes at multiple time scales. We investigate these effects with simulations and measurements to determine their contributions to rotating frame (R1ρ ) relaxation in model systems. Simulations of diffusive and chemical exchange effects on R1ρ dispersion were performed using the Bloch equations. Additionally, R1ρ dispersion was measured in suspensions of Sephadex and latex beads with varying spin locking fields at 9.4 T. A novel analysis method was used to iteratively fit for apparent chemical and diffusive exchange rates with a model by Chopra et al. Single- and double-inflection points in R1ρ dispersion profiles were observed, respectively, in simulations of slow diffusive exchange alone and when combined with rapid chemical exchange. These simulations were consistent with measurements of R1ρ in latex bead suspensions and small-diameter Sephadex beads that showed single- and double-inflection points, respectively. These observations, along with measurements following changes in temperature and pH, are consistent with the combined effects of slow diffusion and rapid -OH exchange processes.
Copyright © 2012 Wiley Periodicals, Inc.
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9 MeSH Terms
A biased ligand for OXE-R uncouples Gα and Gβγ signaling within a heterotrimer.
Blättermann S, Peters L, Ottersbach PA, Bock A, Konya V, Weaver CD, Gonzalez A, Schröder R, Tyagi R, Luschnig P, Gäb J, Hennen S, Ulven T, Pardo L, Mohr K, Gütschow M, Heinemann A, Kostenis E
(2012) Nat Chem Biol 8: 631-8
MeSH Terms: Benzeneacetamides, Benzothiazoles, Biopolymers, Calcium, Cell Line, Cyclic AMP, GTP-Binding Proteins, Humans, Ligands, Receptors, G-Protein-Coupled, Signal Transduction
Show Abstract · Added February 16, 2015
Differential targeting of heterotrimeric G protein versus β-arrestin signaling are emerging concepts in G protein-coupled receptor (GPCR) research and drug discovery, and biased engagement by GPCR ligands of either β-arrestin or G protein pathways has been disclosed. Herein we report on a new mechanism of ligand bias to titrate the signaling specificity of a cell-surface GPCR. Using a combination of biomolecular and virtual screening, we identified the small-molecule modulator Gue1654, which inhibits Gβγ but not Gα signaling triggered upon activation of Gα(i)-βγ by the chemoattractant receptor OXE-R in both recombinant and human primary cells. Gue1654 does not interfere nonspecifically with signaling directly at or downstream of Gβγ. This hitherto unappreciated mechanism of ligand bias at a GPCR highlights both a new paradigm for functional selectivity and a potentially new strategy to develop pathway-specific therapeutics.
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11 MeSH Terms
Fast microtubule dynamics in meiotic spindles measured by single molecule imaging: evidence that the spindle environment does not stabilize microtubules.
Needleman DJ, Groen A, Ohi R, Maresca T, Mirny L, Mitchison T
(2010) Mol Biol Cell 21: 323-33
MeSH Terms: Animals, Biopolymers, Cell Extracts, Cyclopropanes, Kinetics, Meiosis, Microtubules, Molecular Imaging, Ovum, Photobleaching, Pyridines, Thiazoles, Time Factors, Tubulin, Xenopus laevis
Show Abstract · Added March 5, 2014
Metaphase spindles are steady-state ensembles of microtubules that turn over rapidly and slide poleward in some systems. Since the discovery of dynamic instability in the mid-1980s, models for spindle morphogenesis have proposed that microtubules are stabilized by the spindle environment. We used single molecule imaging to measure tubulin turnover in spindles, and nonspindle assemblies, in Xenopus laevis egg extracts. We observed many events where tubulin molecules spend only a few seconds in polymer and thus are difficult to reconcile with standard models of polymerization dynamics. Our data can be quantitatively explained by a simple, phenomenological model-with only one adjustable parameter-in which the growing and shrinking of microtubule ends is approximated as a biased random walk. Microtubule turnover kinetics did not vary with position in the spindle and were the same in spindles and nonspindle ensembles nucleated by Tetrahymena pellicles. These results argue that the high density of microtubules in spindles compared with bulk cytoplasm is caused by local enhancement of nucleation and not by local stabilization. It follows that the key to understanding spindle morphogenesis will be to elucidate how nucleation is spatially controlled.
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15 MeSH Terms
Design parameters and sensitivity analysis of polymer-cladded porous silicon waveguides for small molecule detection.
Jiao Y, Weiss SM
(2010) Biosens Bioelectron 25: 1535-8
MeSH Terms: Biopolymers, Biosensing Techniques, Computer-Aided Design, Equipment Design, Equipment Failure Analysis, Molecular Weight, Polymers, Porosity, Refractometry, Reproducibility of Results, Sensitivity and Specificity, Silicon
Show Abstract · Added April 27, 2017
The relationship between the design parameters and small molecule detection sensitivity of porous silicon waveguides is theoretically and experimentally analyzed. Perturbation theory calculations suggest that the sensitivity asymptotically approaches infinity as the porosity of the waveguide approaches a critical porosity for a given mode and the resonant coupling angle of light into the waveguide approaches 90 degrees. Experimental measurements confirm the trend of the porosity-dependent sensitivity for multiple waveguide modes. Given the limitations of the available measurement apparatus that restricts the maximum coupling angle to 68 degrees, a high sensitivity of 120 degrees/RIU was demonstrated for the detection of 0.8 nm molecules attached inside a polymer-cladded nanoscale porous silicon waveguide. Optimized porous dielectric waveguides enable enhanced small molecule detection sensitivity due to their large available surface area for molecular binding.
Copyright 2009 Elsevier B.V. All rights reserved.
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12 MeSH Terms
Quantifying stochastic effects in biochemical reaction networks using partitioned leaping.
Harris LA, Piccirilli AM, Majusiak ER, Clancy P
(2009) Phys Rev E Stat Nonlin Soft Matter Phys 79: 051906
MeSH Terms: Algorithms, Biopolymers, Calcium Signaling, Computer Simulation, Models, Biological, Models, Statistical, Signal Transduction, Stochastic Processes
Show Abstract · Added June 8, 2016
"Leaping" methods show great promise for significantly accelerating stochastic simulations of complex biochemical reaction networks. However, few practical applications of leaping have appeared in the literature to date. Here, we address this issue using the "partitioned leaping algorithm" (PLA) [L. A. Harris and P. Clancy, J. Chem. Phys. 125, 144107 (2006)], a recently introduced multiscale leaping approach. We use the PLA to investigate stochastic effects in two model biochemical reaction networks. The networks that we consider are simple enough so as to be accessible to our intuition but sufficiently complex so as to be generally representative of real biological systems. We demonstrate how the PLA allows us to quantify subtle effects of stochasticity in these systems that would be difficult to ascertain otherwise as well as not-so-subtle behaviors that would strain commonly used "exact" stochastic methods. We also illustrate bottlenecks that can hinder the approach and exemplify and discuss possible strategies for overcoming them. Overall, our aim is to aid and motivate future applications of leaping by providing stark illustrations of the benefits of the method while at the same time elucidating obstacles that are often encountered in practice.
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8 MeSH Terms
Quality assurance of PASADENA hyperpolarization for 13C biomolecules.
Hövener JB, Chekmenev EY, Harris KC, Perman WH, Tran TT, Ross BD, Bhattacharya P
(2009) MAGMA 22: 123-34
MeSH Terms: Biopolymers, Carbon Isotopes, Equipment Design, Equipment Failure Analysis, Magnetic Resonance Imaging, Magnetic Resonance Spectroscopy, Quality Assurance, Health Care, Reproducibility of Results, Sensitivity and Specificity, United States
Show Abstract · Added March 5, 2014
OBJECT - Define MR quality assurance procedures for maximal PASADENA hyperpolarization of a biological (13)C molecular imaging reagent.
MATERIALS AND METHODS - An automated PASADENA polarizer and a parahydrogen generator were installed. (13)C enriched hydroxyethyl acrylate, 1-(13)C, 2,3,3-d(3) (HEA), was converted to hyperpolarized hydroxyethyl propionate, 1-(13)C, 2,3,3-d(3) (HEP) and fumaric acid, 1-(13)C, 2,3-d(2) (FUM) to hyperpolarized succinic acid, 1-(13)C, 2,3-d(2) (SUC), by reaction with parahydrogen and norbornadiene rhodium catalyst. Incremental optimization of successive steps in PASADENA was implemented. MR spectra and in vivo images of hyperpolarized (13)C imaging agents were acquired at 1.5 and 4.7 T.
RESULTS - Application of quality assurance (QA) criteria resulted in incremental optimization of the individual steps in PASADENA implementation. Optimal hyperpolarization of HEP of P = 20% was achieved by calibration of the NMR unit of the polarizer (B (0) field strength +/- 0.002 mT). Mean hyperpolarization of SUC, P = [15.3 +/- 1.9]% (N = 16) in D (2)O, and P = [12.8 +/- 3.1]% (N = 12) in H (2)O, was achieved every 5-8 min (range 13-20%). An in vivo (13)C succinate image of a rat was produced.
CONCLUSION - PASADENA spin hyperpolarization of SUC to 15.3% in average was demonstrated (37,400 fold signal enhancement at 4.7 T). The biological fate of (13)C succinate, a normally occurring cellular intermediate, might be monitored with enhanced sensitivity.
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10 MeSH Terms
PASADENA hyperpolarization of 13C biomolecules: equipment design and installation.
Hövener JB, Chekmenev EY, Harris KC, Perman WH, Robertson LW, Ross BD, Bhattacharya P
(2009) MAGMA 22: 111-21
MeSH Terms: Biopolymers, Carbon Isotopes, Equipment Design, Equipment Failure Analysis, Magnetic Resonance Imaging, Magnetic Resonance Spectroscopy, Reproducibility of Results, Sensitivity and Specificity
Show Abstract · Added March 5, 2014
OBJECT - The PASADENA method has achieved hyperpolarization of 16-20% (exceeding 40,000-fold signal enhancement at 4.7 T), in liquid samples of biological molecules relevant to in vivo MRI and MRS. However, there exists no commercial apparatus to perform this experiment conveniently and reproducibly on the routine basis necessary for translation of PASADENA to questions of biomedical importance. The present paper describes equipment designed for rapid production of six to eight liquid samples per hour with high reproducibility of hyperpolarization.
MATERIALS AND METHODS - Drawing on an earlier, but unpublished, prototype, we provide diagrams of a delivery circuit, a laminar-flow reaction chamber within a low field NMR contained in a compact, movable housing. Assembly instructions are provided from which a computer driven, semi-automated PASADENA polarizer can be constructed.
RESULTS - Together with an available parahydrogen generator, the polarizer, which can be operated by a single investigator, completes one cycle of hyperpolarization each 52 s. Evidence of efficacy is presented. In contrast to competing, commercially available devices for dynamic nuclear polarization which characteristically require 90 min per cycle, PASADENA provides a low-cost alternative for high throughput.
CONCLUSIONS - This equipment is suited to investigators who have an established small animal NMR and wish to explore the potential of heteronuclear ((13)C and (15)N) MRI, MRS, which harnesses the enormous sensitivity gain offered by hyperpolarization.
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8 MeSH Terms
Biopolymer-released dexamethasone prevents tumor necrosis factor alpha-induced loss of auditory hair cells in vitro: implications toward the development of a drug-eluting cochlear implant electrode array.
Dinh C, Hoang K, Haake S, Chen S, Angeli S, Nong E, Eshraghi AA, Balkany TJ, Van De Water TR
(2008) Otol Neurotol 29: 1012-9
MeSH Terms: Animals, Animals, Newborn, Biopolymers, Cochlear Implants, Delayed-Action Preparations, Dexamethasone, Hair Cells, Auditory, Hearing Loss, Organ of Corti, Prosthesis Design, Rats, Rats, Sprague-Dawley, Tumor Necrosis Factor-alpha
Show Abstract · Added April 18, 2017
HYPOTHESIS - Polymer-eluted dexamethasone (DXM) will retain its ability to protect against tumor necrosis factor alpha (TNFalpha)-induced hair cell (HC) loss.
BACKGROUND - TNFalpha has been shown to be associated with trauma-induced hearing loss. DXM has been demonstrated to protect the cochlea against trauma-induced hearing loss. DXM is currently administered either systemically or locally to treat patients with sudden hearing loss of unknown cause.
METHODS - P-3 organ of Corti explants challenged with an ototoxic level of TNFalpha was the experimental system, and the base form of DXM (DXMb) incorporated into a biorelease polymer (i.e., SIBS) was the otoprotection molecule tested. The efficacy of otoprotection was determined by counts of fluorescein isothiocyanate-phalloidin-stained HCs and changes in gene expression.
RESULTS - HC counts show 1) SIBS alone did not protect HCs from TNFalpha ototoxicity (SIBS versus SIBS + TNFalpha; p < 0.001), and 2) SIBS with DXMb provides a significant level of protection against TNFalpha-induced loss of HCs (TNFalpha + SIBS versus TNFalpha + SIBS/DXMb, 299 mug; p < 0.001). Gene expression results show that polymer-eluted DXMb 1) upregulates antiapoptotic genes (i.e., Bcl-2, Bcl-xl) and downregulates a proapoptotic gene (i.e., Bax) in TNFalpha-challenged explants and 2) downregulates TNFR1 in these explants.
CONCLUSION - Polymer-eluted DXMb retains its otoprotection capabilities in our in vitro test system of TNFalpha-challenged organ of Corti explants by altering the pattern of gene expression to favor survival of TNFalpha-exposed HCs. These results, although in vitro, support the application of polymer containing DXMb to electrode arrays for the conservation of hearing during cochlear implantation.
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13 MeSH Terms
Using low-E resonators to reduce RF heating in biological samples for static solid-state NMR up to 900 MHz.
Gor'kov PL, Chekmenev EY, Li C, Cotten M, Buffy JJ, Traaseth NJ, Veglia G, Brey WW
(2007) J Magn Reson 185: 77-93
MeSH Terms: Biopolymers, Computer-Aided Design, Equipment Design, Equipment Failure Analysis, Heating, Hot Temperature, Lipid Bilayers, Magnetic Resonance Spectroscopy, Magnetics, Powders, Radio Waves, Specimen Handling, Temperature, Transducers
Show Abstract · Added March 5, 2014
RF heating of solid-state biological samples is known to be a destabilizing factor in high-field NMR experiments that shortens the sample lifetime by continuous dehydration during the high-power cross-polarization and decoupling pulses. In this work, we describe specially designed, large volume, low-E 15N-1H solid-state NMR probes developed for 600 and 900 MHz PISEMA studies of dilute membrane proteins oriented in hydrated and dielectrically lossy lipid bilayers. The probes use an orthogonal coil design in which separate resonators pursue their own aims at the respective frequencies, resulting in a simplified and more efficient matching network. Sample heating at the 1H frequency is minimized by a loop-gap resonator which produces a homogeneous magnetic field B1 with low electric field E. Within the loop-gap resonator, a multi-turn solenoid closely matching the shape of the sample serves as an efficient observe coil. We compare power dissipation in a typical lossy bilayer sample in the new low-E probe and in a previously reported 15N-1H probe which uses a double-tuned 4-turn solenoid. RF loss in the sample is measured in each probe by observing changes in the 1H 360 degrees pulse lengths. For the same values of 1H B1 field, sample heating in the new probe was found to be smaller by an order of magnitude. Applications of the low-E design to the PISEMA study of membrane proteins in their native hydrated bilayer environment are demonstrated at 600 and 900 MHz.
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14 MeSH Terms