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https://www.readbyqxmd.com/read/28239762/-1-h-13-c-and-15-n-backbone-chemical-shift-assignments-of-camelid-single-domain-antibodies-against-active-state-%C3%A2%C2%B5-opioid-receptor
#1
Remy Sounier, Yinshan Yang, Joanna Hagelberger, Sébastien Granier, Hélène Déméné
Nanobodies are single chain antibodies that have become a highly valuable and versatile tool for biomolecular and therapeutic research. One application field is the stabilization of active states of flexible proteins, among which G-protein coupled receptors represent a very important class of membrane proteins. Here we present the backbone and side-chain assignment of the (1)H, (13)C and (15)N resonances of Nb33 and Nb39, two nanobodies that recognize and stabilize the µ-opioid receptor to opioids in its active agonist-bound conformation...
February 26, 2017: Biomolecular NMR Assignments
https://www.readbyqxmd.com/read/28236245/modeling-and-design-of-peptidomimetics-to-modulate-protein-protein-interactions
#2
Andrew M Watkins, Richard Bonneau, Paramjit S Arora
We describe a modular approach to identify and inhibit protein-protein interactions (PPIs) that are mediated by protein secondary and tertiary structures with rationally designed peptidomimetics. Our analysis begins with entries of high-resolution complexes in the Protein Data Bank and utilizes conformational sampling, scoring, and design capabilities of advanced biomolecular modeling software to develop peptidomimetics.
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28229262/on-the-use-of-ultracentrifugal-devices-for-routine-sample-preparation-in-biomolecular-magic-angle-spinning-nmr
#3
Abhishek Mandal, Jennifer C Boatz, Travis B Wheeler, Patrick C A van der Wel
A number of recent advances in the field of magic-angle-spinning (MAS) solid-state NMR have enabled its application to a range of biological systems of ever increasing complexity. To retain biological relevance, these samples are increasingly studied in a hydrated state. At the same time, experimental feasibility requires the sample preparation process to attain a high sample concentration within the final MAS rotor. We discuss these considerations, and how they have led to a number of different approaches to MAS NMR sample preparation...
February 22, 2017: Journal of Biomolecular NMR
https://www.readbyqxmd.com/read/28228525/chirality-induced-spin-polarization-places-symmetry-constraints-on-biomolecular-interactions
#4
Anup Kumar, Eyal Capua, Manoj K Kesharwani, Jan M L Martin, Einat Sitbon, David H Waldeck, Ron Naaman
Noncovalent interactions between molecules are key for many biological processes. Necessarily, when molecules interact, the electronic charge in each of them is redistributed. Here, we show experimentally that, in chiral molecules, charge redistribution is accompanied by spin polarization. We describe how this spin polarization adds an enantioselective term to the forces, so that homochiral interaction energies differ from heterochiral ones. The spin polarization was measured by using a modified Hall effect device...
February 22, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28227445/quantitative-estimation-of-electro-osmosis-force-on-charged-particles-inside-a-borosilicate-resistive-pulse-sensor
#5
Mostafa Ghobadi, Yuqian Zhang, Ankit Rana, Ehsan T Esfahani, Leyla Esfandiari, Mostafa Ghobadi, Yuqian Zhang, Ankit Rana, Ehsan T Esfahani, Leyla Esfandiari, Ehsan T Esfahani, Yuqian Zhang, Ankit Rana, Mostafa Ghobadi
Nano and micron-scale pore sensors have been widely used for biomolecular sensing application due to its sensitive, label-free and potentially cost-effective criteria. Electrophoretic and electroosmosis are major forces which play significant roles on the sensor's performance. In this work, we have developed a mathematical model based on experimental and simulation results of negatively charged particles passing through a 2μm diameter solid-state borosilicate pore under a constant applied electric field. The mathematical model has estimated the ratio of electroosmosis force to electrophoretic force on particles to be 77...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28226779/biologically-inspired-design-of-feedback-control-systems-implemented-using-dna-strand-displacement-reactions
#6
Mathias Foo, Rucha Sawlekar, Vishwesh V Kulkarni, Declan G Bates, Mathias Foo, Rucha Sawlekar, Vishwesh V Kulkarni, Declan G Bates, Vishwesh V Kulkarni, Rucha Sawlekar, Declan G Bates, Mathias Foo
The use of abstract chemical reaction networks (CRNs) as a modelling and design framework for the implementation of computing and control circuits using enzyme-free, entropy driven DNA strand displacement (DSD) reactions is starting to garner widespread attention in the area of synthetic biology. Previous work in this area has demonstrated the theoretical plausibility of using this approach to design biomolecular feedback control systems based on classical proportional-integral (PI) controllers, which may be constructed from CRNs implementing gain, summation and integrator operators...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28225259/one-step-ligand-immobilization-and-single-sample-injection-for-regeneration-free-surface-plasmon-resonance-measurements-of-biomolecular-interactions
#7
Xiaoying Wang, Zhiqiang Li, Nguyen Ly, Feimeng Zhou
Surface plasmon resonance (SPR) has been well established as a method of choice for label-free kinetic measurements of biomolecular interactions. The conventional approach involves multiple injections of an analyte of different concentrations into a fluidic channel covered with a fixed ligand density. Optimization of the experimental conditions and assessment of the data quality can be complicated by issues such as disruption of the ligand structure by the regeneration step and limited availability of the sample solution...
February 22, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28225081/biomolecular-condensates-organizers-of-cellular-biochemistry
#8
REVIEW
Salman F Banani, Hyun O Lee, Anthony A Hyman, Michael K Rosen
Biomolecular condensates are micron-scale compartments in eukaryotic cells that lack surrounding membranes but function to concentrate proteins and nucleic acids. These condensates are involved in diverse processes, including RNA metabolism, ribosome biogenesis, the DNA damage response and signal transduction. Recent studies have shown that liquid-liquid phase separation driven by multivalent macromolecular interactions is an important organizing principle for biomolecular condensates. With this physical framework, it is now possible to explain how the assembly, composition, physical properties and biochemical and cellular functions of these important structures are regulated...
February 22, 2017: Nature Reviews. Molecular Cell Biology
https://www.readbyqxmd.com/read/28224489/application-of-hidden-markov-models-in-biomolecular-simulations
#9
Saurabh Shukla, Zahra Shamsi, Alexander S Moffett, Balaji Selvam, Diwakar Shukla
Hidden Markov models (HMMs) provide a framework to analyze large trajectories of biomolecular simulation datasets. HMMs decompose the conformational space of a biological molecule into finite number of states that interconvert among each other with certain rates. HMMs simplify long timescale trajectories for human comprehension, and allow comparison of simulations with experimental data. In this chapter, we provide an overview of building HMMs for analyzing bimolecular simulation datasets. We demonstrate the procedure for building a Hidden Markov model for Met-enkephalin peptide simulation dataset and compare the timescales of the process...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28220417/steady-state-and-kinetics-based-affinity-determination-in-effector-effector-target-interactions
#10
André Reinhard, Thorsten Nürnberger
Dissecting the functional basis of pathogenicity and resistance in the context of plant innate immunity benefits greatly from detailed knowledge about biomolecular interactions, as both resistance and virulence depend on specific interactions between pathogen and host biomolecules. While in vivo systems provide biological context to host-pathogen interactions, these experiments typically cannot provide quantitative biochemical characterization of biomolecular interactions. However, in many cases, the biological function does not only depend on whether an interaction occurs at all, but rather on the "intensity" of the interaction, as quantified by affinity...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28213010/the-pathogenesis-and-pathophysiology-of-gestational-diabetes-mellitus-deductions-from-a-three-part-longitudinal-metabolomics-study-in-china
#11
REVIEW
Kai P Law, Hua Zhang
Gestational diabetes mellitus (GDM) is a form of diabetes that is first recognised during pregnancy, with no evidence of pre-existing type 1 or type 2 diabetes. The prevalence of GDM has been rising steadily over the past few decades, coinciding with the ongoing epidemic of obesity and type 2 diabetes. Although GDM normally disappears after delivery, women who have been previously diagnosed with GDM are at a greater risk of developing gestational diabetes in subsequent pregnancies, and type 2 diabetes later in life...
February 14, 2017: Clinica Chimica Acta; International Journal of Clinical Chemistry
https://www.readbyqxmd.com/read/28212094/characteristics-of-myosin-v-processivity
#12
Jun-Ping Zhang, Yi Liu, Wei Sun, Xiaoyang Zhao, Ta La, Wei-Sheng Guo
Myosin V is a processive doubled-headed biomolecular motor involved in many intracellular organelle and vesicle transport. The unidirectional movement is coupled with the adenosine triphosphate (ATP) hydrolysis and product release cycle. With the progress of experimental techniques and the enhancement of measuring directness, detailed knowledge of the motility of myosin V has been obtained.Following the ATPase cycle, the 4-state mechanochemical model of the myosin V's processive movement is used. The transitions between various states take place in a stochastic manner...
February 14, 2017: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/28211093/gsskat-rapid-gene-set-analysis-and-multiple-testing-correction-for-rare-variant-association-studies-using-weighted-linear-kernels
#13
Nicholas B Larson, Shannon McDonnell, Lisa Cannon Albright, Craig Teerlink, Janet Stanford, Elaine A Ostrander, William B Isaacs, Jianfeng Xu, Kathleen A Cooney, Ethan Lange, Johanna Schleutker, John D Carpten, Isaac Powell, Joan E Bailey-Wilson, Olivier Cussenot, Geraldine Cancel-Tassin, Graham G Giles, Robert J MacInnis, Christiane Maier, Alice S Whittemore, Chih-Lin Hsieh, Fredrik Wiklund, William J Catolona, William Foulkes, Diptasri Mandal, Rosalind Eeles, Zsofia Kote-Jarai, Michael J Ackerman, Timothy M Olson, Christopher J Klein, Stephen N Thibodeau, Daniel J Schaid
Next-generation sequencing technologies have afforded unprecedented characterization of low-frequency and rare genetic variation. Due to low power for single-variant testing, aggregative methods are commonly used to combine observed rare variation within a single gene. Causal variation may also aggregate across multiple genes within relevant biomolecular pathways. Kernel-machine regression and adaptive testing methods for aggregative rare-variant association testing have been demonstrated to be powerful approaches for pathway-level analysis, although these methods tend to be computationally intensive at high-variant dimensionality and require access to complete data...
February 16, 2017: Genetic Epidemiology
https://www.readbyqxmd.com/read/28211059/a-multipolar-approach-to-the-interatomic-covalent-interaction-energy
#14
Evelio Francisco, Daniel Menéndez Crespo, Aurora Costales, Ángel Martín Pendás
Interatomic exchange-correlation energies correspond to the covalent energetic contributions to an interatomic interaction in real space theories of the chemical bond, but their widespread use is severely limited due to their computationally intensive character. In the same way as the multipolar (mp) expansion is customary used in biomolecular modeling to approximate the classical Coulomb interaction between two charge densities ρA(r) and ρB(r), we examine in this work the mp approach to approximate the interatomic exchange-correlation (xc) energies of the Interacting Quantum Atoms method...
February 16, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/28208301/biomolecular-interaction-assays-identified-dual-inhibitors-of-glutaminase-and-glutamate-dehydrogenase-that-disrupt-mitochondrial-function-and-prevent-growth-of-cancer-cells
#15
Min Zhu, Jinzhang Fang, Jingjing Zhang, Zheng Zhang, Jianhui Xie, Yan Yu, Jennifer Jin Ruan, Zhao Chen, Wei Hou, Gensheng Yang, Weike Su, Benfang Helen Ruan
Glutaminase (KGA/isoenzyme GAC) is an emerging and important drug target for cancer. Traditional methods for assaying glutaminase activity are coupled with several other enzymes. Such coupled assays do not permit the direct and stringent characterization of specific glutaminase inhibitors. Ebselen was identified as a potent 9 nM KGA inhibitor in the KGA/glutamate oxidase (GO)/horse radish peroxidase (HRP) coupled assay but showed very weak activity in inhibiting the growth of glutamine-dependent cancer cells...
February 7, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28208081/molecular-synergy-in-biolubrication-the-role-of-cartilage-oligomeric-matrix-protein-comp-in-surface-structuring-of-lubricin
#16
Akanksha Raj, Min Wang, Chao Liu, Liaquat Ali, Niclas G Karlsson, Per M Claesson, Andra Dėdinaitė
HYPOTHESIS: Synovial surfaces are lubricated by biomolecular aggregates that act in synergy, and lubricin is one key biolubricant. Its molecular structure allows extensive hydration and this is conducive to its lubrication performance. However, in order to fullfil its lubrication function it needs to be anchored and oriented on the surface in a proper way. We suggest that cartilage oligomeric matrix protein (COMP) is one of the biomolecules that promotes anchoring of lubricin in a fashion that facilitates lubrication...
June 1, 2017: Journal of Colloid and Interface Science
https://www.readbyqxmd.com/read/28208020/graphene-oxide-induced-perturbation-to-plasma-membrane-and-cytoskeletal-meshwork-sensitize-cancer-cells-to-chemotherapeutic-agents
#17
Jianqiang Zhu, Ming Xu, Ming Gao, Zhihong Zhang, Yong Xu, Tian Xia, Sijin Liu
The outstanding physicochemical properties endow graphene materials (e.g., graphene oxide, GO) with beneficial potentials in diverse biomedical fields such as bioimaging, drug delivery, and biomolecular detection. GO recently emerged as a chemosensitizer; however, the detailed molecular basis underlying GO-conducted sensitization and corresponding biological effects are still elusive. Based on our recent findings that GO treatment at sublethal concentrations could impair the general cellular priming state, including disorders of plasma membrane and cytoskeleton construction, we aimed here to explore the mechanism of GO as a sensitizer to make cancer cells more susceptible to chemotherapeutic agents...
February 20, 2017: ACS Nano
https://www.readbyqxmd.com/read/28207247/ortho-methoxyphenols-as-convenient-oxidative-bioconjugation-reagents-with-application-to-site-selective-heterobifunctional-crosslinkers
#18
Adel M ElSohly, James Irving MacDonald, Nina B Hentzen, Ioana Laura Aanei, Kareem M El Muslemany, Matthew B Francis
The synthesis of complex protein-based bioconjugates has been facilitated greatly by recent developments in chemoselective methods for biomolecular modification. The oxidative coupling of o-aminophenols or catechols with aniline functional groups is chemoselective, mild, and rapid; however, the oxidatively sensitive nature of the electron-rich aromatics and the paucity of commercial sources pose some obstacles to the general use of these reactive strategies. Herein, we identify o-methoxyphenols as air-stable, commercially available derivatives that undergo efficient oxidative couplings with anilines in the presence of periodate as oxidant...
February 16, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28199927/benzimidazole-acrylonitriles-as-multifunctional-push-pull-chromophores-spectral-characterisation-protonation-equilibria-and-nanoaggregation-in-aqueous-solutions
#19
Ema Horak, Robert Vianello, Marijana Hranjec, Svjetlana Krištafor, Grace Karminski Zamola, Ivana Murković Steinberg
Heterocyclic donor-π-acceptor molecular systems based on an N,N-dimethylamino phenylacrylonitrile benzimidazole skeleton have been characterised and are proposed for potential use in sensing applications. The benzimidazole moiety introduces a broad spectrum of useful multifunctional properties to the system including electron accepting ability, pH sensitivity and compatibility with biomolecules. The photophysical characterisation of the prototropic forms of these chromophores has been carried out in both solution and on immobilisation in polymer films...
February 7, 2017: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
https://www.readbyqxmd.com/read/28198086/calcium-independent-activation-of-an-allosteric-network-in-langerin-by-heparin-oligosaccharides
#20
Jonas Hanske, Robert Wawrzinek, Andreas Geissner, Eike-Christian Wamhoff, Katrin Sellrie, Henrik Schmidt, Peter H Seeberger, Christoph Rademacher
The C-type lectin receptor Langerin is a glycan binding protein that serves as an uptake receptor on Langerhans cells and is essential for the formation of Birbeck granules. Whereas most of Langerin´s ligands are recognized via a canonical Ca2+-dependent binding site, interactions with heparins have been proposed to make additional contacts to a secondary, Ca2+-independent site. Glycan array screening and biomolecular NMR spectroscopy were employed to investigate the molecular mechanism of these interactions...
February 14, 2017: Chembiochem: a European Journal of Chemical Biology
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