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https://www.readbyqxmd.com/read/28225259/one-step-ligand-immobilization-and-single-sample-injection-for-regeneration-free-surface-plasmon-resonance-measurements-of-biomolecular-interactions
#1
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
#2
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/28220417/steady-state-and-kinetics-based-affinity-determination-in-effector-effector-target-interactions
#3
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/28211059/a-multipolar-approach-to-the-interatomic-covalent-interaction-energy
#4
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
#5
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/28208020/graphene-oxide-induced-perturbation-to-plasma-membrane-and-cytoskeletal-meshwork-sensitize-cancer-cells-to-chemotherapeutic-agents
#6
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/28198086/calcium-independent-activation-of-an-allosteric-network-in-langerin-by-heparin-oligosaccharides
#7
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
https://www.readbyqxmd.com/read/28193060/-bio-sensing-using-nanoparticle-arrays-on-the-effect-of-analyte-transport-on-sensitivity
#8
N Scott Lynn, Jiří Homola
There has recently been an extensive amount of work regarding the development of optical, electrical, and mechanical (bio)sensors employing planar arrays of surface-bound nanoparticles. The sensor output for these systems is dependent on the rate at which analyte is transported to, and interacts with, each nanoparticle in the array. There has so far been little discussion on the relationship between the design parameters of an array and the interplay of convection, diffusion, and reaction. Moreover, current methods providing such information require extensive computational simulation...
December 20, 2016: Analytical Chemistry
https://www.readbyqxmd.com/read/28192993/quantitative-affinity-determination-by-fluorescence-anisotropy-measurements-of-individual-nanoliter-droplets
#9
Fabrice Gielen, Maren Butz, Eric J Rees, Miklos Erdelyi, Tommaso Moschetti, Marko Hyvönen, Joshua B Edel, Clemens F Kaminski, Florian Hollfelder
Fluorescence anisotropy measurements of reagents compartmentalized into individual nanoliter droplets are shown to yield high-resolution binding curves from which precise dissociation constants (Kd) for protein-peptide interactions can be inferred. With the current platform, four titrations can be obtained per minute (based on ∼100 data points each), with stoichiometries spanning more than 2 orders of magnitude and requiring only tens of microliters of reagents. In addition to affinity measurements with purified components, Kd values for unpurified proteins in crude cell lysates can be obtained without prior knowledge of the concentration of the expressed protein, so that protein purification can be avoided...
January 17, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28191459/epidermal-growth-factor-signaling-towards-proliferation-modeling-and-logic-inference-using-forward-and-backward-search
#10
Adrián Riesco, Beatriz Santos-Buitrago, Javier De Las Rivas, Merrill Knapp, Gustavo Santos-García, Carolyn Talcott
In biological systems, pathways define complex interaction networks where multiple molecular elements are involved in a series of controlled reactions producing responses to specific biomolecular signals. These biosystems are dynamic and there is a need for mathematical and computational methods able to analyze the symbolic elements and the interactions between them and produce adequate readouts of such systems. In this work, we use rewriting logic to analyze the cellular signaling of epidermal growth factor (EGF) and its cell surface receptor (EGFR) in order to induce cellular proliferation...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28188076/cultivation-free-raman-spectroscopic-investigations-of-bacteria
#11
REVIEW
Björn Lorenz, Christina Wichmann, Stephan Stöckel, Petra Rösch, Jürgen Popp
Raman spectroscopy is currently advertised as a hot and ambitious technology that has all of the features needed to characterize and identify bacteria. Raman spectroscopy is rapid, easy to use, noninvasive, and it could complement established microbiological and biomolecular methods in the near future. To bring this vision closer to reality, ongoing research is being conducted on spectral fingerprinting. This can yield a wealth of information, from even single bacteria from various habitats which can be further improved by combining Raman spectroscopy with methods such as stable isotope probing to elucidate microbial interactions...
February 7, 2017: Trends in Microbiology
https://www.readbyqxmd.com/read/28182403/forging-the-basis-for-developing-protein-ligand-interaction-scoring-functions
#12
Zhihai Liu, Minyi Su, Li Han, Jie Liu, Qifan Yang, Yan Li, Renxiao Wang
In structure-based drug design, scoring functions are widely used for fast evaluation of protein-ligand interactions. They are often applied in combination with molecular docking and de novo design methods. Since the early 1990s, a whole spectrum of protein-ligand interaction scoring functions have been developed. Regardless of their technical difference, scoring functions all need data sets combining protein-ligand complex structures and binding affinity data for parametrization and validation. However, data sets of this kind used to be rather limited in terms of size and quality...
February 9, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28181616/na-k-atpase-as-a-target-for-anticancer-metal-based-drugs-insights-into-molecular-interactions-with-selected-gold-iii-complexes
#13
Aleksandra M Bondžić, Goran V Janjić, Miroslav D Dramićanin, Luigi Messori, Lara Massai, Tatjana N Parac Vogt, Vesna M Vasić
Na/K-ATPase is emerging as an important target for a variety of anticancer metal-based drugs. The interactions of Na/K-ATPase (in its E1 state) with three representative and structurally related cytotoxic gold(iii) complexes, i.e. [Au(bipy)(OH)2][PF6], bipy = 2,2'-bipyridine; [Au(py(dmb)-H)(CH3COO)2], py(dmb)-H = deprotonated 6-(1,1-dimethylbenzyl)-pyridine and [Au(bipy(dmb)-H)(OH)][PF6], bipy(c)-H = deprotonated 6-(1,1-dimethylbenzyl)-2,2'-bipyridine, are investigated here in depth using a variety of spectroscopic methods, in combination with docking studies...
February 9, 2017: Metallomics: Integrated Biometal Science
https://www.readbyqxmd.com/read/28156096/manipulation-and-motion-of-organelles-and-single-molecules-in-living-cells
#14
Kamilla Norregaard, Ralf Metzler, Christine M Ritter, Kirstine Berg-Sørensen, Lene B Oddershede
The biomolecule is among the most important building blocks of biological systems, and a full understanding of its function forms the scaffold for describing the mechanisms of higher order structures as organelles and cells. Force is a fundamental regulatory mechanism of biomolecular interactions driving many cellular processes. The forces on a molecular scale are exactly in the range that can be manipulated and probed with single molecule force spectroscopy. The natural environment of a biomolecule is inside a living cell, hence, this is the most relevant environment for probing their function...
February 3, 2017: Chemical Reviews
https://www.readbyqxmd.com/read/28149485/detection-of-side-chain-rearrangements-mediating-the-motions-of-transmembrane-helices-in-molecular-dynamics-simulations-of-g-protein-coupled-receptors
#15
Zied Gaieb, Dimitrios Morikis
Structure and dynamics are essential elements of protein function. Protein structure is constantly fluctuating and undergoing conformational changes, which are captured by molecular dynamics (MD) simulations. We introduce a computational framework that provides a compact representation of the dynamic conformational space of biomolecular simulations. This method presents a systematic approach designed to reduce the large MD simulation spatiotemporal datasets into a manageable set in order to guide our understanding of how protein mechanics emerge from side chain organization and dynamic reorganization...
2017: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/28148957/cooperative-expression-of-atomic-chirality-in-inorganic-nanostructures
#16
Peng-Peng Wang, Shang-Jie Yu, Alexander O Govorov, Min Ouyang
Cooperative chirality phenomena extensively exist in biomolecular and organic systems via intra- and inter-molecular interactions, but study of inorganic materials has been lacking. Here we report, experimentally and theoretically, cooperative chirality in colloidal cinnabar mercury sulfide nanocrystals that originates from chirality interplay between the crystallographic lattice and geometric morphology at different length scales. A two-step synthetic scheme is developed to allow control of critical parameters of these two types of handedness, resulting in different chiral interplays expressed as observables through materials engineering...
February 2, 2017: Nature Communications
https://www.readbyqxmd.com/read/28145686/in-situ-characterization-of-protein-adsorption-onto-nanoparticles-by-fluorescence-correlation-spectroscopy
#17
Li Shang, G Ulrich Nienhaus
Nanotechnology holds great promise for applications in many fields including biology and medicine. Unfortunately, the processes occurring at the interface between nanomaterials and living systems are exceedingly complex and not yet well understood, which has significantly hampered the realization of many nanobiotechnology applications. Whenever nanoparticles (NPs) are incorporated by a living organism, a protein adsorption layer, also known as the "protein corona", forms on the NP surface. Accordingly, living organisms interact with protein-coated rather than bare NPs, and their biological responses depend on the nature of the protein corona...
February 1, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28145117/spectroscopic-evidences-for-strong-hydrogen-bonds-with-selenomethionine-in-proteins
#18
V Rao Mundlapati, Dipak Kumar Sahoo, Sanat Ghosh, Umesh Kumar Purame, Shubhant Pandey, Rudresh Acharya, Nitish Pal, Prince Tiwari, Himansu S Biswal
Careful protein structure analysis unravels many unknown and unappreciated noncovalent interactions that control protein structure; one such unrecognized interaction in protein is selenium centered hydrogen bonds (SeCHBs). We report, for the first time, SeCHBs involving the amide proton and selenium of selenomethionine (Mse), i.e., amide-N-H···Se H-bonds discerned in proteins. Using mass selective and conformer specific high resolution vibrational spectroscopy, gold standard quantum chemical calculations at CCSD(T), and in-depth protein structure analysis, we establish that amide-N-H···Se and amide-N-H···Te H-bonds are as strong as conventional amide-NH···O and amide-NH···O═C H-bonds despite smaller electronegativity of selenium and tellurium than oxygen...
February 2, 2017: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/28134256/the-tumour-suppressor-apc-promotes-hiv-1-assembly-via-interaction-with-gag-precursor-protein
#19
Kei Miyakawa, Mayuko Nishi, Satoko Matsunaga, Akiko Okayama, Masaki Anraku, Ayumi Kudoh, Hisashi Hirano, Hirokazu Kimura, Yuko Morikawa, Naoki Yamamoto, Akira Ono, Akihide Ryo
Diverse cellular proteins and RNAs are tightly regulated in their subcellular localization to exert their local function. Here we report that the tumour suppressor adenomatous polyposis coli protein (APC) directs the localization and assembly of human immunodeficiency virus (HIV)-1 Gag polyprotein at distinct membrane components to enable the efficient production and spread of infectious viral particles. A proteomic analysis and subsequent biomolecular interaction assay reveals that the carboxyl terminus of APC interacts with the matrix region of Gag...
January 30, 2017: Nature Communications
https://www.readbyqxmd.com/read/28130775/delphiforce-a-tool-for-electrostatic-force-calculations-applications-to-macromolecular-binding
#20
Lin Li, Arghya Chakravorty, Emil Alexov
Long-range electrostatic forces play an important role in molecular biology, particularly in macromolecular interactions. However, calculating the electrostatic forces for irregularly shaped molecules immersed in water is a difficult task. Here, we report a new tool, DelPhiForce, which is a tool in the DelPhi package that calculates and visualizes the electrostatic forces in biomolecular systems. In parallel, the DelPhi algorithm for modeling electrostatic potential at user-defined positions has been enhanced to include triquadratic and tricubic interpolation methods...
April 5, 2017: Journal of Computational Chemistry
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