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https://www.readbyqxmd.com/read/28801460/multiplexed-silicon-photonic-sensor-arrays-enable-facile-characterization-of-coagulation-protein-binding-to-nanodiscs-with-variable-lipid-content
#1
Ellen M Muehl, Joshua M Gajsiewicz, Sara M Medfisch, Zachary S B Wiersma, James H Morrissey, Ryan C Bailey
Interactions of soluble proteins with the cell membrane are critical within the blood coagulation cascade. Of particular interest are the interactions of γ-carboxyglutamic acid-rich (GLA) domain-containing clotting proteins with lipids. Variability among conventional analytical methods presents challenges for comparing clotting protein-lipid interactions. Most previous studies have investigated only a single clotting protein and lipid composition and have yielded widely different binding constants. Herein, we demonstrate that a combination of lipid bilayer Nanodiscs and a multiplexed silicon photonic analysis technology enables high-throughput probing of many protein-lipid interactions among blood-clotting proteins...
August 11, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28799205/effects-of-fluorophore-attachment-on-protein-conformation-and-dynamics-studied-by-spfret-and-nmr
#2
Carolina Sanchez, Lena Voith-von-Voithenberg, Lisa Warner, Don C Lamb, Michael Sattler
Fluorescence-based techniques are widely used to study biomolecular conformations, intra- and intermolecular interactions, and conformational dynamics of macromolecules. Especially for fluorescent-based single-molecule experiments, the choice of the fluorophore and labeling position are highly important. Here, we have studied the biophysical and structural effects that are associated with the conjugation of fluorophores to cysteines in the splicing factor U2AF65 by using single pair Förster resonance energy transfer (FRET) and nuclear magnetic resonance (NMR) spectroscopy...
August 10, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28796521/sulfur-as-an-acceptor-to-bromine-in-biomolecular-halogen-bonds
#3
Melissa Coates Ford, Matthew Saxton, Pui Shing Ho
The halogen bond (X-bond) has become an important design element in chemistry, including medicinal chemistry and biomolecular engineering. Although oxygen is the most prevalent and best characterized X-bond acceptor in biomolecules, the interaction is seen with nitrogen, sulfur, and aromatic systems as well. In this study, we characterize the structure and thermodynamics of a Br···S X-bond between a 5-bromouracil base and a phosphorothioate in a model DNA junction. The single crystal structure of the junction shows the geometry of the Br···S to be variable, while calorimetric studies show that the anionic S acceptor is comparable to slightly more stable than the analogous O acceptor, with a -3...
August 10, 2017: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/28793853/equine-skeletal-muscle-adaptations-to-exercise-and-training-evidence-of-differential-regulation-of-autophagosomal-and-mitochondrial-components
#4
Kenneth Bryan, Beatrice A McGivney, Gabriella Farries, Paul A McGettigan, Charlotte L McGivney, Katie F Gough, David E MacHugh, Lisa M Katz, Emmeline W Hill
BACKGROUND: A single bout of exercise induces changes in gene expression in skeletal muscle. Regular exercise results in an adaptive response involving changes in muscle architecture and biochemistry, and is an effective way to manage and prevent common human diseases such as obesity, cardiovascular disorders and type II diabetes. However, the biomolecular mechanisms underlying such responses still need to be fully elucidated. Here we performed a transcriptome-wide analysis of skeletal muscle tissue in a large cohort of untrained Thoroughbred horses (n = 51) before and after a bout of high-intensity exercise and again after an extended period of training...
August 9, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28782927/going-deeper-biomolecular-tools-for-acoustic-and-magnetic-imaging-and-control-of-cellular-function
#5
Dan I Piraner, Arash Farhadi, Hunter C Davis, Di Wu, David Maresca, Jerzy O Szablowski, Mikhail G Shapiro
Most cellular phenomena of interest to mammalian biology occur within the context of living tissues and organisms. However, today's most advanced tools for observing and manipulating cellular function, based on fluorescent or light-controlled proteins, work best in cultured cells, transparent model species, or small, surgically accessed anatomical regions. Their reach into deep tissues and larger animals is limited by photon scattering. To overcome this limitation, we must design biochemical tools that interface with more penetrant forms of energy...
August 7, 2017: Biochemistry
https://www.readbyqxmd.com/read/28780861/characterization-of-protein-protein-interfaces-in-large-complexes-by-solid-state-nmr-solvent-paramagnetic-relaxation-enhancements
#6
Carl Öster, Simone Kosol, Christoph Hartlmüller, Jonathan M Lamley, Dinu Iuga, Andres Oss, Mai-Liis Org, Kalju Vanatalu, Ago Samoson, Tobias Madl, Józef R Lewandowski
Solid-state NMR is becoming a viable alternative for obtaining information about structures and dynamics of large biomolecular complexes including ones that are not accessible to other high resolution biophysical techniques. In this context, methods for probing protein-protein interfaces at atomic resolution are highly desirable. Solvent paramagnetic relaxation enhancements (sPREs) proved to be a powerful method for probing protein-protein interfaces in large complexes in solution but have not been employed towards this goal in the solid state...
August 7, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28780857/barcode-dna-mediated-signal-amplifying-strategy-for-ultrasensitive-biomolecular-detection-on-matrix-assisted-laser-desorption-ionization-time-of-flight-maldi-tof-mass-spectrometry
#7
Raheel Ahmad, Hyowon Jang, Bhagwan S Batule, Hyun Gyu Park
We have devised a barcode DNA-mediated signal amplifying strategy for ultrasensitive biomolecular detection by utilizing matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). As a model target, thrombin was first captured by specific aptamer15 functionalized on magnetic beads (MBs-apt15) and sandwiched through the simultaneous interaction with gold nanoparticles modified with another specific aptamer29 and barcode DNA molecules (apt29-AuNPs-bcDNAs). The sandwiched complex was collected by convenient magnetic separation and then treated with potassium cyanide (KCN) to dissolve the gold nanoparticles (AuNPs) and consequently release the barcode DNA molecules (bcDNAs), which were then again magnetically separated and analyzed by using MALDI-TOF MS...
August 5, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28777495/increased-conformational-flexibility-of-a-macrocycle-receptor-complex-contributes-to-reduced-dissociation-rates
#8
Adrian Glas, Eike-Christian Wamhoff, Dennis M Krüger, Christoph Rademacher, Tom N Grossmann
Constraining a peptide in its bioactive conformation via macrocyclization represents a powerful strategy to design modulators of challenging biomolecular targets. This holds particularly true for the development of inhibitors of protein-protein interactions which often involve interfaces lacking defined binding pockets. Such flat surfaces are demanding targets for traditional small molecules rendering macrocyclic peptides promising scaffolds for novel therapeutics. However, the contribution of peptide dynamics to binding kinetics is barely understood which impedes the design process...
August 4, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28762736/high-resolution-solid-state-nmr-characterization-of-ligand-binding-to-a-protein-immobilized-in-a-silica-matrix
#9
Linda Cerofolini, Stefano Giuntini, Alexandra Louka, Enrico Ravera, Marco Fragai, Claudio Luchinat
Solid state NMR is becoming a powerful tool to detect atomic-level structural features of biomolecules even when they are bound to - or trapped in - solid systems that lack long-range three dimensional order. We here demonstrate that it is possible to probe protein-ligand interactions from a protein-based perspective also when the protein is entrapped in silica, thus translating into biomolecular solid state NMR all the considerations that are usually made to understand the chemical nature of the interaction of a protein with its ligands...
August 1, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28760672/electrochemical-detection-of-interaction-between-capsaicin-and-nucleic-acids-in-comparison-to-agarose-gel-electrophoresis
#10
Nilay Yilmaz, Ece Eksin, Bilge Karacicek, Yasemin Eraç, Arzum Erdem
In this study, the biomolecular interaction occured between nucleic acids and Capsaicin (CPS), the active compound in chilli peppers, which has been reported to have anti-carcinogenic properties, was investigated for the first time herein using disposable electrochemical biosensor. It is aimed to perform the surface-confined interaction between CPS and different types of nucleic acids and under this aim, the experimental conditions were optimized; such as, the concentration of CPS and DNA, DNA immobilizaton time and interaction time etc...
July 28, 2017: Analytical Biochemistry
https://www.readbyqxmd.com/read/28754692/an-in-vitro-tag-and-modify-protein-sample-generation-method-for-singlemolecule-fret
#11
Kambiz M Hamadani, Jesse Howe, Madeleine K Jensen, Peng Wu, Jamie H D Cate, Susan Marqusee
Biomolecular systems exhibit many dynamic and biologically relevant properties, such as conformational fluctuations, multistep catalysis, transient interactions, folding, and allosteric structural transitions. These properties are challenging to detect and engineer using standard ensemble-based techniques. To address this drawback, single-molecule methods offer a way to access conformational distributions, transient states, and asynchronous dynamics inaccessible to these standard techniques. Fluorescence-based single molecule approaches are parallelizable and compatible with multiplexed detection; to date, however, they have remained limited to serial screens of small protein libraries...
July 28, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28750539/octupolar-metastructures-for-a-highly-sensitive-rapid-and-reproducible-phage-based-detection-of-bacterial-pathogens-by-surface-enhanced-raman-scattering
#12
Massimo Rippa, Riccardo Castagna, Marianna Pannico, Pellegrino Musto, Giorgia Borriello, Rubina Paradiso, Giorgio Galiero, Sergio Bolletti Censi, Jun Zhou, Joseph Zyss, Lucia Petti
The development of fast and ultrasensitive methods to detect bacterial pathogens at low concentrations is of high relevance for human and animal health care and diagnostics. In this context, surface-enhanced Raman scattering (SERS) offers the promise of a simplified, rapid, and high-sensitive detection of biomolecular interactions with several advantages over previous assay methodologies. In this work, we have conceived reproducible SERS nanosensors based on tailored multilayer octupolar nanostructures which can combine high enhancement factor and remarkable molecular selectivity...
July 28, 2017: ACS Sensors
https://www.readbyqxmd.com/read/28748401/system-biology-approach-to-identify-potential-receptor-for-targeting-cancer-and-biomolecular-interaction-studies-of-indole-2-1-a-isoquinoline-derivative-as-anticancerous-drug-candidate-against-it
#13
Devender Arora, Ritu Chaudhary, Ajeet Singh
Cancer is a public health concern which is spreading throughout the world. Different approaches have been employed to combat this disease. System biology approach has been used to understand the molecular mechanisms of drugs targeting cancer cell's receptor which have opened-up a window to develop effective drugs for it. We have demonstrated biomolecular interaction studies using the rational drug design of indole[2,1-a]isoquinoline derivative as a potent inhibitor against identified cancerous protein PIK3CA -a catalytic sub-unit of PI3K family protein-and compared its affinity with FDA approved drugs for receptors such as dactolisib, idelalisib, and several others such afatinib, avastin, ceritinib and crizotinib, etc...
July 26, 2017: Interdisciplinary Sciences, Computational Life Sciences
https://www.readbyqxmd.com/read/28745621/investigating-protein-sequence-structure-dynamics-relationships-with-bio3d-web
#14
Shashank Jariwala, Lars Skjærven, Xin-Qiu Yao, Barry J Grant
We demonstrate the usage of Bio3D-web for the interactive analysis of biomolecular structure data. The Bio3D-web application provides online functionality for: (1) The identification of related protein structure sets to user specified thresholds of similarity; (2) Their multiple alignment and structure superposition; (3) Sequence and structure conservation analysis; (4) Inter-conformer relationship mapping with principal component analysis, and (5) comparison of predicted internal dynamics via ensemble normal mode analysis...
July 16, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28743534/complementary-uses-of-small-angle-x-ray-scattering-and-x-ray-crystallography
#15
REVIEW
Monica C Pillon, Alba Guarné
Most proteins function within networks and, therefore, protein interactions are central to protein function. Although stable macromolecular machines have been extensively studied, dynamic protein interactions remain poorly understood. Small-angle X-ray scattering probes the size, shape and dynamics of proteins in solution at low resolution and can be used to study samples in a large range of molecular weights. Therefore, it has emerged as a powerful technique to study the structure and dynamics of biomolecular systems and bridge fragmented information obtained using high-resolution techniques...
July 22, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28742972/stimuli-responsive-directional-vesicular-assembly-with-tunable-surface-functionality-and-impact-on-enzyme-inhibition
#16
Amrita Sikder, Debes Ray, Vinod K Aswal, Suhrit Ghosh
The article describes the self-assembly of a series of unsymmetrical bola-shaped π-amphiphiles (NDI-1, NDI-1a, NDI-2, NDI-3, and NDI-4) consisting of a hydrophobic naphthalene-diimide (NDI) chromophore attached to a nonionic hydrophilic wedge and an anionic headgroup in the two opposite arms of the central NDI. By design, only a single hydrazide group is linked either on the ionic or nonionic arm of the NDI. NDI-1 and NDI-1a are regioisomers differing only in the location of the hydrazide group, placed in the nonionic or ionic arm, respectively...
August 8, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/28733669/high-resolution-imaging-of-a-single-gliding-protofilament-of-tubulins-by-hs-afm
#17
Jakia Jannat Keya, Daisuke Inoue, Yuki Suzuki, Toshiya Kozai, Daiki Ishikuro, Noriyuki Kodera, Takayuki Uchihashi, Arif Md Rashedul Kabir, Masayuki Endo, Kazuki Sada, Akira Kakugo
In vitro gliding assay of microtubules (MTs) on kinesins has provided us with valuable biophysical and chemo-mechanical insights of this biomolecular motor system. Visualization of MTs in an in vitro gliding assay has been mainly dependent on optical microscopes, limited resolution of which often render them insufficient sources of desired information. In this work, using high speed atomic force microscopy (HS-AFM), which allows imaging with higher resolution, we monitored MTs and protofilaments (PFs) of tubulins while gliding on kinesins...
July 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28726873/local-decomposition-of-imaginary-polarizabilities-and-dispersion-coefficients
#18
Ignat Harczuk, Balazs Nagy, Frank Jensen, Olav Vahtras, Hans Ågren
We present a new way to compute the two-body contribution to the dispersion energy using ab initio theory. By combining the complex polarization propagator method and the LoProp transformation, local contributions to the Casimir-Polder interaction is obtained. The full dispersion energy in dimer systems consisting of pairs of molecules including H2, N2, CO, CH4, pyridine, and benzene is investigated, where anisotropic as well as isotropic models of dispersion are obtained using a decomposition scheme for the dipole-dipole polarizability...
July 20, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28723204/crossed-surface-relief-gratings-as-nanoplasmonic-biosensors
#19
Srijit Nair, Carlos Escobedo, Ribal Georges Sabat
We present an original, low-cost nanoplasmonic (bio)sensor based on crossed surface relief gratings (CSRGs) generated from orthogonally superimposed surface relief gratings (SRGs) on gold-coated azo-glass substrate. This surface plasmon resonance (SPR)-based sensing approach is unique, since the light transmitted through a CSRG is zero except in the narrow bandwidth where the SPR conversion occurs, enabling quantitative monitoring of only the plasmonic signal from biomolecular interactions in real time. We validated the individual SRG plasmonic signature of CSRGs by observing their respective SPR excitation peaks, and tested them to detect both bulk and near-surface refractive index (RI) changes...
March 24, 2017: ACS Sensors
https://www.readbyqxmd.com/read/28721939/two-faces-of-competition-target-mediated-reverse-signalling-in-microrna-and-mitogen-activated-protein-kinase-regulatory-networks
#20
REVIEW
Yongjin Jang, Min A Kim, Yoosik Kim
Biomolecular regulatory networks are organised around hubs, which can interact with a large number of targets. These targets compete with each other for access to their common hubs, but whether the effect of this competition would be significant in magnitude and in function is not clear. In this review, the authors discuss recent in vivo studies that analysed the system level retroactive effects induced by target competition in microRNA and mitogen-activated protein kinase regulatory networks. The results of these studies suggest that downstream targets can regulate the overall state of their upstream regulators, and thus cannot be ignored in analysing biomolecular networks...
August 2017: IET Systems Biology
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