keyword
MENU ▼
Read by QxMD icon Read
search

biomolecular interaction

keyword
https://www.readbyqxmd.com/read/28936029/silicon-nanoporous-membranes-as-a-rigorous-platform-for-validation-of-biomolecular-transport-models
#1
Benjamin J Feinberg, Jeff C Hsiao, Jaehyun Park, Andrew L Zydney, William H Fissell, Shuvo Roy
Microelectromechanical systems (MEMS), a technology that resulted from significant innovation in semiconductor fabrication, have recently been applied to the development of silicon nanopore membranes (SNM). In contrast to membranes fabricated from polymeric materials, SNM exhibit slit-shaped pores, monodisperse pore size, constant surface porosity, zero pore overlap, and sub-micron thickness. This development in membrane fabrication is applied herein for the validation of the XDLVO (extended Derjaguin, Landau, Verwey, and Overbeek) theory of membrane transport within the context of hemofiltration...
August 15, 2017: Journal of Membrane Science
https://www.readbyqxmd.com/read/28929969/cellnetvis-a-web-tool-for-visualization-of-biological-networks-using-force-directed-layout-constrained-by-cellular-components
#2
Henry Heberle, Marcelo Falsarella Carazzolle, Guilherme P Telles, Gabriela Vaz Meirelles, Rosane Minghim
BACKGROUND: The advent of "omics" science has brought new perspectives in contemporary biology through the high-throughput analyses of molecular interactions, providing new clues in protein/gene function and in the organization of biological pathways. Biomolecular interaction networks, or graphs, are simple abstract representations where the components of a cell (e.g. proteins, metabolites etc.) are represented by nodes and their interactions are represented by edges. An appropriate visualization of data is crucial for understanding such networks, since pathways are related to functions that occur in specific regions of the cell...
September 13, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28929734/label-free-and-high-throughput-detection-of-biomolecular-interactions-using-a-flatbed-scanner-biosensor
#3
Ugur Aygun, Oguzhan Avci, Elif Seymour, Hakan Urey, M Selim Ünlu, Ayca Yalcin Ozkumur
Fluorescence based microarray detection systems provide sensitive measurements, however variation of probe immobilization and poor repeatability negatively affect the final readout, and thus quantification capability of these systems. Here, we demonstrate a label-free and high-throughput optical biosensor that can be utilized for calibration of fluorescence microarrays. The sensor employs a commercial flatbed scanner, and we demonstrate transformation of this low cost (100 USD) system into an Interferometric Reflectance Imaging Sensor through hardware and software modifications...
September 20, 2017: ACS Sensors
https://www.readbyqxmd.com/read/28926974/block-v-rtx-domain-of-adenylate-cyclase-from-bordetella-pertussis-a-conformationally-dynamic-scaffold-for-protein-engineering-applications
#4
REVIEW
Beyza Bulutoglu, Scott Banta
The isolated Block V repeats-in-toxin (RTX) peptide domain of adenylate cyclase (CyaA) from Bordetella pertussis reversibly folds into a β-roll secondary structure upon calcium binding. In this review, we discuss how the conformationally dynamic nature of the peptide is being engineered and employed as a switching mechanism to mediate different protein functions and protein-protein interactions. The peptide has been used as a scaffold for diverse applications including: a precipitation tag for bioseparations, a cross-linking domain for protein hydrogel formation and as an alternative scaffold for biomolecular recognition applications...
September 17, 2017: Toxins
https://www.readbyqxmd.com/read/28924921/mg-2-induced-dna-compaction-condensation-and-phase-separation-in-gene-delivery-vehicles-based-on-zwitterionic-phospholipids-a-dynamic-light-scattering-and-surface-enhanced-raman-spectroscopic-study
#5
Erhan Süleymanoğlu
Despite the significant efforts towards applying improved non-destructive and label-free measurements of biomolecular structures of lipid-based gene delivery vectors, little is achieved in terms of their structural relevance in gene transfections. Better understanding of structure-activity relationships of lipid-DNA complexes and their gene expression efficiencies thus becomes an essential issue. Raman scattering offers a complimentary measurement technique for following the structural transitions of both DNA and lipid vesicles employed for their transfer...
September 18, 2017: Journal of Biological Inorganic Chemistry: JBIC
https://www.readbyqxmd.com/read/28921497/quantitative-analysis-of-nucleic-acid-stability-with-ligands-under-high-pressure-to-design-novel-drugs-targeting-g-quadruplexes
#6
Shuntaro Takahashi, Naoki Sugimoto
Nucleic acids (DNA and RNA) can form various non-canonical structures. Because some serious diseases are caused by the conformational change of G-quadruplex DNA structures, the development of ligands that bind and stabilize G-quadruplex DNA is of interest to the field of nucleic acid chemistry. Volumetric changes (ΔV) in the biomolecular reaction include the structural change of biomolecules and hydration behaviors, which provide information about the tertiary interaction between G-quadruplex DNA and ligands...
September 18, 2017: Current Protocols in Nucleic Acid Chemistry
https://www.readbyqxmd.com/read/28921104/development-of-constant-ph-simulation-methods-in-implicit-solvent-and-applications-in-biomolecular-systems
#7
REVIEW
Fernando Luís Barroso daSilva, Luis Gustavo Dias
pH is a critical parameter for biological and technological systems directly related with electrical charges. It can give rise to peculiar electrostatic phenomena, which also makes them more challenging. Due to the quantum nature of the process, involving the forming and breaking of chemical bonds, quantum methods should ideally by employed. Nevertheless, due to the very large number of ionizable sites, different macromolecular conformations, salt conditions, and all other charged species, the CPU time cost simply becomes prohibitive for computer simulations, making this a quite complex problem...
September 18, 2017: Biophysical Reviews
https://www.readbyqxmd.com/read/28920687/manipulating-protein-protein-interactions-in-nrps-type-ii-pcps
#8
Matt J Jaremko, D John Lee, Ashay Patel, Victoria Winslow, Stanley J Opella, J Andrew McCammon, Michael D Burkart
In an effort to elucidate and engineer interactions in type II nonribosomal peptide synthetases, we analyzed biomolecular recognition between the essential peptidyl carrier proteins and adenylation domains using NMR spectroscopy, molecular dynamics, and mutational studies. Three peptidyl carrier proteins, PigG, PltL, and RedO, in addition to their cognate adenylation domains, PigI, PltF, and RedM, were investigated for their cross species activity. Of the three peptidyl carrier proteins, only PigG, showed substantial cross-pathway activity...
September 18, 2017: Biochemistry
https://www.readbyqxmd.com/read/28916835/plasmon-coupled-whispering-gallery-modes-on-nanodisk-arrays-for-signal-enhancements
#9
Tae Young Kang, Wonju Lee, Heesang Ahn, Dong-Myeong Shin, Chang-Seok Kim, Jin-Woo Oh, Donghyun Kim, Kyujung Kim
Metallic nanostructures including single and double nanodisks are successfully used to enhance the localized electric field in vicinity of microcavity in whispering gallery mode (WGM) sensor. We demonstrate numerical calculations of plasmonic coupling of WGMs to single and double nanodisk arrays on a planar substrate. We then experimentally confirmed that the resonance wavelength of WGM sensor was dramatically shifted by adoption of single and double nanodisks on the surface of microcavity in the WGM sensor...
September 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28910854/characterizing-the-nano-bio-interface-using-microscopic-techniques-imaging-the-cell-system-is-just-as-important-as-imaging-the-nanoparticle-system
#10
Christie M Sayes, Henry Lujan
The rapid growth of nanotechnology and its industries has elevated the need to understand the risks associated with handling, using, and disposing of nanomaterials. These risks can be assessed through exposure measurement and hazard identification. One of the common challenges associated with quantifying nanomaterials in products, waste, humans, or the environment is the lack of tools available to measure concentration. The ability of refined tools and techniques to qualitatively detect nanoparticles in complex matrices has been demonstrated...
September 14, 2017: Current Protocols in Chemical Biology
https://www.readbyqxmd.com/read/28905203/adaptive-resolution-simulations-of-biomolecular-systems
#11
Julija Zavadlav, Staš Bevc, Matej Praprotnik
In this review article, we discuss and analyze some recently developed hybrid atomistic-mesoscopic solvent models for multiscale biomolecular simulations. We focus on the biomolecular applications of the adaptive resolution scheme (AdResS), which allows solvent molecules to change their resolution back and forth between atomistic and coarse-grained representations according to their positions in the system. First, we discuss coupling of atomistic and coarse-grained models of salt solution using a 1-to-1 molecular mapping-i...
September 13, 2017: European Biophysics Journal: EBJ
https://www.readbyqxmd.com/read/28901745/terminating-dna-tile-assembly-with-nanostructured-caps
#12
Deepak K Agrawal, Ruoyu Jiang, Seth Reinhart, Abdul M Mohammed, Tyler D Jorgenson, Rebecca Schulman
Precise control over the nucleation, growth, and termination of self-assembly processes is a fundamental tool for controlling product yield and assembly dynamics. Mechanisms for altering these processes programmatically could allow the use of simple components to self-assemble complex final products or to design processes allowing for dynamic assembly or reconfiguration. Here we use DNA tile self-assembly to develop general design principles for building complexes that can bind to a growing biomolecular assembly and terminate its growth by systematically characterizing how different DNA origami nanostructures interact with the growing ends of DNA tile nanotubes...
September 18, 2017: ACS Nano
https://www.readbyqxmd.com/read/28898077/simulation-of-reversible-protein-protein-binding-and-calculation-of-binding-free-energies-using-perturbed-distance-restraints
#13
Jan Walther Perthold, Chris Oostenbrink
Virtually all biological processes depend on the interaction between proteins at some point. The correct prediction of biomolecular binding free-energies has many interesting applications in both basic and applied pharmaceutical research. While recent advances in the field of molecular dynamics (MD) simulations have proven the feasibility of the calculation of protein-protein binding free energies, the large conformational freedom of proteins and complex free energy landscapes of binding processes make such calculations a difficult task...
September 12, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28890161/self-assembly-of-repeat-proteins-concepts-and-design-of-new-interfaces
#14
Daniel Sanchez-deAlcazar, Sara H Mejias, Kevin Erazo, Begoña Sot, Aitziber L Cortajarena
In Nature, assembled protein structures offer the most complex functional structures. The understanding of the mechanisms ruling protein-protein interactions opens the door to manipulate protein assemblies in a rational way. Proteins are versatile scaffolds with great potential as tools in nanotechnology and biomedicine because of their chemical, structural, and functional versatility. Currently, bottom-up self-assembly based on biomolecular interactions of small and well-defined components, is an attractive approach to biomolecular engineering and biomaterial design...
September 7, 2017: Journal of Structural Biology
https://www.readbyqxmd.com/read/28890155/antibiotic-induced-microbiota-perturbation-causes-gut-endocannabinoidome-changes-hippocampal-neuroglial-reorganization-and-depression-in-mice
#15
F Guida, F Turco, M Iannotta, D De Gregorio, I Palumbo, G Sarnelli, A Furiano, F Napolitano, S Boccella, L Luongo, M Mazzitelli, A Usiello, F De Filippis, F A Iannotti, F Piscitelli, D Ercolini, V de Novellis, V Di Marzo, R Cuomo, S Maione
The microbiota-gut-brain axis (MGBA) regulates the reciprocal interaction between chronic inflammatory bowel and psychiatric disorders. This interaction involves multiple pathways that are highly debated. We examined the behavioural, biochemical and electrophysiological alterations, as well as gut microbiota composition in a model of antibiotic-induced experimental dysbiosis. Inflammation of the small intestine was also assessed. Mice were exposed to a mixture of antimicrobials for 2weeks. Afterwards, they received Lactobacillus casei DG (LCDG) or a vehicle for up to 7days via oral gavage...
September 7, 2017: Brain, Behavior, and Immunity
https://www.readbyqxmd.com/read/28887532/nano-integrated-suspended-polymeric-microfluidics-spmf-platform-for-ultra-sensitive-bio-molecular-recognition-of-bovine-growth-hormones
#16
Hamid Sadabadi, Muthukumaran Packirisamy
The development of sensitive platforms for the detection of biomolecules recognition is an extremely important problem in clinical diagnostics. In microcantilever (MC) transducers, surface-stress is induced upon bimolecular interaction which is translated into MC deflection. This paper presents a cost-effective and ultra-sensitive MC-based biosensing platform. To address these goals, the need for costly high-resolution read-out system has been eliminated by reducing the cantilever compliance through developing a polymer-based cantilever...
September 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28886512/physicochemical-study-of-biomolecular-interactions-between-lysosomotropic-surfactants-and-bovine-serum-albumin
#17
Tomasz Janek, Żaneta Czyżnikowska, Jacek Łuczyński, Eduardo J Gudiña, Lígia R Rodrigues, Joanna Gałęzowska
The interactions between two cationic lysosomotropic surfactants (2-dodecanoyloxyethyl)trimethylammonium bromide (DMM-11) and (2-dodecanoyloxypropyl)trimethylammonium bromide (DMPM-11) with bovine serum albumin (BSA) in Hepes buffer (pH=7.4) were systematically studied by surface tension, fluorescence and circular dichroism (CD) spectroscopy and isothermal titration calorimetry (ITC). Furthermore, the size of the micellar aggregates and the polydispersity indexes of both cationic surfactants were studied by dynamic light scattering technique (DLS)...
August 30, 2017: Colloids and Surfaces. B, Biointerfaces
https://www.readbyqxmd.com/read/28880211/dual-mode-electro-optical-techniques-for-biosensing-applications-a-review
#18
REVIEW
José Juan-Colás, Steven Johnson, Thomas F Krauss
The monitoring of biomolecular interactions is a key requirement for the study of complex biological processes and the diagnosis of disease. Technologies that are capable of providing label-free, real-time insight into these interactions are of great value for the scientific and clinical communities. Greater understanding of biomolecular interactions alongside increased detection accuracy can be achieved using technology that can provide parallel information about multiple parameters of a single biomolecular process...
September 7, 2017: Sensors
https://www.readbyqxmd.com/read/28869274/probing-the-modulated-formation-of-gold-nanoparticles-beta-lactoglobulin-corona-complexes-and-their-applications
#19
Jiang Yang, Bo Wang, Youngsang You, Woo-Jin Chang, Ke Tang, Yi-Cheng Wang, Wenzhao Zhang, Feng Ding, Sundaram Gunasekaran
Understanding the interactions between proteins and nanoparticles (NPs) along with the underlying structural and dynamic information is of utmost importance to exploit nanotechnology for biomedical applications. Upon adsorption onto a NP surface, proteins form a well-organized layer, termed the corona, that dictates the identity of the NP-protein complex and governs its biological pathways. Given its high biological relevance, in-depth molecular investigations and applications of NPs-protein corona complexes are still scarce, especially since different proteins form unique corona patterns, making identification of the biomolecular motifs at the interface critical...
September 4, 2017: Nanoscale
https://www.readbyqxmd.com/read/28861068/protein-protein-interactions-in-virus-host-systems
#20
REVIEW
Anderson F Brito, John W Pinney
To study virus-host protein interactions, knowledge about viral and host protein architectures and repertoires, their particular evolutionary mechanisms, and information on relevant sources of biological data is essential. The purpose of this review article is to provide a thorough overview about these aspects. Protein domains are basic units defining protein interactions, and the uniqueness of viral domain repertoires, their mode of evolution, and their roles during viral infection make viruses interesting models of study...
2017: Frontiers in Microbiology
keyword
keyword
77241
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"