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https://www.readbyqxmd.com/read/28437105/a-virtual-environment-for-studying-the-docking-interactions-of-rigid-biomolecules-with-haptics
#1
Georgios Iakovou, Steven Hayward, Stephen Laycock
Haptic technology facilitates user interaction with the virtual world via the sense of touch. In molecular docking, haptics enables the user to sense the interaction forces during the docking process. Here we describe a haptics-assisted interactive software tool, called Haptimol RD, for the study of docking interactions. By utilising GPU-accelerated proximity querying methods very large systems can now be studied. Methods for force scaling, multipoint collision response and haptic navigation are described that address force stability issues that are particular to the interactive docking of large systems...
April 24, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28436296/synthesis-characterization-dna-and-hsa-binding-studies-of-isomeric-pd-ii-antitumor-complexes-using-spectrophotometry-techniques
#2
Sareh Zareian-Jahromi, Hassan Mansouri-Torshizi
Two new Palladium(II) isomeric complexes, [Pd(Gly)(Leu)](I) and [Pd(Gly)(Ile)](II), where Gly is glycine, and Leu and Ile are isomeric amino acids (leucine and isoleucine), have been synthesized and characterized by elemental analysis, molar conductivity measurements, FT-IR, (1)H NMR and UV-Vis. The complexes have been tested for their In vitro cytotoxicity against cancer cell line K562 and their binding properties to calf thymus DNA (CT-DNA) and human serum albumin (HSA) have also been investigated by multispectroscopic techniques...
April 23, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28432684/characterization-of-interactions-of-metal-containing-nanoparticles-with-biomolecules-by-ce-an-update-2012-2016
#3
REVIEW
Svetlana S Aleksenko, Magdalena Matczuk, Andrei R Timerbaev
The methodological developments and applications of CE related to studying biotransformations of metal-based nanoscale particles of impending medicinal use are overviewed. This is an update to a previous review article (Aleksenko, S. S., Shmykov, A. Y., Oszwałdowski, S., Timerbaev, A. R., Metallomics 2012, 4, 1141-1148) and it covers the research papers published within the last five years. As was anticipated in that review, CE can now be seen as a customary technique in the analysis of biomolecular interactions that exert an impact on the mechanism of action of nanoparticles, comprising metabolism, delivery, cell processing, and targeting...
April 22, 2017: Electrophoresis
https://www.readbyqxmd.com/read/28431169/spa-ln-a-scoring-function-of-ligand-nucleic-acid-interactions-via-optimizing-both-specificity-and-affinity
#4
Zhiqiang Yan, Jin Wang
Nucleic acids have been widely recognized as potential targets in drug discovery and aptamer selection. Quantifying the interactions between small molecules and nucleic acids is critical to discover lead compounds and design novel aptamers. Scoring function is normally employed to quantify the interactions in structure-based virtual screening. However, the predictive power of nucleic acid-ligand scoring functions is still a challenge compared to other types of biomolecular recognition. With the rapid growth of experimentally determined nucleic acid-ligand complex structures, in this work, we develop a knowledge-based scoring function of nucleic acid-ligand interactions, namely SPA-LN...
April 20, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28430221/numerical-simulation-on-the-performance-analysis-of-a-graphene-coated-optical-fiber-plasmonic-sensor-at-anti-crossing
#5
Jeeban Kumar Nayak, Rajan Jha
A graphene-based surface plasmon resonance sensor using D-shaped fiber in anti-crossing has been designed. Silver as a plasmon active metal is followed by graphene, which helps in preventing oxidation and shows better adsorption efficiency to biomolecules. A wavelength interrogation technique based on the finite element method has been used to evaluate performance parameters. Design parameters such as thickness of silver, residual cladding, and GeO<sub>2</sub> dopant concentration have been optimized...
April 20, 2017: Applied Optics
https://www.readbyqxmd.com/read/28426223/over-destabilization-of-protein-protein-interaction-in-generalized-born-model-and-utility-of-energy-density-integration-cutoff
#6
Yukinobu Mizuhara, Dan Parkin, Koji Umezawa, Jun Ohnuki, Mitsunori Takano
The generalize Born (GB) model is frequently used in MD simulations of biomolecular systems in aqueous solution. The GB model is usually based on the so-called Coulomb field approximation (CFA) for the energy density integration. In this study, we report that the GB model with CFA overdestabilizes the long-range electrostatic attraction between oppositely-charged molecules (ionic bond forming two-helix system and kinesin-tubulin system) when the energy density integration cutoff, rmax, which is used to calculate the Born energy, is set to a large value...
April 20, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28426045/enzyme-coated-janus-nanoparticles-that-selectively-bind-cell-receptors-as-a-function-of-the-concentration-of-glucose
#7
Gabriele Rucinskaite, Sebastian A Thompson, Sureyya Paterson, Roberto de la Rica
A method is proposed for controlling the number of nanoparticles bound to cell membranes via RGDS peptide-integrin interactions. It consists of propelling nanoparticles bearing the peptides with enzymes (glucose oxidase), which disrupts biomolecular interactions as a function of the concentration of enzyme substrate (glucose).
April 20, 2017: Nanoscale
https://www.readbyqxmd.com/read/28424990/proteomic-analysis-of-the-hippocampus-in-mouse-models-of-trigeminal-neuralgia-and-inescapable-shock-induced-depression
#8
Qing-Huan Guo, Qing-He Tong, Ning Lu, Hong Cao, Liu Yang, Yu-Qiu Zhang
To investigate the behavioral and biomolecular similarity between neuralgia and depression, a trigeminal neuralgia (TN) mouse model was established by constriction of the infraorbital nerve (CION) to mimic clinical trigeminal neuropathic pain. A mouse learned helplessness (LH) model was developed to investigate inescapable foot-shock-induced psychiatric disorders like depression in humans. Mass spectrometry was used to assess changes in the biomolecules and signaling pathways in the hippocampus from TN or LH mice...
April 19, 2017: Neuroscience Bulletin
https://www.readbyqxmd.com/read/28417365/quantifying-cbm-carbohydrate-interactions-using-microscale-thermophoresis
#9
Haiyang Wu, Cédric Y Montanier, Claire Dumon
MicroScale Thermophoresis (MST) is an emerging technology for studying a broad range of biomolecular interactions with high sensitivity. The affinity constant can be obtained for a wide range of molecules within minutes based on reactions in microliters. Here, we describe the application of MST in quantifying two CBM-carbohydrate interactions, a CBM3a toward cellulose nanocrystals and a CBM4 against xylohexaose.
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28412902/nanosafety-towards-safer-nanoparticles-by-design
#10
Neus G Bastús, Víctor Puntes
The continuous development of Nanotechnology is progressively introducing nanoparticles into society. However, little is known about the safety of nanoparticles and functions of engineered nanomaterials, in particular how the physicochemical properties of the materials relate to mechanisms of injury at the nano-bio interface. While comprehensive knowledge on the potential toxicity of NPs is still lacking, as time goes by and research in the field continues, different aspects, such as interactions with the immune system, perturbation of cellular membranes, transportation of toxic moieties and others are emerging as potentially hazardous aspects of NPs...
April 13, 2017: Current Medicinal Chemistry
https://www.readbyqxmd.com/read/28407563/recent-advances-in-fret-for-the-study-of-protein-interactions-and-dynamics
#11
REVIEW
Kenji Okamoto, Yasushi Sako
Förster/fluorescence resonance energy transfer (FRET) has been extensively used to detect the binding state or conformation of biomolecules. In the past few decades, various in vitro and in vivo applications of FRET measurement have been developed, including FRET probes, in-cell measurements, single-molecule measurements, and combination with computer simulation. In this review, we describe recent advances in FRET methods for examining biomolecular interactions and dynamics: (i) phasor plot analysis for quantitative analysis of protein interactions, (ii) single-molecule FRET measurement for detecting conformational dynamics in live cells, and (iii) data assimilation using molecular dynamics simulation to evaluate conformation of the whole protein...
April 10, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28399632/predicting-binding-free-energies
#12
David L Mobley, Michael K Gilson
Binding free energy calculations based on molecular simulations provide predicted affinities for biomolecular complexes. These calculations begin with a detailed description of a system, including its chemical composition and the interactions among its components. Simulations of the system are then used to compute thermodynamic information, such as binding affinities. Because of their promise for guiding molecular design, these calculations have recently begun to see widespread applications in early-stage drug discovery...
April 7, 2017: Annual Review of Biophysics
https://www.readbyqxmd.com/read/28399366/polarizable-force-field-for-dna-based-on-the-classical-drude-oscillator-i-refinement-using-quantum-mechanical-base-stacking-and-conformational-energetics
#13
Justin A Lemkul, Alexander D MacKerell
Empirical force fields seek to relate the configuration of a set of atoms to its energy, thus yielding the forces governing its dynamics, using classical physics rather than more expensive quantum mechanical calculations that are computationally intractable for large systems. Most force fields used to simulate biomolecular systems use fixed atomic partial charges, neglecting the influence of electronic polarization, instead making use of a mean-field approximation that may not be transferable across environments...
April 19, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28394606/is-the-solution-activity-derivative-sufficient-to-parameterize-ion-ion-interactions-in-aqueous-solution-ions-for-tip5p-water
#14
Vahid Satarifard, Sadra Kashefolgheta, Ana Vila Verde, Andrea Grafmueller
Biomolecular processes involve hydrated ions, and thus molecular simulations of such processes require accurate force-field parameters for these ions. In the best force-fields, both ion-water and anion-cation interactions are explicitly parameterized. First, the ion Lennard-Jones parameters are optimized to reproduce, e.g., single ion solvation free energies; then ion-pair interactions are often adjusted to match experimental activity or activity derivatives. Here we apply this approach to derive optimized parameters for concentrated NaCl, KCl, MgCl2 and CaCl2 salt solutions, to be used with the TIP5P water model...
April 10, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28388089/critical-comparison-of-biomembrane-force-fields-protein-lipid-interactions-at-the-membrane-interface
#15
Angelica Sandoval-Perez, Kristyna Pluhackova, Rainer A Böckmann
Molecular dynamics (MD) simulations offer the possibility to study biological processes at high spatial and temporal resolution often not reachable by experiments. Corresponding biomolecular force field parameters have been developed for a wide variety of molecules ranging from inorganic ligands and small organic molecules over proteins and lipids to nucleic acids. Force fields have typically been parametrized and validated on thermodynamic observables and structural characteristics of individual compounds, e...
April 20, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28383863/-how-i-explore%C3%A2-hla-class-ii-by-ultrastructure-in-toxic-epidermal-necrolysis
#16
REVIEW
G E Piérard, A Dowlati, C Piérard-Franchimont, P Paquet, P Delvenne
Toxic epidermal necrolysis (TEN, Lyell syndrome) is a severe paroxystic drug reaction whose inductive mechanisms remain poorly understood. The HLA glycoproteins are possibly involved in the disease process. Such investigations rely on biomolecular methods, and suggest specific interactions between some drugs or their metabolites and some HLA groups according to ethnicity of the TEN patients. Electron microscopy following the immunogold method for revealing HLA-DR did not disclose any evidence for distinguishing distinct patterns on Langerhans cell membrane between the initial and the resolution phases of TEN...
June 2016: Revue Médicale de Liège
https://www.readbyqxmd.com/read/28376614/benchmarking-a-fast-proton-titration-scheme-in-implicit-solvent-for-biomolecular-simulations
#17
Fernando Luis Barroso da Silva, Donal MacKernan
pH is a key parameter for technological and biological processes, intimately related with biomolecular charge. As such, it controls biomolecular conformation and inter molecular interactions, for example protein/RNA stability and folding, enzyme activity, regulation through conformational switches,protein-polyelectrolyte association, and protein-RNA interactions. pH also plays an important role in technological systems in food, brewing, pharma, bioseparations and biomaterials in general. Predicting the structure of large proteins and complexes remains a great challenge, experimentally; industrially; and theoretically, despite the variety of numerical schemes available ranging from Poisson-Boltzmann approaches to explicit solvent based methods...
April 4, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28369121/sequence-dependency-of-canonical-base-pair-opening-in-the-dna-double-helix
#18
Viveca Lindahl, Alessandra Villa, Berk Hess
The flipping-out of a DNA base from the double helical structure is a key step of many cellular processes, such as DNA replication, modification and repair. Base pair opening is the first step of base flipping and the exact mechanism is still not well understood. We investigate sequence effects on base pair opening using extensive classical molecular dynamics simulations targeting the opening of 11 different canonical base pairs in two DNA sequences. Two popular biomolecular force fields are applied. To enhance sampling and calculate free energies, we bias the simulation along a simple distance coordinate using a newly developed adaptive sampling algorithm...
April 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28364684/biophysical-and-molecular-docking-approaches-for-the-investigation-of-biomolecular-interactions-between-amphotericin-b-and-bovine-serum-albumin
#19
Muslim Raza, Aftab Ahmad, Feng Yue, Zahid Khan, Yang Jiang, Yun Wei, Saleem Raza, Wang Wen He, Faheem Ullah Khan, Yuan Qipeng
Exogenous drug as an antidote to treat various infections get absorbed in the blood circulatory system of a human can directly contact with transporter proteins such as serum albumin. Therefore, for rational drug discovery, understanding the biomolecular interaction between drugs and protein is highly important. In this contribution, we describe the possible interactions between an antifungal drug Amphotericin B (AmB) and Bovine Serum Albumin (BSA) using multi-spectroscopic techniques and further confirmed through in-silico approaches...
March 23, 2017: Journal of Photochemistry and Photobiology. B, Biology
https://www.readbyqxmd.com/read/28364249/surface-plasmon-resonance-based-concentration-determination-assay-label-free-and-antibody-free-quantification-of-morpholinos
#20
Jordan Boutilier, Hong M Moulton
Surface plasmon resonance (SPR) is a physical process that allows label-free and real-time detection of biomolecular interactions. SPR provides a rapid and quantitative method for studying interactions of macromolecules such as proteins and nucleic acids. Antisense Morpholino oligomers are widely used to regulate gene expression and the US FDA has approved a Morpholino drug for treatment of Duchenne muscular dystrophy. Here, we describe an antibody-free, label-free, high-throughput, and walk-away SPR method for quantification of Morpholino compounds extracted from biological specimens...
2017: Methods in Molecular Biology
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