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molecular dynamics

Srilata Ballu, Ramesh Itteboina, Sree Kanth Sivan, Vijjulatha Manga
Staphylococcus aureus is a gram positive bacterium. It is the leading cause of skin and respiratory infections, osteomyelitis, Ritter's disease, endocarditis, and bacteraemia in the developed world. We employed combined studies of 3D QSAR, molecular docking which are validated by molecular dynamics simulations and in silico ADME prediction have been performed on Isothiazoloquinolones inhibitors against methicillin resistance Staphylococcus aureus. Three-dimensional quantitative structure-activity relationship (3D-QSAR) study was applied using comparative molecular field analysis (CoMFA) with Q2 of 0...
December 20, 2017: Computational Biology and Chemistry
Huacheng Xu, Laodong Guo
Dissolved organic matter (DOM) is ubiquitous and plays an important role in regulating water quality, ecological function, and the fate and transport of trace elements and pollutants in aquatic environments. Both the colloidal precursors (i.e. <1 kDa) and bulk DOM collected from a freshwater estuary were incubated in the dark for 21 days to examine dynamic changes in molecular size and composition induced by microbial degradation and self-assembly. Results showed that the concentrations of total organic carbon, carbohydrates, and protein-like substances decreased by 11-30% during incubation, while those of humic- and fulvic-like substances remained relatively constant, indicating humic substances are more resistant to microbial utilization compared to carbohydrates and protein-like DOM...
February 7, 2018: Water Research
Kumar Padmapriya, Ritu Barthwal
Plant derived small molecules, which interact with and stabilize G-quadruplex DNA, act as inhibitors of telomere elongation and oncogene expression in humans. The inhibition of telomerase enzyme has immense potential since it is over expressed in most cancer cells. Interaction of palmatine, an antitumor alkaloid, to parallel G-quadruplex DNA, [d(TTGGGGT)]4 and [d(TTAGGGT)]4 , has been investigated using Nuclear Magnetic Resonance (NMR), fluorescence and Circular Dichroism (CD) spectroscopy. Titrations were monitored by recording1 H and31 P NMR spectra and solution structure of palmatine-[d(TTGGGGT)]4 complex was obtained by restrained Molecular Dynamics (rMD) simulations using distance restraints from 2D NOESY spectra...
February 20, 2018: Biochimie
Katharina F Sonnen, Volker M Lauschke, Julia Uraji, Henning J Falk, Yvonne Petersen, Maja C Funk, Mathias Beaupeux, Paul François, Christoph A Merten, Alexander Aulehla
How signaling dynamics encode information is a central question in biology. During vertebrate development, dynamic Notch signaling oscillations control segmentation of the presomitic mesoderm (PSM). In mouse embryos, this molecular clock comprises signaling oscillations of several pathways, i.e., Notch, Wnt, and FGF signaling. Here, we directly address the role of the relative timing between Wnt and Notch signaling oscillations during PSM patterning. To this end, we developed a new experimental strategy using microfluidics-based entrainment that enables specific control of the rhythm of segmentation clock oscillations...
February 22, 2018: Cell
Trung Hai Nguyen, Chao Zhang, Ewald Weichselbaum, Denis G Knyazev, Peter Pohl, Paolo Carloni
Proton transport at water/membrane interfaces plays a fundamental role for a myriad of bioenergetic processes. Here we have performed ab initio molecular dynamics simulations of proton transfer along two phosphatidylcholine bilayers. As found in previous theoretical studies, the excess proton is preferably located at the water/membrane interface. Further, our simulations indicate that it interacts not only with phosphate head groups, but also with water molecules at the interfaces. Interfacial water molecules turn out to be oriented relative to the lipid bilayers, consistently with experimental evidence...
2018: PloS One
Yingjie Zhang, Mohammad Heiranian, Blanka Janicek, Zoe Budrikis, Stefano Zapperi, Pinshane Huang, Harley T Johnson, Narayana R Aluru, Joseph W Lyding, Nadya Mason
Spatially non-uniform strain is important for engineering the pseudo-magnetic field and band structure of graphene. Despite the wide interest in strain engineering, there is still a lack of control on device-compatible strain patterns due to the limited understanding of the structure-strain relationship. Here we study the effect of substrate corrugation and curvature on the strain profiles of graphene via combined experimental and theoretical studies of a model system - graphene on closely packed SiO2 nanospheres with different diameters (20 - 200 nm)...
February 23, 2018: Nano Letters
Yilin Meng, Cen Gao, David K Clawson, Shane Atwell, Marjanne Russell, Michal Vieth, Benoît Roux
Understanding protein conformational variability remains a challenge in drug discovery. The issue arises in protein kinases, whose multiple conformational states can affect the binding of small-molecule inhibitors. To overcome this challenge, we propose a comprehensive computational framework based on Markov State Models (MSMs). Our framework integrates the information from explicit-solvent molecular dynamics simulations to accurately rank-order the accessible conformational variants of a target protein. We tested the methodology using Abl kinase with a reference and blind-test set...
February 23, 2018: Journal of Chemical Theory and Computation
Kartheek Pitta, Marimuthu Krishnan
DNA damages alter genetic information and adversely affect gene expression pathways leading to various complex genetic disorders and cancers. DNA repair proteins recognize and rectify DNA damages with high fidelity. A critical molecular event that occurs during most protein-mediated DNA repair processes is the extrusion of orphaned bases at the damaged site facilitated by specific repairing enzymes. The molecular-level understanding of the mechanism, dynamics, and energetics of base extrusion is necessary to elucidate the molecular basis of protein-mediated DNA damage repair...
February 23, 2018: Journal of Chemical Information and Modeling
Tamer M Sakr, Mohammed A Khedr, Hassan M Rashed, Maged E Mohamed
l-Phosphinothricin (glufosinate or 2-amino-4-((hydroxy(methyl) phosphinyl) butyric acid ammonium salt (AHPB)), which is a structural analog of glutamate, is a recognized herbicide that acts on weeds through inhibition of glutamine synthetase. Due to the structural similarity between phosphinothricin and some bisphosphonates (BPs), this study focuses on investigating the possibility of repurposing phosphinothricin as a bisphosphonate analogue, particularly in two medicine-related activities: image probing and as an anti-cancer drug...
February 23, 2018: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
Eloise Keeling, Andrew J Lotery, David A Tumbarello, J Arjuna Ratnayaka
Chronic degeneration of the Retinal Pigment Epithelium (RPE) is a precursor to pathological changes in the outer retina. The RPE monolayer, which lies beneath the neuroretina, daily internalises and digests large volumes of spent photoreceptor outer segments. Impaired cargo handling and processing in the endocytic/phagosome and autophagy pathways lead to the accumulation of lipofuscin and pyridinium bis-retinoid A2E aggregates and chemically modified compounds such as malondialdehyde and 4-hydroxynonenal within RPE...
February 23, 2018: Cells
Simone Queiroz Pantaleão, Eric Allison Philot, Pedro Túlio de Resende-Lara, Angélica Nakagawa Lima, David Perahia, Maria Atanassova Miteva, Ana Ligia Scott, Kathia Maria Honorio
Dipeptidyl peptidase-4 (DPP-4) is a target to treat type II diabetes mellitus. Therefore, it is important to understand the structural aspects of this enzyme and its interaction with drug candidates. This study involved molecular dynamics simulations, normal mode analysis, binding site detection and analysis of molecular interactions to understand the protein dynamics. We identified some DPP-4 functional motions contributing to the exposure of the binding sites and twist movements revealing how the two enzyme chains are interconnected in their bioactive form, which are defined as chains A (residues 40-767) and B (residues 40-767)...
February 23, 2018: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
Brian Doherty, Xiang Zhong, Orlando Acevedo
Molecular simulations of ionic liquids can provide deeper insight into the relationship between intermolecular interactions and macroscopic measurements for the solvents. However, many existing force fields have multiple shortcomings, including poor solvent dynamics, the underestimation of hydrogen bonding strength, and errors in solvent interactions/organization. A new force field, called OPLS-VSIL, has been developed for imidazolium-based ionic liquids featuring a novel topology incorporating a virtual site bisecting the nitrogen atoms that offloads negative charge to inside the plane of the ring...
February 23, 2018: Journal of Physical Chemistry. B
Alan Ianeselli, Simone Orioli, Giovanni Spagnolli, Pietro Faccioli, Lorenzo Cupellini, Sandro Jurinovich, Benedetta Mennucci
Circular Dichroism (CD) is known to be an excellent tool for the determination of protein secondary structure due to fingerprint signatures of α and β domains. However, CD spectra are also sensitive to the 3D arrangement of the chain as a result of the excitonic nature of additional signals due to the aromatic residues. This double sensitivity, when extended to time-resolved experiments, should allow protein folding to be monitored with high spatial resolution. To date, the exploitation of this very appealing idea has been limited, due to the difficulty in relating the observed spectral evolution to specific configurations of the chain...
February 23, 2018: Journal of the American Chemical Society
Melaine A Kuenemann, Denis Fourches
The With-No-Lysine (WNK) serine/threonine kinase family constitutes a unique and distinctive branch of the kinome. The four proteins of this family (WNK1/2/3/4) are involved in blood pressure regulation, body fluid, and electrolyte homeostasis. Herein, we modeled and analyzed the binding modes of all publicly-available small orthosteric and allosteric binders (including WNK463 and WNK467) experimentally tested towards any of the WNK family member. To do so, we relied on state-of-the-art cheminformatics approaches including structure-based molecular docking and molecular dynamics simulations...
February 23, 2018: Molecular Informatics
Juan Camilo Molano-Arevalo, Walter Gonzalez, Kevin Jeanne Dit Fouque, Jaroslava Miksovska, Philippe Maitre, Francisco Fernandez-Lima
Nicotinamide adenine dinucleotide (NAD) is found in all living cells where the oxidized (NAD+ ) and reduced (NADH) forms play important roles in many enzymatic reactions. However, little is known about NAD+ and NADH conformational changes and kinetics as a function of the cell environment. In the present work, an analytical workflow is utilized to study NAD+ and NADH dynamics as a function of the organic content in solution using fluorescence lifetime spectroscopy and in the gas-phase using trapped ion mobility spectrometry coupled to mass spectrometry (TIMS-MS) and infrared multiple photon dissociation (IRMPD) spectroscopy...
February 23, 2018: Physical Chemistry Chemical Physics: PCCP
Mounika Gosika, Prabal K Maiti
The adsorption of PAMAM dendrimers at solid/water interfaces has been extensively studied, and is mainly driven by electrostatic and van der Waals interactions between the substrate and the dendrimers. However, the pH dependence of the adsorption driven predominantly by the van der Waals interactions is poorly explored, although it is crucial for investigating the potentiality of these dendrimers in supercapacitors and surface patterning. Motivated by this aspect, we have studied the adsorption behavior of PAMAM dendrimers of generations 2 (G2) to 5 (G5) with pH and salt concentration variation, on a charge neutral graphene substrate, using fully atomistic molecular dynamics simulations...
February 23, 2018: Soft Matter
Federico Fogolari, Alessandra Corazza, Gennaro Esposito
Free energy is the key quantity to describe the thermodynamics of biological systems. In this perspective we consider the calculation of free energy, enthalpy and entropy from end-point molecular dynamics simulations. Since the enthalpy may be calculated as the ensemble average over equilibrated simulation snapshots the difficulties related to free energy calculation are ultimately related to the calculation of the entropy of the system and in particular of the solvent entropy. In the last two decades implicit solvent models have been used to circumvent the problem and to take into account solvent entropy implicitly in the solvation terms...
2018: Frontiers in Molecular Biosciences
Kamelia M Osman, Ashgan M Hessain, Usama H Abo-Shama, Zeinab M Girh, Saleh A Kabli, Hassan A Hemeg, Ihab M Moussa
Escherichia coli is a recognized zoonotic food-borne pathogen; however, the use of polymerase chain reaction (PCR) in the underdeveloped countries to differentiate pathogenic from non-pathogenic E. coli is a problematic issue. Our grail was to assess the phenotypic virulence markers motility, hemolysin, congo red agar, embryo lethality assay and serum resistance for pathogenic E. coli (PEC) correlated to PCR tests which is currently used world-wide to evaluate the PEC. The 448 strains of Escherichia coli that were isolated from different sources, were characterized for phenotypic virulence factors such as motility, hemolysin, Congo red binding, Embryo Lethality assay (ELA) and serum resistance, as well as antibiotic susceptibility using disc diffusion method to 23 antibiotics ...
February 2018: Saudi Journal of Biological Sciences
Stephen J Clark, Ricard Argelaguet, Chantriolnt-Andreas Kapourani, Thomas M Stubbs, Heather J Lee, Celia Alda-Catalinas, Felix Krueger, Guido Sanguinetti, Gavin Kelsey, John C Marioni, Oliver Stegle, Wolf Reik
Parallel single-cell sequencing protocols represent powerful methods for investigating regulatory relationships, including epigenome-transcriptome interactions. Here, we report a single-cell method for parallel chromatin accessibility, DNA methylation and transcriptome profiling. scNMT-seq (single-cell nucleosome, methylation and transcription sequencing) uses a GpC methyltransferase to label open chromatin followed by bisulfite and RNA sequencing. We validate scNMT-seq by applying it to differentiating mouse embryonic stem cells, finding links between all three molecular layers and revealing dynamic coupling between epigenomic layers during differentiation...
February 22, 2018: Nature Communications
Jongrae Kim, Mathias Foo, Declan G Bates
Measurement techniques in biology are now able to provide data on the trajectories of multiple individual molecules simultaneously, motivating the development of techniques for the stochastic spatio-temporal modelling of biomolecular networks. However, standard approaches based on solving stochastic reaction-diffusion equations are computationally intractable for large-scale networks. We present a novel method for modeling stochastic and spatial dynamics in biomolecular networks using a simple form of the Langevin equation with noisy kinetic constants...
February 22, 2018: Scientific Reports
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