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https://www.readbyqxmd.com/read/27913731/disentangling-polydispersity-in-the-pcna-p15paf-complex-a-disordered-transient-and-multivalent-macromolecular-assembly
#1
Tiago N Cordeiro, Po-Chia Chen, Alfredo De Biasio, Nathalie Sibille, Francisco J Blanco, Jochen S Hub, Ramon Crehuet, Pau Bernadó
The intrinsically disordered p15(PAF) regulates DNA replication and repair when interacting with the Proliferating Cell Nuclear Antigen (PCNA) sliding clamp. As many interactions between disordered proteins and globular partners involved in signaling and regulation, the complex between p15(PAF) and trimeric PCNA is of low affinity, forming a transient complex that is difficult to characterize at a structural level due to its inherent polydispersity. We have determined the structure, conformational fluctuations, and relative population of the five species that coexist in solution by combining small-angle X-ray scattering (SAXS) with molecular modelling...
December 1, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27911884/desorption-of-water-from-hydrophilic-mcm-41-mesopores-positron-annihilation-ftir-and-md-simulation-studies
#2
Priya Maheshwari, D Dutta, T Muthulakshmi, B Chakraborty, N Raje, P K Pujari
The desorption mechanism of water from the hydrophilic mesopores of MCM-41 was studied using positron annihilation lifetime spectroscopy (PALS) and attenuated total reflection Fourier transform infrared spectroscopy supplemented with molecular dynamics (MD) simulation. PALS results indicated that water molecules do not undergo sequential evaporation in a simple layer-by-layer manner during desorption from MCM-41 mesopores. The results suggested that the water column inside the uniform cylindrical mesopore become stretched during desorption and induces cavitation (as seen in the case of ink-bottle type pores) inside it, keeping a dense water layer at the hydrophilic pore wall, as well as a water plug at both the open ends of the cylindrical pore, until the water was reduced to a certain volume fraction where the pore catastrophically empties...
December 2, 2016: Journal of Physics. Condensed Matter: An Institute of Physics Journal
https://www.readbyqxmd.com/read/27909522/safety-and-necessity-of-thermal-esophageal-probes-during-radiofrequency-ablation-for-the-treatment-of-atrial-fibrillation
#3
Antonio Fasano, Prof Emeritus, Luca Anfuso Md, Stefano Bozzi Md, Claudio Pandozi Prof
BACKGROUND: Radiofrequency ablation is extensively used to achieve pulmonary veins isolation for the cure of atrial fibrillation. Luminal esophageal temperature can be monitored by means of suitable probes to prevent the onset of lesions. OBJECTIVE: To compute the thermal field generated by the ablation, to investigate the interaction between the electromagnetic field and the probe sensors, and to provide a safe interpretation of the temperature detected by the probe, supported by clinical data...
June 2016: Journal of Atrial Fibrillation
https://www.readbyqxmd.com/read/27907857/membrane-effects-of-dihydropyrimidine-analogues-with-larvicidal-activity
#4
Mariela E Sánchez-Borzone, Maria E Mariani, Virginia Miguel, Raquel M Gleiser, Bharti Odhav, Katharigatta N Venugopala, Daniel A García
Two recently synthesized dihydropyrimidines (DHPMs) analogues have demonstrated larvicide and repellent activity against Anopheles arabiensis. DHPMs high lipophilicity suggests that these compounds may interact directly with the membrane and modify their biophysical properties. The purpose of the present study was to characterize the interaction of both compounds with artificial membranes. Changes on the properties of DPPC films were studied using Langmuir monolayers. The presence of DHPMs in the subphase modified the interfacial characteristics of DPPC compression isotherms, causing the expansion of the monolayer, inducing the disappearance of DPPC phase transition and increasing the molecular packing of the film...
November 24, 2016: Colloids and Surfaces. B, Biointerfaces
https://www.readbyqxmd.com/read/27907142/ibisa_tools-a-computational-toolkit-for-ion-binding-state-analysis-in-molecular-dynamics-trajectories-of-ion-channels
#5
Kota Kasahara, Kengo Kinoshita
Ion conduction mechanisms of ion channels are a long-standing conundrum. Although the molecular dynamics (MD) method has been extensively used to simulate ion conduction dynamics at the atomic level, analysis and interpretation of MD results are not straightforward due to complexity of the dynamics. In our previous reports, we proposed an analytical method called ion-binding state analysis to scrutinize and summarize ion conduction mechanisms by taking advantage of a variety of analytical protocols, e.g., the complex network analysis, sequence alignment, and hierarchical clustering...
2016: PloS One
https://www.readbyqxmd.com/read/27903910/structural-insights-into-dynamics-of-recu-hj-complex-formation-elucidates-key-role-of-ntr-and-stalk-region-toward-formation-of-reactive-state
#6
Sagar Khavnekar, Sarath Chandra Dantu, Svetlana Sedelnikova, Sylvia Ayora, John Rafferty, Avinash Kale
Holliday junction (HJ) resolving enzyme RecU is involved in DNA repair and recombination. We have determined the crystal structure of inactive mutant (D88N) of RecU from Bacillus subtilis in complex with a 12 base palindromic DNA fragment at a resolution of 3.2 Å. This structure shows the stalk region and the essential N-terminal region (NTR) previously unseen in our DNA unbound structure. The flexible nature of the NTR in solution was confirmed using SAXS. Thermofluor studies performed to assess the stability of RecU in complex with the arms of an HJ indicate that it confers stability...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27901172/conformational-states-of-hamp-domains-interacting-with-sensory-rhodopsin-membrane-systems-an-integrated-all-atom-and-coarse-grained-molecular-dynamics-simulation-approach
#7
Bikash Ranjan Sahoo, Toshimichi Fujiwara
Understanding the downstream signaling mechanism of sensory rhodopsin and its cognate transducer complex (srII-htrII) has long been a challenge in the field of photoreceptor research. Here, an integration of all-atom and coarse-grained (CG) molecular dynamics (MD) simulations in different srII-htrII complex states is carried out. It is shown that the cytoplasmic four-helix HAMP dimer gives rise to a gear-box model interaction with discrete hydrophobic packing in Natronomonas pharaonis (Np). Structural analysis in all-atom and CG-MD reveals a stable conformational state in the physiological environment (323 K and 1...
November 30, 2016: Molecular BioSystems
https://www.readbyqxmd.com/read/27901162/molecular-dynamics-simulations-and-kelvin-probe-force-microscopy-to-study-of-cholesterol-induced-electrostatic-nanodomains-in-complex-lipid-mixtures
#8
E Drolle, W F D Bennett, K Hammond, E Lyman, M Karttunen, Z Leonenko
The molecular arrangement of lipids and proteins within biomembranes and monolayers gives rise to complex film morphologies as well as regions of distinct electrical surface potential, topographical and electrostatic nanoscale domains. To probe these nanodomains in soft matter is a challenging task both experimentally and theoretically. This work addresses the effects of cholesterol, lipid composition, lipid charge, and lipid phase on the monolayer structure and the electrical surface potential distribution...
November 30, 2016: Soft Matter
https://www.readbyqxmd.com/read/27901156/hydration-and-self-aggregation-of-a-neutral-cosolute-from-dielectric-relaxation-spectroscopy-and-md-simulations-the-case-of-1-3-dimethylurea
#9
Vira Agieienko, Dominik Horinek, Richard Buchner
The influence of the amphiphile 1,3-dimethylurea (1,3-DMU) on the dynamic properties of water was studied using dielectric relaxation spectroscopy. The experiment provided evidence for substantial retardation of water reorientation in the hydration shell of 1,3-DMU, leading to a separate slow-water relaxation in addition to contributions from bulk-like and fast water as well as from the solute. From the amplitudes of the resolved water modes effective hydration numbers were calculated, showing that each 1,3-DMU molecule effectively freezes the reorientation of 1-2 water molecules...
November 30, 2016: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/27901138/understanding-the-self-assembly-of-amino-ester-based-benzene-1-3-5-tricarboxamides-using-molecular-dynamics-simulations
#10
Karteek K Bejagam, Richard C Remsing, Michael L Klein, Sundaram Balasubramanian
Amino ester-based benzene-1,3,5-tricarboxamides (BTAs) are widely studied experimentally for their facile self-assembly, which leads to strong three-fold hydrogen bonded supramolecular polymers. Understanding the supramolecular assembly of these BTAs is complicated by the presence of two types of dimers, based on the nature of the intermolecular hydrogen bonding pattern: amide-amide (AA) and amide-carboxylate (AC). AA dimers form three hydrogen bonds between the two molecules, are typical of BTA stacks, and act as a basic building block of assembly...
November 30, 2016: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/27900580/buckling-analysis-of-defective-cross-linked-functionalized-single-and-double-walled-carbon-nanotubes-with-polyethylene-chains-using-molecular-dynamics-simulations
#11
S Ajori, R Ansari, H Parsapour
Functionalized carbon nanotubes (CNTs) can be used for improving the mechanical properties and load transfer in nanocomposites. In this research, the buckling behavior of perfect and defective cross-linked functionalized CNTs with polyethylene (PE) chains is studied employing molecular dynamics (MD) simulations. Two different configurations with the consideration of vacancy defects, namely mapped and wrapped, are selected. According to the results, critical buckling force of cross-linked functionalized CNTs with PE chains increases as compared to pure CNTs, especially in the case of double-walled carbon nanotubes (DWCNTs)...
December 2016: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/27899437/allosteric-control-of-antibody-prion-recognition-through-oxidation-of-a-disulfide-bond-between-the-ch-and-cl-chains
#12
Jun Zhao, Ruth Nussinov, Buyong Ma
Molecular details of the recognition of disordered antigens by their cognate antibodies have not been studied as extensively as folded protein antigens and much is still unknown. To follow the conformational changes in the antibody and cross-talk between its subunits and with antigens, we performed molecular dynamics (MD) simulations of the complex of Fab and prion-associated peptide in the apo and bound forms. We observed that the inter-chain disulfide bond in constant domains restrains the conformational changes of Fab, especially the loops in the CH1 domain, resulting in inhibition of the cross-talk between Fab subdomains that thereby may prevent prion peptide binding...
November 29, 2016: Protein Engineering, Design & Selection: PEDS
https://www.readbyqxmd.com/read/27897348/enzymatic-activity-and-thermodynamic-stability-of-biliverdin-ix%C3%AE-reductase-are-maintained-by-an-active-site-serine
#13
Wen-Ting Chu, Natasha M Nesbitt, Dmitri V Gnatenko, Zongdong Li, Beibei Zhang, Markus A Seeliger, Seamus Browne, Timothy J Mantle, Wadie F Bahou, Jin Wang
Biliverdin reductase IXβ (BLVRB) is a crucial enzyme in heme metabolism. Recent studies in humans have identified a loss-of-function mutation (Ser111Leu) that unmasks a fundamentally important role in hematopoiesis. We have applied experimental and thermodynamic modeling studies to provide further insight into role of the cofactor in substrate accessibility and protein folding properties regulating BLVRB catalytic mechanisms. Site-directed mutagenesis with molecular dynamic (MD) simulations establish the critical role of NAD(P)H-dependent conformational changes on substrate accessibility by forming the "hydrophobic pocket", along with identification of a single key residue (Arg35) modulating NAD(P)H/NADH selectivity...
November 29, 2016: Chemistry: a European Journal
https://www.readbyqxmd.com/read/27897077/understanding-the-conformational-flexibility-and-electrostatic-properties-of-curcumin-in-the-active-site-of-rhache-via-molecular-docking-molecular-dynamics-and-charge-density-analysis
#14
Saravanan Kandasamy, Kalaiarasi Chinnasamy, Kumaradhas Poomani
Acetylcholinesterase (AChE) is an important enzyme responsible for Alzheimer disease (AD), as per report, keto-enol form of curcumin inhibits this enzyme. The present study aims to understand the binding mechanism of keto-enol curcumin with the recombinant human Acetylcholinesterase (rhAChE) from its conformational flexibility, intermolecular interactions, charge density distribution and the electrostatic properties at the active site of rhAChE. To accomplish this, a molecular docking analysis of curcumin with the rhAChE was performed, which gives the structure and conformation of curcumin in the active site of rhAChE...
November 29, 2016: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/27896494/endohedral-metalloborofullerenes-m-b44-m-ca-sr-ba-a-computational-investigation
#15
Le Yang, Peng Jin, Qinghua Hou, Lanlan Li
For the first time, the structures, stabilities and electronic properties of alkaline-earth metal doped B44 fullerenes were investigated by means of density functional theory calculations. Our results reveal that M@B44 (M = Ca, Sr, Ba) possess endohedral configurations as their lowest energy structures, whereas the exohedral form is favored when metal is Be or Mg. The large binding energies and sizable HOMO-LUMO gap energies of Ca@B44, Sr@B44 and Ba@B44 suggest the considerable possibility to achieve these novel endohedral borofullerenes experimentally...
December 2016: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/27891211/from-linked-open-data-to-molecular-interaction-studying-selectivity-trends-for-ligands-of-the-human-serotonin-and-dopamine-transporter
#16
Barbara Zdrazil, Eva Hellsberg, Michael Viereck, Gerhard F Ecker
Retrieval of congeneric and consistent SAR data sets for protein targets of interest is still a laborious task to do if no appropriate in-house data set is available. However, combining integrated open data sources (such as the Open PHACTS Discovery Platform) with workflow tools now offers the possibility of querying across multiple domains and tailoring the search to the given research question. Starting from two phylogenetically related protein targets of interest (the human serotonin and dopamine transporters), the whole chemical compound space was explored by implementing a scaffold-based clustering of compounds possessing biological measurements for both targets...
September 14, 2016: MedChemComm
https://www.readbyqxmd.com/read/27890821/molecular-dynamics-driven-drug-discovery-leaping-forward-with-confidence
#17
REVIEW
Aravindhan Ganesan, Michelle L Coote, Khaled Barakat
Given the significant time and financial costs of developing a commercial drug, it remains important to constantly reform the drug discovery pipeline with novel technologies that can narrow the candidates down to the most promising lead compounds for clinical testing. The past decade has witnessed tremendous growth in computational capabilities that enable in silico approaches to expedite drug discovery processes. Molecular dynamics (MD) has become a particularly important tool in drug design and discovery...
November 24, 2016: Drug Discovery Today
https://www.readbyqxmd.com/read/27890678/hot-spot-mapping-of-protein-surfaces-with-tempol-bovine-pancreatic-rnase-a-as-a-model-system
#18
Neri Niccolai, Edoardo Morandi, Simone Gardini, Valentino Costabile, Roberta Spadaccini, Orlando Crescenzi, Delia Picone, Ottavia Spiga, Andrea Bernini
TEMPOL spin-label has been used to identify surface exposure of protein nuclei from NMR analysis of the induced paramagnetic relaxation enhancements (PRE). The absence of linear dependence between atom depths and observed PRE reveals that specific mechanisms drive the approach of the paramagnet to the protein surface. RNase A represents a unique protein system to explore the fine details of the information offered by TEMPOL induced PRE, due to the abundance of previous results, obtained in solution and in the crystal, dealing with surface dynamics behavior of this protein...
November 24, 2016: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/27888840/nmr-solution-structure-determination-of-large-rna-protein-complexes
#19
REVIEW
Deepak Kumar Yadav, Peter J Lukavsky
Structure determination of RNA-protein complexes is essential for our understanding of the multiple layers of RNA-mediated posttranscriptional regulation of gene expression. Over the past 20years, NMR spectroscopy became a key tool for structural studies of RNA-protein interactions. Here, we review the progress being made in NMR structure determination of large ribonucleoprotein assemblies. We discuss approaches for the design of RNA-protein complexes for NMR structural studies, established and emerging isotope and segmental labeling schemes suitable for large RNPs and how to gain distance restraints from NOEs, PREs and EPR and orientational information from RDCs and SAXS/SANS in such systems...
November 2016: Progress in Nuclear Magnetic Resonance Spectroscopy
https://www.readbyqxmd.com/read/27886326/molecular-dynamics-simulation-of-amino-acid-ionic-liquids-near-a-graphene-electrode-effects-of-alkyl-side-chain-length
#20
Behnoosh Sadeghi Moghadam, Mohammad Razmkhah, Mohammad Taghi Hamed Mosavian, Fatemeh Moosavi
Electric double layer (EDL) supercapacitors, using ionic liquid electrolytes, have been receiving a great deal of attention in response to the growing demand for energy storage systems. In the present study, the nanoscopic structure of amino acid ionic liquids (AAILs) as biodegradable electrolytes near a neutral graphene surface was studied by molecular dynamics (MD) simulation. In order to explore the influence of the anion type and structure, the effect of the alkyl side-chain length of amino acids on the EDL was investigated...
November 25, 2016: Physical Chemistry Chemical Physics: PCCP
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