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Molecular Dynamics Simulations

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https://www.readbyqxmd.com/read/30098463/aptasensor-designed-via-the-stochastic-tunneling-basin-hopping-method-for-biosensing-of-vascular-endothelial-growth-factor
#1
Hung-Wei Yang, Shin-Pon Ju, Che-Hao Cheng, Ying-Tzu Chen, Yu-Sheng Lin, See-Tong Pang
The Systematic Evolution Ligands by Exponential Enrichment (SELEX) is common used for selection of high affinity single-stranded DNA (ssDNA) aptamer with target protein. However, we do not know what the most stable configuration of the selected aptamer bound with target protein is. Therefore, a systematic search process using the stochastic tunneling-basin hopping (STUN-BH) method is proposed to find the most stable configuration of the ssDNA aptamer specific for vascular endothelial growth factor (VEGF) capture (AptVEGF ; 5'-TGTGGGGGTGGACGGGCCGGGTAGA-3')...
August 2, 2018: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/30097974/papain-loaded-poly-%C3%AE%C2%B5-caprolactone-nanoparticles-in-silico-and-in-vitro-studies
#2
Yasemin Budama-Kilinc, Rabia Cakir-Koc, Serda Kecel-Gunduz, Tolga Zorlu, Yagmur Kokcu, Bilge Bicak, Zeynep Karavelioglu, Aysen E Ozel
Papain is a protease enzyme with therapeutic properties that are very valuable for medical applications. Poly(ε-caprolactone) (PCL) is an ideal polymeric carrier for controlled drug delivery systems due to its low biodegradability and its high biocompatibility. In this study, the three-dimensional structure and action mechanism of papain were investigated by in vitro and in silico experiments using molecular dynamics (MD) and molecular docking methods to elucidate biological functions. The results showed that the size of papain-loaded PCL nanoparticles (NPs) and the polydispersity index (PDI) of the NPs were 242...
August 10, 2018: Journal of Fluorescence
https://www.readbyqxmd.com/read/30097767/investigating-the-structural-properties-of-the-active-conformation-btl2-of-a-lipase-from-geobacillus-thermocatenulatus-in-toluene-using-molecular-dynamic-simulations-and-engineering-btl2-via-in-silico-mutation
#3
Aslı Yenenler, Alessandro Venturini, Huseyin Cahit Burduroglu, Osman Uğur Sezerman
The discovery or development of thermoalkalophilic lipases that show high levels of catalytic activity in organic solvents would have important industrial ramifications. However, this goal is yet to be achieved because organic solvents induce structural changes in lipases that suppress their catalytic abilities. A deep understanding of these structural changes to lipases in the presence of organic solvents is required before strategies can be devised to stop them from occurring. In this work, we investigated the effects of an organic reaction medium, toluene, on the structure of the Bacillus thermocatenulatus lipase BTL2 using MD simulation...
August 10, 2018: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/30097643/targeting-nucleotide-binding-domain-of-multidrug-resistance-associated-protein-1-mrp1-for-the-reversal-of-multi-drug-resistance-in-cancer
#4
Divya Dhasmana, Ashutosh Singh, Rohit Shukla, Timir Tripathi, Neha Garg
Multidrug resistance (MDR) is the major cause, by which cancer cells expel the drugs out, developing a challenge against the current chemotherapeutic drugs regime. This mechanism is attributed to the over expression of ABC transporters like MRP1 on the surface of cells. Since nucleotide binding domains (NBD) of ABC transporters are the site of ATP binding and hydrolysis, thereby in this study we have targeted NBD1 of MRP1using molecular docking and molecular dynamic simulations (MDS). The compounds present in the FDA approved library were docked against NBD1 of the human multidrug resistance associated protein 1 (PDB ID: 2CBZ)...
August 10, 2018: Scientific Reports
https://www.readbyqxmd.com/read/30097175/allosteric-kras4b-can-modulate-sos1-fast-and-slow-ras-activation-cycles
#5
Tsung-Jen Liao, Hyunbum Jang, David Fushman, Ruth Nussinov
Membrane-anchored Ras family proteins are activated by guanine nucleotide exchange factors such as SOS1. The CDC25 domain of SOS1 catalyzes GDP-to-GTP exchange, thereby activating Ras. Here, we aim to decipher the activation mechanism of KRas4B, a significantly mutated oncogene. We perform large-scale molecular dynamics simulations on 12 SOS1 systems, scrutinizing each step in two possible KRas4B activation cycles, fast and slow. To activate KRas4B at the CDC25 catalytic site, the allosteric site in the Ras exchanger motif (REM) domain of SOS1 needs to recruit a (nucleotide-bound) KRas4B molecule...
July 24, 2018: Biophysical Journal
https://www.readbyqxmd.com/read/30096696/determination-of-interactions-between-human-serum-albumin-and-niraparib-through-multi-spectroscopic-and-computational-methods
#6
Na Gan, Qiaomei Sun, Peixiao Tang, Di Wu, Tonghui Xie, Yongkui Zhang, Hui Li
The interactions between 2-{4-[(3S)-piperidin-3-yl] phenyl}-2H-indazole-7-carboxamide (niraparib) and human serum albumin (HSA) were investigated through fluorescence and computational studies. Fluorescence experiments showed that the static quenching mechanism and the binding constant of the HSA-niraparib system at a single binding site was approximately 4 × 104  L mol-1 . Thermodynamic constants indicated that the binding of niraparib to HSA was mainly driven by electrostatic interactions. Competition experiments and molecular docking simulations revealed that niraparib bound to site III of HSA...
August 1, 2018: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
https://www.readbyqxmd.com/read/30096242/all-hydrocarbon-staples-and-their-effect-over-peptide-conformation-under-different-force-fields
#7
Bianca Villavicencio, Rodrigo Ligabue-Braun, Hugo Verli
Olefinic staples enhance alpha-helical content and conformational stability in peptides, maintaining a structural scaffold that allows the emulation of specific regions of protein surfaces for therapeutical purposes. The ability to anticipate the efficacy of the staple addition to a peptide through computational simulations may contribute to lower the costs associated with rational drug design. We evaluated the capability of different force fields to reproduce the effect of all-hydrocarbon staples on molecular dynamics simulations...
August 10, 2018: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/30096240/the-presence-and-role-of-midplane-cholesterol-in-lipid-bilayers-containing-registered-or-antiregistered-phase-domains
#8
Michael D Weiner, Gerald W Feigenson
Three-component lipid mixtures can produce coexisting liquid ordered (Lo) and liquid disordered (Ld) phases, a model for eukaryotic plasma membrane rafts. In compositionally symmetric bilayers with two phase-separated leaflets, phase domains of the two leaflets may align through registration, where domains are found across from domains of the same phase, or else antiregistration, where domains are found across from domains of the opposite phase. This alignment could serve as a method of information communication across the plasma membrane...
August 10, 2018: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/30095921/interaction-of-proteins-with-polyelectrolytes-a-comparison-between-theory-and-experiment
#9
Xiao Xu, Stefano Angioletti-Uberti, Yan Lu, Joachim Dzubiella, Matthias Ballauff
We discuss recent investigations of the interaction of polyelectrolytes with proteins. In particular, we review our recent studies on the interaction of simple proteins as human serum albumin (HSA) or lysozyme with linear polyelectrolytes, charged dendrimers, charged networks, and polyelectrolyte brushes. In all cases discussed here we combined experimental work with molecular dynamics (MD) simulations and meanfield theories. In particular, isothermal titration calorimetry (ITC) has been employed to obtain the respective binding constants Kb and the Gibbs free energy of binding...
August 10, 2018: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/30095901/concentration-dependent-membrane-selective-activity-of-human-ll37-peptides-modified-with-collagen-binding-domain-sequences
#10
Lindsay D Lozeau, Sina Youssefian, Nima Rahbar, Terri A Camesano, Marsha W Rolle
Antimicrobial peptides (AMPs) such as LL37 are promising alternatives to antibiotics to treat wound infections due to their broad activity, immunomodulatory functions, and low likelihood of antimicrobial resistance. To deliver LL37 to chronic wounds, we developed two chimeric LL37 peptides with C-terminal collagen binding domains (CBD) derived from collagenase (cCBD-LL37) and fibronectin (fCBD-LL37), as a strategy for noncovalent tethering of LL37 onto collagen-based, commercially available wound dressings...
August 10, 2018: Biomacromolecules
https://www.readbyqxmd.com/read/30095840/nonlinear-optical-responses-of-self-assembled-monolayers-functionalized-with-indolino-oxazolidine-photoswitches
#11
Claire Tonnelé, Kornelia Pielak, Jean Deviers, Luca Muccioli, Benoît Champagne, Frédéric Castet
A computational approach combining molecular dynamic simulations and density functional theory (DFT) calculations is implemented to evaluate the second-order nonlinear optical (NLO) responses of photoresponsive self-assembled monolayers (SAMs) based on indolino-oxazolidine molecular switches. These numerical simulations provide a complete atomistic picture of the morphology of the SAMs, revealing a high degree of positional disorder and an almost isotropic orientation of the chromophores. Subsequent DFT calculations, carried out to evaluate the average first hyperpolarizability of indolino-oxazolidine switches within the SAM, predict that the structural disorder does not significantly reduce the NLO contrast compared to that of the isolated molecules...
August 10, 2018: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/30095336/induction-of-aneurysmogenic-high-positive-wall-shear-stress-gradient-by-wide-angle-at-cerebral-bifurcations-independent-of-flow-rate
#12
Alexandra Lauric, James E Hippelheuser, Adel M Malek
OBJECTIVE Endothelium adapts to wall shear stress (WSS) and is functionally sensitive to positive (aneurysmogenic) and negative (protective) spatial WSS gradients (WSSG) in regions of accelerating and decelerating flow, respectively. Positive WSSG causes endothelial migration, apoptosis, and aneurysmal extracellular remodeling. Given the association of wide branching angles with aneurysm presence, the authors evaluated the effect of bifurcation geometry on local apical hemodynamics. METHODS Computational fluid dynamics simulations were performed on parametric bifurcation models with increasing angles having: 1) symmetrical geometry (bifurcation angle 60°-180°), 2) asymmetrical geometry (daughter angles 30°/60° and 30°/90°), and 3) curved parent vessel (bifurcation angles 60°-120°), all at baseline and double flow rate...
August 10, 2018: Journal of Neurosurgery
https://www.readbyqxmd.com/read/30095268/unravelling-the-effects-of-a-site-cations-on-nonradiative-electron-hole-recombination-in-lead-bromide-perovskites-time-domain-ab-initio-analysis
#13
Jinlu He, Wei-Hai Fang, Run Long
Lead bromide perovskites APbBr3 (A = Cs, MA, FA) hold great promise in optoelectronics and photovoltaics. Because the bandgap of the three materials are similar, and also because the A site cation does not contribute to band edges, leading one to expect minor influence of A site cation on the excited-state lifetime of the perovskites. Experiments defy the expectation. By performing ab initio nonadiabatic (NA) molecular dynamics combined with time-domain density functional simulations, we demonstrate that the nonradiative electron-hole recombination times are on the order FAPbBr3 > MAPbBr3 > CsPbBr3, which are determined by the NA electron-phonon coupling because decoherence times are similar...
August 10, 2018: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/30094683/spices-a-particle-based-molecular-structure-line-notation-and-support-library-for-mesoscopic-simulation
#14
Karina van den Broek, Mirco Daniel, Matthias Epple, Hubert Kuhn, Jonas Schaub, Achim Zielesny
Simplified Particle Input ConnEction Specification (SPICES) is a particle-based molecular structure representation derived from straightforward simplifications of the atom-based SMILES line notation. It aims at supporting tedious and error-prone molecular structure definitions for particle-based mesoscopic simulation techniques like Dissipative Particle Dynamics by allowing for an interplay of different molecular encoding levels that range from topological line notations and corresponding particle-graph visualizations to 3D structures with support of their spatial mapping into a simulation box...
August 9, 2018: Journal of Cheminformatics
https://www.readbyqxmd.com/read/30094474/terahertz-electric-field-induced-membrane-electroporation-by-molecular-dynamics-simulations
#15
Jingchao Tang, Hairong Yin, Jialu Ma, Wenfei Bo, Yang Yang, Jin Xu, Yiyao Liu, Yubin Gong
In this paper, the membrane electroporation induced by the terahertz electric field is simulated by means of the molecular dynamics method. The influences of the waveform and frequency of the applied terahertz electric field on the electroporation and the unique features of the process of the electroporation with the applied terahertz electric field are given. It shows that whether the electroporation can happen depends on the waveform of the applied terahertz electric field when the magnitude is not large enough...
August 9, 2018: Journal of Membrane Biology
https://www.readbyqxmd.com/read/30094445/atomistic-reverse-nonequilibrium-molecular-dynamics-simulation-of-the-viscosity-of-ionic-liquid-1-n-butyl-3-methylimidazolium-bis-trifluoromethylsulfonyl-imide-bmim-tf-2-n
#16
Rouhollah Safinejad, Nargess Mehdipour, Hossein Eslami
The shear viscosity of room-temperature ionic liquid (IL) 1-n-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide [bmim][Tf2N] is calculated over a temperature range 298-353 K, using the reverse nonequilibrium molecular dynamics simulation technique. The results of this work show that while the use of equilibrium molecular dynamics simulation techniques might be inefficient for viscosity calculations of ILs, the reverse nonequilibrium molecular dynamics technique is an efficient tool for this purpose...
August 10, 2018: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/30093931/computational-screening-of-metal-organic-frameworks-for-membrane-based-co-2-n-2-h-2-o-separations-best-materials-for-flue-gas-separation
#17
Hilal Daglar, Seda Keskin
It has become a significant challenge to select the best metal-organic frameworks (MOFs) for membrane-based gas separations because the number of synthesized MOFs is growing exceptionally fast. In this work, we used high-throughput computational screening to identify the top MOF membranes for flue gas separation. Grand canonical Monte Carlo and molecular dynamics simulations were performed to assess adsorption and diffusion properties of CO2 and N2 in 3806 different MOFs. Using these data, selectivities and permeabilities of MOF membranes were predicted and compared with those of conventional membranes, polymers, and zeolites...
August 2, 2018: Journal of Physical Chemistry. C, Nanomaterials and Interfaces
https://www.readbyqxmd.com/read/30093407/structural-insight-into-proline-cis-trans-isomerization-of-unfolded-proteins-catalyzed-by-the-trigger-factor-chaperone
#18
Soichiro Kawagoe, Hiroshi Nakagawa, Hiroyuki Kumeta, Koichiro Ishimori, Tomohide Saio
Molecular chaperones often possess functional modules that are specialized in assisting the formation of specific structural elements, such as disulfide bridges and peptidyl-prolyl bonds in the cis form, in the client protein. A ribosome-associated molecular chaperone called trigger factor (TF), which has a peptidyl-prolyl cis/trans isomerase (PPIase) domain, acts as a highly efficient catalyst in the folding process limited by peptidyl-prolyl isomerization. Herein, we report on the mechanism through which TF recognizes the proline residue in the unfolded client protein during the cis/trans isomerization process...
August 9, 2018: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/30093168/a-patient-with-hereditary-attr-and-a-novel-agel-p-ala578pro-amyloidosis
#19
Meera Sridharan, W Edward Highsmith, Paul J Kurtin, Michael T Zimmermann, Jason D Theis, Surendra Dasari, David Dingli
Hereditary amyloidosis represents a group of diseases in which mutant proteins are deposited in various organs leading to their dysfunction. Correct identification of the amyloid-causing protein is critical because this will determine the optimal therapy for the patient. The most common type of hereditary amyloidosis is due to mutant transthyretin (ATTRm) deposition and often presents with heart failure or peripheral neuropathy. We report the first known case of a patient who had amyloidosis both due to a mutant transthyretin (p...
August 7, 2018: Mayo Clinic Proceedings
https://www.readbyqxmd.com/read/30093037/studies-on-the-binding-characteristics-of-three-polysaccharides-with-different-molecular-weight-and-flavonoids-from-corn-silk-maydis-stigma
#20
Qingwen Guo, Qiqi Ma, Zihan Xue, Xudong Gao, Haixia Chen
Polysaccharides and flavonoids co-existed in corn silk (Maydis stigma) could interact inevitably during processing and digestion. In this study, the binding interaction between three polysaccharides with different molecular weight and flavonoids from corn silk was characterized using molecular dynamic and thermodynamic simulation. And the corn silk polysaccharides-flavonoids complex (CSP - CSF complex) was characterized using fourier transform infrared (FT-IR) spectra, circular dichroism (CD), scanning electron microscope (SEM) and differential scanning calorimetry (DSC)...
October 15, 2018: Carbohydrate Polymers
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