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https://www.readbyqxmd.com/read/28346078/molecular-dynamics-simulation-of-three-plastic-additives-diffusion-in-polyethylene-terephthalate
#1
Bo Li, Zhi-Wei Wang, Qin-Bao Lin, Chang-Ying Hu
Accurate diffusion coefficient data of additives in polymer is of paramount importance for estimating the migration of the additives over time. In this article it is shown how this diffusion coefficient can be estimated for three plastic additives [2-(2'-hydroxy-5'-methylphenyl) (UV-P), 2, 6-di-tert-butyl-4-methylphenol (BHT) and di-(2-ethylhexyl) phthalate (DEHP)] in polyethylene terephthalate (PET) using the molecular dynamics (MD) simulation method. MD simulations were performed at temperatures of 293-433 K...
March 27, 2017: Food Additives & Contaminants. Part A, Chemistry, Analysis, Control, Exposure & Risk Assessment
https://www.readbyqxmd.com/read/28345907/simulating-protein-mediated-hydrolysis-of-atp-and-other-nucleoside-triphosphates-by-combining-qm-mm-molecular-dynamics-with-advances-in-metadynamics
#2
Rui Sun, Olaseni Sode, James F Dama, Gregory A Voth
The protein mediated hydrolysis of nucleoside triphosphates such as ATP or GTP is one of the most important and challenging biochemical reactions in nature. The chemical environment (water structure, catalytic metal, and amino acid residues) adjacent to the hydrolysis site contains hundreds of atoms, usually greatly limiting the amount of the free energy sampling that one can achieve from computationally demanding electronic structure calculations such as QM/MM simulations. Therefore, the combination of QM/MM molecular dynamics with the recently developed Transition-tempered Metadynamics (TTMetaD), an enhanced sampling method that can provide a high-quality free energy estimate at an early stage in a simulation, is an ideal approach to address the biomolecular nucleoside triphosphate hydrolysis problem...
March 27, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28345904/ligand-selectivity-mechanism-and-conformational-changes-in-guanine-riboswitch-by-molecular-dynamics-simulations-and-free-energy-calculations
#3
Guodong Hu, Aijing Ma, Ji Hua Wang
Riboswitches regulate gene expression through direct and specific interactions with small metabolite molecules. Binding of a ligand to its RNA target is high selectivity and affinity and induces conformational changes of the RNA's secondary and tertiary structure. The structural difference of two purine riboswitches aptamers is caused by only one single mutation, where cytosine 74 in the guanine riboswitch is corresponding to a uracil 74 in adenine riboswitch. Here we employed molecular dynamics (MD) simulation, molecular mechanics Poisson Boltzmann surface area (MM-PBSA) and thermodynamic integration computational methodologies to evaluate the energetic and conformational changes of ligands binding to purine riboswitches...
March 27, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28342136/molecular-basis-of-p450-oletje-an-investigation-of-substrate-binding-mechanism-and-major-pathways
#4
Juan Du, Lin Liu, Li Zhong Guo, Xiao Jun Yao, Jian Ming Yang
Cytochrome P450 OleTJE has attracted much attention for its ability to catalyze the decarboxylation of long chain fatty acids to generate alkenes, which are not only biofuel molecule, but also can be used broadly for making lubricants, polymers and detergents. In this study, the molecular basis of the binding mechanism of P450 OleTJE for arachidic acid, myristic acid, and caprylic acid was investigated by utilizing conventional molecular dynamics simulation and binding free energy calculations. Moreover, random acceleration molecular dynamics (RAMD) simulations were performed to uncover the most probable access/egress channels for different fatty acids...
March 25, 2017: Journal of Computer-aided Molecular Design
https://www.readbyqxmd.com/read/28338133/stereoselective-binding-of-agonists-to-the-%C3%AE-2-adrenergic-receptor-insights-into-molecular-details-and-thermodynamics-from-molecular-dynamics-simulations
#5
Anita Plazinska, Wojciech Plazinski
The β2-adrenergic receptor (β2-AR) is one of the most studied G-protein-coupled receptors. When interacting with ligand molecules, it exhibits a binding characteristic that is strongly dependent on ligand stereoconfiguration. In particular, many experimental and theoretical studies confirmed that stereoisomers of an important β2-AR agonist, fenoterol, are associated with diverse mechanisms of binding and activation of β2-AR. The objective of the present study was to explore the stereoselective binding of fenoterol to β2-AR through the application of an advanced computational methodology based on enhanced-sampling molecular dynamics simulations and potentials of interactions tailored to investigate the stereorecognition effects...
March 24, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28330346/a-new-approach-to-molecular-dynamics-with-non-adiabatic-and-spin-orbit-effects-with-applications-to-qm-mm-simulations-of-thiophene-and-selenophene
#6
Marek Pederzoli, Jiří Pittner
We present surface hopping dynamics on potential energy surfaces resulting from the spin-orbit splitting, i.e., surfaces corresponding to the eigenstates of the total electronic Hamiltonian including the spin-orbit coupling. In this approach, difficulties arise because of random phases of degenerate eigenvectors and possibility of crossings of the resulting mixed states. Our implementation solves these problems and allows propagation of the coefficients both in the representation of the spin free Hamiltonian and directly in the "diagonal representation" of the mixed states...
March 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28330175/exploration-of-the-binding-modes-of-l-asparaginase-complexed-with-its-amino-acid-substrates-by-molecular-docking-dynamics-and-simulation
#7
Erva Rajeswara Reddy, Rajulapati Satish Babu, Potla Durthi Chandrasai, Pola Madhuri
Acute lymphocytic leukemia (ALL) is an outrageous disease worldwide. L-Asparagine (L-Asn) and L-glutamine (L-Gln) deamination plays crucial role in ALL treatment. Role of Erwinaze(®) (L-asparaginase from Erwinia chrysanthemi) in regulation of L-Asn and L-Gln has been confirmed by the experimental studies. Therapeutic research against ALL remained elusive with the lack of structural information on Erwinaze(®) enzyme. In this present study, homology model of the Erwinaze(®) was developed using MODELLER and the same was validated by various quality indexing tools...
June 2016: 3 Biotech
https://www.readbyqxmd.com/read/28327752/umbrella-sampling-molecular-dynamics-simulations-reveal-concerted-ion-movement-through-g-quadruplex-dna-channels
#8
Parisa Akhshi, Gang Wu
We have applied the umbrella sampling (US) method in all-atom molecular dynamics (MD) simulations to obtain potential of mean force (PMF) profiles for ion transport through three representative G-quadruplex DNA channels: [d(TG4T)]4, [d(G3T4G4)]2, and d[G4(T4G4)3]. The US MD results are in excellent agreement with those obtained previously with the adaptive biasing force (ABF) method. We then utilized the unique features in the US MD method to investigate multi-ion effects in [d(G3T4G4)]2 and discovered that the concerted ion movement is crucial for fully explaining the unusual experimental results on ion movement in this particular G-quadruplex system...
March 22, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28321247/investigations-on-binding-pattern-of-kinase-inhibitors-with-ppar%C3%AE-molecular-docking-molecular-dynamic-simulations-and-free-energy-calculation-studies
#9
Mohit Mazumder, Prija Ponnan, Umashankar Das, Samudrala Gourinath, Haseeb Ahmad Khan, Jian Yang, Meena Kishore Sakharkar
Peroxisome proliferator-activated receptor gamma (PPARγ) is a potential target for the treatment of several disorders. In view of several FDA approved kinase inhibitors, in the current study, we have investigated the interaction of selected kinase inhibitors with PPARγ using computational modeling, docking, and molecular dynamics simulations (MDS). The docked conformations and MDS studies suggest that the selected KIs interact with PPARγ in the ligand binding domain (LBD) with high positive predictive values...
2017: PPAR Research
https://www.readbyqxmd.com/read/28319781/systematic-study-of-imidazoles-inhibiting-ido1-via-the-integration-of-molecular-mechanics-and-quantum-mechanics-calculations
#10
Yi Zou, Fang Wang, Yan Wang, Wenjie Guo, Yihua Zhang, Qiang Xu, Yisheng Lai
Indoleamine 2,3-dioxygenase 1 (IDO1) is regarded as an attractive target for cancer immunotherapy. To rationalize the detailed interactions between IDO1 and its inhibitors at the atomic level, an integrated computational approach by combining molecular mechanics and quantum mechanics methods was employed in this report. Specifically, the binding modes of 20 inhibitors was initially investigated using the induced fit docking (IFD) protocol, which outperformed other two docking protocols in terms of correctly predicting ligand conformations...
March 14, 2017: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28318252/molecular-dynamics-in-mixed-solvents-reveals-protein-ligand-interactions-improves-docking-and-allows-accurate-binding-free-energy-predictions
#11
Juan Pablo Arcon, Lucas A Alfredo Defelipe, Carlos Pablo Modenutti, Elias Daniel Lopez, Daniel Alvarez-Garcia, Xavier Barril, Adrian Gustavo Turjanski, Marcelo A Marti
One of the most important biological processes at the molecular level is the formation of protein-ligand complexes. Therefore, determining their structure and underlying key interactions is of paramount relevance and has direct applications in drug development. Due to its low cost relative to its experimental sibling, Molecular Dynamics (MD) simulations in the presence of different solvent probes mimicking specific type of interactions have been increasingly used to analyze protein binding sites and reveal protein-ligand interaction hot spots...
March 20, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28318251/molecular-simulation-studies-on-the-binding-selectivity-of-type-i-inhibitors-in-the-complexes-with-ros1-versus-alk
#12
Yuanxin Tian, Yonghuan Yu, Yudong Shen, Hua Wan, Shan Chang, Tingting Zhang, Shanhe Wan, Jiajie Zhang
ROS1 and ALK are promising targets of anti-cancer drugs for non small cell lung cancer. Since they have 49% amide acid sequence homology in the kinases domain and 77% identity at the ATP binding area, some ALK inhibitors also showed some significant responses for ROS1 in the clinical trial, such as the type-I binding inhibitor crizotinib and PF-06463922. As a newly therapeutic target, selective ROS1 inhibitor is relative rarely. Moreover, the molecular basis for the selectivity of ROS1 versus ALK still remains unclear...
March 20, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28314372/exploring-fluorescent-dyes-at-biomimetic-interfaces-with-second-harmonic-generation-and-molecular-dynamics
#13
Giuseppe Licari, Lukasz Cwiklik, Pavel Jungwirth, Eric Vauthey
The adsorption of a DNA fluorescent probe belonging to the thiazole orange family at the dodecane/water and dodecane/phospholipid/water interfaces has been investigated using a combination of surface second harmonic generation (SSHG) and all-atomistic molecular dynamics (MD) simulations. Both approaches point to a high affinity of the cationic dye for the dodecane/water interface with a Gibbs free energy of adsorption on the order of -45 kJ/mol. Similar affinity was observed with a monolayer of negatively charged DPPG (1,2-dipalmitoyl-sn-glycero-3-phospho-rac-(1-glycerol)) lipids...
March 27, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/28304156/probing-the-time-dependency-of-cyclooxygenase-1-inhibitors-by-computer-simulations
#14
Yasmin Shamsudin Khan, Hugo Gutiérrez-de-Terán, Johan Åqvist
Time-dependent inhibition of the cyclooxygenases (COX) by a range of nonsteroidal anti-inflammatory drugs has been described since the first experimental assays of COX were performed. Slow tight-binding inhibitors of COX-1 bind in a two-step mechanism in which the EI → EI* transition is slow and practically irreversible. Since then, various properties of the inhibitors have been proposed to cause or affect the time dependency. Conformational changes in the enzyme have also been proposed to cause the time dependency, but no particular structural feature has been identified...
March 23, 2017: Biochemistry
https://www.readbyqxmd.com/read/28299743/computational-approaches-to-matrix-metalloprotease-drug-design
#15
Tanya Singh, B Jayaram, Olayiwola Adedotun Adekoya
Matrix metalloproteinases (MMPs) are a family of zinc-containing enzymes required for homeostasis. These enzymes are an important class of drug targets as their over expression is associated with many disease states. Most of the inhibitors reported against this class of proteins have failed in clinical trials due to lack of specificity. In order to assist in drug design endeavors for MMP targets, a computationally tractable pathway is presented, comprising, (1) docking of small molecule inhibitors against the target MMPs, (2) derivation of quantum mechanical charges on the zinc ion in the active site and the amino acids coordinating with zinc including the inhibitor molecule, (3) molecular dynamics simulations on the docked ligand-MMP complexes, and (4) evaluation of binding affinities of the ligand-MMP complexes via an accurate scoring function for zinc containing metalloprotein-ligand complexes...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28298161/a-simulation-investigation-on-interaction-mechanism-between-ebola-nucleoprotein-and-vp35-peptide
#16
Jing-Na Ding, Yan-Jun Zhang, Hui Zhong, Cheng-Cheng Ao, Ju-Guang Han
Ebola viruses (EBOV) will induce acute hemorrhagic fever fatally to humans and nonhuman primates. The combination of EBOV VP35 peptide with nucleoprotein N-terminal (NPNTD) is proposed based on static crystal structures in recent studies, but VP35 binding mechanism and conformational dynamics are still unclear. This investigation, using Molecular Dynamic (MD) simulation and Molecular Mechanics Generalized Born Surface Area (MM-GB/SA) energy calculation, more convincingly proves the greater roles of the protein binding mechanisms than do hints from the static crystal structure observations...
March 15, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28297603/improving-the-efficiency-of-non-equilibrium-sampling-in-the-aqueous-environment-via-implicit-solvent-simulations
#17
Hui Liu, Fu Chen, Huiyong Sun, Dan Li, Tingjun Hou
By means of estimators based on non-equilibrium work, equilibrium free energy differences or potentials of mean force (PMFs) of a system of interest can be computed from biased molecular dynamics (MD) simulations. The approach, however, is often plagued by slow conformational sampling and poor convergence, especially when the solvent effects are taken into account. Here, as a possible way to alleviate the problem, several widely used implicit-solvent models, which are derived from the analytic generalized Born (GB) equation and implemented in the AMBER suite of programs, were employed in free energy calculations based on non-equilibrium work and evaluated for their abilities to emulate explicit water...
March 23, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28296211/deleterious-effects-of-nonsynonymous-single-nucleotide-variants-of-human-il-1%C3%AE-gene
#18
Yue-Hui Zhang, Jia Song, Jing Zhang, Jiang Shao
The IL-1β gene is currently topic of interest for its important role in the pathogenesis of intervertebral disc degeneration. The new sequencing technology makes it crucial to study the effects of variants in IL-1β. Thus, 714 IL-1β variants with evidence supporting were collected from the EMBL database. Among them, 62 were nonsynonymous single nucleotide variants (nsSNVs). Furthermore, six common nsSNVs were predicted to have damaging effects by SIFT, PolyPhen, PROVEAN and SNPs&GO. Based on the constructed three-dimensional structure of pro-IL-1β, rs375479974 with a mutation of Phe to Ser was proposed to reduce the stability of the pro-IL-1β protein...
March 15, 2017: Chemical Biology & Drug Design
https://www.readbyqxmd.com/read/28293633/combined-ligand-structure-based-virtual-screening-and-molecular-dynamics-simulations-of-steroidal-androgen-receptor-antagonists
#19
Yuwei Wang, Rui Han, Huimin Zhang, Hongli Liu, Jiazhong Li, Huanxiang Liu, Paola Gramatica
The antiandrogens, such as bicalutamide, targeting the androgen receptor (AR), are the main endocrine therapies for prostate cancer (PCa). But as drug resistance to antiandrogens emerges in advanced PCa, there presents a high medical need for exploitation of novel AR antagonists. In this work, the relationships between the molecular structures and antiandrogenic activities of a series of 7α-substituted dihydrotestosterone derivatives were investigated. The proposed MLR model obtained high predictive ability...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28291369/ultrashort-single-walled-carbon-nanotubes-insert-into-pulmonary-surfactant-monolayer-via-self-rotating-poration-and-mechanical-inhibition
#20
Tongtao Yue, Yan Xu, Shixin Li, Zhen Luo, Xianren Zhang, Fang Huang
It has been widely accepted that longer single-walled carbon nanotubes (SWCNTs) exhibit higher toxicity by causing severe pneumonia once inhaled, yet relatively little is known regarding the potential toxicity of ultrashort SWCNTs, which are of central importance to their development as suitable vehicles for biomedical applications. Here, by combining coarse-grained molecular dynamics (CGMD), pulling simulations, and scaling analysis, we demonstrate that the inhalation toxicity of ultrashort SWCNTs (1.5 nm < l < 5...
March 14, 2017: Journal of Physical Chemistry. B
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