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Molecular dynamics simulation free energy

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https://www.readbyqxmd.com/read/29690584/novel-inhibitor-discovery-of-staphylococcus-aureus-sortase-b-and-the-mechanism-confirmation-via-molecular-modeling
#1
Guizhen Wang, Xiyan Wang, Lin Sun, Yawen Gao, Xiaodi Niu, Hongsu Wang
SortaseB (SrtB) plays a critical role in Staphylococcus aureus ( S. aureus ) infections. According to the reports in the literature, SrtB can anchor the IsdC to the cell wall to capture iron from the host to achieve a successful invasion. On the other hand, SrtB could also affect the adhesion of S. aureus to host cells based on previous studies. Here, we report about a novel SrtB inhibitor, coptisine, a natural compound that does not exhibit antibacterial activity but can inhibit the SrtB activity in vitro...
April 23, 2018: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/29684323/molecular-dynamics-simulations-of-glyphosate-in-a-dppc-lipid-bilayer
#2
Ezequiel N Frigini, J J López Cascales, Rodolfo D Porasso
Extensive Molecular Dynamics simulations have been performed to study the effect of Glyphosate (in their neutral and charged forms, GLYP and GLYP2- , respectively) on fully hydrated DiPalmitoylPhosphatidylCholine (DPPC) lipid bilayer. First, we calculated the free energy profile (using the Umbrella Sampling technique) for both states of charge of glyphosate. The minimum value for the free energy for GLYP is ∼-60 kJ.mol-1 located at z=±1.7 nm (from the lipid bilayer center), and there is almost no maximum at the center of the lipid bilayer...
April 20, 2018: Chemistry and Physics of Lipids
https://www.readbyqxmd.com/read/29683178/an-interplay-of-electrostatic-and-excluded-volume-interactions-in-the-conformational-behavior-of-a-dipolar-chain-theory-and-computer-simulations
#3
Yu D Gordievskaya, Yu A Budkov, E Yu Kramarenko
The effect of an interplay between electrostatic and excluded volume interactions on the conformational behavior of a dipolar chain has been studied theoretically and by means of molecular dynamics simulations. Every monomer unit of the dipolar chain comprises a dipole formed by a charged group of the chain and an oppositely charged counterion. The counterion is assumed to freely move around the chain but keeping the distance between oppositely charged ions (the dipole length) fixed. The novelty of the developed mean-field theory is that variations of the dipole parameters (the dipole length and the counterion size) have been accounted for in both electrostatic and excluded volume contributions to the total free energy of the dipolar chain...
April 23, 2018: Soft Matter
https://www.readbyqxmd.com/read/29678106/uncertainty-quantification-in-alchemical-free-energy-methods
#4
Agastya P Bhati, Shunzhou Wan, Yuan Hu, Brad Sherborne, Peter Vivian Coveney
The alchemical free energy methods have gained much importance recently from several reports of improved ligand-protein binding affinity predictions based on their implementation using molecular dynamics simulation. A large number of variants of such methods implementing different accelerated sampling techniques and free energy estimators are available, each claimed to be better than the others in its own way. However, the key features of reproducibility and the quantification of the associated uncertainties in such methods have barely been discussed...
April 20, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/29677600/interactions-of-2-phenyl-benzotriazole-xenobiotic-compounds-with-human-cytochrome-p450-cyp1a1-by-means-of-docking-molecular-dynamics-simulations-and-mm-gbsa-calculations
#5
Karel Mena-Ulecia, Desmond MacLeod-Carey
2-phenyl-benzotriazole xenobiotic compounds (PBTA-4, PBTA-6, PBTA-7 and PBTA-8) that were previously isolated and identified in waters of the Yodo river, in Japan (Nukaya et al., 2001; Ohe et al., 2004; Watanabe et al., 2001) were characterized as powerful pro-mutagens. In order to predict the activation mechanism of these pro-mutagens, we designed a computational biochemistry protocol, which includes, docking experiments, molecular dynamics simulations and free energy decomposition calculations to obtain information about the interaction of 2-phenyl-benzotriazole molecules into the active center of cytochrome P450-CYP1A1 (CYP1A1)...
April 7, 2018: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/29677482/allosteric-ligands-for-the-pharmacologically-important-flavivirus-target-ns5-from-zinc-database-based-on-pharmacophoric-points-free-energy-calculations-and-dynamics-correlation
#6
Abbas Khan, Shoaib Saleem, Muhammad Idrees, Syed Shujait Ali, Muhammad Junaid, Aman Chandra Kaushik, Dong-Qing Wei
Dengue virus belongs to a group of human pathogens, which causes different diseases, dengue hemorrhagic fever and dengue shock syndrome in humans. It possesses RNA as a genetic material and is replicated with the aid of NS5 protein. RNA-dependent RNA polymerase (RdRp) is an important domain of NS5 in the replication of that virus. The catalytic process activity of RdRp is making it an important target for antiviral chemical therapy. To date, No FDA drug has been approved and marketed for the treatment of diseases caused by Dengue virus...
April 11, 2018: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/29674291/molecular-modeling-on-porphyrin-derivatives-as-%C3%AE-5-subunit-inhibitor-of-20s-proteasome
#7
Muhammad Arba, Andry Nur-Hidayat, Ruslin, Muhammad Yusuf, Sumarlin, Rukman Hertadi, Setyanto Tri Wahyudi, Slamet Ibrahim Surantaadmaja, Daryono H Tjahjono
The ubiquitin-proteasome system plays an important role in protein quality control. Currently, inhibition of the proteasome has been validated as a promising approach in anticancer therapy. The 20S core particle of the proteasome harbors β5 subunit which is a crucial active site in proteolysis. Targeting proteasome β5 subunit which is responsible for the chymotrypsin-like activity of small molecules has been regarded as an important way for achieving therapeutics target. In the present study, a series of porphyrin derivatives bearing either pyridine or pyrazole rings as meso-substituents were designed and evaluated as an inhibitor for the β5 subunit of the proteasome by employing molecular docking and dynamics simulations...
April 16, 2018: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/29671687/exploring-the-interactional-details-between-aldose-reductase-akr1b1-and-3-mercapto-5h-1-2-4-triazino-5-6-b-indole-5-acetic-acid-through-molecular-dynamics-simulations
#8
Jiu-Yu Zhan, Ke Ma, Qing-Chuan Zheng, Guang-Hui Yang, Hong-Xing Zhang
Aldose reductase (AKR1B1) has been considered as a significant target for designing drugs to counteract the development of diabetic complications. In the present study, molecular dynamics (MD) simulations and molecular mechanics generalized Born surface area (MM-GB/SA) calculations were performed to make sure which tautomer is the preferred one among three tautomeric forms (Mtia1, Mtia2, and Mtia3) of 3-Mercapto-5H-1,2,4-triazino[5,6-b]indole-5-acetic acid (Mtia) for binding to AKR1B1. The overall structural features and the results of calculated binding free energies indicate that Mtia1 and Mtia2 have more superiority than Mtia3 in terms of binding to AKR1B1...
April 19, 2018: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/29670852/a-molecular-study-on-drug-delivery-system-based-on-carbon-nanotube-compared-to-silicon-carbide-nanotube-for-encapsulation-of-platinum-based-anticancer-drug
#9
Zahra Khatti, Seyed Majid Hashemianzadeh, Seyed Ali Shafiei
Purpose: Drug delivery has a critical role in the treatment of cancer, in particular, carbon nanotubes for their potential use in various biomedical devices and therapies. From many other materials which could be more biocompatible and biodegradable and which could form single-walled nanotubes, silicon carbide was selected. Methods: To compare two drug delivery systems based on single-walled nanotubes, molecular dynamic simulations were applied and encapsulation behavior of the drug carboplatin was investigated inside the silicon carbide nanotube and the carbon nanotube...
March 2018: Advanced Pharmaceutical Bulletin
https://www.readbyqxmd.com/read/29670215/nanomanufacturing-of-silicon-surface-with-a-single-atomic-layer-precision-via-mechanochemical-reactions
#10
Lei Chen, Jialin Wen, Peng Zhang, Bingjun Yu, Cheng Chen, Tianbao Ma, Xinchun Lu, Seong H Kim, Linmao Qian
Topographic nanomanufacturing with a depth precision down to atomic dimension is of importance for advancement of nanoelectronics with new functionalities. Here we demonstrate a mask-less and chemical-free nanolithography process for regio-specific removal of atomic layers on a single crystalline silicon surface via shear-induced mechanochemical reactions. Since chemical reactions involve only the topmost atomic layer exposed at the interface, the removal of a single atomic layer is possible and the crystalline lattice beneath the processed area remains intact without subsurface structural damages...
April 18, 2018: Nature Communications
https://www.readbyqxmd.com/read/29669415/accelerated-enveloping-distribution-sampling-enabling-sampling-of-multiple-end-states-while-preserving-local-energy-minima
#11
Jan Walther Perthold, Chris Oostenbrink
Enveloping distribution sampling (EDS) is an efficient approach to calculate multiple free-energy differences from a single molecular dynamics (MD) simulation. However, the construction of an appropriate reference state Hamiltonian that samples all states efficiently is not straightforward. We propose a novel approach for the construction of the EDS reference state Hamiltonian, related to a previously described procedure to smoothen energy landscapes. In contrast to previously suggested EDS approaches, our reference-state Hamiltonian preserves local energy minima of the combined end-states...
April 18, 2018: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/29666235/mass-and-heat-transfer-between-evaporation-and-condensation-surfaces-atomistic-simulation-and-solution-of-boltzmann-kinetic-equation
#12
Vasily V Zhakhovsky, Alexei P Kryukov, Vladimir Yu Levashov, Irina N Shishkova, Sergey I Anisimov
Boundary conditions required for numerical solution of the Boltzmann kinetic equation (BKE) for mass/heat transfer between evaporation and condensation surfaces are analyzed by comparison of BKE results with molecular dynamics (MD) simulations. Lennard-Jones potential with parameters corresponding to solid argon is used to simulate evaporation from the hot side, nonequilibrium vapor flow with a Knudsen number of about 0.02, and condensation on the cold side of the condensed phase. The equilibrium density of vapor obtained in MD simulation of phase coexistence is used in BKE calculations for consistency of BKE results with MD data...
April 16, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29665428/enhanced-sampling-of-the-glutamate-receptor-ligand-binding-domain
#13
REVIEW
Albert Y Lau
The majority of excitatory synaptic transmission in the central nervous system is mediated by ionotropic glutamate receptors (iGluRs). These membrane-bound protein assemblies consist of modular domains that can be genetically isolated and expressed, which has resulted in a plethora of crystal structures of individual domains in different conformations bound to different ligands. These structures have presented opportunities for molecular dynamics (MD) simulation studies. To examine the free energies that govern molecular behavior, simulation strategies and algorithms have been developed, collectively called enhanced sampling methods This review focuses on the use of enhanced sampling MD simulations of isolated iGluR ligand-binding domains to characterize thermodynamic properties important to receptor function...
April 14, 2018: Neuroscience Letters
https://www.readbyqxmd.com/read/29663897/computational-study-of-imidazolylporphyrin-derivatives-as-a-radiopharmaceutical-ligand-kit-for-melanoma
#14
Fransiska Kurniawan, Rahmana E Kartasasmita, Naoki Yoshioka, Abdul Mutalib, Daryono H Tjahjono
Melanoma is the most aggressive type of skin cancer. Metastatic melanoma is extremely difficult to treat with current therapy methods such as surgery. On the other hand, it is a good opportunity to develop a radiopharmaceutical using a radionuclide such as technetium (Tc) for diagnostic and rhenium (Re) for therapeutic purposes. T3,4BCPP has been be used as a radioimaging agent for melanoma cancers experimentally. The aim of the present research was to design new imidazolylporphyrin derivatives with better selectivity and higher affinity than those of T3,4BCPP by molecular modeling...
April 16, 2018: Current Computer-aided Drug Design
https://www.readbyqxmd.com/read/29661309/protein-adsorption-onto-polysaccharides-comparison-of-chitosan-and-chitin-polymers
#15
Mohammad Yahyaei, Faramarz Mehrnejad, Hossein Naderi-Manesh, Ali Hossein Rezayan
Chitosan (CHS) and chitin (CHT) biopolymers have found many applications in the field of controlled-release drug delivery systems. Herein, molecular dynamics (MD) simulation and binding free energy calculations were used to investigate the potentials of CHS and CHT polymers for the controlled release of follicle-stimulating hormone (FSH). The results indicated that FSH conformation did not change in the presence of CHS and CHT. In addition, FSH-polymer interactions caused stability of the 310 -helix structure of the alpha subunits of FSH (FSHα)...
July 1, 2018: Carbohydrate Polymers
https://www.readbyqxmd.com/read/29660291/the-molecular-mechanism-underlying-ligand-binding-to-the-membrane-embedded-site-of-a-g-protein-coupled-receptor
#16
Xiao-Jing Yuan, Stefano Raniolo, Vittorio Limongelli, Yechun Xu
The crystal structure of P2Y1 receptor (P2Y1R), a class A GPCR, revealed a special extra-helical site for its antagonist, BPTU, which locates in between the membrane and the protein. However, due to the limitation of crystallization experiments, the membrane was mimicked by use of detergents and the information related to the binding of BPTU to the receptor in the membrane environment is rather limited. In the present work, we conducted a total of ~7.5 µs all-atom simulations in explicit solvent using conventional molecular dynamics and multiple enhanced sampling methods, with models of BPTU and a POPC bilayer, both in the absence and presence of P2Y1R...
April 16, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/29658431/in-silico-identification-and-screening-of-cyp24a1-inhibitors-3d-qsar-pharmacophore-mapping-and-molecular-dynamics-analysis
#17
Jayaraj John Marshal, Gopinath Krishnasamy, Jung-Kul Lee, Karthikeyan Muthusamy
Vitamin D is a key signalling molecule that plays a vital role in the regulation of calcium-phosphate homeostasis and bone remodelling. The circulating biologically active form of vitamin D is regulated by the catabolic mechanism of cytochrome P450 24-hydroxylase (CYP24A1) enzyme. The over-expression of CYP24A1 negatively regulates the vitamin D level, which is the causative agent of chronic kidney disease, osteoporosis, and several types of cancers. In this study, we found three potential lead molecules adverse to CYP24A1 through structure-based, atom-based pharmacophore and e-pharmacophore-based screening methods...
April 16, 2018: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/29657661/thermodynamic-mechanism-and-interfacial-structure-of-kaolinite-intercalation-and-surface-modification-by-alkane-surfactants-with-neutral-and-ionic-head-groups
#18
Shuai Zhang, Qinfu Liu, Hongfei Cheng, Feng Gao, Cun Liu, Brian J Teppen
Intercalation and surface modification of clays with surfactants are the essential process to tailor the clays' surface chemistry for their extended applications. A full understanding of the interaction mechanism of surfactants with clay surfaces is crucial to engineer clay surfaces for meeting a particular requirement of industrial applications. In this study, the thermodynamic mechanism involved in the intercalation and surface modification of methanol preintercalated kaolinite by three representative alkane surfactants with different head groups, dodecylamine, cetyltrimethylammonium chloride (CTAC), and sodium stearate, were investigated using the adaptive biasing force accelerated molecular dynamics simulations...
April 27, 2017: Journal of Physical Chemistry. C, Nanomaterials and Interfaces
https://www.readbyqxmd.com/read/29655321/-trampoline-ejection-of-organic-molecules-from-graphene-and-graphite-via-kev-cluster-ions-impacts
#19
Stanislav V Verkhoturov, Mikołaj Gołuński, Dmitriy S Verkhoturov, Sheng Geng, Zbigniew Postawa, Emile A Schweikert
We present the data on ejection of molecules and emission of molecular ions caused by single impacts of 50 keV C60 2+ on a molecular layer of deuterated phenylalanine (D8Phe) deposited on free standing, 2-layer graphene. The projectile impacts on the graphene side stimulate the abundant ejection of intact molecules and the emission of molecular ions in the transmission direction. To gain insight into the mechanism of ejection, Molecular Dynamic simulations were performed. It was found that the projectile penetrates the thin layer of graphene, partially depositing the projectile's kinetic energy, and molecules are ejected from the hot area around the hole that is made by the projectile...
April 14, 2018: Journal of Chemical Physics
https://www.readbyqxmd.com/read/29652495/peptidic-macrocycles-conformational-sampling-and-thermodynamic-characterization
#20
Anna Sophia Kamenik, Uta Lessel, Julian E Fuchs, Thomas Fox, Klaus R Liedl
Macrocycles are of considerable interest as highly specific drug candidates, yet they challenge standard conformer generators with their large number of rotatable bonds and conformational restrictions. Here, we present a molecular dynamics-based routine that bypasses current limitations in conformational sampling and extensively profiles the free energy landscape of peptidic macrocycles in solution. We perform accelerated molecular dynamics simulations to capture a diverse conformational ensemble. By applying an energetic cutoff, followed by geometric clustering we demonstrate the striking robustness and efficiency of the approach in identifying highly populated conformational states of cyclic peptides...
April 13, 2018: Journal of Chemical Information and Modeling
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