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Molecular dynamics simulation free energy

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https://www.readbyqxmd.com/read/28445637/control-of-charge-carriers-trapping-and-relaxation-in-hematite-by-oxygen-vacancy-charge-ab-initio-non-adiabatic-molecular-dynamics
#1
Zhaohui Zhou, Jin Liu, Run Long, Linqiu Li, Liejin Guo, Oleg V Prezhdo
Ultrafast charge recombination in hematite (α-Fe2O3) severely limits its applications in solar energy conversion and utilization, for instance, in photo-electrochemical water splitting. We report the first time-domain ab initio study of charge relaxation dynamics in α-Fe2O3 with and without the oxygen vacancy (Ov) defect, using non-adiabatic molecular dynamics implemented within time-dependent density functional theory. The simulations show that the hole trapping is the rate-limiting step in the electron-hole recombination process for both neutral and ionized Ov systems...
April 26, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28445123/changes-in-the-free-energy-landscape-of-p38%C3%AE-map-kinase-through-its-canonical-activation-and-binding-events-as-studied-by-enhanced-molecular-dynamics-simulations
#2
Antonija Kuzmanic, Ludovico Sutto, Giorgio Saladino, Angel R Nebreda, Francesco L Gervasio, Modesto Orozco
p38α is a Ser/Thr protein kinase involved in a variety of cellular processes and pathological conditions, which makes it a promising pharmacological target. Although the activity of the enzyme is highly regulated, its molecular mechanism of activation remains largely unexplained, even after decades of research. By using state-of-the-art molecular dynamics simulations, we decipher the key elements of the complex molecular mechanism refined by evolution to allow for a fine tuning of p38α kinase activity. Our study describes for the first time the molecular effects of different regulators of the enzymatic activity, and provides an integrative picture of the activation mechanism that explains the seemingly contradictory X-ray and NMR data...
April 26, 2017: ELife
https://www.readbyqxmd.com/read/28440827/molecular-dynamics-investigations-of-membrane-bound-cyp2c19-polymorphisms-reveal-distinct-mechanisms-for-peripheral-variants-by-long-range-effects-on-the-enzymatic-activity
#3
Ying-Lu Cui, Rong-Ling Wu
Increasing sophistication in methods used to account for human polymorphisms in susceptibility to drug metabolism has been one of the success stories in the prevention of adverse drug reactions. Genetic polymorphisms in drug-metabolizing enzymes can affect enzyme activity and cause differences in treatment response or drug toxicity. CYP2C19 is one of the most highly polymorphic CYP enzymes and acts on 10-15% of drugs in current clinical use. Despite the number of experimental analyses carried out for this system, the detailed structural basis for altered catalytic properties of polymorphic CYP2C19 variants remains unexplained at the atomic level...
April 25, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28438697/predicting-drug-loading-in-pla-peg-nanoparticles
#4
M Meunier, A Goupil, P Lienard
Polymer nanoparticles present advantageous physical and biopharmaceutical properties as drug delivery systems compared to conventional liquid formulations. Active pharmaceutical ingredients (APIs) are often hydrophobic, thus not soluble in conventional liquid delivery. Encapsulating the drugs in polymer nanoparticles can improve their pharmacological and bio-distribution properties, preventing rapid clearance from the bloodstream. Such nanoparticles are commonly made of non-toxic amphiphilic self-assembling block copolymers where the core (poly-[D,L-lactic acid] or PLA) serves as a reservoir for the API and the external part (Poly-(Ethylene-Glycol) or PEG) serves as a stealth corona to avoid capture by macrophage...
April 21, 2017: International Journal of Pharmaceutics
https://www.readbyqxmd.com/read/28437616/neural-network-and-nearest-neighbour-algorithms-for-enhancing-sampling-of-molecular-dynamics
#5
Raimondas Galvelis, Yuji Sugita
The free energy calculations of complex chemical and biological systems with molecular dynamics (MD) are inefficient due to multiple local minima separated by high-energy barriers. The minima can be escaped using an enhanced sampling method such as metadynamics, which apply bias (i.e. importance sampling) along a set of collective variables (CV), but the maximum number of CVs (or dimensions) is severely limited. We propose a high-dimensional bias potential method (NN2B) based on two machine learning algorithms: the nearest neighbour density estimator (NNDE) and the artificial neural network (ANN) for the bias potential approximation...
April 24, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28435965/conformational-and-hydration-properties-modulate-ice-recognition-by-type-i-antifreeze-protein-and-its-mutants
#6
Sandipan Chakraborty, Biman Jana
The mechanism of ice recognition by antifreeze protein (AFP) is a topic of recent interest. Here, using equilibrium simulations and free energy calculations, we provide structural rationale to the observed experimental anomalies on type I AFP (wfAFP isoform HPLC6) and its mutants as well as probe the molecular origin of ice recognition by them. Our results clearly demonstrate that the interplay between the conformational and hydration properties dictates the ice binding ability of type I AFP and its mutants...
April 24, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28435964/kinetics-of-co2-diffusion-in-human-carbonic-anhydrase-a-study-using-molecular-dynamics-simulations-and-the-markov-state-model
#7
Gong Chen, Xian Kong, Diannan Lu, Jianzhong Wu, Zheng Liu
Molecular dynamics (MD) simulations, in combination with the Markov-state model (MSM), were applied to probe CO2 diffusion from an aqueous solution into the active site of human carbonic anhydrase II (hCA-II), an enzyme useful for enhanced CO2 capture and utilization. The diffusion process in the hydrophobic pocket of hCA-II was illustrated in terms of a two-dimensional free-energy landscape. We found that CO2 diffusion in hCA-II is a rate-limiting step in the CO2 diffusion-binding-reaction process. The equilibrium distribution of CO2 shows its preferential accumulation within a hydrophobic domain in the protein core region...
April 24, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28433036/an-eqt-based-cdft-approach-for-thermodynamic-properties-of-confined-fluid-mixtures
#8
M H Motevaselian, N R Aluru
We present an empirical potential-based quasi-continuum theory (EQT) to predict the structure and thermodynamic properties of confined fluid mixtures. The central idea in the EQT is to construct potential energies that integrate important atomistic details into a continuum-based model such as the Nernst-Planck equation. The EQT potentials can be also used to construct the excess free energy functional, which is required for the grand potential in the classical density functional theory (cDFT). In this work, we use the EQT-based grand potential to predict various thermodynamic properties of a confined binary mixture of hydrogen and methane molecules inside graphene slit channels of different widths...
April 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28433027/potential-of-mean-force-for-insertion-of-antimicrobial-peptide-melittin-into-a-pore-in-mixed-dopc-dopg-lipid-bilayer-by-molecular-dynamics-simulation
#9
Yuan Lyu, Ning Xiang, Xiao Zhu, Ganesan Narsimhan
Antimicrobial peptides (AMPs) inactivate microorganisms by forming transmembrane pores in a cell membrane through adsorption and aggregation. Energetics of addition of an AMP to a transmembrane pore is important for evaluation of its formation and growth. Such information is essential for the characterization of pore forming ability of peptides in cell membranes. This study quantifies the potential of mean force through molecular dynamics (MD) simulation for the addition of melittin, a naturally occurring AMP, into a DOPC/DOPG mixed bilayer, a mimic of bacterial membrane, for different extents of insertion into either a bilayer or a pore consisting of three to six transmembrane peptides...
April 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28432980/discovery-of-potential-inhibitor-against-human-acetylcholinesterase-a-molecular-docking-and-molecular-dynamics-investigation
#10
Surya Pratap Singh, Dwijendra Gupta
Alzheimer's disease (AD) is a progressive neurodegenerative disease of central nervous system among elderly people. Human acetylcholinesterase (hAChE), an important enzyme in neuronal signaling, is responsible for the degradation of acetylcholine which in turn prevents the post synaptic signal transmissions. hAChE has been an attractive target of drug discovery for the search of therapeutics against AD. In the recent past hAChE has become hot target for the investigation of new potential therapeutics. We performed virtual screening of entire database against hAChE...
April 12, 2017: Computational Biology and Chemistry
https://www.readbyqxmd.com/read/28432959/molecular-dynamics-simulation-studies-of-novel-%C3%AE-lactamase-inhibitor
#11
Farhan Ul Haq, Asma Abro, Saad Raza, Klaus R Liedl, Syed Sikander Azam
New Delhi Metallo-β-Lactamase-1 (NDM-1) has drawn great attention due to its diverse antibiotic resistant activity. It can hydrolyze almost all clinically available β-lactam antibiotics. To inhibit the activity of NDM-1 a new strategy is proposed using computational methods. Molecular dynamics (MD) simulations are used to analyze the molecular interactions between selected inhibitor candidates and NDM-1 structure. The enzyme-ligand complex is subject to binding free energy calculations using MM(PB/GB)SA methods...
April 4, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28429940/density-functional-theory-and-car-parrinello-molecular-dynamics-study-of-the-hydrogen-producing-mechanism-of-the-co-dmgbf2-2-and-co-dmgh-2-cobaloxime-complexes-in-the-acetonitrile-water-solvent
#12
Jinfan Chen, Patrick H-L Sit
The catalytic hydrogen-producing processes of two prototypical cobaloxime catalysts Co(dmgBF2)2 (dmgBF2=difluoroboryl-dimethylglyoxime) and Co(dmgH)2 (dmgH=dimethylglyoxime), were studied by Density Functional Theory (DFT) and Car-Parrinello molecular dynamics (CPMD) simulations in the explicit acetonitrile-water solvent. Our study demonstrates the key role of water molecules as shuttles to deliver protons to the cobalt active centers of these catalysts. However, the transfer of protons to the cobalt centers also competes with the diffusion of the proton away from the complex via the hydrogen bond network of water...
April 21, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/28423907/effects-of-active-site-mutations-on-specificity-of-nucleobase-binding-in-human-dna-polymerase-%C3%AE
#13
Melek N Ucisik, Sharon Hammes-Schiffer
Human DNA polymerase η (Pol η) plays a vital role in protection against skin cancer caused by damage from ultraviolet light. This enzyme rescues stalled replication forks at cyclobutane thymine-thymine dimers (TTDs) by inserting nucleotides opposite these DNA lesions. Residue R61 is conserved in the Pol η enzymes across species, but the corresponding residue, as well as its neighbor S62, is different in other Y-family polymerases, Pol ι and Pol κ. Herein, R61 and S62 are mutated to their Pol ι and Pol κ counterparts...
April 20, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28423900/methodology-for-the-simulation-of-molecular-motors-at-different-scales
#14
Abhishek Singharoy, Christophe Chipot
Millisecond-scale conformational transitions represent a seminal challenge for traditional molecular dynamics simulations, even with the help of high-end supercomputer architectures. Such events are particularly relevant to the study of molecular motors-proteins or abiological constructs that convert chemical energy into mechanical work. Here, we present a hybrid-simulation scheme combining an array of methods including elastic network models, transition path sampling, and advanced free-energy methods, possibly in conjunction with generalized-ensemble schemes to deliver a viable option for capturing the millisecond-scale motor steps of biological motors...
April 20, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28418682/mesoscale-simulation-and-machine-learning-of-asphaltene-aggregation-phase-behavior-and-molecular-assembly-landscapes
#15
Jiang Wang, Mohit A Gayatri, Andrew L Ferguson
Asphaltenes constitute the heaviest fraction of the aromatic group in crude oil. Aggregation and precipitation of asphaltenes during petroleum processing costs the petroleum industry billions of dollars each year due to downtime and production inefficiencies. Asphaltene aggregation proceeds via a hierarchical self-assembly process that is well-described by the Yen-Mullins model. Nevertheless, the microscopic details of the emergent cluster morphologies and their relative stability under different processing conditions remain poorly understood...
April 26, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28418655/accuracy-test-of-the-opls-aa-force-field-for-calculating-free-energies-of-mixing-and-comparison-with-pac-mac
#16
Augustinus J M Sweere, Johannes G E M Fraaije
We have calculated the excess free energy of mixing of 1053 binary mixtures with the OPLS-AA force field using two different methods: thermodynamic integration (TI) of molecular dynamics simulations and the Pair Configuration to Molecular Activity Coefficient (PAC-MAC) method. PAC-MAC is a force field based quasi-chemical method for predicting miscibility properties of various binary mixtures. The TI calculations yield a root mean squared error (RMSE) compared to experimental data of 0.132 kBT (0.37 kJ/mol)...
April 24, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28418442/network-analysis-and-percolation-transition-in-hydrogen-bonded-clusters-nitric-acid-and-water-extracted-by-tributyl-phosphate
#17
Michael J Servis, David T Wu, Jenifer C Braley
Extraction of polar molecules by amphiphilic species results in a complex variety of clusters whose topologies and energetics control phase behavior and efficiency of liquid-liquid separations. A computational approach including quantum mechanical vibrational frequency calculations and molecular dynamics simulation with intermolecular network theory is used to provide a robust assessment of extractant and polar solute association through hydrogen bonding in the tributyl phosphate (TBP)/HNO3/H2O/dodecane system for the first time...
April 18, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28418440/an-all-atom-molecular-dynamics-study-of-the-anti-interferon-signaling-of-ebola-virus-interaction-mechanisms-of-ebov-vp24-binding-to-karyopherin-alpha5
#18
Jing-Na Ding, Yan-Jun Zhang, Hui Zhong, Cheng-Cheng Ao, Jing Li, Ju-Guang Han
Ebola virus (EBOV) is highly lethal due to virally encoded immune antagonists, and the combination of EBOV VP24 with karyopherin alpha (KPNA) will trigger anti-interferon (IFN) signaling. The crystal structure of VP24-KPNA5 has been proposed in recent studies, but the precise binding mechanisms are still unclear. In order to explore the VP24-KPNA5 protein binding micro-mechanisms, Molecular Dynamic (MD) simulations and Molecular Mechanics Generalized Born Surface Area (MM-GB/SA) energy calculation are performed...
April 18, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28417976/revealing-inhibition-difference-between-pfi-2-enantiomers-against-setd7-by-molecular-dynamics-simulations-binding-free-energy-calculations-and-unbinding-pathway-analysis
#19
Yuzhen Niu, Danfeng Shi, Lanlan Li, Jingyun Guo, Huanxiang Liu, Xiaojun Yao
SETD7 is associated with multiple diseases related signaling pathways. (R)-PFI-2 is the first SETD7 inhibitor with nanomolar inhibitory potency. The activity of (R)-PFI-2 is about 500 times over that of (S)-PFI-2. Understanding the mechanism behind this difference will be helpful to discovery and design of more potent SETD7 inhibitors. A computational study combining molecular dynamics simulation, binding free energy calculations, and residue interaction network (RIN) was performed on the (S)-PFI-2/SETD7 and (R)-PFI-2/SETD7 complexes to explore the molecular mechanism behind the different inhibition activity...
April 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28414935/cdna-cloning-molecular-modeling-and-docking-calculations-of-l-type-lectins-from-swartzia-simplex-var-grandiflora-leguminosae-papilionoideae-a-member-of-the-tribe-swartzieae
#20
Paulo A C Maranhão, Claudener S Teixeira, Bruno L Sousa, Ito L Barroso-Neto, José E Monteiro-Júnior, Andreia V Fernandes, Marcio V Ramos, Ilka M Vasconcelos, José F C Gonçalves, Bruno A M Rocha, Valder N Freire, Thalles B Grangeiro
The genus Swartzia is a member of the tribe Swartzieae, whose genera constitute the living descendants of one of the early branches of the papilionoid legumes. Legume lectins comprise one of the main families of structurally and evolutionarily related carbohydrate-binding proteins of plant origin. However, these proteins have been poorly investigated in Swartzia and to date, only the lectin from S. laevicarpa seeds (SLL) has been purified. Moreover, no sequence information is known from lectins of any member of the tribe Swartzieae...
April 14, 2017: Phytochemistry
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