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MD simulation

Kun Li, Yi Tao, Zhongwu Li, Jingjie Sha, Yunfei Chen
By means of molecular dynamics (MD) simulations and density functional theory (DFT) calculations, we demonstrate that stretched and charged graphene can act as ion sieve membranes. It is observed that loading 30% strain on graphene can induce pores in the dense electron cloud to allow ions to pass through the aromatic rings. Meanwhile, charged surface is helpful to peel the hydration layers from the ions and decrease the energy barrier for ion translocation through nanopores. Our results suggest that with membrane charge density of 6...
November 16, 2017: Nanotechnology
Denan Zhang, Lei Liu, Lin Pang, Qing Jin, Kehui Ke, Ming Hu, Jingbo Yang, Weifang Ma, Hongbo Xie, Xiujie Chen
Glycogen synthase kinase-3 beta (GSK-3β) is involved in multiple signaling pathways. Consistent with its critical roles in normal cells, abnormalities in GSK-3β activity have been implicated in diabetes, heart disease, Parkinson disease and Alzheimer's disease. In this study, a series of new scaffolds of small molecule inhibitors of GSK-3β were identified by virtual screening and bioassay. Candidates that adhere to drug-like criteria from a virtual library of compounds were tested using computational docking studies...
November 16, 2017: Journal of Cellular Biochemistry
Zhujiang Hua, Yang Zhao, Shuhong Dong, Peishi Yu, Yu Liu, Ning Wei, Junhua Zhao
From the macro- to the nanoscale, kirigami structures show novel and tunable properties by tailoring the original two-dimensional sheets. In this study, the large stretchability and failure behavior in graphene nanoribbon kirigami (GNR-k) are obtained using the finite element (FE) method and molecular dynamics (MD) simulations. The carbon-carbon bond in the FE method is equivalent to a nonlinear Timoshenko beam based on the Tersoff-Brenner potential. All the results from the present FE method are in reasonable agreement with those from our MD simulations using the REBO potential...
November 16, 2017: Soft Matter
Qing-Qing Pan, Shuang-Bao Li, Ying-Chen Duan, Yong Wu, Ji Zhang, Yun Geng, Liang Zhao, Zhong-Min Su
The interface characteristic is a crucial factor determining the power conversion efficiency of organic solar cells (OSCs). In this work, our aim is to conduct a comparative study on the interface characteristics between the very famous non-fullerene acceptor, ITIC, and a fullerene acceptor, PC71BM by combining molecular dynamics simulations with density functional theory. Based on some typical interface models of the acceptor ITIC or PC71BM and the donor PBDB-T selected from MD simulation, besides the evaluation of charge separation/recombination rates, the relative positions of Frenkel exciton (FE) states and the charge transfer states along with their oscillator strengths are also employed to estimate the charge separation abilities...
November 16, 2017: Physical Chemistry Chemical Physics: PCCP
Amit Chaudhary, Birendra Singh Yadav, Swati Singh, Pramod Kumar Maurya, Alok Mishra, Shweta Srivastva, Pritish Kumar Varadwaj, Nand Kumar Singh, Ashutosh Mani
Background: Ficus religiosa L. is generally known as Peepal and belongs to family Moraceae. The tree is a source of many compounds having high medicinal value. In gastrointestinal tract, histamine H2 receptors have key role in histamine-stimulated gastric acid secretion. Their over stimulation causes its excessive production which is responsible for gastric ulcer. Objective: This study aims to screen the range of phytochemicals present in F. religiosa for binding with human histamine H2 and identify therapeutics for a gastric ulcer from the plant...
October 2017: Pharmacognosy Magazine
Mohammad M Sultan, Rajiah Aldrin Denny, Ray Unwalla, Frank Lovering, Vijay S Pande
Bruton tyrosine kinase (BTK) is a key enzyme in B-cell development whose improper regulation causes severe immunodeficiency diseases. Design of selective BTK therapeutics would benefit from improved, in-silico structural modeling of the kinase's solution ensemble. However, this remains challenging due to the immense computational cost of sampling events on biological timescales. In this work, we combine multi-millisecond molecular dynamics (MD) simulations with Markov state models (MSMs) to report on the thermodynamics, kinetics, and accessible states of BTK's kinase domain...
November 15, 2017: Scientific Reports
Zhen Wang, Li Ping Cheng, Xing Hua Zhang, Wan Pang, Liang Li, Jin Long Zhao
Neuraminidase (NA) is one of the particular potential targets for novel antiviral therapy. In this work, a series of neuraminidase inhibitors with the cyclohexene scaffold were studied based upon the combination of 3D-QSAR, molecular docking, and molecular dynamics techniques. The results indicate that the built 3D-QSAR models yield reliable statistical information: the correlation coefficient (r(2)) and cross-validation coefficient (q(2)) of CoMFA (comparative molecular field analysis) are 0.992 and 0.819; the r(2) and q(2) of CoMSIA (comparative molecular similarity analysis) are 0...
November 4, 2017: Bioorganic & Medicinal Chemistry Letters
Luigi Sbailò, Frank Noé
Molecular Dynamics-Green's Function Reaction Dynamics (MD-GFRD) is a multiscale simulation method for particle dynamics or particle-based reaction-diffusion dynamics that is suited for systems involving low particle densities. Particles in a low-density region are just diffusing and not interacting. In this case, one can avoid the costly integration of microscopic equations of motion, such as molecular dynamics (MD), and instead turn to an event-based scheme in which the times to the next particle interaction and the new particle positions at that time can be sampled...
November 14, 2017: Journal of Chemical Physics
Xuewei Liu, Danfeng Shi, Shuangyan Zhou, Hongli Liu, Huanxiang Liu, Xiaojun Yao
Molecular dynamics (MD) simulations can provide not only plentiful dynamical structural information on biomacromolecules but also a wealth of energetic information about protein and ligand interactions. Such information is very important to understanding the structure-function relationship of the target and the essence of protein-ligand interactions and to guiding the drug discovery and design process. Thus, MD simulations have been applied widely and successfully in each step of modern drug discovery. Areas covered: In this review, the authors review the applications of MD simulations in novel drug discovery, including the pathogenic mechanisms of amyloidosis diseases, virtual screening and the interaction mechanisms between drugs and targets...
November 15, 2017: Expert Opinion on Drug Discovery
Jing Su, Xinguo Liu, Shaolong Zhang, Fangfang Yan, Qinggang Zhang, Jianzhong Chen
Bromodomains (BRDs) have been an attractive candidate for development of efficient inhibitors toward gene transcription. Molecular dynamics (MD) simulations followed by principal component (PC) analysis were performed to investigate binding selectivity of inhibitors RVX297, BSP, JQ1, SF2523 and CPD2 toward two domains (BD1 and BD2) of bromodomain-containing protein 4 (BRD4). The results show that inhibitor bindings exert different effect on motions of the BC-loops in BD1 and BD2. The rank of binding free energies calculated by using molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) method agrees with the one determined by experiment...
November 15, 2017: Chemical Biology & Drug Design
Yi Cai, Hao Liu, Haifeng Chen
The human immunodeficiency virus (HIV) is a retrovirus which infects T lymphocyte of human body and causes Immunodeficiency. Reverse transcriptase inhibitors (RTIs) can inhibit some functions of RT, preventing virus synthesis (double-stranded DNA), so that HIV virus replication can be reduced. Experimental results indicate a series of benzimidazole-based inhibitors which target HIV RT-associate RNase to inhibit the reverse transcription of HIV virus. However, the allosteric mechanism is still unclear. Here, molecular dynamics simulations and dynamics fluctuation network analysis were used to reveal the binding mode between the inhibitors and RT-associate RNase...
November 15, 2017: Chemical Biology & Drug Design
Wisman Acharige Monika Madhavi, M S Samantha Weerasinghe, Konstantin I Momot
Rotational motion of water molecules plays the dominant role in determining NMR spin relaxation properties of liquid water and many biological tissues. The traditional theory of NMR spin relaxation predominantly uses the assumption that the reorientational dynamics of water molecules is described by a continuous-time rotational-diffusion random walk with a single rotational diffusion coefficient. However, recent experimental and theoretical studies have demonstrated that water reorientation occurs via large, discrete angle jumps superimposed on a continuous-time rotational diffusion process...
November 14, 2017: Journal of Physical Chemistry. B
Himanshu Joshi, Prabal K Maiti
Engineering the synthetic nanopores through lipid bilayer membrane to access the interior of a cell is a long persisting challenge in biotechnology. Here, we demonstrate the stability and dynamics of a tile-based 6-helix DNA nanotube (DNT) embedded in POPC lipid bilayer using the analysis of 0.2 μs long equilibrium MD simulation trajectories. We observe that the head groups of the lipid molecules close to the lumen cooperatively tilt towards the hydrophilic sugar-phosphate backbone of DNA and form a toroidal structure around the patch of DNT protruding in the membrane...
November 10, 2017: Nucleic Acids Research
Alexander B Kuhn, Sebastian Kube, Anne R Karow-Zwick, Daniel Seeliger, Patrick Garidel, Michaela Blech, Lars V Schäfer
Monoclonal antibody (mAb) based therapeutics often require high concentration formulations. Unfortunately, highly concentrated antibody solutions often have biophysical properties that are disadvantageous for therapeutic development, such as high viscosity, solubility limitations, precipitation issues, or liquid-liquid phase separation. In this work, we present a computational rational design principle for improving the thermodynamic stability of mAb solutions through targeted point mutations. Two publicly available IgG1 monoclonal antibodies that exhibit high viscosity at high concentrations were used as model systems...
November 14, 2017: Journal of Physical Chemistry. B
Syed Tarique Moin, Thomas S Hofer
The ab initio quantum mechanical charge field molecular dynamics (QMCF-MD) simulation approach was successfully applied to Fe(2+)-P and Fe(3+)-P in water to evaluate their structural, dynamical and energetic properties. Based on the structural data, it was found that Fe(2+)-P accommodates one water molecule in the first coordination sphere of the Fe(2+) ion including the four nitrogen atoms of the porphyrin system coordinating with central metal species. On the other hand, two water molecules were coordinated to Fe(3+)-P, thus forming a hexa-coordinated species...
November 14, 2017: Physical Chemistry Chemical Physics: PCCP
Oleksandr Yakovenko, Steven J M Jones
We report the implementation of molecular modeling approaches developed as a part of the 2016 Grand Challenge 2, the blinded competition of computer aided drug design technologies held by the D3R Drug Design Data Resource ( ). The challenge was focused on the ligands of the farnesoid X receptor (FXR), a highly flexible nuclear receptor of the cholesterol derivative chenodeoxycholic acid. FXR is considered an important therapeutic target for metabolic, inflammatory, bowel and obesity related diseases (Expert Opin Drug Metab Toxicol 4:523-532, 2015), but in the context of this competition it is also interesting due to the significant ligand-induced conformational changes displayed by the protein...
November 13, 2017: Journal of Computer-aided Molecular Design
Peshala/P Thibotuwawa Gamage, Fardin Khalili, Md/Khurshidul Azad, Hansen/A Mansy
Inspiratory flow in a multi-generation pig lung airways was numerically studied at a steady inlet flow rate of 3.2×10-4 m3/s corresponding to a Reynolds number of 1150 in the trachea. The model was validated by comparing velocity distributions with previous measurements and simulations in simplified airway geometries. Simulation results provided detailed maps of the axial and secondary flow patterns at different cross sections of the airway tree. The vortex core regions in the airways were visualized using absolute helicity values and suggested the presence of secondary flow vortices where two counter rotating vortices were observed at the main bifurcation and in many other bifurcations...
November 13, 2017: Journal of Biomechanical Engineering
Jenny Fagerland, Daniela Pappalardo, Björn Schmidt, Per-Olof Syrén, Anna Finne Wistrand
Peptides are often attached to polymer materials, as bioactive components, for the control of interactions between the material and its surrounding proteins and cells. However, synthesizing peptides and attaching them to polymers can be challenging and laborious. Herein, we describe the grafting of oligopeptides to an aliphatic polyester, using a one-step chemo-enzymatic synthesis with papain as the biocatalyst. To enable enzyme-mediated functionalization of the polyester, ethyl hept-6-enoylalaninate (grafter) was synthesized and attached to polylactide chains using thiol-ene click reactions...
November 13, 2017: Biomacromolecules
Hiroya Tanaka, Hideo Iizuka, Yuriy V Pershin, Massimiliano Di Ventra
Ionic Coulomb blockade in nanopores is a phenomenon that shares some similarities but also differences with its electronic ounterpart. Here, we investigate extensively this phenomenon using all-atom molecular dynamics of ionic transport through nanopores of about one nanometer in diameter and up to several nanometers in length. Our goal is to better understand the role of atomic roughness and structure of the pore walls in facilitating ionic Coulomb blockade. Our numerical results reveal the following general trends...
November 13, 2017: Nanotechnology
Thana Sutthibutpong, Triwit Rattanarojpong, Pongsak Khunrae
Local conformational changes and global unfolding pathways of wildtype xyn11A recombinant and its mutated structures were studied through a series of atomistic molecular dynamics (MD) simulations, along with enzyme activity assays at three incubation temperatures to investigate the effects of mutations at three different sites to the thermostability. The first mutation was to replace an unstable negatively charged residue at a surface beta turn near the active site (D32G) by a hydrophobic residue. The second mutation was to create a disulfide bond (S100C/N147C) establishing a strong connection between an alpha helix and a distal beta hairpin associated with the thermally sensitive Thumb loop, and the third mutation add an extra hydrogen bond (A155S) to the same alpha helix...
November 13, 2017: Journal of Biomolecular Structure & Dynamics
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