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Molecular dynamics simulation channel

Vivek Sharma, Pablo G Jambrina, Markus Kaukonen, Edina Rosta, Peter R Rich
Proton pumping A-type cytochrome c oxidase (CcO) terminates the respiratory chains of mitochondria and many bacteria. Three possible proton transfer pathways (D, K, and H channels) have been identified based on structural, functional, and mutational data. Whereas the D channel provides the route for all pumped protons in bacterial A-type CcOs, studies of bovine mitochondrial CcO have led to suggestions that its H channel instead provides this route. Here, we have studied H-channel function by performing atomistic molecular dynamics simulations on the entire, as well as core, structure of bovine CcO in a lipid-solvent environment...
November 13, 2017: Proceedings of the National Academy of Sciences of the United States of America
Yuxiang Li, Zaixing Yang, Yanlong Wang, Zhuanling Bai, Tao Zheng, Xing Dai, Shengtang Liu, Daxiang Gui, Wei Liu, Meng Chen, Lanhua Chen, Juan Diwu, Lingyan Zhu, Ruhong Zhou, Zhifang Chai, Thomas E Albrecht-Schmitt, Shuao Wang
Many environmental pollutants inherently exist in their anionic forms and are therefore highly mobile in natural water systems. Cationic framework materials that can capture those pollutants are highly desirable but scarcely reported. Here we present a mesoporous cationic thorium-based MOF (SCU-8) containing channels with a large inner diameter of 2.2 nm and possessing a high surface area of 1360 m(2) g(-1). The anion-exchange properties of SCU-8 were explored with many anions including small oxo anions like ReO4(-) and Cr2O7(2-) as well as anionic organic dyes like methyl blue and the persistent organic pollutant, perfluorooctane sulfonate (PFOS)...
November 7, 2017: Nature Communications
Jianbo Liu
Direct dynamics trajectories were calculated at the B3LYP/6-31G* level of theory to examine the intra-base pair proton transfer and dissociation of the deprotonated guanine (G)·cytosine (C) base pair under different excitation conditions, and to explore the origin of the nonstatistical product branching reported in a collision-induced dissociation (CID) experiment (Phys. Chem. Chem. Phys. 2016, 18, 32222). Trajectories for thermal excitation were initiated at two major conformers G·[C-H](-) (hydrogen-bonded guanine and N1-deprotonated cytosine) and G·[C-H](-)_PT (formed by proton transfer from the N1 of guanine to the N3 of deprotonated cytosine), and at their transition state (TS)...
November 8, 2017: Physical Chemistry Chemical Physics: PCCP
Youguo Yan, Zihan Dong, Yingnan Zhang, Pan Wang, Timing Fang, Jun Zhang
In tight oil reservoirs, nanopore throat acting as the narrowest section of fluidic channel determines the oil transport performance; injecting CO2 is found to significantly promote the oil flow. Despite substantial efforts, the underlying transport mechanism of above phenomenon remains unclear. Employing molecular dynamics simulation, the oil transport through a nanopore throat is studied. A high energy barrier derived of conformation deformation, oil/pore interaction and Jamin effect is found to impede the oil transport...
November 8, 2017: Physical Chemistry Chemical Physics: PCCP
Tyler J Harpole, Lucie Delemotte
The expansion of computational power, better parameterization of force fields, and the development of novel algorithms to enhance the sampling of the free energy landscape of proteins have allowed molecular dynamics (MD) simulations to become an indispensable tool to understand the function of biomolecules. The temporal and spatial resolution of MD simulation allows for the study of a vast number of processes of interest. Here, we review the computational efforts to uncover the conformational free energy landscapes of a subset of membrane proteins: ion channels, transporters and G-protein coupled receptors...
November 4, 2017: Biochimica et Biophysica Acta
Shuo Zhang, Olli H Pakarinen, Matilda Backholm, Flyura Djurabekova, Kai Nordlund, Juhani Keinonen, Tieshan Wang
In this work, we first simulated the amorphization of crystalline quartz under 50 keV <sup>23</sup>Na ion irradiation with classical molecular dynamics (MD). We then used binary collision approximation algorithms to simulate the Rutherford backscattering spectrometry in channeling conditions (RBS-C) from these irradiated MD cells, and compared the RBS-C spectra with experiments. The simulated RBS-C results show an agreement with experiments in the evolution of amorphization as a function of dose, showing what appears to be (by this measure) full amorphization at about 2...
November 6, 2017: Journal of Physics. Condensed Matter: An Institute of Physics Journal
Shouli Yuan, Bin Gao, Shunyi Zhu
The Kv1.2 channel plays an important role in the maintenance of resting membrane potential and the regulation of the cellular excitability of neurons, whose silencing or mutations can elicit neuropathic pain or neurological diseases (e.g., epilepsy and ataxia). Scorpion venom contains a variety of peptide toxins targeting the pore region of this channel. Despite a large amount of structural and functional data currently available, their detailed interaction modes are poorly understood. In this work, we choose four Kv1...
November 1, 2017: Toxins
Shuang Hou, Ruo-Xu Gu, Dong-Qing Wei
Destabilization of cellular ionic homeostasis by toxic β-amyloid (Aβ) channels/barrels, which is a pathogenic mechanism for Alzheimer's disease (AD), is inhibited by a novel anti-AD drug candidate wgx-50 significantly in our previous biological experiments. In this work, molecular dynamics simulations are conducted to investigate wgx-50-Aβ channels/barrels interactions, as well as the ion conductance inhibition mechanism. Ion influx from the extracellular side to the central pore, which is found in apo-form simulations, is blocked by wgx-50 ligands that bind to the hydrophobic rings at the entrance of the channels/barrels...
November 15, 2017: Journal of Chemical Information and Modeling
D Zanuttini, I Blum, L Rigutti, F Vurpillot, J Douady, E Jacquet, P-M Anglade, B Gervais
The molecular electronic states of the SiO(2+) dication have been investigated in a joint theoretical and experimental analysis. The use of a tip-shaped sample for tomographic atom probe analysis offers the unique opportunity to produce and to analyze the lifetime of some excited states of this dication. The perturbation brought by the large electric field of the polarized tip along the ion trajectory is analyzed by means of molecular dynamics simulation. For the typical electric fields used in the experiment, the lowest energy triplet states spontaneously dissociate, while the lowest energy singlet states do not...
October 28, 2017: Journal of Chemical Physics
Alper Tunga Celebi, Murat Barisik, Ali Beskok
Motivated by electrowetting-based flow control in nano-systems, water transport in graphene nano-channels is investigated as a function of the applied electric field. Molecular dynamics simulations are performed for deionized water confined in graphene nano-channels subjected to opposing surface charges, creating an electric field across the channel. Water molecules respond to the electric field by reorientation of their dipoles. Oxygen and hydrogen atoms in water face the anode and cathode, respectively, and hydrogen atoms get closer to the cathode compared to the oxygen atoms near the anode...
October 28, 2017: Journal of Chemical Physics
Themis Lazaridis, Gerhard Hummer
An important limitation of standard classical molecular dynamics simulations is the inability to make or break chemical bonds. This restricts severely our ability to study processes that involve even the simplest of chemical reactions, the transfer of a proton. Existing approaches for allowing proton transfer in the context of classical mechanics are rather cumbersome and have not achieved widespread use and routine status. Here we reconsider the combination of molecular dynamics with periodic stochastic proton hops...
November 14, 2017: Journal of Chemical Information and Modeling
Wen Fan, Jige Chen, Xiaoling Lei, Haiping Fang
Ionic hydration shells are the most noticeable microscopic feature in an aqueous salt solution, and have attracted attention due to their possible contribution to its flow behavior. In this paper, we find by molecular dynamic simulations that an S-shaped velocity profile is induced by the ionic hydration shells in the nano channel flow. Our theoretical analysis implies a linear relationship between the energy density inside the first hydration shell of the ions and the deformation strength of the velocity profiles of aqueous salt solutions, where the deformation strength is quantified by the curvature length defined by the linear deviation extended from the velocity profile...
November 2, 2017: Physical Chemistry Chemical Physics: PCCP
Carlo Guardiani, Olena A Fedorenko, Stephen K Roberts, Igor A Khovanov
Ion channel selectivity is essential for their function, yet the molecular basis of a channel's ability to select between ions is still rather controversial. In this work, using a combination of molecular dynamics simulations and electrophysiological current measurements we analyze the ability of the NaChBac channel to discriminate between calcium and sodium. Our simulations show that a single calcium ion can access the Selectivity Filter (SF) interacting so strongly with the glutamate ring so as to remain blocked inside...
November 1, 2017: Physical Chemistry Chemical Physics: PCCP
Giovanni Gonzalez-Gutierrez, Yuhang Wang, Gisela D Cymes, Emad Tajkhorshid, Claudio Grosman
Remarkable advances have been made toward the structural characterization of ion channels in the last two decades. However, the unambiguous assignment of well-defined functional states to the obtained structural models has proved challenging. In the case of the superfamily of nicotinic-receptor channels (also referred to as pentameric ligand-gated ion channels [pLGICs]), for example, two different types of model of the open-channel conformation have been proposed on the basis of structures solved to resolutions better than 4...
October 31, 2017: Journal of General Physiology
Ramachandran Gnanasekaran
We calculate communication maps for HIV-1 Reverse Transcriptase (RT) to elucidate energy transfer pathways between deoxythymidine triphosphate (dTTP) and other parts of the protein. This approach locates energy transport channels from the dTTP to remote regions of the protein via residues and water molecules. We examine the water dynamics near the catalytic site of HIV-1 RT by molecular dynamics (MD) simulations. We find that, within the catalytic site, the relaxation of water molecules is similar to that of the hydration water molecules present in other proteins and the relaxation time scale is fast enough to transport energy and helps in communication between dTTP and other residues in the system...
November 8, 2017: Physical Chemistry Chemical Physics: PCCP
Andrea Carrer, Alessandro Leparulo, Giulia Crispino, Catalin Dacian Ciubotaru, Oriano Marin, Francesco Zonta, Mario Bortolozzi
Mutations of the GJB1 gene encoding connexin 32 (Cx32) cause the X-linked form of Charcot-Marie-Tooth disease (CMTX1), a demyelinating peripheral neuropathy for which there is no cure. A growing body of evidence indicates that ATP release through Cx32 hemichannels in Schwann cells could be critical for nerve myelination, but it is unknown if CMTX1 mutations alter the cytosolic Ca2+-dependent gating mechanism that controls Cx32 hemichannel opening and ATP release. The current study uncovered that loss of the C-terminus in Cx32 (R220X mutation), which causes a severe CMTX1 phenotype, inhibits hemichannel opening during a canonical IP3-mediated increase in cytosolic Ca2+ in HeLa cells...
October 25, 2017: Human Molecular Genetics
Nina E Ottosson, Malin Silverå Ejneby, Xiongyu Wu, Samira Yazdi, Peter Konradsson, Erik Lindahl, Fredrik Elinder
Many pharmaceutical drugs against neurological and cardiovascular disorders exert their therapeutic effects by binding to specific sites on voltage-gated ion channels of neurons or cardiomyocytes. To date, all molecules targeting known ion channel sites bind to protein pockets that are mainly surrounded by water. We describe a lipid-protein drug-binding pocket of a potassium channel. We synthesized and electrophysiologically tested 125 derivatives, analogs, and related compounds to dehydroabietic acid. Functional data in combination with docking and molecular dynamics simulations mapped a binding site for small-molecule compounds at the interface between the lipid bilayer and the transmembrane segments S3 and S4 of the voltage-sensor domain...
October 2017: Science Advances
Maximilian Scheurer, Daria Brisker-Klaiman, Andreas Dreuw
Photoinduced biochemical reactions are ubiquitously governed by derivatives of flavin, which is a key player in a manifold of cellular redox reactions. The photoreactivity of flavins is also one of their greatest disadvantages as the molecules are sensitive to photodegradation. To prevent this unfavorable reaction, UV-light-exposed archaea bacteria, such as Halobacterium salinarum, manage the task of protecting flavin derivatives by dodecin, a protein which stores flavins and efficiently photoprotects them...
November 8, 2017: Journal of Physical Chemistry. B
Nicolas E Martin, Siddharth Malik, Nicolas Calimet, Jean-Pierre Changeux, Marco Cecchini
Pentameric ligand-gated ion channels (pLGICs) mediate intercellular communication at synapses through the opening of an ion pore in response to the binding of a neurotransmitter. Despite the increasing availability of high-resolution structures of pLGICs, a detailed understanding of the functional isomerization from closed to open (gating) and back is currently missing. Here, we provide the first atomistic description of the transition from open to closed (un-gating) in the glutamate-gated chloride channel (GluCl) from Caenorhabditis Elegans...
October 2017: PLoS Computational Biology
Alvin Yu, Albert Y Lau
Ionotropic glutamate receptors (iGluRs) are ligand-gated ion channels that are responsible for the majority of excitatory transmission at the synaptic cleft. Mechanically speaking, agonist binding to the ligand binding domain (LBD) activates the receptor by triggering a conformational change that is transmitted to the transmembrane region, opening the ion channel pore. We use fully atomistic molecular dynamics simulations to investigate the binding process in the α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptor, an iGluR subtype...
November 9, 2017: Journal of Physical Chemistry. B
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