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Molecular dynamics simulation channel

Kai Szuttor, Tamal Roy, Steffen Hardt, Christian Holm, Jens Smiatek
We use mesoscopic lattice-Boltzmann/molecular dynamics simulations to study the stretching behavior of a single tethered polymer in micro- and nanochannels. In particular, we are interested in the connection between fluid flow properties and the force on the polymer chain. An analytical expression for the stretching force is proposed, which linearly depends on the number of monomers and the boundary shear rate. In agreement with theory, the numerical findings reveal that the influence of hydrodynamic interactions can be ignored, which is also supported by results of additional Langevin dynamics simulations...
July 21, 2017: Journal of Chemical Physics
Emre Lacin, Prafulla Aryal, Ian W Glaaser, Karthik Bodhinathan, Eric Tsai, Nidaa Marsh, Stephen J Tucker, Mark S P Sansom, Paul A Slesinger
G protein-gated inwardly rectifying potassium (GIRK) channels control neuronal excitability in the brain and are implicated in several different neurological diseases. The anionic phospholipid phosphatidylinositol 4,5 bisphosphate (PIP2) is an essential cofactor for GIRK channel gating, but the precise mechanism by which PIP2 opens GIRK channels remains poorly understood. Previous structural studies have revealed several highly conserved, positively charged residues in the "tether helix" (C-linker) that interact with the negatively charged PIP2 However, these crystal structures of neuronal GIRK channels in complex with PIP2 provide only snapshots of PIP2's interaction with the channel and thus lack details about the gating transitions triggered by PIP2 binding...
July 18, 2017: Journal of General Physiology
Kamolrat Somboon, Jitti Niramitranon, Prapasiri Pongprayoon
Pseudomonas aeruginosa is an important nosocomial human pathogen. The major difficulty in the fight against this pathogen is the relative impermeability of its outer membrane (OM). Only specific substrates can penetrate through the OM of P. aeruginosa via substrate-specific porins, so this has become one of the most problematic drug-resistant pathogens. Carbapenems are the most effective drugs for treating P. aeruginosa infections. One such carbapenem that is applied in cases of P. aeruginosa infection is imipenem (IMI), which uses outer membrane carboxylate channel D1 (OccD1) as a point of entry into the pathogen...
August 2017: Journal of Molecular Modeling
L Chiodo, T E Malliavin, L Maragliano, G Cottone
The determination of the conformational states corresponding to diverse functional roles of ligand gated ion channels is subject of intense investigation with various techniques, from X-rays structure determination to electrophysiology and computational modeling. Even with a certain number of structures becoming recently available, only few major structural features distinguishing conductive open channel from the non conductive resting protein have been highlighted, while high-resolution details are still missing...
June 30, 2017: Biophysical Chemistry
Karl F Herold, Olaf S Andersen, Hugh C Hemmings
General anesthetics revolutionized medicine by allowing surgeons to perform more complex and much longer procedures. This widely used class of drugs is essential to patient care, yet their exact molecular mechanism(s) are incompletely understood. One early hypothesis over a century ago proposed that nonspecific interactions of anesthetics with the lipid bilayer lead to changes in neuronal function via effects on membrane properties. This model was supported by the Meyer-Overton correlation between anesthetic potency and lipid solubility and despite more recent evidence for specific protein targets, in particular ion-channels, lipid bilayer-mediated effects of anesthetics is still under debate...
July 10, 2017: European Biophysics Journal: EBJ
Catarina A Carvalheda, Andrei V Pisliakov
Cytochrome cbb3 (or C-type) oxidases are a highly divergent group and the least studied members of the heme-copper oxidases (HCOs) superfamily. HCOs couple the reduction of oxygen at the end of the respiratory chain to the active proton translocation across the membrane, contributing to establishment of an electrochemical gradient essential for ATP synthesis. Cbb3 oxidases exhibit unique structural and functional features and have an essential role in the metabolism of many clinically relevant human pathogens...
July 7, 2017: Biochemical and Biophysical Research Communications
May Siksik, Vikram Krishnamurthy
This paper proposes a multi-dielectric Brownian Dynamics (BD) simulation framework for Design-Space-Exploration (DSE) studies of ion-channel permeation. The goal of such DSE studies is to estimate the channel modeling-parameters that minimize the mean-squared-error between the simulated and expected "permeation characteristics". To address this computational challenge, we use a methodology based on statistical inference that utilizes knowledge of channel structure to prune the design space. We demonstrate the proposed framework and DSE methodology using a case study based on the KcsA ion channel in which the design space is successfully reduced from a 6-dimensional space to a 2-dimensional space...
July 4, 2017: IEEE Transactions on Nanobioscience
Amin Reza Zolghadr, Maryam Heydari Dokoohaki
Molecular dynamics (MD) simulations are conducted to suggest a mechanism of action for the aminopropyl dibromocarbazole derivative (P7C3) small molecule, which protects neurons from apoptotic cell death. At first, the influence of embedded Aβ42 stacks on the structure of membrane is studied. Then, the effect of P7C3 molecules on the Aβ42 fibril enriched membrane and Aβ42 fibril depleted membrane (when Aβ42 fibrils are originally dissolved in the aqueous phase) are evaluated. Also, the formation of an amyloid ion channel in the Aβ42 enriched membrane is examined by calculating deuterium order parameter, density profile, and surface thickness...
July 20, 2017: Journal of Chemical Information and Modeling
Renjith Sasimohanan Pillai, Hervé Jobic, Michael Marek Koza, Farid Nouar, Christian Serre, Guillaume Maurin, Naseem Ahmed Ramsahye
The diffusivity of CO2 and N2 in the small-pore titanium-based bis(phosphonate) metal-organic framework MIL-91(Ti) was explored by using a combination of quasielastic neutron scattering measurements and molecular dynamics simulations. These two techniques were used to determine the loading dependence of the self-diffusivity, corrected and transport diffusivities of these two gases to complement our previously reported thermodynamics study, which revealed that this material was a promising candidate for CO2 /N2 separation...
July 10, 2017: Chemphyschem: a European Journal of Chemical Physics and Physical Chemistry
Jun Li, Michele R Richards, Elena N Kitova, John S Klassen
The gas-phase conformations of dimers of the channel-forming membrane peptide gramicidin A (GA), produced from isobutanol or aqueous solutions of GA-containing nanodiscs (NDs), are investigated using electrospray ionization-ion mobility separation-mass spectrometry (ESI-IMS-MS) and molecular dynamics (MD) simulations. The IMS arrival times measured for (2GA + 2Na)(2+) ions from isobutanol reveal three different conformations, with collision cross-sections (Ω) of 683 Å(2) (conformation 1, C1), 708 Å(2) (C2), and 737 Å(2) (C3)...
July 5, 2017: Journal of the American Society for Mass Spectrometry
Abdolreza Javidialesaadi, George Stan
Powerful AAA+ biological nanomachines, such as ClpY, form hexameric ring structures, which selectively process abnormal proteins targeted for degradation by unfolding and threading them through a narrow central channel. The molecular details of this process are not yet fully understood. We perform Langevin dynamics simulations using a coarse-grained model of substrate proteins (SPs), Titin I27 and its V13P variant, threading through the ClpY pore. We probe the effect of ClpY surface heterogeneity and changes in pore width on SP orientation and the direction of applied force during SP unfolding...
July 18, 2017: Journal of Physical Chemistry. B
Maria Musgaard, Teresa Paramo, Laura Domicevica, Ole Juul Andersen, Philip C Biggin
Developments in structural biology mean that the number of different ion channel structures has increased significantly in recent years. Structures of ion channels enable us to rationalize how mutations may lead to channelopathies. However, determining the structures of ion channels is still not trivial, especially as they necessarily exist in many distinct functional states. Therefore, the use of computational modelling can provide complementary information that can refine working hypotheses of both wild type and mutant ion channels...
June 29, 2017: Neuropharmacology
M Morciano, M Fasano, A Nold, C Braga, P Yatsyshin, D N Sibley, B D Goddard, E Chiavazzo, P Asinari, S Kalliadasis
We investigate the hydrodynamic properties of a Lennard-Jones fluid confined to a nanochannel using molecular dynamics simulations. For channels of different widths and hydrophilic-hydrophobic surface wetting properties, profiles of the fluid density, stress, and viscosity across the channel are obtained and analysed. In particular, we propose a linear relationship between the density and viscosity in confined and strongly inhomogeneous nanofluidic flows. The range of validity of this relationship is explored in the context of coarse grained models such as dynamic density functional-theory...
June 28, 2017: Journal of Chemical Physics
Lamia Mlayeh, Eva-Maria Krammer, Marc Léonetti, Martine Prévost, Fabrice Homblé
The voltage-dependent anion-selective channel (VDAC) is the main pathway for inorganic ions and metabolites through the mitochondrial outer membrane. Studies recently demonstrated that membrane lipids regulate its function. It remains, however, unclear how this regulation takes place. In this study, we show that phospholipids are key regulators of Phaseolus VDAC function and, furthermore, that the salt concentration modulates this regulation. Both selectivity and voltage dependence of Phaseolus VDAC are very sensitive to a change in the lipid polar head from PC to PE...
June 27, 2017: Biochimica et Biophysica Acta
Laura Zanetti-Polzi, Massimiliano Aschi, Andrea Amadei, Isabella Daidone
Flavoproteins, containing flavin chromophores, are enzymes capable of transferring electrons at very high speeds. The ultrafast photoinduced electron-transfer (ET) kinetics of riboflavin binding protein to the excited riboflavin was studied by femtosecond spectroscopy and found to occur within a few hundred femtoseconds [ Zhong and Zewail, Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 11867-11872 ]. This ultrafast kinetics was attributed to the presence of two aromatic rings that could transfer the electron to riboflavin: the side chains of tryptophan 156 and tyrosine 75...
July 7, 2017: Journal of Physical Chemistry Letters
Ziqin Rong, Penghao Xiao, Miao Liu, Wenxuan Huang, Daniel C Hannah, William Scullin, Kristin A Persson, Gerbrand Ceder
In this work, we identify a new potential Mg battery cathode structure Mo3(PO4)3O, which is predicted to exhibit ultra-fast Mg(2+) diffusion and relatively high voltage based on first-principles density functional theory calculations. Nudged elastic band calculations reveal that the migration barrier of the percolation channel is only ∼80 meV, which is remarkably low, and comparable to the best Li-ion conductors. This low barrier is verified by ab initio molecular dynamics and kinetic Monte Carlo simulations...
June 30, 2017: Chemical Communications: Chem Comm
Marek Havrila, Petr Stadlbauer, Barira Islam, Michal Otyepka, Jiri Sponer
G-quadruplexes (GQs) are key non-canonical DNA and RNA architectures stabilized by desolvated monovalent cations present in their central channels. We analyze extended atomistic molecular dynamics simulations (~ 580 µs in total) of GQs with eleven monovalent cation parametrizations, assessing GQ overall structural stability, dynamics of internal cations and distortions of the G-tetrad geometries. Majority of simulations were executed with the SPC/E water model, however, test simulations with TIP3P and OPC water models are also reported...
June 28, 2017: Journal of Chemical Theory and Computation
Lu Liu, Hui Yu, Lianjuan Yang, Xi Zhao, Xuri Huang
No abstract text is available yet for this article.
June 28, 2017: Journal of Biomolecular Structure & Dynamics
Luba Simhaev, Nael A McCarty, Robert C Ford, Hanoch Senderowitz
Cystic fibrosis (CF) is a lethal, genetic disease found in particular in humans of European origin which is caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) chloride channel. The search for CF therapies acting by modulating the impaired function of mutant CFTR will be greatly advanced by high resolution structures of CFTR in different states. To date, two medium resolution electron microscopy (EM) structures of CFTR are available (one of a distant zebrafish (Danio rerio) CFTR ortholog and one of human CFTR)...
July 18, 2017: Journal of Chemical Information and Modeling
Pius S Padayatti, Josephine H Leung, Paween Mahinthichaichan, Emad Tajkhorshid, Andrii Ishchenko, Vadim Cherezov, S Michael Soltis, J Baz Jackson, C David Stout, Robert B Gennis, Qinghai Zhang
The nicotinamide nucleotide transhydrogenase (TH) is an integral membrane enzyme that uses the proton-motive force to drive hydride transfer from NADH to NADP(+) in bacteria and eukaryotes. Here we solved a 2.2-Å crystal structure of the TH transmembrane domain (Thermus thermophilus) at pH 6.5. This structure exhibits conformational changes of helix positions from a previous structure solved at pH 8.5, and reveals internal water molecules interacting with residues implicated in proton translocation. Together with molecular dynamics simulations, we show that transient water flows across a narrow pore and a hydrophobic "dry" region in the middle of the membrane channel, with key residues His42(α2) (chain A) being protonated and Thr214(β) (chain B) displaying a conformational change, respectively, to gate the channel access to both cytoplasmic and periplasmic chambers...
July 5, 2017: Structure
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