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Molecular dynamics simulation channel

Kolattukudy P Santo, Aleksey Vishnyakov, Yefim Brun, Alexander V Neimark
This work explores interactions of functionalized nanoparticles (NP) with polymer brushes (PB) in a binary mixture of good and poor solvents. NP-PB systems are used in multiple applications, and we are particularly interested in the problem of chromatographic separation of NPs on polymer-grafted porous columns. This process involves NP flow through the pore channels with walls covered by PBs. NP-PB adhesion is governed by adsorption of polymer chains to NP surface and entropic repulsion caused by the polymer chain confinement between NP and the channel wall...
September 15, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
Christian J Burnham, Niall J English
An extensive suite of nonequilibrium molecular-dynamics (NEMD) simulations have been performed for ∼60 ns of human aquaporin 4 in externally applied circularly polarized (CP) electric fields, applied axially along channels. These external fields were 0.05 V/Å in intensity and 100 GHz in frequency. This has the effect of "electro-pumping" the water through the pores as prototypical biochannels, from conversion of molecules' spin angular momentum to linear momentum in the asymmetric heterogeneous-frictional environment of the pores, thus inducing overall net flow...
September 14, 2017: Journal of Physical Chemistry Letters
Kevin Speyer, Claudio Pastorino
We study the influence of chain stiffness on droplet flow in a nano-channel, coated with semiflexible hydrophobic polymers by means of non-equilibrium molecular-dynamics simulations. The studied system is then a moving droplet in the slit channel, coexisting with its vapor and subjected to periodic boundary conditions in the flow direction. The polymer chains, grafted by the terminal bead to the confining walls, are described by a coarse-grained model that accounts for chain connectivity, excluded volume interactions and local chain stiffness...
September 11, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
Flávio O Sanches-Neto, Nayara D Coutinho, Valter H Carvalho-Silva
A number of experimental and theoretical papers accounted almost exclusively for two channels in the reaction of atomic hydrogen with methanol: H-abstraction from the methyl (R1) and hydroxyl (R2) functional groups. Recently, several astrochemical studies claimed the importance of another channel for this reaction, which is crucial for kinetic simulations related to the abundance of molecular constituents in planetary atmospheres: methyl radical and water formation (R3 channel). Here, motivated by the lack of and uncertainties about the experimental and theoretical kinetic rate constants for the third channel, we developed first-principles Car-Parrinello molecular dynamics thermalized at two significant temperatures - 300 and 2500 K...
September 11, 2017: Physical Chemistry Chemical Physics: PCCP
Ketan Malhotra, Arnab Modak, Shivangi Nangia, Tyler H Daman, Umut Gunsel, Victoria L Robinson, Dejana Mokranjac, Eric R May, Nathan N Alder
The phospholipid cardiolipin mediates the functional interactions of proteins that reside within energy-conserving biological membranes. However, the molecular basis by which this lipid performs this essential cellular role is not well understood. We address this role of cardiolipin using the multisubunit mitochondrial TIM23 protein transport complex as a model system. The early stages of protein import by this complex require specific interactions between the polypeptide substrate receptor, Tim50, and the membrane-bound channel-forming subunit, Tim23...
September 2017: Science Advances
Andrew H Beaven, Alexander J Sodt, Richard Walter Pastor, Roger E Koeppe, Olaf S Andersen, Wonpil Im
Previous experiments have shown that the lifetime of a gramicidin A dimer channel (which forms from two non-conducting monomers) in a lipid bilayer is modulated by mutations of the tryptophan (Trp) residues at the bilayer-water interface. We explore this further using extensive molecular dynamics simulations of various gA dimer and monomer mutants at the Trp positions in phosphatidylcholine bilayers with different tail lengths. gA interactions with the surrounding bilayer are strongly modulated by mutating these Trp residues...
September 4, 2017: Journal of Chemical Theory and Computation
Anup Arunrao Deshpande, Monika Sharma, Anand Kumar Bachhawat
Cystine transporters are a clinically important class of transporters found in bacteria, pathogenic fungi and mammalian cells. Despite their significance, very little is known about the mechanism of substrate recognition and transport. We have carried out studies on the plasma membrane Candida glabrata cystine transporter, CgCYN1 a member of the amino acid-polyamine-organocation (APC) transporter superfamily. A homology model of CgCYN1 was generated by using crystal structures of three known bacterial APC transporters followed by further refinement using molecular dynamics simulations...
September 1, 2017: Biochimica et Biophysica Acta
Giulio Alberini, Fabio Benfenati, Luca Maragliano
Tight-junctions between epithelial cells of biological barriers are specialized molecular structures that regulate the flux of solutes across the barrier, parallel to cell walls. The tight-junction backbone is made of strands of transmembrane proteins from the claudin family, but the molecular mechanism of its function is still not completely understood. Recently, the crystal structure of a mammalian claudin-15 was reported, displaying for the first time the detailed features of transmembrane and extracellular domains...
2017: PloS One
Adam D Martinac, Navid Bavi, Omid Bavi, Boris Martinac
There are great opportunities in the manipulation of bacterial mechanosensitive (MS) ion channels for specific and targeted drug delivery purposes. Recent research has shown that these ion channels have the potential to be converted into nanovalves through clever use of magnetic nanoparticles and magnetic fields. Using a combination of molecular dynamics (MD) simulations and the finite element (FE) modelling, this study investigates the theoretical feasibility of opening the MscL channel (MS channel of large conductance of E...
2017: PloS One
Pakhuri Mehta, Shubham Srivastava, Bhanwar Singh Choudhary, Manish Sharma, Ruchi Malik
Multidrug resistance along with side-effects of available anti-epileptic drugs and unavailability of potent and effective agents in submicromolar quantities presents the biggest therapeutic challenges in anti-epileptic drug discovery. The molecular modeling techniques allow us to identify agents with novel structures to match the continuous urge for its discovery. KCNQ2 channel represents one of the validated targets for its therapy. The present study involves identification of newer anti-epileptic agents by means of a computer-aided drug design adaptive protocol involving both structure-based virtual screening of Asinex library using homology model of KCNQ2 and 3D-QSAR based virtual screening with docking analysis, followed by dG bind and ligand efficiency calculations with ADMET studies, of which 20 hits qualified all the criterions...
August 31, 2017: Journal of Receptor and Signal Transduction Research
Yuri A Nedialkov, Kristopher Opron, Hailey L Caudill, Fadi Assaf, Amanda J Anderson, Robert I Cukier, Guowei Wei, Zachary F Burton
Based on molecular dynamics simulations and functional studies, a conformational mechanism is posited for forward translocation by RNA polymerase (RNAP). In a simulation of a ternary elongation complex, the clamp and downstream cleft were observed to close. Hinges within the bridge helix and trigger loop supported generation of translocation force against the RNA-DNA hybrid resulting in opening of the furthest upstream i-8 RNA-DNA bp, establishing conditions for RNAP sliding. The β flap tip helix and the most N-terminal β' Zn finger engage the RNA, indicating a path of RNA threading out of the exit channel...
August 30, 2017: Transcription
Davide Sala, Silvia Ciambellotti, Andrea Giachetti, Paola Turano, Antonio Rosato
We investigated the kinetics of the release of iron(II) ions from the internal cavity of human H ferritin as a function of pH. Extensive molecular dynamics (MD) simulations of the entire 24-mer ferritin provided atomic-level information on the release mechanism. Iron ions exit via the C3 channels. Double protonation of His residues at pH 4 facilitates the removal of the iron ligands within the channel through the formation of salt bridges, resulting in a significantly lower release energy barrier than pH 9...
August 30, 2017: Journal of Chemical Information and Modeling
Travis J A Craddock, Philip Kurian, Jordane Preto, Kamlesh Sahu, Stuart R Hameroff, Mariusz Klobukowski, Jack A Tuszynski
Anesthesia blocks consciousness and memory while sparing non-conscious brain activities. While the exact mechanisms of anesthetic action are unknown, the Meyer-Overton correlation provides a link between anesthetic potency and solubility in a lipid-like, non-polar medium. Anesthetic action is also related to an anesthetic's hydrophobicity, permanent dipole, and polarizability, and is accepted to occur in lipid-like, non-polar regions within brain proteins. Generally the protein target for anesthetics is assumed to be neuronal membrane receptors and ion channels, however new evidence points to critical effects on intra-neuronal microtubules, a target of interest due to their potential role in post-operative cognitive dysfunction (POCD)...
August 29, 2017: Scientific Reports
Qichao Luo, Liping Chen, Xi Cheng, Yuqin Ma, Xiaona Li, Bing Zhang, Li Li, Shilei Zhang, Fei Guo, Yang Li, Huaiyu Yang
Two-pore domain potassium (K2P) channels generate leak currents that are responsible for the maintenance of the resting membrane potential, and they are thus potential drug targets for treating diseases. Here, we identify N-(4-cholorphenyl)-N-(2-(3,4-dihydrosioquinolin-2(1H)-yl)-2-oxoethyl)methanesulfonamide (TKDC) as an inhibitor of the TREK subfamily, including TREK-1, TREK-2 and TRAAK channels. Using TKDC as a chemical probe, a study combining computations, mutagenesis and electrophysiology reveals a K2P allosteric ligand-binding site located in the extracellular cap of the channels...
August 29, 2017: Nature Communications
Birce Onal, Daniel Gratz, Thomas J Hund
Atrial fibrillation (AF) affects more than 3 million people per year in the U.S., and is associated with high morbidity and mortality. Both electrical and structural remodeling contribute to AF, but the molecular pathways underlying AF pathogenesis are not well understood. Recently, a role for Ca(2+)/calmodulin-dependent protein kinase II (CaMKII) in regulation of persistent "late" sodium current (INa,L) has been identified. While INa,L inhibition is emerging as a potential antiarrhythmic strategy in AF patients, little is known about the mechanism linking INa,L to atrial arrhythmogenesis...
August 25, 2017: American Journal of Physiology. Heart and Circulatory Physiology
Mahdi Bagherpoor Helabad, Tahereh Ghane, Marco Reidelbach, Anna Lena Woelke, Ernst Walter Knapp, Petra Imhof
Proton transfer in cytochrome c oxidase from the cellular inside to the binuclear redox center (BNC) can occur through two distinct pathways, the D- and K-channels. For the protein to function as both a redox enzyme and a proton pump, proton transfer into the protein toward the BNC or toward a proton loading site (and ultimately through the membrane) must be highly regulated. The PR → F transition is the first step in a catalytic cycle that requires proton transfer from the bulk at the N-side to the BNC. Molecular dynamics simulations of the PR → F intermediate of this transition, with 16 different combinations of protonation states of key residues in the D- and K-channel, show the impact of the K-channel on the D-channel to be protonation-state dependent...
August 22, 2017: Biophysical Journal
Marawan Ahmed, Horia Jalily Hasani, Aravindhan Ganesan, Michael Houghton, Khaled Barakat
Abnormalities in the human Nav1.5 (hNav1.5) voltage-gated sodium ion channel (VGSC) are associated with a wide range of cardiac problems and diseases in humans. Current structural models of hNav1.5 are still far from complete and, consequently, their ability to study atomistic interactions of this channel is very limited. Here, we report a comprehensive atomistic model of the hNav1.5 ion channel, constructed using homology modeling technique and refined through long molecular dynamics simulations (680 ns) in the lipid membrane bilayer...
2017: Drug Design, Development and Therapy
Sudip Chakraborty, Hemant Kumar, Chandan Dasgupta, Prabal K Maiti
Understanding the properties of strongly confined water is important for a variety of applications such as fast flow and desalination devices, voltage generation, flow sensing, and nanofluidics. Confined water also plays an important role in many biological processes such as flow through ion channels. Water in the bulk exhibits many unusual properties that arise primarily from the presence of a network of hydrogen bonds. Strong confinement in structures such as carbon nanotubes (CNTs) substantially modifies the structural, thermodynamic, and dynamic (both translational and orientational) properties of water by changing the structure of the hydrogen bond network...
August 15, 2017: Accounts of Chemical Research
Jiaye Su, Yunzhen Zhao, Chang Fang, Syed Bilal Ahmed, Yue Shi
Nanoparticles are highly versatile and exhibit broad applications in tuning material properties. Herein, we show through molecular dynamics simulations the possibility of a nanometer water pump, driven by the motion of nanoparticles (NPs) on a membrane surface. Surprisingly, considerable net water flux can be induced through a carbon nanotube (CNT) that is perpendicular to the NP motion. The water transport can occur in a highly controllable fashion, not only by using a single NP with different forces, but also by varying the CNT length or the NP number...
August 23, 2017: Physical Chemistry Chemical Physics: PCCP
Jingwei Zhou, Yue Huang, Chunyan Cheng, Kai Wang, Ruibo Wu
The development of novel isoform/class-selective inhibitors is still of great biological and medical significance to conquer the continuously reported side effects for the histone deacetylase (HDAC) drugs. The first potent HDAC allosteric inhibitor was discovered last year, and this allosteric inhibitor design is thought to be a promising strategy to overcome the current challenges in HDAC inhibitor design. However, the detailed allosteric mechanism and its remote regulatory effects on the catalytic/inhibitor activity of HDAC are still unclear...
August 25, 2017: Journal of Chemical Information and Modeling
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