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Molecular dynamics simulation channel

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#1
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
#2
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
#3
Maria V Yelshanskaya, Samaneh Mesbahi-Vasey, Maria G Kurnikova, Alexander I Sobolevsky
AMPA subtype ionotropic glutamate receptors mediate fast excitatory neurotransmission and are implicated in numerous neurological diseases. Ionic currents through AMPA receptor channels can be allosterically regulated via different sites on the receptor protein. We used site-directed mutagenesis and patch-clamp recordings to probe the ion channel extracellular collar, the binding region for noncompetitive allosteric inhibitors. We found position and substitution-dependent effects for introduced mutations at this region on AMPA receptor gating...
April 21, 2017: Scientific Reports
#4
Madhusmita Tripathy, Sunil Kumar P B, Abhijit P Deshpande
The extent of phase separation and water percolation in sulfonated membranes are the key to their performance in fuel cells. Toward this, the effect of hydration on the morphology and transport characteristics of sulfonated poly(ether ether ketone), sPEEK, membrane is investigated using atomistic molecular dynamics simulation at various hydration levels($\lambda$: number of water molecules per sulfonate group). The evolution of local morphology is investigated using structural correlations and minimum pair distances...
April 21, 2017: Journal of Physical Chemistry. B
#5
Abhijit Mondal, Frank B Sachse, Alonso P Moreno
Gap junction channels play a vital role in intercellular communication by connecting cytoplasm of adjoined cells through arrays of channel-pores formed at the common membrane junction. Their structure and properties vary depending on the connexin isoform(s) involved in forming the full gap junction channel. Lack of information on the molecular structure of gap junction channels has limited the development of computational tools for single channel studies. Currently, we rely on cumbersome experimental techniques that have limited capabilities...
2017: Frontiers in Physiology
#6
Michail Papanikolaou, Michael Frank, Dimitris Drikakis
This paper investigates the effect of surface roughness on fluid viscosity using molecular dynamics simulations. The three-dimensional model consists of liquid argon flowing between two solid walls whose surface roughness was modeled using fractal theory. In tandem with previously published experimental work, our results show that, while the viscosity in smooth channels remains constant across the channel width, in the presence of surface roughness it increases close to the walls. The increase of the boundary viscosity is further accentuated by an increase in the depth of surface roughness...
March 2017: Physical Review. E
#7
REVIEW
J Rydzewski, W Nowak
Computational simulations in biophysics describe the dynamics and functions of biological macromolecules at the atomic level. Among motions particularly important for life are the transport processes in heterogeneous media. The process of ligand diffusion inside proteins is an example of a complex rare event that can be modeled using molecular dynamics simulations. The study of physical interactions between a ligand and its biological target is of paramount importance for the design of novel drugs and enzymes...
April 1, 2017: Physics of Life Reviews
#8
Martin B Ulmschneider, Jakob P Ulmschneider, J Alfredo Freites, Gunnar von Heijne, Douglas J Tobias, Stephen H White
Hydrophobic amino acids are abundant in transmembrane (TM) helices of membrane proteins. Charged residues are sparse, apparently due to the unfavorable energetic cost of partitioning charges into nonpolar phases. Nevertheless, conserved arginine residues within TM helices regulate vital functions, such as ion channel voltage gating and integrin receptor inactivation. The energetic cost of arginine in various positions along hydrophobic helices has been controversial. Potential of mean force (PMF) calculations from atomistic molecular dynamics simulations predict very large energetic penalties, while in vitro experiments with Sec61 translocons indicate much smaller penalties, even for arginine in the center of hydrophobic TM helices...
April 13, 2017: European Biophysics Journal: EBJ
#9
REVIEW
Steven V Molinski, Zoltán Bozóky, Surtaj H Iram, Saumel Ahmadi
Although membrane proteins represent most therapeutically relevant drug targets, the availability of atomic resolution structures for this class of proteins has been limited. Structural characterization has been hampered by the biophysical nature of these polytopic transporters, receptors, and channels, and recent innovations to in vitro techniques aim to mitigate these challenges. One such class of membrane proteins, the ATP-binding cassette (ABC) superfamily, are broadly expressed throughout the human body, required for normal physiology and disease-causing when mutated, yet lacks sufficient structural representation in the Protein Data Bank...
2017: International Journal of Medicinal Chemistry
#10
Jan-Philipp Machtens, Rodolfo Briones, Claudia Alleva, Bert L de Groot, Christoph Fahlke
Electrical cell signaling requires adjustment of ion channel, receptor, or transporter function in response to changes in membrane potential. For the majority of such membrane proteins, the molecular details of voltage sensing remain insufficiently understood. Here, we present a molecular dynamics simulation-based method to determine the underlying charge movement across the membrane-the gating charge-by measuring electrical capacitor properties of membrane-embedded proteins. We illustrate the approach by calculating the charge transfer upon membrane insertion of the HIV gp41 fusion peptide, and validate the method on two prototypical voltage-dependent proteins, the Kv1...
April 11, 2017: Biophysical Journal
#11
Jafar Ghorbanian, Ali Beskok
This paper concentrates on the unconventional temperature profiles and heat fluxes observed in non-equilibrium molecular dynamics (MD) simulations of force-driven liquid flows in nano-channels. Using MD simulations of liquid argon flows in gold nano-channels, we investigate the manifestation of the first law of thermodynamics for the MD system, and compare it with that of the continuum fluid mechanics. While the energy equation for the continuum system results in heat conduction determined by viscous heating, the first law of thermodynamics in the MD system includes an additional slip-heating term...
April 19, 2017: Physical Chemistry Chemical Physics: PCCP
#12
Prafulla Aryal, Viwan Jarerattanachat, Michael V Clausen, Marcus Schewe, Conor McClenaghan, Liam Argent, Linus J Conrad, Yin Y Dong, Ashley C W Pike, Elisabeth P Carpenter, Thomas Baukrowitz, Mark S P Sansom, Stephen J Tucker
The mechanosensitive two-pore domain (K2P) K(+) channels (TREK-1, TREK-2, and TRAAK) are important for mechanical and thermal nociception. However, the mechanisms underlying their gating by membrane stretch remain controversial. Here we use molecular dynamics simulations to examine their behavior in a lipid bilayer. We show that TREK-2 moves from the "down" to "up" conformation in direct response to membrane stretch, and examine the role of the transmembrane pressure profile in this process. Furthermore, we show how state-dependent interactions with lipids affect the movement of TREK-2, and how stretch influences both the inner pore and selectivity filter...
March 24, 2017: Structure
#13
YinBo Zhu, FengChao Wang, HengAn Wu
The freezing and melting of low-dimensional materials, either via a first-order phase transition or without any discontinuity in thermodynamic, still remain a matter of debate. Melting (superheating) in two-dimensional (2D) ice is fundamentally different from that in bulk counterpart. Here, we perform comprehensive molecular dynamics simulations of the superheating of monolayer ice in graphene nanocapillaries to understand the nature of melting transition in 2D water/ice. We find four different superheating (melting) scenarios can happen in the superheating of monolayer square-like ice, which are closely related to the lateral pressure and the channel width...
April 7, 2017: Journal of Chemical Physics
#14
Akio Kitao, Yasutaka Nishihara
Flagellar motors utilize the motive force of protons and other ions as an energy source. To elucidate the mechanisms of ion permeation and torque generation, it is essential to investigate the structure of the motor stator complex; however, the atomic structure of the transmembrane region of the stator has not been determined experimentally. We recently constructed an atomic model structure of the transmembrane region of the Escherichia coli MotA/B stator complex based on previously published disulfide cross-linking and tryptophan scanning mutations...
2017: Methods in Molecular Biology
#15
Matthew P Harrigan, Keri A McKiernan, Veerabahu Shanmugasundaram, Rajiah Aldrin Denny, Vijay S Pande
Two-pore domain potassium (K2P) channel ion conductance is regulated by diverse stimuli that directly or indirectly gate the channel selectivity filter (SF). Recent crystal structures for the TREK-2 member of the K2P family reveal distinct "up" and "down" states assumed during activation via mechanical stretch. We performed 195 μs of all-atom, unbiased molecular dynamics simulations of the TREK-2 channel to probe how membrane stretch regulates the SF gate. Markov modeling reveals a novel "pinched" SF configuration that stretch activation rapidly destabilizes...
April 4, 2017: Scientific Reports
#16
Takaoki Koyanagi, Kevin J Cao, Geoffray Leriche, David Onofrei, Gregory P Holland, Michael Mayer, David Sept, Jerry Yang
This paper presents a new hybrid lipid that fuses the ideas of molecular tethering of lipid tails used by archaea and the integration of cholesterol groups used by eukaryotes, thereby leveraging two strategies employed by nature to increase lipid packing in membranes. Liposomes comprised of pure hybrid lipids exhibited a 5-30-fold decrease in membrane leakage of small ions and molecules compared to liposomes that used only one strategy (lipid tethering or cholesterol incorporation) to increase membrane integrity...
March 29, 2017: Chemistry: a European Journal
#17
Alisha D Caliman, Yinglong Miao, J Andrew McCammon
Activation of the first sphingosine-1-phosphate receptor (S1PR1 ) promotes permeability of the blood brain barrier, astrocyte and neuronal protection, and lymphocyte egress from secondary lymphoid tissues. Although an agonist often activates the S1PR1 , the receptor exhibits high levels of basal activity. In this study, we performed long-timescale molecular dynamics and accelerated molecular dynamics (aMD) simulations to investigate activation mechanisms of the ligand-free (apo) S1PR1 . In the aMD enhanced sampling simulations, we observed four independent events of activation, which is characterized by close interaction between Y311(7...
March 28, 2017: Protein Science: a Publication of the Protein Society
#18
Nohad Gresh, Sehr Naseem-Khan, Louis Lagardère, Jean-Philip Piquemal, Judit E Sponer, Jiri Sponer
Stacking of guanine quartets (GQs) can trigger the formation of DNA or RNA quadruple helices, which play numerous biochemical roles. The GQs are stabilized by alkali cations, mainly K(+) and Na(+), which can reside in, or channel through, the central axis of the GQ stems. Further, ion conduction through GQ wires can be leveraged for nanochemistry applications. G-quadruplex systems have been extensively studied by classical molecular dynamics (MD) simulations using pair-additive force fields or by quantum-chemical (QC) calculations...
April 13, 2017: Journal of Physical Chemistry. B
#19
Alexander J Sodt, Andrew H Beaven, Olaf S Andersen, Wonpil Im, Richard W Pastor
To change conformation, a protein must deform the surrounding bilayer. In this work, a three-dimensional continuum elastic model for gramicidin A in a lipid bilayer is shown to describe the sensitivity to thickness, curvature stress, and the mechanical properties of the lipid bilayer. A method is demonstrated to extract the gramicidin-lipid boundary condition from all-atom simulations that can be used in the three-dimensional continuum model. The boundary condition affects the deformation dramatically, potentially much more than typical variations in the material stiffness do as lipid composition is changed...
March 28, 2017: Biophysical Journal
#20
Andrew H Beaven, Andreia M Maer, Alexander J Sodt, Huan Rui, Richard W Pastor, Olaf S Andersen, Wonpil Im
Integral membrane protein function can be modulated by the host bilayer. Because biological membranes are diverse and nonuniform, we explore the consequences of lipid diversity using gramicidin A channels embedded in phosphatidylcholine (PC) bilayers composed of equimolar mixtures of di-oleoyl-PC and di-erucoyl-PC (dC18:1+dC22:1, respectively), di-palmitoleoyl-PC and di-nervonoyl-PC (dC16:1+dC24:1, respectively), and di-eicosenoyl-PC (pure dC20:1), all of which have the same average bilayer chain length. Single-channel lifetime experiments, molecular dynamics simulations, and a simple lipid compression model are used in tandem to gain insight into lipid redistribution around the channel, which partially alleviates the bilayer deformation energy associated with channel formation...
March 28, 2017: Biophysical Journal
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