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Molecular dynamics simulation channel

Parisa Akhshi, Gang Wu
We have applied the umbrella sampling (US) method in all-atom molecular dynamics (MD) simulations to obtain potential of mean force (PMF) profiles for ion transport through three representative G-quadruplex DNA channels: [d(TG4T)]4, [d(G3T4G4)]2, and d[G4(T4G4)3]. The US MD results are in excellent agreement with those obtained previously with the adaptive biasing force (ABF) method. We then utilized the unique features in the US MD method to investigate multi-ion effects in [d(G3T4G4)]2 and discovered that the concerted ion movement is crucial for fully explaining the unusual experimental results on ion movement in this particular G-quadruplex system...
March 22, 2017: Physical Chemistry Chemical Physics: PCCP
Chan Cao, Shuqing Wang, Tanxing Cui, Xun-Cheng Su, James J Chou
The calcium (Ca(2+)) uniporter of mitochondria is a holocomplex consisting of the Ca(2+)-conducting channel, known as mitochondrial calcium uniporter (MCU), and several accessory and regulatory components. A previous electrophysiology study found that the uniporter has high Ca(2+) selectivity and conductance and this depends critically on the conserved amino acid sequence motif, DXXE (Asp-X-X-Glu) of MCU. A recent NMR structure of the MCU channel from Caenorhabditis elegans revealed that the DXXE forms two parallel carboxylate rings at the channel entrance that seem to serve as the ion selectivity filter, although direct ion interaction of this structural motif has not been addressed...
March 21, 2017: Proceedings of the National Academy of Sciences of the United States of America
A Simon, M Rapacioli, G Rouaut, G Trinquier, F X Gadéa
We present dynamical studies of the dissociation of polycyclic aromatic hydrocarbon (PAH) radical cations in their ground electronic states with significant internal energy. Molecular dynamics simulations are performed, the electronic structure being described on-the-fly at the self-consistent-charge density functional-based tight binding (SCC-DFTB) level of theory. The SCC-DFTB approach is first benchmarked against DFT results. Extensive simulations are achieved for naphthalene [Formula: see text], pyrene [Formula: see text] and coronene [Formula: see text] at several energies...
April 28, 2017: Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences
Rodolfo Briones, Camilo Aponte-Santamaría, Bert L de Groot
Hydrophobic matching, lipid sorting, and protein oligomerization are key principles by which lipids and proteins organize in biological membranes. The Aquaporin-0 channel (AQP0), solved by electron crystallography (EC) at cryogenic temperatures, is one of the few protein-lipid complexes of which the structure is available in atomic detail. EC and room-temperature molecular dynamics (MD) of dimyristoylglycerophosphocholine (DMPC) annular lipids around AQP0 show similarities, however, crystal-packing and temperature might affect the protein surface or the lipids distribution...
2017: Frontiers in Physiology
Chattip Kurehong, Chalermpol Kanchanawarin, Busaba Powthongchin, Panchika Prangkio, Gerd Katzenmeier, Chanan Angsuthanasombat
The Bordetella pertussis CyaA-hemolysin (CyaA-Hly) domain was previously demonstrated to be an important determinant for hemolysis against target erythrocytes and ion-channel formation in planar lipid bilayers (PLBs). Here, net-charge variations in the pore-lining helix of thirteen related RTX cytolysins including CyaA-Hly were revealed by amino acid sequence alignments, reflecting their different degrees of hemolytic activity. To analyze possible functional effects of net-charge alterations on hemolytic activity and channel formation of CyaA-Hly, specific mutations were made at Gln(574) or Glu(581) in its pore-lining α3 of which both residues are highly conserved Lys in the three highly active RTX cytolysins (i...
March 16, 2017: Toxins
Patrick O Saboe, Chiara Rapisarda, Shreyas Kaptan, Yu-Shan Hsiao, Samantha R Summers, Rita De Zorzi, Danijela Dukovski, Jiaheng Yu, Bert L de Groot, Manish Kumar, Thomas Walz
Compared to other aquaporins (AQPs), lens-specific AQP0 is a poor water channel, and its permeability was reported to be pH-dependent. To date, most water conduction studies on AQP0 were performed on protein expressed in Xenopus oocytes, and the results may therefore also reflect effects introduced by the oocytes themselves. Experiments with purified AQP0 reconstituted into liposomes are challenging because the water permeability of AQP0 is only slightly higher than that of pure lipid bilayers. By reconstituting high amounts of AQP0 and using high concentrations of cholesterol to reduce the permeability of the lipid bilayer, we improved the signal-to-noise ratio of water permeability measurements on AQP0 proteoliposomes...
March 14, 2017: Biophysical Journal
Monika R VanGordon, Gaurav Gyawali, Steven W Rick, Susan B Rempe
Channelrhodopsins (ChR1 and ChR2) are light-activated ion channels that enable photomobility of microalgae from the genus Chlamydomonas. Despite common use of ChR2 in optogenetics for selective control and monitoring of individual neurons in living tissue, the protein structures remain unresolved. Instead, a crystal structure of the ChR chimera (C1C2), an engineered combination of helices I-V from ChR1, without its C-terminus, and helices VI-VII from ChR2, is used as a template for ChR2 structure prediction...
March 14, 2017: Biophysical Journal
Weixin Qian, Kentaro Doi, Satoyuki Kawano
Electrokinetic phenomena in micro/nanofluidic channels have attracted considerable attention because precise control of molecular transport in liquids is required to optically and electrically capture the behavior of single molecules. However, the detailed mechanisms of polymer transport influenced by electroosmotic flows and electric fields in micro/nanofluidic channels have not yet been elucidated. In this study, a Langevin dynamics simulation was used to investigate the electrokinetic transport of single-stranded DNA (ssDNA) in a cylindrical nanochannel, employing a coarse-grained bead-spring model that quantitatively reproduced the radius of gyration, diffusion coefficient, and electrophoretic mobility of the polymer...
March 14, 2017: Biophysical Journal
Evelyne Deplazes
Disulfide-rich peptides isolated from the venom of arthropods and marine animals are a rich source of potent and selective modulators of ion channels. This makes these peptides valuable lead molecules for the development of new drugs to treat neurological disorders. Consequently, much effort goes into understanding their mechanism of action. This paper presents an overview of how molecular simulations have been used to study the interactions of disulfide-rich venom peptides with ion channels and membranes. The review is focused on the use of docking, molecular dynamics simulations, and free energy calculations to (i) predict the structure of peptide-channel complexes; (ii) calculate binding free energies including the effect of peptide modifications; and (iii) study the membrane-binding properties of disulfide-rich venom peptides...
February 27, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
Catarina A Carvalheda, Andrei V Pisliakov
Heme-copper oxidases are membrane protein complexes that catalyse the final step of the aerobic respiration, namely the reduction of oxygen to water. The energy released during catalysis is coupled to the active translocation of protons across the membrane, which contributes to the establishment of an electrochemical gradient that is used for ATP synthesis. The distinctive C-type (or cbb3) cytochrome c oxidases, which are mostly present in proteobacteria, exhibit a number of unique structural and functional features, including high catalytic activity at low oxygen concentrations...
March 1, 2017: Biochimica et Biophysica Acta
Hadi Alizadeh, Jamal Davoodi, Hashem Rafii-Tabar
Connexins are a 21-member membrane protein family constituting channels evolved in direct communication between adjacent cells by passaging cytoplasmic molecules and ions. Hexametrical assembly of connexin proteins in plasma membrane forms a wide aqueous pore known as connexin hemichannel. These hemichannels mediate cytoplasm and extracellular milieu communication both in many external tissues and in the central nervous system. In this study, a series of molecular dynamics simulations has been performed to investigate the effect of applied static and alternating electric fields on the stability and conformation of human connexin26 hemichannel...
February 20, 2017: Journal of Molecular Graphics & Modelling
Karunakar Reddy Pothula, Naresh N Dhanasekar, Usha Lamichhane, Farhan Younas, Daniel Pletzer, Roland Benz, Mathias Winterhalter, Ulrich Kleinekathöfer
The OccK protein subfamily located in the outer membrane of Pseudomonas aeruginosa contains dynamic channels with several conformational states that range from open to closed forms. The molecular determinants of the OccK channels that contribute to the diverse gating has, however, remained elusive so far. Performing molecular dynamics simulations (MD) on OccK5 (OpdH) as an example, local fluctuations of loop L7 mediated by a single residue were identified that effectively gate the channel. The features of this gate residue were studied by single-channel electrophysiology and site-directed mutagenesis demonstrating that this gate residue indeed confers unique gating properties to the OccK channels...
March 3, 2017: Journal of Physical Chemistry. B
Jing Kong, Zheng Bo, Huachao Yang, Jinyuan Yang, Xiaorui Shuai, Jianhua Yan, Kefa Cen
The behavior of ion diffusion in nano-confined spaces and its temperature dependence provide important fundamental information about electric double-layer capacitors (EDLCs) employing nano-sized active materials. In this work, the ion diffusion coefficients of NaCl electrolyte confined within neutral and charged graphene nanochannels at different temperatures are investigated using molecular dynamics simulations. The results show that ions confined in neutral nanochannels diffuse faster (along the graphene surfaces) than those in bulk solution, which could be attributed to the relatively smaller concentration in confined spaces and the solvophobic nature of graphene surfaces...
March 3, 2017: Physical Chemistry Chemical Physics: PCCP
Lucia Kocincová, Miroslava Jarešová, Jan Byška, Július Parulek, Helwig Hauser, Barbora Kozlíková
BACKGROUND: Protein function is determined by many factors, namely by its constitution, spatial arrangement, and dynamic behavior. Studying these factors helps the biochemists and biologists to better understand the protein behavior and to design proteins with modified properties. One of the most common approaches to these studies is to compare the protein structure with other molecules and to reveal similarities and differences in their polypeptide chains. RESULTS: We support the comparison process by proposing a new visualization technique that bridges the gap between traditionally used 1D and 3D representations...
February 15, 2017: BMC Bioinformatics
M A Nosir, L Martin-Gondre, G A Bocan, R Díez Muiño
We present an extensive theoretical study of N2 adsorption mechanisms on an Fe(111) surface. We combine the static analysis of a six-dimensional potential energy surface (6D-PES), based on ab initio density functional theory (DFT) calculations for the system, with quasi-classical trajectory (QCT) calculations to simulate the adsorption dynamics. There are four molecular adsorption states, usually called γ, δ, α, and ε, arising from our DFT calculations. We find that N2 adsorption in the γ-state is non-activated, while the threshold energy is associated with the entrance channel for the other three adsorption states...
February 28, 2017: Physical Chemistry Chemical Physics: PCCP
Yihao Zhang, Krithika Abiraman, He Li, David M Pierce, Anastasios V Tzingounis, George Lykotrafitis
Super-resolution microscopy recently revealed that, unlike the soma and dendrites, the axon membrane skeleton is structured as a series of actin rings connected by spectrin filaments that are held under tension. Currently, the structure-function relationship of the axonal structure is unclear. Here, we used atomic force microscopy (AFM) to show that the stiffness of the axon plasma membrane is significantly higher than the stiffnesses of dendrites and somata. To examine whether the structure of the axon plasma membrane determines its overall stiffness, we introduced a coarse-grain molecular dynamics model of the axon membrane skeleton that reproduces the structure identified by super-resolution microscopy...
February 2017: PLoS Computational Biology
Ishan Ghai, Alessandro Pira, Mariano Andrea Scorciapino, Igor Bodrenko, Lorraine Benier, Matteo Ceccarelli, Mathias Winterhalter, Richard Wagner
A major challenge in the discovery of the new antibiotics against Gram-negative bacteria is to achieve sufficiently fast permeation in order to avoid high doses causing toxic side effects. So far, suitable assays for quantifying the uptake of charged antibiotics into bacteria are lacking. We apply an electrophysiological zero-current assay using concentration gradients of β-lactamase inhibitors combined with single-channel conductance to quantify their flux rates through OmpF. Molecular dynamic simulations provide in addition details on the interactions between the nanopore wall and the charged solutes...
March 6, 2017: Journal of Physical Chemistry Letters
Irina Volokhina, Yury Gusev, Svyatoslav Mazilov, Yelizaveta Moiseeva, Mikhail Chumakov
The single-stranded transfer DNA from the Ti plasmid of the soil bacteria Agrobacterium nonspecifically integrates into the plant chromosome and is inherited at subsequent cell divisions. How it is transferred across host membranes is unknown, but it is believed that VirE2 proteins form a membrane-spanning pore or channel in a lipid bilayer and possibly mediate the delivery of the single-stranded transfer DNA-VirD2-VirE2 complex to the plant cell chromosomes. The aim of this work was to perform a computer simulation of VirE2's pore-forming capacity and an evaluation of constructed VirE2 complexes...
February 9, 2017: Computational Biology and Chemistry
Padmani Sandhu, Yusuf Akhter
Iron is an essential metal ion required for the various physiological activities of bacteria. The pathogenic bacteria remain dependent on the host cell for their iron requirements and evolved with specialized scavenging machinery in the form of iron chelating siderophores. Mycobacterium tuberculosis has two types of siderophore molecules, mycobactin and carboxymycobactin. These are synthesized inside bacterial cells and need to be transported outside by specialized membrane associated proteins. MmpL5-MmpS5 (mycobacterial membrane protein large5-mycobacterial membrane protein small5) complex has been linked to the export of non-ferrated siderophores to extracellular environment but the precise molecular mechanism involved was largely unknown...
February 14, 2017: Journal of Inorganic Biochemistry
Birgit Stallmeyer, Johanna Kuß, Stefan Kotthoff, Sven Zumhagen, Kirsty S Vowinkel, Susanne Rinne, Lina A Matschke, Corinna Friedrich, Ellen Schulze-Bahr, Stephan Rust, Guiscard Seebohm, Niels Decher, Eric Schulze-Bahr
Rationale: Familial sinus node and atrioventricular (AV) conduction dysfunction is a rare disorder that leads to paroxysmal dizziness, fatigue and syncope due to a temporarily or permanent reduced heart rate. To date, only a few genes for familial sinus and/or AV conduction dysfunction are known and the majority of cases remain etiologically unresolved. Objective: We aim to identify the disease gene in a large three-generation family (n=25) with autosomal dominant sinus node dysfunction (SND) and AV block (AVB) and to characterise the mutation-related pathomechanisms in familial SND+AVB...
February 20, 2017: Circulation Research
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