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Molecular dynamics simulation channel

Moon-Ki Choi, Hyunki Kim, Byung Ho Lee, Teayeop Kim, Junsuk Rho, Moon Ki Kim, Kyunghoon Kim
Carbon nanotube (CNT) has been considered as a prominent nano-channel in cell membranes because of their prominent ion-conductance and ion-selectivity, offering agents for biomimetic channel platform. Using a coarse-grained molecular dynamics simulation, we clarify a construction mechanism of vertical CNT nano-channels in the lipid membrane for a long period, that has been difficult to observe in previous CNT-lipid interaction simulations. The result shows that both lipid coating density and length of CNT affect the suitable fabrication condition for a vertical and stable CNT-channel...
January 15, 2018: Nanotechnology
Heather B Mayes, Sangyun Lee, Andrew D White, Gregory A Voth, Jessica M J Swanson
Despite several years of research, the ion exchange mechanisms in chloride/proton antiporters and many other coupled transporters are not yet understood at the molecular level. Here, we present a novel approach to kinetic modeling and apply it to ion exchange in ClC-ec1. Our multiscale kinetic model (MKM) is developed by 1) calculating the state-to-state rate coefficients with reactive and polarizable molecular dynamics simulations, 2) optimizing these rates in a global kinetic network, and 3) predicting new electrophysiological results...
January 14, 2018: Journal of the American Chemical Society
Dorit Shemesh, Robert Benny Gerber
The photochemistry of acrylic acid is of considerable atmospheric importance. However, the mechanisms and the timescales of the reactions involved are unknown. In this work, the products, yields and reaction pathways of acrylic acid photochemistry are investigated theoretically by molecular dynamics simulations on the ππ* excited state. Two methods were used to describe the excited state: the semi-empirical OM2/MRCI and the ab initio ADC(2). Over one hundred trajectories were computed with each method. A rich variety of reaction channels including mechanisms, timescales and yields, are predicted for the single potential energy surface used...
January 11, 2018: Journal of Physical Chemistry Letters
Taylor E T Hughes, David T Lodowski, Kevin W Huynh, Aysenur Yazici, John Del Rosario, Abhijeet Kapoor, Sandip Basak, Amrita Samanta, Xu Han, Sudha Chakrapani, Z Hong Zhou, Marta Filizola, Tibor Rohacs, Seungil Han, Vera Y Moiseenkova-Bell
The transient receptor potential vanilloid 5 (TRPV5) channel is a member of the transient receptor potential (TRP) channel family, which is highly selective for Ca2+, that is present primarily at the apical membrane of distal tubule epithelial cells in the kidney and plays a key role in Ca2+ reabsorption. Here we present the structure of the full-length rabbit TRPV5 channel as determined using cryo-EM in complex with its inhibitor econazole. This structure reveals that econazole resides in a hydrophobic pocket analogous to that occupied by phosphatidylinositides and vanilloids in TRPV1, thus suggesting conserved mechanisms for ligand recognition and lipid binding among TRPV channels...
January 2018: Nature Structural & Molecular Biology
Li Ding, Yanying Wei, Libo Li, Tao Zhang, Haihui Wang, Jian Xue, Liang-Xin Ding, Suqing Wang, Jürgen Caro, Yury Gogotsi
Molecular sieving membranes with sufficient and uniform nanochannels that break the permeability-selectivity trade-off are desirable for energy-efficient gas separation, and the arising two-dimensional (2D) materials provide new routes for membrane development. However, for 2D lamellar membranes, disordered interlayer nanochannels for mass transport are usually formed between randomly stacked neighboring nanosheets, which is obstructive for highly efficient separation. Therefore, manufacturing lamellar membranes with highly ordered nanochannel structures for fast and precise molecular sieving is still challenging...
January 11, 2018: Nature Communications
Jamal Adiban, Yousef Jamali, Hashem Rafii-Tabar
CaV channels are transmembrane proteins that mediate and regulate ions fluxes across cell membranes, and they are activated in response to action potentials to allow Ca2+ influx. Since ion channels are composed of charge or polar groups, an external alternating electric field may affect the ion-selective membrane transport and the performance of the channel. In this paper, we have investigated the effect of an external GHz electric field on the dynamics of calcium ions in the selectivity filter of the CaV Ab channel...
January 11, 2018: Proteins
Han Wen, Wenjun Zheng
As a prototype cellular sensor, the TRPV1 cation channel undergoes a closed-to-open gating transition in response to various physical and chemical stimuli including noxious heat. Despite recent progress, the molecular mechanism of heat activation of TRPV1 gating remains enigmatic. Toward decrypting the structural basis of TRPV1 heat activation, we performed extensive molecular dynamics simulations (with cumulative simulation time of ∼11 μs) for the wild-type channel and a constitutively active double mutant at different temperatures (30, 60, and 72°C), starting from a high-resolution closed-channel structure of TRPV1 solved by cryo-electron microscopy...
January 9, 2018: Biophysical Journal
Junghoon Ha, Yu Xu, Takeharu Kawano, Tyler Hendon, Lia Baki, Sumanta Garai, Andreas Papapetropoulos, Ganesh Thakur, Leigh D Plant, Diomedes E Logothetis
Inwardly rectifying potassium (Kir) channels establish and regulate the resting membrane potential of excitable cells in the heart, brain and other peripheral tissues. Phosphatidylinositol 4,5-bisphosphate (PIP2) is a key direct activator of ion channels, including Kir channels. The gasotransmitter carbon monoxide has been shown to regulate Kir channel activity by altering channel-PIP2 interactions.  Here, we tested in two cellular models the effects and mechanism of action of another gasotransmitter, hydrogen sulfide (H2S), thought to play a key role in cellular responses under ischemic conditions...
January 9, 2018: Journal of Biological Chemistry
Feng Yu
Microsolvated bimolecular nucleophilic substitution (SN2) reaction of monohydrated hydrogen peroxide anion [HOO-(H2O)] with methyl chloride (CH3Cl) has been investigated with direct chemical dynamics simulations at the M06-2X/6-31+G(d,p) level of theory. Dynamic exit-channel pathways and corresponding reaction mechanisms at the atomic level are revealed in detail. Accordingly, a product distribution of 0.85:0.15 is obtained for Cl-:Cl-(H2O), which is consistent with a previous experiment [D. L. Thomsen et al...
January 7, 2018: Journal of Chemical Physics
Alexander C Forse, Miguel I Gonzalez, Rebecca L Siegelman, Velencia J Witherspoon, Sudi Jawahery, Rocio Mercado, Phillip J Milner, Jeffrey D Martell, Berend Smit, Bernhard Blümich, Jeffrey R Long, Jeffrey A Reimer
Metal-organic frameworks are promising materials for energy-efficient gas separations, but little is known about the diffusion of adsorbates in materials featuring one-dimensional porosity at the nanoscale. An understanding of the interplay between framework structure and gas diffusion is crucial for the practical application of these materials as adsorbents or in mixed-matrix membranes, since the rate of gas diffusion within the adsorbent pores impacts the required size (and therefore cost) of the adsorbent column or membrane...
January 4, 2018: Journal of the American Chemical Society
Ning Xiang, Yuan Lyu, Xiao Zhu, Ganesan Narsimhan
Some amyloid related proteins/peptides are involved in aggregation and pore formation in phospholipid membranes (cell membranes), which result in a variety of neurological disorders such as Alzheimer's disease, Parkinson's disease and Huntington disease. In this research, the mechanism of pore formation by β amyloid (Aβ) peptides was investigated using molecular dynamics simulation by simulating the interaction of the Aβ(11-42) peptide, with a lipid membrane and the potential of the mean force of interaction was evaluated...
January 4, 2018: Physical Chemistry Chemical Physics: PCCP
Panisak Boonamnaj, Pornthep Sompornpisut
The voltage-gated proton-selective channel (Hv1) conducts protons in response to changes in membrane potential. The Hv1 protein forms dimers in the membrane. Crystal structures of Hv1 channels have revealed that the primary contacts between the two monomers are in the C-terminal domain (CTD), which forms a coiled-coil structure. The role of Hv1-CTD in channel assembly and activity is not fully understood. Here, molecular dynamics (MD) simulations of full-length and truncated CTD models of human and mouse Hv1 channels reveal a strong contribution of the CTD to the packing of the transmembrane domains...
January 1, 2018: Journal of Physical Chemistry. B
Guilherme H M Salvador, Juliana I Dos Santos, Rafael J Borges, Marcos R M Fontes
The myotoxic mechanism for PLA2-like toxins has been proposed recently to be initiated by an allosteric change induced by a fatty acid binding to the protein, leading to the alignment of the membrane docking site (MDoS) and membrane disrupting site (MDiS). Previous structural studies performed by us demonstrated that MjTX-II, a PLA2-like toxin isolated from Bothrops moojeni, presents a different mode of ligand-interaction, with its hydrophobic channels caused by natural amino acid substitutions and an insertion...
December 26, 2017: Biochimica et Biophysica Acta
Qiwen Liao, Shengnan Li, Shirley Weng In Siu, Binrui Yang, Chen Huang, Judy Yuet-Wa Chan, Jean-Étienne Morlighem, Clarence Tsun Ting Wong, Gandhi Radis-Baptista, Simon Ming-Yuen Lee
Palythoa caribaeorum (class Anthozoa) is a zoanthid that together jellyfishes, hydra, and sea anemones, which are venomous and predatory, belongs to the Phyllum Cnidaria. The distinguished feature in these marine animals is the cnidocytes in the body tissues, responsible for toxin production and injection that are used majorly for prey capture and defense. With exception for other anthozoans, the toxin cocktails of zoanthids have been scarcely studied and are poorly known. Here, based on the analysis of P. caribaeorum transcriptome, numerous predicted venom-featured polypeptides were identified, including allergens, neurotoxins, membrane-active and Kunitz-like peptides (PcKuz)...
December 29, 2017: Journal of Proteome Research
Kshatresh Dutta Dubey, Sason Shaik
The driving force for the electron transfer (ET) step in the catalytic cycle of cytochrome P450BM3, is investigated using three sets of 1 µs molecular dynamic simulations for the resting state of P450 in complex with the flavin (FMN) in the reductase domain. These sets involve: (i) substrate-free (SF), (ii) substrate (N-palmitoyl glycine, i.e NPG)-bound (SB), and (iii) SB with the semiquinone radical-anion (SQ-) of FMN. Starting from the X-ray structure of the SF heme domain, we observe that the α1 helix (of the reductase) and the C helix (of the heme) undergo reorientation to a parallel orientation, which is the thermochemically stable form...
December 26, 2017: Journal of the American Chemical Society
Zhijun Xu, Weilong Zhao, Ziqiu Wang, Yang Yang, Nita Sahai
Bone is a hierarchical biocomposite material in which a collagen fibril matrix self-assembled in a three-dimensional (3-D) pseudohexagonal array controls many important processes in mineralization such as providing the pathways by which calcium and phosphate species are delivered and a template for the earliest nucleation sites, determining the spatial distribution of the mineral and the topology for binding of associated non-collagenous proteins. However, the structural characteristics of collagen molecules in the fibril remain unclear at the atomic level...
December 20, 2017: Physical Chemistry Chemical Physics: PCCP
Rebecca J Howard, Vincenzo Carnevale, Lucie Delemotte, Ute A Hellmich, Brad S Rothberg
Ion translocation across biological barriers is a fundamental requirement for life. In many cases, controlling this process-for example with neuroactive drugs-demands an understanding of rapid and reversible structural changes in membrane-embedded proteins, including ion channels and transporters. Classical approaches to electrophysiology and structural biology have provided valuable insights into several such proteins over macroscopic, often discontinuous scales of space and time. Integrating these observations into meaningful mechanistic models now relies increasingly on computational methods, particularly molecular dynamics simulations, while surfacing important challenges in data management and conceptual alignment...
December 16, 2017: Biochimica et Biophysica Acta
Jos Eacute Silva, Mario Roberto Meneghetti
New aspects of the formation and growth mechanism of gold nanorods (AuNRs) during seed-mediated colloidal synthesis are revealed from the results of molecular dynamics simulations. The model systems consist of cetyltrimethylammonium bromide (CTAB) units adsorbed on low-index (Au(110), Au(100) and Au(111)) and high-index (Au(250)) gold surfaces. The CTAB units are adsorbed as adjacent cylindrical micelles when the relative number of adsorbed bromide ions is small. At later AuNR growth stages, the number of bromide ions increases as the [AuBr2]- species pass through the channels between the adsorbed micelles on the gold surface...
December 15, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
Zonglin Gu, Leigh D Plant, Xuanyu Meng, Jose Manuel Perez-Aguilar, Zegao Wang, Mingdong Dong, Diomedes E Logothetis, Ruhong Zhou
Molybdenum disulfide (MoS2) nanomaterial has recently found various applications in the biomedical field mainly due to its outstanding physicochemical properties. However, little is known about its interactions with biological systems at the atomic level, which intimately relates to the biocompatibility of the material. To provide insights into the effects of MoS2 in biological entities, we investigated the interactions of MoS2 with proteins from a functionally important membrane family, the ubiquitous potassium (K+) channels...
December 13, 2017: ACS Nano
Jing Yang, Alessandro Piai, Hong-Bin Shen, James J Chou
Nuclear magnetic resonance (NMR) has been an important source of structural restraints for solving structures of oligomeric transmembrane domains (TMDs) of cell surface receptors and viral membrane proteins. In NMR studies, oligomers are assembled using inter-protomer distance restraints. But, for oligomers that are higher than dimer, these distance restraints all have two-fold directional ambiguity, and resolving such ambiguity often requires time-consuming trial-and-error calculations using restrained molecular dynamics (MD) with simulated annealing (SA)...
December 12, 2017: Scientific Reports
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