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https://www.readbyqxmd.com/read/27907142/ibisa_tools-a-computational-toolkit-for-ion-binding-state-analysis-in-molecular-dynamics-trajectories-of-ion-channels
#1
Kota Kasahara, Kengo Kinoshita
Ion conduction mechanisms of ion channels are a long-standing conundrum. Although the molecular dynamics (MD) method has been extensively used to simulate ion conduction dynamics at the atomic level, analysis and interpretation of MD results are not straightforward due to complexity of the dynamics. In our previous reports, we proposed an analytical method called ion-binding state analysis to scrutinize and summarize ion conduction mechanisms by taking advantage of a variety of analytical protocols, e.g., the complex network analysis, sequence alignment, and hierarchical clustering...
2016: PloS One
https://www.readbyqxmd.com/read/27907003/mapping-cholesterol-interaction-sites-on-serotonin-transporter-through-coarse-grained-molecular-dynamics
#2
Mariarosaria Ferraro, Matteo Masetti, Maurizio Recanatini, Andrea Cavalli, Giovanni Bottegoni
Serotonin transporter (SERT) modulates serotonergic signaling via re-uptake of serotonin in pre-synaptic cells. The inclusion in cholesterol-enriched membrane domains is crucial for SERT activity, suggesting a cross-talk between the protein and the sterol. Here, we develop a protocol to identify potential cholesterol interaction sites coupling statistical analysis to multi-microsecond coarse-grained molecular dynamics simulations of SERT in a previously validated raft-like membrane model. Six putative sites were found, including a putative CRAC motif on TM4 and a CARC motif on TM10...
2016: PloS One
https://www.readbyqxmd.com/read/27905555/the-complex-nature-of-calcium-cation-interactions-with-phospholipid-bilayers
#3
Adéla Melcrová, Sarka Pokorna, Saranya Pullanchery, Miriam Kohagen, Piotr Jurkiewicz, Martin Hof, Pavel Jungwirth, Paul S Cremer, Lukasz Cwiklik
Understanding interactions of calcium with lipid membranes at the molecular level is of great importance in light of their involvement in calcium signaling, association of proteins with cellular membranes, and membrane fusion. We quantify these interactions in detail by employing a combination of spectroscopic methods with atomistic molecular dynamics simulations. Namely, time-resolved fluorescent spectroscopy of lipid vesicles and vibrational sum frequency spectroscopy of lipid monolayers are used to characterize local binding sites of calcium in zwitterionic and anionic model lipid assemblies, while dynamic light scattering and zeta potential measurements are employed for macroscopic characterization of lipid vesicles in calcium-containing environments...
December 1, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27902924/simple-mechanisms-of-early-life-simulation-model-on-the-origin-of-semi-cells
#4
Adrian Klein, Martin Bock, Wolfgang Alt
The development of first cellular structures played an important role in the early evolution of life. Early evolution of life probably took place on a molecular level in a reactive environment. The iron-sulfur theory postulates the formation of cell-like structures on catalytic surfaces. Experiments show that H2S together with FeS and other metallic centers drive auto-catalytic surface reactions, in which organic molecules such as pyruvic and amino acids occur. It is questionable which mechanisms are needed to form cell-like structures under these conditions...
November 27, 2016: Bio Systems
https://www.readbyqxmd.com/read/27901172/conformational-states-of-hamp-domains-interacting-with-sensory-rhodopsin-membrane-systems-an-integrated-all-atom-and-coarse-grained-molecular-dynamics-simulation-approach
#5
Bikash Ranjan Sahoo, Toshimichi Fujiwara
Understanding the downstream signaling mechanism of sensory rhodopsin and its cognate transducer complex (srII-htrII) has long been a challenge in the field of photoreceptor research. Here, an integration of all-atom and coarse-grained (CG) molecular dynamics (MD) simulations in different srII-htrII complex states is carried out. It is shown that the cytoplasmic four-helix HAMP dimer gives rise to a gear-box model interaction with discrete hydrophobic packing in Natronomonas pharaonis (Np). Structural analysis in all-atom and CG-MD reveals a stable conformational state in the physiological environment (323 K and 1...
November 30, 2016: Molecular BioSystems
https://www.readbyqxmd.com/read/27901162/molecular-dynamics-simulations-and-kelvin-probe-force-microscopy-to-study-of-cholesterol-induced-electrostatic-nanodomains-in-complex-lipid-mixtures
#6
E Drolle, W F D Bennett, K Hammond, E Lyman, M Karttunen, Z Leonenko
The molecular arrangement of lipids and proteins within biomembranes and monolayers gives rise to complex film morphologies as well as regions of distinct electrical surface potential, topographical and electrostatic nanoscale domains. To probe these nanodomains in soft matter is a challenging task both experimentally and theoretically. This work addresses the effects of cholesterol, lipid composition, lipid charge, and lipid phase on the monolayer structure and the electrical surface potential distribution...
November 30, 2016: Soft Matter
https://www.readbyqxmd.com/read/27897200/lipid-ii-independent-antimicrobial-mechanism-of-nisin-depends-on-its-crowding-and-degree-of-oligomerization
#7
Ashutosh Prince, Padmani Sandhu, Pankaj Kumar, Eva Dash, Shingarika Sharma, Manoranjan Arakha, Suman Jha, Yusuf Akhter, Mohammed Saleem
Nisin inhibits bacterial growth by generating pores in cell membrane and interrupting cell-wall biosynthesis through specific lipid II interaction. However, the role of the hinge region and C-terminus residues of the peptide in antibacterial action of nisin is largely unknown. Here, using molecular dynamics simulations and experimental approach, we report that at high concentration regimes of nisin, interaction with phospholipids may equally deform the bacterial cell membranes even under significantly varying amounts of lipid-II...
November 29, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27894676/a-multiscale-biomechanical-model-of-platelets-correlating-with-in-vitro-results
#8
Peng Zhang, Li Zhang, Marvin J Slepian, Yuefan Deng, Danny Bluestein
Using dissipative particle dynamics (DPD) combined with coarse grained molecular dynamics (CGMD) approaches, we developed a multiscale deformable platelet model to accurately describe the molecular-scale intra-platelet constituents and biomechanical properties of platelets in blood flow. Our model includes the platelet bilayer membrane, cytoplasm and an elaborate elastic cytoskeleton. Correlating numerical simulations with published in-vitro experiments, we validated the biorheology of the cytoplasm, the elastic response of membrane to external stresses, and the stiffness of the cytoskeleton actin filaments, resulting in an accurate representation of the molecular-level biomechanical microstructures of platelets...
November 11, 2016: Journal of Biomechanics
https://www.readbyqxmd.com/read/27886553/mechanical-stress-regulates-transport-in-a-compliant-3d-model-of-the-blood-brain-barrier
#9
Paul P Partyka, George A Godsey, John R Galie, Mary C Kosciuk, Nimish K Acharya, Robert G Nagele, Peter A Galie
Transport of fluid and solutes is tightly controlled within the brain, where vasculature exhibits a blood-brain barrier and there is no organized lymphatic network facilitating waste transport from the interstitial space. Here, using a compliant, three-dimensional co-culture model of the blood-brain barrier, we show that mechanical stimuli exerted by blood flow mediate both the permeability of the endothelial barrier and waste transport along the basement membrane. Application of both shear stress and cyclic strain facilitates tight junction formation in the endothelial monolayer, with and without the presence of astrocyte endfeet in the surrounding matrix...
November 17, 2016: Biomaterials
https://www.readbyqxmd.com/read/27886543/interactions-among-triphenyltin-degradation-phospholipid-synthesis-and-membrane-characteristics-of-bacillus-thuringiensis-in-the-presence-of-d-malic-acid
#10
Linlin Wang, Wenying Yi, Jinshao Ye, Huaming Qin, Yan Long, Meng Yang, Qusheng Li
Degradation pathway and surface biosorption of triphenyltin (TPT) by effective microbes have been investigated in the past. However, unclear interactions among membrane components and TPT binding and transport are still obstacles to understanding TPT biotransformation. To reveal the mechanism involved, the phospholipid expression, membrane potential, cellular mechanism and molecular dynamics between TPT and fatty acids (FAs) during the TPT degradation process in the presence of d-malic acid (DMA) were studied...
November 22, 2016: Chemosphere
https://www.readbyqxmd.com/read/27884599/influence-of-sequence-and-lipid-type-on-membrane-perturbation-by-human-and-rat-amyloid-%C3%AE-peptide-1-42
#11
Anne M Brown, David R Bevan
The hallmark characteristics of plaque formation and neuronal cell death in Alzheimer's disease (AD) are caused principally by the amyloid β-peptide (Aβ). Aβ sequence and lipid composition are essential variables to consider when elucidating the impact of biological membranes on Aβ structure and the effect of Aβ on membrane integrity. Atomistic molecular dynamics simulations testing two Aβ sequences, human and rat Aβ (HAβ and RAβ, respectively), and five lipid types were performed to assess the effect of these variables on membrane perturbation and potential link to AD phenotype differences based on differences in sequence...
November 21, 2016: Archives of Biochemistry and Biophysics
https://www.readbyqxmd.com/read/27881302/crystal-structure-of-a-full-length-human-tetraspanin-reveals-a-cholesterol-binding-pocket
#12
Brandon Zimmerman, Brendan Kelly, Brian J McMillan, Tom C M Seegar, Ron O Dror, Andrew C Kruse, Stephen C Blacklow
Tetraspanins comprise a diverse family of four-pass transmembrane proteins that play critical roles in the immune, reproductive, genitourinary, and auditory systems. Despite their pervasive roles in human physiology, little is known about the structure of tetraspanins or the molecular mechanisms underlying their various functions. Here, we report the crystal structure of human CD81, a full-length tetraspanin. The transmembrane segments of CD81 pack as two largely separated pairs of helices, capped by the large extracellular loop (EC2) at the outer membrane leaflet...
November 3, 2016: Cell
https://www.readbyqxmd.com/read/27879668/structure-functional-basis-of-ion-transport-in-sodium-calcium-exchanger-ncx-proteins
#13
REVIEW
Moshe Giladi, Reut Shor, Michal Lisnyansky, Daniel Khananshvili
The membrane-bound sodium-calcium exchanger (NCX) proteins shape Ca(2+) homeostasis in many cell types, thus participating in a wide range of physiological and pathological processes. Determination of the crystal structure of an archaeal NCX (NCX_Mj) paved the way for a thorough and systematic investigation of ion transport mechanisms in NCX proteins. Here, we review the data gathered from the X-ray crystallography, molecular dynamics simulations, hydrogen-deuterium exchange mass-spectrometry (HDX-MS), and ion-flux analyses of mutants...
November 22, 2016: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/27874097/molecular-insight-into-affinities-of-gallated-and-nongallated-proanthocyanidins-dimers-to-lipid-bilayers
#14
Wei Zhu, Le Xiong, Jinming Peng, Xiangyi Deng, Jun Gao, Chun-Mei Li
Experimental studies have proved the beneficial effects of proanthocyanidins (Pas) relating to interaction with the cell membrane. But the detailed mechanisms and structure-function relationship was unclear. In present study, molecular dynamics (MD) simulations were used to study the interactions of four PA dimers with a lipid bilayer composed of 1:1 mixed 1-palmitoyl-2-oleoyl phosphatidylcholine (POPC) and 1-palmitoyl-2-oleoyl phosphatidylethanolamine (POPE). The results showed that the gallated PA dimers had much higher affinities to the bilayer with lower binding free energies compared with nongallated PA dimers...
November 22, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27874065/antimicrobial-peptide-potency-is-facilitated-by-greater-conformational-flexibility-when-binding-to-gram-negative-bacterial-inner-membranes
#15
Sarah-Beth T A Amos, Louic S Vermeer, Philip M Ferguson, Justyna Kozlowska, Matthew Davy, Tam T Bui, Alex F Drake, Christian D Lorenz, A James Mason
The interaction of antimicrobial peptides (AMPs) with the inner membrane of Gram-negative bacteria is a key determinant of their abilities to exert diverse bactericidal effects. Here we present a molecular level understanding of the initial target membrane interaction for two cationic α-helical AMPs that share structural similarities but have a ten-fold difference in antibacterial potency towards Gram-negative bacteria. The binding and insertion from solution of pleurocidin or magainin 2 to membranes representing the inner membrane of Gram-negative bacteria, comprising a mixture of 128 anionic and 384 zwitterionic lipids, is monitored over 100 ns in all atom molecular dynamics simulations...
November 22, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27872296/mechanism-of-gating-by-calcium-in-connexin-hemichannels
#16
William Lopez, Jayalakshmi Ramachandran, Abdelaziz Alsamarah, Yun Luo, Andrew L Harris, Jorge E Contreras
Aberrant opening of nonjunctional connexin hemichannels at the plasma membrane is associated with many diseases, including ischemia and muscular dystrophy. Proper control of hemichannel opening is essential to maintain cell viability and is achieved by physiological levels of extracellular Ca(2+), which drastically reduce hemichannel activity. Here we examined the role of conserved charged residues that form electrostatic networks near the extracellular entrance of the connexin pore, a region thought to be involved in gating rearrangements of hemichannels...
November 21, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27870912/atp-hydrolysis-induced-conformational-changes-in-the-vitamin-b12-transporter-btucd-revealed-by-md-simulations
#17
Chao Pan, Jingwei Weng, Wenning Wang
ATP binding cassette (ABC) transporters utilize the energy of ATP hydrolysis to uni-directionally transport substrates across cell membrane. ATP hydrolysis occurs at the nucleotide-binding domain (NBD) dimer interface of ABC transporters, whereas substrate translocation takes place at the translocation pathway between the transmembrane domains (TMDs), which is more than 30 angstroms away from the NBD dimer interface. This raises the question of how the hydrolysis energy released at NBDs is "transmitted" to trigger the conformational changes at TMDs...
2016: PloS One
https://www.readbyqxmd.com/read/27866853/functional-annotation-of-ion-channel-structures-by-molecular-simulation
#18
Jemma L Trick, Sivapalan Chelvaniththilan, Gianni Klesse, Prafulla Aryal, E Jayne Wallace, Stephen J Tucker, Mark S P Sansom
Ion channels play key roles in cell membranes, and recent advances are yielding an increasing number of structures. However, their functional relevance is often unclear and better tools are required for their functional annotation. In sub-nanometer pores such as ion channels, hydrophobic gating has been shown to promote dewetting to produce a functionally closed (i.e., non-conductive) state. Using the serotonin receptor (5-HT3R) structure as an example, we demonstrate the use of molecular dynamics to aid the functional annotation of channel structures via simulation of the behavior of water within the pore...
November 8, 2016: Structure
https://www.readbyqxmd.com/read/27862971/structural-snapshots-of-the-%C3%AE-barrel-assembly-machinery
#19
REVIEW
Jeremy Bakelar, Susan K Buchanan, Nicholas Noinaj
The β-barrel assembly machinery (BAM) is a multi-component complex responsible for the biogenesis of β-barrel outer membrane proteins (OMPs) in Gram-negative bacteria, with conserved systems in both mitochondria and chloroplasts. Given its importance in the integrity of the outer membrane and in the assembly of surface exposed virulence factors, BAM is an attractive therapeutic target against pathogenic bacteria, particularly multi-drug resistant strains. While the mechanism for how BAM functions remains elusive, previous structural studies have described each of the individual components of BAM, offering only a few clues to how the complex functions...
November 14, 2016: FEBS Journal
https://www.readbyqxmd.com/read/27862455/ph-gated-chloride-transport-by-triazine-based-tripodal-semicage
#20
Arundhati Roy, Debasis Saha, Prashant Sahebrao Mandal, Arnab Mukherjee, Pinaki Talukdar
Triazine-based pre-organized tripodal receptors are reported as efficient transmembrane Cl- carriers. These receptors were designed based on triazine core and 3,7-diazabicyclo[3.3.1]nonane arms to facilitate preorganized cavity formation. Each bicyclic arm was further functionalized to control protonation and lipophilicity which are crucial for their efficient anion binding and effective transport through liposomal membranes. The benzyl substituted receptor was the most effective ion transporter followed by the pentafluorobenzyl substituted derivative...
November 16, 2016: Chemistry: a European Journal
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