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https://www.readbyqxmd.com/read/28640814/a-novel-algorithm-identifies-stress-induced-alterations-in-mitochondrial-connectivity-and-inner-membrane-structure-from-confocal-images
#1
Mathieu Ouellet, Gérald Guillebaud, Valerie Gervais, David Lupien St-Pierre, Marc Germain
Mitochondria exist as a highly interconnected network that is exquisitely sensitive to variations in nutrient availability, as well as a large array of cellular stresses. Changes in length and connectivity of this network, as well as alterations in the mitochondrial inner membrane (cristae), regulate cell fate by controlling metabolism, proliferation, differentiation, and cell death. Given the key roles of mitochondrial dynamics, the process by which mitochondria constantly fuse and fragment, the measure of mitochondrial length and connectivity provides crucial information on the health and activity of various cell populations...
June 22, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28640808/transmembrane-helical-interactions-in-the-cftr-channel-pore
#2
Jhuma Das, Andrei A Aleksandrov, Liying Cui, Lihua He, John R Riordan, Nikolay V Dokholyan
Mutations in the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) gene affect CFTR protein biogenesis or its function as a chloride channel, resulting in dysregulation of epithelial fluid transport in the lung, pancreas and other organs in cystic fibrosis (CF). Development of pharmaceutical strategies to treat CF requires understanding of the mechanisms underlying channel function. However, incomplete 3D structural information on the unique ABC ion channel, CFTR, hinders elucidation of its functional mechanism and correction of cystic fibrosis causing mutants...
June 22, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28640581/molecular-insight-of-water-desalination-across-multilayer-graphene-oxide-membranes
#3
Bo Chen, Haifeng Jiang, Xiang Liu, Xuejiao Hu
Transport of ionic solutions through graphene oxide (GO) membranes is a complicated issue because the complex and tortuous structure inside make it very hard to clarify. Using molecular dynamics (MD) simulations, we investigated the mechanism of water transport and ions movement across the multilayer graphene oxide. The significant flow rate is considerably influenced by the structural parameters of GO membranes. Due to the size effect on shrunken real flow area, there is disagreement between classical continuum model and nano-scaled flow...
June 22, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28636909/electric-field-induced-protein-translocation-via-a-conformational-transition-in-secdf-an-md-study
#4
Emel Ficici, Daun Jeong, Ioan Andricioaei
SecDF is an important component of the Sec protein translocation machinery embedded in the bacterial membrane, which is associated with many functions, such as stabilizing other Sec translocon components within the membrane, maintaining the transmembrane (TM) potential, and facilitating the ATP-independent stage of the translocation mechanism. Related studies suggest that SecDF undergoes functionally important conformational changes that involve mainly its P1-head domain and that these changes are coupled with the proton motive force (Δp)...
June 20, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28636363/distinct-protein-hydration-water-species-defined-by-spatially-resolved-spectra-of-intermolecular-vibrations
#5
Viren Sureshkumar Pattni, Tatiana Vasilevskaya, Walter Thiel, Matthias Heyden
In this molecular dynamics simulation study, we analyze intermolecular vibrations in the hydration shell of a solvated enyzme, the membrane type 1--matrix metalloproteinase, with high spatial resolution. Our approach allows us to characterize vibrational signatures of the local hydrogen bond network, the translational mobility of water molecules, as well as the molecular entropy, in specific local environments. Our study demonstrates the heterogeneity of water properties within the hydration shell of a complex biomolecule...
June 21, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28636028/supramolecular-functional-assemblies-dynamic-membrane-transporters-and-peptide-nanotubular-composites
#6
Alberto Fuertes, Marisa Juanes, Juan R Granja, Javier Montenegro
The fabrication of functional molecular devices constitutes one of the most important current challenges for chemical sciences. The complex processes accomplished by living systems continuously demand the assistance of non-covalent interactions between molecular building blocks. Additionally, these building blocks (proteins, membranes, nucleotides) are also constituted by self-assembled structures. Therefore, supramolecular chemistry is the discipline required to understand the properties of the minimal self-assembled building blocks of living systems and to develop new functional smart materials...
June 21, 2017: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/28632757/molecular-mechanism-of-drp1-assembly-studied-in-vitro-by-cryo-electron-microscopy
#7
Kaustuv Basu, Driss Lajoie, Tristan Aumentado-Armstrong, Jin Chen, Roman I Koning, Blaise Bossy, Mihnea Bostina, Attila Sik, Ella Bossy-Wetzel, Isabelle Rouiller
Mitochondria are dynamic organelles that continually adapt their morphology by fusion and fission events. An imbalance between fusion and fission has been linked to major neurodegenerative diseases, including Huntington's, Alzheimer's, and Parkinson's diseases. A member of the Dynamin superfamily, dynamin-related protein 1 (DRP1), a dynamin-related GTPase, is required for mitochondrial membrane fission. Self-assembly of DRP1 into oligomers in a GTP-dependent manner likely drives the division process. We show here that DRP1 self-assembles in two ways: i) in the presence of the non-hydrolysable GTP analog GMP-PNP into spiral-like structures of ~36 nm diameter; and ii) in the presence of GTP into rings composed of 13-18 monomers...
2017: PloS One
https://www.readbyqxmd.com/read/28630812/molecular-properties-of-a-dtd-channelrhodopsin-from-guillardia-theta
#8
Yumeka Yamauchi, Masae Konno, Shota Ito, Satoshi P Tsunoda, Keiichi Inoue, Hideki Kandori
Microbial rhodopsins are membrane proteins found widely in archaea, eubacteria and eukaryotes (fungal and algal species). They have various functions, such as light-driven ion pumps, light-gated ion channels, light sensors and light-activated enzymes. A light-driven proton pump bacteriorhodopsin (BR) contains a DTD motif at positions 85, 89, and 96, which is unique to archaeal proton pumps. Recently, channelrhodopsins (ChRs) containing the DTD motif, whose sequential identity is ~20% similar to BR and to cation ChRs in Chlamydomonas reinhardtii (CrCCRs), were found...
2017: Biophysics and Physicobiology
https://www.readbyqxmd.com/read/28628337/buckling-under-pressure-curvature-based-lipid-segregation-and-stability-modulation-in-cardiolipin-containing-bilayers
#9
Kevin J Boyd, Nathan N Alder, Eric R May
Mitochondrial metabolic function is affected by the morphology and protein organization of the mitochondrial inner membrane (MIM). Cardiolipin (CL) is a unique tetra-acyl lipid that is involved in the maintenance of the highly-curved shape of the MIM as well as spatial organization of the proteins necessary for respiration and oxidative phosphorylation. Cardiolipin has been suggested to self-organize into lipid domains due to its inverted conical molecular geometry, though the driving forces for this organization are not fully understood...
June 19, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/28628083/molecular-basis-of-selective-mitochondrial-fusion-by-heterotypic-action-between-opa1-and-cardiolipin
#10
Tadato Ban, Takaya Ishihara, Hiroto Kohno, Shotaro Saita, Ayaka Ichimura, Katsumi Maenaka, Toshihiko Oka, Katsuyoshi Mihara, Naotada Ishihara
Mitochondria are highly dynamic organelles that undergo frequent fusion and fission. Optic atrophy 1 (OPA1) is an essential GTPase protein for both mitochondrial inner membrane (IM) fusion and cristae morphology. Under mitochondria-stress conditions, membrane-anchored L-OPA1 is proteolytically cleaved to form peripheral S-OPA1, leading to the selection of damaged mitochondria for mitophagy. However, molecular details of the selective mitochondrial fusion are less well understood. Here, we showed that L-OPA1 and cardiolipin (CL) cooperate in heterotypic mitochondrial IM fusion...
June 19, 2017: Nature Cell Biology
https://www.readbyqxmd.com/read/28627570/determination-of-bending-rigidity-and-tilt-modulus-of-lipid-membranes-from-real-space-fluctuation-analysis-of-molecular-dynamics-simulations
#11
M Doktorova, D Harries, G Khelashvili
We have recently developed a novel computational methodology (termed RSF for Real-Space Fluctuations) to quantify the bending rigidity and tilt modulus of lipid membranes from real-space analysis of fluctuations in the tilt and splay degrees of freedom as sampled in molecular dynamics (MD) simulations. In this article, we present a comprehensive study that combines results from the application of the RSF method to a wide range of lipid bilayer systems that encompass membranes of different fluidities and sizes, including lipids with saturated and unsaturated lipid tails, single and multi-component lipid systems, as well as non-standard lipids such as the four-tailed cardiolipin...
June 19, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28627472/molecular-dynamics-as-a-tool-for-in-silico-screening-of-skin-permeability
#12
Paolo Rocco, Francesco Cilurzo, Paola Minghetti, Giulio Vistoli, Alessandro Pedretti
Prediction of skin permeability can have manifold applications ranging from drug delivery to toxicity prediction. Along with the semi-empirical or mechanistic models proposed in the last decades, Molecular Dynamics simulations have recently become a fruitful tool for investigating membrane permeability, in particular as they allow the involved mechanisms to be modelled at a molecular level. Despite their significant structural complexity, Molecular Dynamics simulations can also be utilized to study permeation through the lipid matrix that characterizes the stratum corneum...
June 13, 2017: European Journal of Pharmaceutical Sciences
https://www.readbyqxmd.com/read/28624444/distribution-lipid-bilayer-affinity-and-kinetics-of-the-metabolic-effects-of-dinoseb-in-the-liver
#13
Gabriela Bueno Franco Salla, Lívia Bracht, Anacharis Babeto de Sá-Nakanishi, Angela Valderrama Parizotto, Fabrício Bracht, Rosane Marina Peralta, Adelar Bracht
Dinoseb is a highly toxic pesticide of the dinitrophenol group. Its use has been restricted, but it can still be found in soils and waters in addition to being a component of related pesticides that, after ingestion by humans or animals, can originate the compound by enzymatic hydrolysis. As most dinitrophenols, dinoseb uncouples oxidative phosphorylation. In this study, distribution, lipid bilayer affinity and kinetics of the metabolic effects of dinoseb were investigated, using mainly the isolated perfused rat liver, but also isolated mitochondria and molecular dynamics simulations...
June 15, 2017: Toxicology and Applied Pharmacology
https://www.readbyqxmd.com/read/28623230/flexible-body-motions-of-calmodulin-and-the-farnesylated-hypervariable-region-yield-a-high-affinity-interaction-enabling-k-ras4b-membrane-extraction
#14
Hyunbum Jang, Avik Banerjee, Tanmay Chavan, Vadim Gaponenko, Ruth Nussinov
In calmodulin (CaM)-rich environments, oncogenic KRAS plays a critical role in adenocarcinomas by promoting PI3K/Akt signaling. We previously proposed that at elevated calcium levels in cancer, CaM recruits PI3Kα to the membrane and extracts K-Ras4B from the membrane, organizing a K-Ras4B/CaM/PI3Kα ternary complex. CaM can thereby replace a missing receptor tyrosine kinase signal to fully activate PI3Kα. Recent experimental data show that CaM selectively promotes K-Ras signaling, but not of N-Ras or H-Ras...
June 16, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28622469/free-energy-calculations-of-microcin-j25-variants-binding-to-the-fhua-receptor
#15
Pin-Kuang Lai, Yiannis N Kaznessis
Computer simulations are performed to study the antimicrobial peptide microcin J25 (MJ25), a 21-mer peptide with an unusual lasso structure and high activity against Gram-negative bacteria. MJ25 has intracellular targets. The initial step for MJ25 acquisition in bacterial cells is binding to the outer membrane receptor FhuA. Molecular dynamics simulation is implemented to study the binding mechanism of MJ25 to FhuA and to search for important binding residues. The absolute binding free energy calculated from combined free energy perturbation (FEP) and thermodynamic integration (TI) methods agrees well with experimental data...
June 16, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28621369/transport-of-nanoparticles-across-pulmonary-surfactant-monolayer-a-molecular-dynamics-study
#16
Yan Xu, Li Deng, Hao Ren, Xianren Zhang, Fang Huang, Tongtao Yue
Pulmonary nanodrug delivery is an emerging concept, especially for targeted lung cancer therapy. Once inhaled, the nanoparticles (NPs) acting as drug carriers need to efficiently cross the pulmonary surfactant monolayer (PSM) of lung alveoli, which act as the first barrier for external particles entering the lung. Herein, by performing molecular dynamics simulations, we study how inhaled NPs interact with the PSM, particularly focusing on the transport of NPs with different properties across the PSM. While hydrophilic NPs translocate directly across the PSM, transport of hydrophobic NPs is achieved as the PSM wraps them...
June 16, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28620219/molecular-dynamics-exploration-of-poration-and-leaking-caused-by-kalata-b1-in-hiv-infected-cell-membrane-compared-to-host-and-hiv-membranes
#17
Wanapinun Nawae, Supa Hannongbua, Marasri Ruengjitchatchawalya
The membrane disruption activities of kalata B1 (kB1) were investigated using molecular dynamics simulations with membrane models. The models were constructed to mimic the lipid microdomain formation in membranes of HIV particle, HIV-infected cell, and host cell. The differences in the lipid ratios of these membranes caused the formation of liquid ordered (lo) domains of different sizes, which affected the binding and activity of kB1. Stronger kB1 disruptive activity was observed for the membrane with small sized lo domain...
June 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28620035/molecular-interactions-shaping-the-tetraspanin-web
#18
REVIEW
Sjoerd J van Deventer, Vera-Marie E Dunlock, Annemiek B van Spriel
To facilitate the myriad of different (signaling) processes that take place at the plasma membrane, cells depend on a high degree of membrane protein organization. Important mediators of this organization are tetraspanin proteins. Tetraspanins interact laterally among themselves and with partner proteins to control the spatial organization of membrane proteins in large networks called the tetraspanin web. The molecular interactions underlying the formation of the tetraspanin web were hitherto mainly described based on their resistance to different detergents, a classification which does not necessarily correlate with functionality in the living cell...
June 15, 2017: Biochemical Society Transactions
https://www.readbyqxmd.com/read/28618626/stochastic-lattice-model-of-synaptic-membrane-protein-domains
#19
Yiwei Li, Osman Kahraman, Christoph A Haselwandter
Neurotransmitter receptor molecules, concentrated in synaptic membrane domains along with scaffolds and other kinds of proteins, are crucial for signal transmission across chemical synapses. In common with other membrane protein domains, synaptic domains are characterized by low protein copy numbers and protein crowding, with rapid stochastic turnover of individual molecules. We study here in detail a stochastic lattice model of the receptor-scaffold reaction-diffusion dynamics at synaptic domains that was found previously to capture, at the mean-field level, the self-assembly, stability, and characteristic size of synaptic domains observed in experiments...
May 2017: Physical Review. E
https://www.readbyqxmd.com/read/28617850/molecular-determinants-for-the-thermodynamic-and-functional-divergence-of-uniporter-glut1-and-proton-symporter-xyle
#20
Meng Ke, Yafei Yuan, Xin Jiang, Nieng Yan, Haipeng Gong
GLUT1 facilitates the down-gradient translocation of D-glucose across cell membrane in mammals. XylE, an Escherichia coli homolog of GLUT1, utilizes proton gradient as an energy source to drive uphill D-xylose transport. Previous studies of XylE and GLUT1 suggest that the variation between an acidic residue (Asp27 in XylE) and a neutral one (Asn29 in GLUT1) is a key element for their mechanistic divergence. In this work, we combined computational and biochemical approaches to investigate the mechanism of proton coupling by XylE and the functional divergence between GLUT1 and XylE...
June 15, 2017: PLoS Computational Biology
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