keyword
MENU ▼
Read by QxMD icon Read
search

Molecular dynamics membrane

keyword
https://www.readbyqxmd.com/read/29148803/hsdhodh-microdomain-membrane-interactions-are-influenced-by-the-lipid-composition
#1
Eduardo Festozo Vicente, Indra Dev Sahu, Edson Crusca, Luis Guilherme Mansor Basso, Claudia Elisabeth Munte, Antonio Jose Costa-Filho, Gary A Lorigan, Eduardo Maffud Maffud Cilli
Human dihydroorotate dehydrogenase (HsDHODH) enzyme has been studied as selective target for inhibitors to block the enzyme activity, intending to prevent proliferative diseases. The N-terminal microdomain seems to play an important role in the enzyme function. However, the molecular mechanism of action and dynamics of this region are not totally understood yet. This study analyzes the interaction and conformation in model membranes of HsDHODH microdomain using peptide analogues containing the paramagnetic amino acid TOAC at strategic positions...
November 17, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/29144280/selective-ion-permeation-through-strained-and-charged-graphene-membranes
#2
Kun Li, Yi Tao, Zhongwu Li, Jingjie Sha, Yunfei Chen
By means of molecular dynamics (MD) simulations and density functional theory (DFT) calculations, we demonstrate that stretched and charged graphene can act as ion sieve membranes. It is observed that loading 30% strain on graphene can induce pores in the dense electron cloud to allow ions to pass through the aromatic rings. Meanwhile, charged surface is helpful to peel the hydration layers from the ions and decrease the energy barrier for ion translocation through nanopores. Our results suggest that with membrane charge density of 6...
November 16, 2017: Nanotechnology
https://www.readbyqxmd.com/read/29138410/pla2-like-proteins-myotoxic-mechanism-a-dynamic-model-description
#3
Rafael J Borges, Ney Lemke, Marcos R M Fontes
Phospholipase A2-like (PLA2-like) proteins contribute to the development of muscle necrosis in Viperidae snake bites and are not efficiently neutralized by current antivenom treatments. The toxic mechanisms of PLA2-like proteins are devoid of catalytic activity and not yet fully understood, although structural and functional experiments suggest a dimeric assembly and that the C-terminal residues are essential to myotoxicity. Herein, we characterized the functional mechanism of bothropic PLA2-like structures related to global and local measurements using the available models in the Protein Data Bank and normal mode molecular dynamics (NM-MD)...
November 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29135688/membrane-microdomains-and-the-regulation-of-hdl-biogenesis
#4
Jacques Genest, Adel Schwertani, Hong Y Choi
PURPOSE OF REVIEW: The major cardio-protective function of HDL is to remove excess cellular cholesterol in the process of HDL particle formation and maturation. The HDL biogenic procedure requiring protein-lipid interactions has been incompletely understood, and here we discuss recent progress and insights into the mechanism of HDL biogenesis. RECENT FINDINGS: The initial and rate-limiting step of HDL biogenesis is the interaction between apoA-I and plasma membrane microdomains created by ATP-binding cassette transporter A1 (ABCA1) transporter...
November 11, 2017: Current Opinion in Lipidology
https://www.readbyqxmd.com/read/29134655/protein-components-of-postsynaptic-density-lattice-a-backbone-structure-for-type-i-excitatory-synapses
#5
Tatsuo Suzuki, Kiyokazu Kametani, Weiheng Guo, Weidong Li
It is essential to study the molecular architecture of postsynaptic density (PSD) to understand the molecular mechanism underlying the dynamic nature of PSD, one of the bases of synaptic plasticity. A well-known model for the architecture of PSD of type I excitatory synapses basically comprises of several scaffolding proteins (scaffold protein model). On the contrary, "PSD lattice" observed through electron microscopy has been considered a basic backbone of type I PSDs. However, major constituents of the PSD lattice and the relationship between the PSD lattice and the scaffold protein model, are unknown...
November 14, 2017: Journal of Neurochemistry
https://www.readbyqxmd.com/read/29133163/non-visual-arrestins-regulate-the-focal-adhesion-formation-via-small-gtpases-rhoa-and-rac1-independently-of-gpcrs
#6
Whitney M Cleghorn, Nada Bulus, Seunghyi Kook, Vsevolod V Gurevich, Roy Zent, Eugenia V Gurevich
Arrestins recruit a variety of signaling proteins to active phosphorylated G protein-coupled receptors in the plasma membrane and to the cytoskeleton. Loss of arrestins leads to decreased cell migration, altered cell shape, and an increase in focal adhesions. Small GTPases of the Rho family are molecular switches that regulate actin cytoskeleton and affect a variety of dynamic cellular functions including cell migration and cell morphology. Here we show that non-visual arrestins differentially regulate RhoA and Rac1 activity to promote cell spreading via actin reorganization, and focal adhesion formation via two distinct mechanisms...
November 11, 2017: Cellular Signalling
https://www.readbyqxmd.com/read/29132840/d-peptides-as-inhibitors-of-pr3-membrane-interactions
#7
Ksenia Maximova, Tom Venken, Nathalie Reuter, Joanna Trylska
Proteinase 3 (PR3) is a neutrophil serine protease present in cytoplasmic granules but also expressed at the neutrophil surface where it mediates proinflammatory effects. Studies of the underlying molecular mechanisms have been hampered by the lack of inhibitors of the PR3 membrane anchorage. Indeed while there exist inhibitors of the catalytic activity of PR3, its membrane interfacial binding site (IBS) is distinct from its catalytic site. The IBS has been characterized both by mutagenesis experiments and molecular modeling...
November 10, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29131636/template-guided-assembly-of-silk-fibroin-on-cellulose-nanofibers-for-robust-nanostructures-with-ultrafast-water-transport
#8
Rui Xiong, Ho Shin Kim, Shuaidi Zhang, Sunghan Kim, Volodymyr F Korolovych, Ruilong Ma, Yaroslava G Yingling, Canhui Lu, Vladimir V Tsukruk
The construction of multilength scaled hierarchical nanostructures from diverse natural components is critical in the progress toward all-natural nanocomposites with structural robustness and versatile added functionalities. Here, we report a spontaneous formation of peculiar "shish kebab" nanostructures with the periodic arrangement of silk fibroin domains along straight segments of cellulose nanofibers. We suggest that the formation of these shish kebab nanostructures is facilitated by the preferential organization of heterogeneous (β-sheets and amorphous silk) domains along the cellulose nanofiber driven by modulated axial distribution of crystalline planes, hydrogen bonding, and hydrophobic interactions as suggested by all-atom molecular dynamic simulations...
November 17, 2017: ACS Nano
https://www.readbyqxmd.com/read/29130892/surface-effects-on-ionic-coulomb-blockade-in-nanometer-size-pores
#9
Hiroya Tanaka, Hideo Iizuka, Yuriy V Pershin, Massimiliano Di Ventra
Ionic Coulomb blockade in nanopores is a phenomenon that shares some similarities but also differences with its electronic ounterpart. Here, we investigate extensively this phenomenon using all-atom molecular dynamics of ionic transport through nanopores of about one nanometer in diameter and up to several nanometers in length. Our goal is to better understand the role of atomic roughness and structure of the pore walls in facilitating ionic Coulomb blockade. Our numerical results reveal the following general trends...
November 13, 2017: Nanotechnology
https://www.readbyqxmd.com/read/29129571/photo-triggered-recognition-between-host-and-guest-compounds-in-a-giant-vesicle-encapsulating-photo-pierceable-vesicles
#10
Kentaro Suzuki, Koichiro Machida, Kazuo Yamaguchi, Tadashi Sugawara
Here, we used centrifugal precipitation to construct a giant vesicle (GV) encapsulating smaller giant vesicles (GV-in-GV) which comprises a photo-resistant outer GV and a photo-pierceable inner GV; the outer GV contained a fluorescent probe (SYBR Green I) in its inner water pool, and the inner GV contained double-stranded DNA (dsDNA) in its inner water pool. The phospholipid membrane of the inner GV was made photo-pierceable by inclusion of ca. 15mol% of a caged phospholipid in its membrane. Immediately after exposure of the GV-in-GVs to UV irradiation, strong fluorescence was detected in the inner water pool of the outer GV, indicating that dsDNA had been released from the inner GV and had complexed with the fluorescent probe...
November 9, 2017: Chemistry and Physics of Lipids
https://www.readbyqxmd.com/read/29125878/insight-into-the-interactions-residue-snorkeling-and-membrane-disordering-potency-of-a-single-antimicrobial-peptide-into-different-lipid-bilayers
#11
Majid Jafari, Faramarz Mehrnejad, Farahnoosh Doustdar
Pardaxin, with a bend-helix-bend-helix structure, is a membrane-active antimicrobial peptide that its membrane activity depends on the lipid bilayer composition. Herein, all-atom molecular dynamics (MD) simulations were performed to provide further molecular insight into the interactions, structural dynamics, orientation behavior, and cationic residues snorkeling of pardaxin in the DMPC, DPPC, POPC, POPG, POPG/POPE (3:1), and POPG/POPE (1:3) lipid bilayers. The results showed that the C-terminal helix of the peptide was maintained in all six types of the model-bilayers and pardaxin was tilted into the DMPC, DPPC, and POPG/POPE mixed bilayers more than the POPC and POPG bilayers...
2017: PloS One
https://www.readbyqxmd.com/read/29125472/membrane-vesiculation-induced-by-proteins-of-the-dengue-virus-envelope-studied-by-molecular-dynamics-simulations
#12
Ricardo de Oliveira Dos Santos Soares, Leandro Oliveira Bortot, David van der Spoel, Antonio Caliri
Biological membranes are continuously remodeled in the cell by specific membrane-shaping machineries to form, for example, tubes and vesicles. We examine fundamental mechanisms involved in the vesiculation processes induced by a cluster of envelope (E) and membrane (M) proteins of the Dengue Virus (DENV) using molecular dynamics simulations and a coarse-grained model. We show that an arrangement of three E-M heterotetramers (EM3) works as a bending unit and an ordered cluster of five such units generates a closed vesicle, reminiscent of the virus budding process...
November 10, 2017: Journal of Physics. Condensed Matter: An Institute of Physics Journal
https://www.readbyqxmd.com/read/29125278/grafting-commercial-surfactants-brij-ciej-and-peg-to-electrodes-via-aryldiazonium-salts
#13
Ophélie Squillace, Charles Esnault, Jean-François Pilard, Guillaume Brotons
Grafting commercial surfactants appears to be a simple way to modify electrodes and conducting interfaces, avoiding the synthesis of complex organic molecules. A new surface functionalisation route is presented to build surfactants coatings with monolayer thicknesses grafting molecules considered as non-reactive. A monolayer of -SO2Cl functions (from a para-benzene sulfonyl chloride) was first electro-grafted. It shown a high reactivity toward weak nucleophiles commonly found on surfactants end-moieties such as hydroxyl groups (-OH) and it was used to covalently graft: 1) non-ionic diblock oligomers (Brij or CiEj, CxH2x+1(OCH2CH2)nOH with x=16 and n=23 for Brij58; x=16 and n=10 for Brij C10; x=16 and n=2 for Brij52); 2) Poly (ethylene glycol) PEG short chains (PEO9 for (OCH2CH2)nOH with n=9); and mixed formula...
November 10, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/29123973/cholera-toxin-b-subunit-induces-local-curvature-on-lipid-bilayers
#14
Weria Pezeshkian, Lina J Nåbo, John H Ipsen
The B subunit of the bacterial cholera toxin (CTxB) is responsible for the toxin binding to the cell membrane and its intracellular trafficking. CTxB binds to the monosialotetrahexosyl ganglioside at the plasma membrane of the target cell and mediates toxin internalization by endocytosis. CTxB induces a local membrane curvature that is essential for its clathrin-independent uptake. Using all-atom molecular dynamics, we show that CTxB induces local curvature, with the radius of curvature around 36 nm. The main feature of the CTxB molecular structure that causes membrane bending is the protruding alpha helices in the middle of the protein...
November 2017: FEBS Open Bio
https://www.readbyqxmd.com/read/29123470/regulation-of-ampa-receptor-trafficking-by-protein-ubiquitination
#15
REVIEW
Jocelyn Widagdo, Sumasri Guntupalli, Se E Jang, Victor Anggono
The molecular mechanisms underlying plastic changes in the strength and connectivity of excitatory synapses have been studied extensively for the past few decades and remain the most attractive cellular models of learning and memory. One of the major mechanisms that regulate synaptic plasticity is the dynamic adjustment of the α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA)-type glutamate receptor content on the neuronal plasma membrane. The expression of surface AMPA receptors (AMPARs) is controlled by the delicate balance between the biosynthesis, dendritic transport, exocytosis, endocytosis, recycling and degradation of the receptors...
2017: Frontiers in Molecular Neuroscience
https://www.readbyqxmd.com/read/29123095/thermal-crumpling-of-perforated-two-dimensional-sheets
#16
David Yllanes, Sourav S Bhabesh, David R Nelson, Mark J Bowick
Thermalized elastic membranes without distant self-avoidance are believed to undergo a crumpling transition when the microscopic bending stiffness is comparable to kT, the scale of thermal fluctuations. Most potential physical realizations of such membranes have a bending stiffness well in excess of experimentally achievable temperatures and are therefore unlikely ever to access the crumpling regime. We propose a mechanism to tune the onset of the crumpling transition by altering the geometry and topology of the sheet itself...
November 9, 2017: Nature Communications
https://www.readbyqxmd.com/read/29122611/effect-of-ergosterol-on-the-fungal-membrane-properties-all-atom-and-coarse-grained-molecular-dynamics-study
#17
Elena Ermakova, Yuriy Zuev
Cell membranes are complex multicomponent systems consisting of thousands of different lipids with numerous embedded membrane proteins and many types of sterols. We used all-atom and coarse-grained molecular dynamics simulations to study the structural and dynamical properties of phospholipid bilayers containing four types of phospholipids and different amount of ergosterol, main sterol component in the fungal membranes. To characterize the influence of ergosterol on the membrane properties we analyzed the surface area per lipid, bilayer thickness, area compressibility modulus, mass density profiles, deuterium order parameters, and lateral diffusion coefficients...
November 6, 2017: Chemistry and Physics of Lipids
https://www.readbyqxmd.com/read/29120672/an-electrostatic-and-probabilistic-simulation-model-to-describe-neurosecretion-at-the-synaptic-scale
#18
A E Macias-Medri, Jacinto A Liendo, Ricardo J Silva
A hybrid simulation model (macro-molecular dynamics and Monte Carlo method) is proposed to reproduce neurosecretion and exocytosis. A theory has been developed for vesicular dynamics based on quasi-static electric interactions and a simple transition-state model for the vesicular fusion. Under the non-equilibrium electric conditions in an electrolytic fluid, it is considered that the motion of each synaptic vesicle is influenced by electrostatic forces exerted by the membranes of the synaptic bouton, other vesicles, the intracellular and intravesicular fluids, and external elements to the neuron...
November 9, 2017: Network: Computation in Neural Systems
https://www.readbyqxmd.com/read/29120602/porphyrin-assisted-docking-of-a-thermophage-portal-protein-into-lipid-bilayers-nanopore-engineering-and-characterization
#19
Benjamin Cressiot, Sandra J Greive, Wei Si, Tomas C Pascoa, Mehrnaz Mojtabavi, Maria Chechik, Huw T Jenkins, Xueguang Lu, Ke Zhang, Aleksei Aksimentiev, Alfred A Antson, Meni Wanunu
Nanopore-based sensors for nucleic acid sequencing and single-molecule detection typically employ pore-forming membrane proteins with hydrophobic external surfaces, suitable for insertion into a lipid bilayer. In contrast, hydrophilic pore-containing molecules, such as DNA origami, have been shown to require chemical modification to favor insertion into a lipid environment. In this work, we describe a strategy for inserting polar proteins with an inner pore into lipid membranes, focusing here on a circular 12-subunit assembly of the thermophage G20c portal protein...
November 15, 2017: ACS Nano
https://www.readbyqxmd.com/read/29119782/intracellular-protein-labeling-probes-for-multicolor-single-molecule-imaging-of-immune-receptor-adaptor-molecular-dynamics
#20
Ryota Sato, Jun Kozuka, Masahiro Ueda, Reiko Mishima, Yutaro Kumagai, Akimasa Yoshimura, Masafumi Minoshima, Shin Mizukami, Kazuya Kikuchi
Single-molecule imaging (SMI) has been widely utilized to investigate biomolecular dynamics and protein-protein interactions in living cells. However, multicolor SMI of intracellular proteins is challenging because of high background signals and other limitations of current fluorescence labeling approaches. To achieve reproducible intracellular SMI, a labeling probe ensuring both efficient membrane permeability and minimal non-specific binding to cell components is essential. We developed near-infrared (NIR) fluorescent probes for protein-labeling, which specifically binds to a mutant β-lactamase tag...
November 9, 2017: Journal of the American Chemical Society
keyword
keyword
78833
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"