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https://www.readbyqxmd.com/read/28432921/gates-for-soluble-and-membrane-proteins-and-two-trafficking-systems-ift-and-lift-establish-a-dynamic-ciliary-signaling-compartment
#1
REVIEW
Victor L Jensen, Michel R Leroux
Primary cilia are microtubule-based organelles found on most mammalian cell surfaces. They possess a soluble matrix and membrane contiguous with the cell body cytosol and plasma membrane, and yet, have distinct compositions that can be modulated to enable dynamic signal transduction. Here, we discuss how specialized ciliary compartments are established using a coordinated network of gating, trafficking and targeting activities. Cilium homeostasis is maintained by a size-selective molecular mesh that limits soluble protein entry, and by a membrane diffusion barrier localized at the transition zone...
April 19, 2017: Current Opinion in Cell Biology
https://www.readbyqxmd.com/read/28431242/structural-and-functional-analysis-of-a-%C3%AE-2-adrenergic-receptor-complex-with-grk5
#2
Konstantin E Komolov, Yang Du, Nguyen Minh Duc, Robin M Betz, João P G L M Rodrigues, Ryan D Leib, Dhabaleswar Patra, Georgios Skiniotis, Christopher M Adams, Ron O Dror, Ka Young Chung, Brian K Kobilka, Jeffrey L Benovic
The phosphorylation of agonist-occupied G-protein-coupled receptors (GPCRs) by GPCR kinases (GRKs) functions to turn off G-protein signaling and turn on arrestin-mediated signaling. While a structural understanding of GPCR/G-protein and GPCR/arrestin complexes has emerged in recent years, the molecular architecture of a GPCR/GRK complex remains poorly defined. We used a comprehensive integrated approach of cross-linking, hydrogen-deuterium exchange mass spectrometry (MS), electron microscopy, mutagenesis, molecular dynamics simulations, and computational docking to analyze GRK5 interaction with the β2-adrenergic receptor (β2AR)...
April 20, 2017: Cell
https://www.readbyqxmd.com/read/28430444/molecular-structuring-and-percolation-transition-in-hydrated-sulfonated-poly-ether-ether-ketone-membranes
#3
Madhusmita Tripathy, Sunil Kumar P B, Abhijit P Deshpande
The extent of phase separation and water percolation in sulfonated membranes are the key to their performance in fuel cells. Toward this, the effect of hydration on the morphology and transport characteristics of sulfonated poly(ether ether ketone), sPEEK, membrane is investigated using atomistic molecular dynamics simulation at various hydration levels($\lambda$: number of water molecules per sulfonate group). The evolution of local morphology is investigated using structural correlations and minimum pair distances...
April 21, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28429746/the-small-g-protein-arf6-expressed-in-keratinocytes-by-hgf-stimulation-is-a-regulator-for-skin-wound-healing
#4
Yuki Miura, Van Ngo Thai Bich, Momoko Furuya, Hiroshi Hasegawa, Satoru Takahashi, Naohiro Katagiri, Tsunaki Hongu, Yuji Funakoshi, Norihiko Ohbayashi, Yasunori Kanaho
The earlier step of cutaneous wound healing process, re-epithelialization of the wounded skin, is triggered by a variety of growth factors. However, molecular mechanisms through which growth factors trigger skin wound healing are less understood. Here, we demonstrate that hepatocyte growth factor (HGF)/c-Met signaling-induced expression of the small G protein Arf6 mRNA in keratinocytes is essential for the skin wound healing. Arf6 mRNA expression was dramatically induced in keratinocytes at the wounded skin, which was specifically suppressed by the c-Met inhibitor...
April 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28429411/nanodiscs-for-inpharma-nmr-characterization-of-gpcrs-ligand-binding-to-the-human-a2a-adenosine-receptor
#5
Kai Fredriksson, Philip Lottmann, Sonja Hinz, Iounut Onila, Aliaksei Shymanets, Christian Harteneck, Christa E Müller, Christian Griesinger, Thomas E Exner
G-protein-coupled-receptors (GPCRs) are of fundamental importance for signal transduction through cell membranes. This makes them important drug targets, but structure-based drug design (SBDD) is still hampered by the limitations for structure determination of unmodified GPCRs. We show that the interligand NOEs for pharmacophore mapping (INPHARMA) method can provide valuable information on ligand poses inside the binding site of the unmodified human A2A adenosine receptor reconstituted in nanodiscs. By comparing experimental INPHARMA spectra with back-calculated spectra based on ligand poses obtained from molecular dynamics simulations, a complex structure for A2A R with the low-affinity ligand 3-pyrrolidin-1-ylquinoxalin-2-amine was determined based on the X-ray structure of ligand ZM-241,358 in complex with a modified A2A R...
April 21, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28429314/evolutionary-origin-of-euglena
#6
Bożena Zakryś, Rafał Milanowski, Anna Karnkowska
Euglenids (Excavata, Discoba, Euglenozoa, Euglenida) is a group of free-living, single-celled flagellates living in the aquatic environments. The uniting and unique morphological feature of euglenids is the presence of a cell covering called the pellicle. The morphology and organization of the pellicle correlate well with the mode of nutrition and cell movement. Euglenids exhibit diverse modes of nutrition, including phagotrophy and photosynthesis. Photosynthetic species (Euglenophyceae) constitute a single subclade within euglenids...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28429276/enhancing-thermal-stability-of-a-highly-concentrated-insulin-formulation-with-pluronic-f-127-for-long-term-use-in-microfabricated-implantable-devices
#7
Jason Li, Michael K Chu, Brian Lu, Sako Mirzaie, Kuan Chen, Claudia R Gordijo, Oliver Plettenburg, Adria Giacca, Xiao Yu Wu
Development of highly concentrated formulations of protein and peptide drugs is a major challenge due to increased susceptibility to aggregation and precipitation. Numerous drug delivery systems including implantable and wearable controlled-release devices require thermally stable formulations with high concentrations due to limited device sizes and long-term use. Herein we report a highly concentrated insulin gel formulation (up to 80 mg/mL, corresponding to 2200 IU/mL), stabilized with a non-ionic amphiphilic triblock copolymer (i...
April 20, 2017: Drug Delivery and Translational Research
https://www.readbyqxmd.com/read/28428758/modulation-of-asymmetric-flux-in-heterotypic-gap-junctions-by-pore-shape-particle-size-and-charge
#8
Abhijit Mondal, Frank B Sachse, Alonso P Moreno
Gap junction channels play a vital role in intercellular communication by connecting cytoplasm of adjoined cells through arrays of channel-pores formed at the common membrane junction. Their structure and properties vary depending on the connexin isoform(s) involved in forming the full gap junction channel. Lack of information on the molecular structure of gap junction channels has limited the development of computational tools for single channel studies. Currently, we rely on cumbersome experimental techniques that have limited capabilities...
2017: Frontiers in Physiology
https://www.readbyqxmd.com/read/28427876/polar-n-terminal-residues-conserved-in-type-2-secretion-pseudopilins-determine-subunit-targeting-and-membrane-extraction-steps-during-fibre-assembly
#9
Javier Santos-Moreno, Alexandra East, Ingrid Guilvout, Nathalie Nadeau, Peter J Bond, Guy Tran Van Nhieu, Olivera Francetic
Bacterial type 2 secretion systems (T2SS), type 4 pili (T4P) and archaeal flagella assemble fibres from initially membrane-embedded pseudopilin and pilin subunits. Fibre subunits are made as precursors with positively charged N-terminal anchors, whose cleavage via the prepilin peptidase, essential for pilin membrane extraction and assembly, is followed by N-methylation of the mature (pseudo)pilin N-terminus. The conserved Glu residue at position 5 (E5) of mature (pseudo)pilins is essential for assembly. Unlike T4 pilins, where E5 residue substitutions also abolish N-methylation, the E5A variant of T2SS pseudopilin PulG remains N-methylated, but is affected in interaction with the T2SS component PulM...
April 17, 2017: Journal of Molecular Biology
https://www.readbyqxmd.com/read/28426820/the-influence-of-cell-membrane-and-snap25-linker-loop-on-the-dynamics-and-unzipping-of-snare-complex
#10
Yi Shi, Yong Zhang, Jizhong Lou
The soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) complex is composed of three neuronal proteins VAMP2, Syntaxin and SNAP25, which plays a core role during the process of membrane fusion. The zipping assembly of the SNARE complex releases energies and drives the vesicle and cell membrane into close proximity. In this study, we use all-atom molecular dynamics simulations to probe the dynamics of SNARE and its unzipping process in the context of membrane at the atomistic details...
2017: PloS One
https://www.readbyqxmd.com/read/28426222/structural-and-dynamical-properties-of-tetra-alkyl-ammonium-bromide-aqueous-solutions-a-molecular-dynamics-simulation-study-using-a-polarizable-force-field
#11
Dengpan Dong, Justin B Hooper, Dmitry Bedrov
Understanding the behavior of aqueous solutions containing tetra-alkyl ammonium (TAA) cations is of great significance in a number of applications, including polymer membranes for fuel cells. In this work, a polarizable force field has been used to preform atomistic molecular dynamics (MD) simulations of aqueous solutions containing tetra-methyl ammonium (TMA) or tetra-butyl ammonium (TBA) cations and Br counterions. Extensive MD simulations of TMA-Br/water and TBA-Br/water systems were conducted as a function of solution composition (ion pair : water molar ratios of 1:10, 1:20, 1:30, 1:63, 1:500) at atmospheric pressure and 298K...
April 20, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28426203/tyrosine-kinase-activation-and-conformational-flexibility-lessons-from-src-family-tyrosine-kinases
#12
Yilin Meng, Matthew P Pond, Benoît Roux
Protein kinases are enzymes that catalyze the covalent transfer of the γ-phosphate of an adenosine triphosphate (ATP) molecule onto a tyrosine, serine, threonine, or histidine residue in the substrate and thus send a chemical signal to networks of downstream proteins. They are important cellular signaling enzymes that regulate cell growth, proliferation, metabolism, differentiation, and migration. Unregulated protein kinase activity is often associated with a wide range of diseases, therefore making protein kinases major therapeutic targets...
April 20, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28425718/testing-high-concentrations-of-membrane-active-antibiotic-chlorhexidine-via-computational-titration-and-calorimetry
#13
Brad Van Oosten, Drew Marquardt, Thad A Harroun
Coarse grained strategies for membrane simulations are designed to increase the time and length scales of molecular dynamics simulations. For membrane active antibiotics, the concentration dependence of their action presents a tremendous challenge in simulation scale. In this study we examine the effects of concentration for the popular membrane active antibacterial drug chlorhexidine. It presents an interesting biophysical modelling test, where from experimental experience we know that model membranes of DMPC can absorb very high quantities of the drug without disruption...
April 20, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28425152/nmr-structures-and-molecular-dynamics-simulation-of-hylin-a1-peptide-analogs-interacting-with-micelles
#14
Edson Crusca, Amanda Souza Câmara, Carolina Oliveira Matos, Reinaldo Marchetto, Eduardo Maffud Cilli, Luciano Morais Lião, Aline Lima de Oliveira
Antimicrobial peptides are recognized candidates with pharmaceutical potential against epidemic emerging multi-drug resistant bacteria. In this study, we use nuclear magnetic resonance spectroscopy and molecular dynamics simulations to determine the unknown structure and evaluate the interaction with dodecylphosphatidylcholine (DPC) and sodium dodecylsulphate (SDS) micelles with three W(6) -Hylin-a1 analogs antimicrobial peptides (HyAc, HyK, and HyD). The HyAc, HyK, and HyD bound to DPC micelles are all formed by a unique α-helix structure...
April 20, 2017: Journal of Peptide Science: An Official Publication of the European Peptide Society
https://www.readbyqxmd.com/read/28422265/nanoporous-poly-3-hexylthiophene-thin-film-structures-from-self-organization-of-a-tunable-molecular-bottlebrush-scaffold
#15
Suk-Kyun Ahn, Jan-Michael Y Carrillo, Jong K Keum, Jihua Chen, David Uhrig, Bradley S Lokitz, Bobby G Sumpter, S Michael Kilbey
The ability to widely tune the design of macromolecular bottlebrushes provides access to self-assembled nanostructures formed by microphase segregation in melt, thin film and solution that depart from structures adopted by simple linear copolymers. A series of random bottlebrush copolymers containing poly(3-hexylthiophene) (P3HT) and poly(d,l-lactide) (PLA) side chains grafted on a poly(norbornene) backbone were synthesized via ring-opening metathesis polymerization (ROMP) using the grafting through approach...
April 19, 2017: Nanoscale
https://www.readbyqxmd.com/read/28420794/structural-features-and-lipid-binding-domain-of-tubulin-on-biomimetic-mitochondrial-membranes
#16
David P Hoogerheide, Sergei Y Noskov, Daniel Jacobs, Lucie Bergdoll, Vitalii Silin, David L Worcester, Jeff Abramson, Hirsh Nanda, Tatiana K Rostovtseva, Sergey M Bezrukov
Dimeric tubulin, an abundant water-soluble cytosolic protein known primarily for its role in the cytoskeleton, is routinely found to be associated with mitochondrial outer membranes, although the structure and physiological role of mitochondria-bound tubulin are still unknown. There is also no consensus on whether tubulin is a peripheral membrane protein or is integrated into the outer mitochondrial membrane. Here the results of five independent techniques-surface plasmon resonance, electrochemical impedance spectroscopy, bilayer overtone analysis, neutron reflectometry, and molecular dynamics simulations-suggest that α-tubulin's amphipathic helix H10 is responsible for peripheral binding of dimeric tubulin to biomimetic "mitochondrial" membranes in a manner that differentiates between the two primary lipid headgroups found in mitochondrial membranes, phosphatidylethanolamine and phosphatidylcholine...
April 18, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28420346/linoleic-acid-is-this-the-key-that-unlocks-the-quantum-brain-insights-linking-broken-symmetries-in-molecular-biology-mood-disorders-and-personalistic-emergentism
#17
REVIEW
Massimo Cocchi, Chiara Minuto, Lucio Tonello, Fabio Gabrielli, Gustav Bernroider, Jack A Tuszynski, Francesco Cappello, Mark Rasenick
In this paper we present a mechanistic model that integrates subneuronal structures, namely ion channels, membrane fatty acids, lipid rafts, G proteins and the cytoskeleton in a dynamic system that is finely tuned in a healthy brain. We also argue that subtle changes in the composition of the membrane's fatty acids may lead to down-stream effects causing dysregulation of the membrane, cytoskeleton and their interface. Such exquisite sensitivity to minor changes is known to occur in physical systems undergoing phase transitions, the simplest and most studied of them is the so-called Ising model, which exhibits a phase transition at a finite temperature between an ordered and disordered state in 2- or 3-dimensional space...
April 19, 2017: BMC Neuroscience
https://www.readbyqxmd.com/read/28413881/molecular-mechanism-on-stabilizing-huntingtin-n17-helical-structure-in-micelle-environment
#18
Leili Zhang, Hongsuk Kang, Francisco X Vázquez, Leticia Marisel Toledo-Sherman, Binquan Luan, Ruhong Zhou
Huntington's disease is a deadly neurodegenerative disease caused by the fibrilization of huntingtin (HTT) exon-1 protein mutants. Despite extensive efforts over the past decade, much remains unknown about the structures of (mutant) HTT exon-1 and their enigmatic roles in aggregation. Particularly, whether the first 17 residues in the N-terminal (HTT-N17) adopt a helical or a coiled structure remains unclear. Here, with the rigorous study of molecular dynamics simulations, we explored the most possible structures of HTT-N17 in both dodecylphosphocholine (DPC) micelles and aqueous solution, using three commonly applied force fields (OPLS-AA/L, CHARMM36 and AMBER99sb*-ILDNP) to examine the underlying molecular mechanism and rule out the potential artifacts...
April 17, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28412347/interaction-of-kras4b-with-anionic-membranes-a-special-role-for-pip2
#19
Michael C Gregory, Mark A McLean, Stephen G Sligar
KRas4b is a small G-protein whose constitutively active oncogenic mutants are present in 90% of pancreatic cancers. Using fully post-translationally modified KRAS4b, we investigated the role of lipid identity in the recruitment of KRas4b to a membrane surface of defined composition. Application of a newly developed single frequency fluorescence anisotropy decay experiment to this system revealed that KRas4b has a significant binding preference for Nanodisc bilayers containing PIP2. We conducted molecular dynamics simulations to look for an origin of this specificity...
April 13, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28412156/tyrosine-oxidation-and-nitration-in-transmembrane-peptides-is-connected-to-lipid-peroxidation
#20
Silvina Bartesaghminni, Daniel Herrera, Débora M Martinez, Ariel Petruk, Verónica Demicheli, Madia Trujillo, Marcelo A Martí, Darío A Estrín, Rafael Radi
Tyrosine nitration is an oxidative post-translational modification that can occur in proteins associated to hydrophobic bio-structures such as membranes and lipoproteins. In this work, we have studied tyrosine nitration in membranes using a model system consisting of phosphatidylcholine liposomes with pre-incorporated tyrosine-containing 23 amino acid transmembrane peptides. Tyrosine residues were located at positions 4, 8 or 12 of the amino terminal, resulting in different depths in the bilayer. Tyrosine nitration was accomplished by exposure to peroxynitrite and a peroxyl radical donor or hemin in the presence of nitrite...
April 13, 2017: Archives of Biochemistry and Biophysics
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