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Membrane curvature

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https://www.readbyqxmd.com/read/27914065/computational-design-of-membrane-curvature-sensing-peptides
#1
Armando Jerome de Jesus, Hang Yin
Computer simulations have become an indispensable tool in studying molecular biological systems. The unmatched spatial and temporal resolution that it offers enables for microscopic-level views into the dynamics and mechanics of biological systems. Recent advances in hardware resources have also opened up to computer simulations the investigation of longer timescale biological processes and larger systems. The study of membrane proteins or peptides especially benefits from simulations due to difficulties related to crystallization of such proteins in a membrane environment...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27903801/inhibition-of-an-aquatic-rhabdovirus-demonstrates-promise-of-a-broad-spectrum-antiviral-for-use-in-aquaculture
#2
Bethany F Balmer, Rachel L Powers, Ting-Hu Zhang, Jihye Lee, Frederic Vigant, Benhur Lee, Michael E Jung, Maureen K Purcell, Kevin Snekvik, Hector C Aguilar
: Many enveloped viruses cause devastating disease in aquaculture, resulting in significant economic impact. LJ001 is a broad-spectrum antiviral compound that inhibits enveloped viral infections by specifically targeting phospholipids in the lipid bilayer via production of singlet oxygen ((1)O2). This stabilizes positive curvature and decreases membrane fluidity, which inhibits viral-cell membrane fusion during viral entry. Based on previous mammalian studies and the requirement of light for activation of LJ001, we hypothesized that LJ001 may be useful as a preventative and/or therapeutic agent for enveloped viral infections in aquaculture...
November 30, 2016: Journal of Virology
https://www.readbyqxmd.com/read/27892522/sars-cov-fusion-peptides-induce-membrane-surface-ordering-and-curvature
#3
Luis G M Basso, Eduardo F Vicente, Edson Crusca, Eduardo M Cilli, Antonio J Costa-Filho
Viral membrane fusion is an orchestrated process triggered by membrane-anchored viral fusion glycoproteins. The S2 subunit of the spike glycoprotein from severe acute respiratory syndrome (SARS) coronavirus (CoV) contains internal domains called fusion peptides (FP) that play essential roles in virus entry. Although membrane fusion has been broadly studied, there are still major gaps in the molecular details of lipid rearrangements in the bilayer during fusion peptide-membrane interactions. Here we employed differential scanning calorimetry (DSC) and electron spin resonance (ESR) to gather information on the membrane fusion mechanism promoted by two putative SARS FPs...
November 28, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27873063/-a%C3%A2-new-technique-to-facilitate-donor-preparation-for-dmek-surgery
#4
P W Rieck, T Engels
BACKGROUND: Descemet membrane endothelial keratoplasty (DMEK) is becoming more and more the method of choice to treat corneal endothelial diseases in specialized centers. The reasons that prevent this technique from becoming widespread are the delicate donor tissue preparation. By inverting the curvature of the cornea from convex to concave after mounting onto an artificial anterior chamber, we developed a combined manual delamination and hydrodissection technique, which allows a rapid and endothelium-preserving method of separating donor Descemet membranes from the underlying stroma...
November 21, 2016: Der Ophthalmologe: Zeitschrift der Deutschen Ophthalmologischen Gesellschaft
https://www.readbyqxmd.com/read/27872254/a-family-of-membrane-shaping-proteins-at-er-subdomains-regulates-pre-peroxisomal-vesicle-biogenesis
#5
Amit S Joshi, Xiaofang Huang, Vineet Choudhary, Tim P Levine, Junjie Hu, William A Prinz
Saccharomyces cerevisiae contains three conserved reticulon and reticulon-like proteins that help maintain ER structure by stabilizing high membrane curvature in ER tubules and the edges of ER sheets. A mutant lacking all three proteins has dramatically altered ER morphology. We found that ER shape is restored in this mutant when Pex30p or its homologue Pex31p is overexpressed. Pex30p can tubulate membranes both in cells and when reconstituted into proteoliposomes, indicating that Pex30p is a novel ER-shaping protein...
November 21, 2016: Journal of Cell Biology
https://www.readbyqxmd.com/read/27869216/erratum-lipid-membrane-mediated-attraction-between-curvature-inducing-objects
#6
Casper van der Wel, Afshin Vahid, Anđela Šarić, Timon Idema, Doris Heinrich, Daniela J Kraft
No abstract text is available yet for this article.
November 21, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27853010/femtosecond-laser-assisted-deep-anterior-lamellar-keratoplasty-with-big-bubble-technique-for-keratoconus
#7
Yan Lu, Xiangfei Chen, Liping Yang, Chunyan Xue, Zhenping Huang
PURPOSE: The purpose of this study was to evaluate the clinical results after deep anterior lamellar keratoplasty (DALK) assisted by the femtosecond laser with big-bubble technique for keratoconus. METHODS: A case series of 22 eyes in 19 patients with keratoconus was enrolled in the study. The 500-kHz VisuMax femtosecond laser (Carl Zeiss Meditec AG, Jena, Germany) was used to create a vertical side cut on donor and recipient corneas. Intraoperative and postoperative complications, uncorrected visual acuity, best-corrected visual acuity, corneal curvature, and central corneal thickness were evaluated in all patients...
September 2016: Indian Journal of Ophthalmology
https://www.readbyqxmd.com/read/27851940/a-coiled-coil-peptide-shaping-lipid-bilayers-upon-fusion
#8
Martin Rabe, Christopher Aisenbrey, Kristyna Pluhackova, Vincent de Wert, Aimee L Boyle, Didjay F Bruggeman, Sonja A Kirsch, Rainer A Böckmann, Alexander Kros, Jan Raap, Burkhard Bechinger
A system based on two designed peptides, namely the cationic peptide K, (KIAALKE)3, and its complementary anionic counterpart called peptide E, (EIAALEK)3, has been used as a minimal model for membrane fusion, inspired by SNARE proteins. Although the fact that docking of separate vesicle populations via the formation of a dimeric E/K coiled-coil complex can be rationalized, the reasons for the peptides promoting fusion of vesicles cannot be fully explained. Therefore it is of significant interest to determine how the peptides aid in overcoming energetic barriers during lipid rearrangements leading to fusion...
November 15, 2016: Biophysical Journal
https://www.readbyqxmd.com/read/27849600/mapping-membrane-activity-in-undiscovered-peptide-sequence-space-using-machine-learning
#9
Ernest Y Lee, Benjamin M Fulan, Gerard C L Wong, Andrew L Ferguson
There are some ∼1,100 known antimicrobial peptides (AMPs), which permeabilize microbial membranes but have diverse sequences. Here, we develop a support vector machine (SVM)-based classifier to investigate ⍺-helical AMPs and the interrelated nature of their functional commonality and sequence homology. SVM is used to search the undiscovered peptide sequence space and identify Pareto-optimal candidates that simultaneously maximize the distance σ from the SVM hyperplane (thus maximize its "antimicrobialness") and its ⍺-helicity, but minimize mutational distance to known AMPs...
November 29, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27834997/exploiting-lipid-permutation-symmetry-to-compute-membrane-remodeling-free-energies
#10
Greg Bubnis, Herre Jelger Risselada, Helmut Grubmüller
A complete physical description of membrane remodeling processes, such as fusion or fission, requires knowledge of the underlying free energy landscapes, particularly in barrier regions involving collective shape changes, topological transitions, and high curvature, where Canham-Helfrich (CH) continuum descriptions may fail. To calculate these free energies using atomistic simulations, one must address not only the sampling problem due to high free energy barriers, but also an orthogonal sampling problem of combinatorial complexity stemming from the permutation symmetry of identical lipids...
October 28, 2016: Physical Review Letters
https://www.readbyqxmd.com/read/27832339/vitrectomy-and-scleral-imbrication-in-patients-with-myopic-traction-maculopathy-and-macular-hole-retinal-detachment
#11
Yoshimasa Ando, Akito Hirakata, Arisa Ohara, Reiji Yokota, Tadashi Orihara, Kazunari Hirota, Takashi Koto, Makoto Inoue
PURPOSE: To determine the outcomes of vitrectomy with scleral imbrication in highly myopic eyes with either myopic traction maculopathy (MTM) or macular hole retinal detachment (MHRD). METHODS: The medical records of 17 patients who had undergone vitrectomy with internal limiting membrane (ILM) peeling and scleral imbrication for MTM or MHRD were reviewed. The best-corrected visual acuities (BCVAs), the axial length, the macular hole (MH) closure rate, and the shape of the posterior segment determined by optical coherence tomography were evaluated...
November 10, 2016: Graefe's Archive for Clinical and Experimental Ophthalmology
https://www.readbyqxmd.com/read/27823927/physical-mechanisms-of-micro-and-nanodomain-formation-in-multicomponent-lipid-membranes
#12
REVIEW
Friederike Schmid
This article summarizes a variety of physical mechanisms proposed in the literature, which can generate micro- and nanodomains in multicomponent lipid bilayers and biomembranes. It mainly focusses on lipid-driven mechanisms that do not involve direct protein-protein interactions. Specifically, it considers (i) equilibrium mechanisms based on lipid-lipid phase separation such as critical cluster formation close to critical points, and multiple domain formation in curved geometries, (ii) equilibrium mechanisms that stabilize two-dimensional microemulsions, such as the effect of linactants and the effect of curvature-composition coupling in bilayers and monolayers, and (iii) non-equilibrium mechanisms induced by the interaction of a biomembrane with the cellular environment, such as membrane recycling and the pinning effects of the cytoplasm...
November 5, 2016: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/27821736/c-terminal-domain-of-mammalian-complexin-1-localizes-to-highly-curved-membranes
#13
Jihong Gong, Ying Lai, Xiaohong Li, Mengxian Wang, Jeremy Leitz, Yachong Hu, Yunxiang Zhang, Ucheor B Choi, Daniel Cipriano, Richard A Pfuetzner, Thomas C Südhof, Xiaofei Yang, Axel T Brunger, Jiajie Diao
In presynaptic nerve terminals, complexin regulates spontaneous "mini" neurotransmitter release and activates Ca(2+)-triggered synchronized neurotransmitter release. We studied the role of the C-terminal domain of mammalian complexin in these processes using single-particle optical imaging and electrophysiology. The C-terminal domain is important for regulating spontaneous release in neuronal cultures and suppressing Ca(2+)-independent fusion in vitro, but it is not essential for evoked release in neuronal cultures and in vitro...
November 22, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27806910/structure-and-function-of-pspa-and-vipp1-n-terminal-peptides-insights-into-the-membrane-stress-sensing-and-mitigation
#14
Christopher McDonald, Goran Jovanovic, B A Wallace, Oscar Ces, Martin Buck
The phage shock protein (Psp) response maintains integrity of the inner membrane (IM) in response to extracytoplasmic stress conditions and is widely distributed amongst enterobacteria. Its central component PspA, a member of the IM30 peripheral membrane protein family, acts as a major effector of the system through its direct association with the IM. Under non-stress conditions PspA also negatively regulates its own expression via direct interaction with the AAA+ ATPase PspF. PspA has a counterpart in cyanobacteria called Vipp1, which is implicated in protection of the thylakoid membranes...
October 30, 2016: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/27806280/influence-of-ganglioside-gm1-concentration-on-lipid-clustering-and-membrane-properties-and-curvature
#15
Dhilon S Patel, Soohyung Park, Emilia L Wu, Min Sun Yeom, Göran Widmalm, Jeffery B Klauda, Wonpil Im
Gangliosides are a class of glycosphingolipids (GSLs) with amphiphilic character that are found at the outer leaflet of the cell membranes, where their ability to organize into special domains makes them vital cell membrane components. However, a molecular understanding of GSL-rich membranes in terms of their clustered organization, stability, and dynamics is still elusive. To gain molecular insight into the organization and dynamics of GSL-rich membranes, we performed all-atom molecular-dynamics simulations of bicomponent ganglioside GM1 in 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) phospholipid bilayers with varying concentrations of GM1 (10%, 20%, and 30%)...
November 1, 2016: Biophysical Journal
https://www.readbyqxmd.com/read/27806264/membrane-shape-instability-induced-by-protein-crowding
#16
Zhiming Chen, Ehsan Atefi, Tobias Baumgart
Peripheral proteins can bend membranes through several different mechanisms, including scaffolding, wedging, oligomerization, and crowding. The crowding effect in particular has received considerable attention recently, in part because it is a colligative mechanism-implying that it could, in principle, be explored by any peripheral protein. Here we sought to clarify to what extent this mechanism is exploited by endocytic accessory proteins. We quantitatively investigate membrane curvature generation by means of a GUV shape stability assay...
November 1, 2016: Biophysical Journal
https://www.readbyqxmd.com/read/27794305/the-role-of-compression-in-the-simultaneous-masker-phase-effect
#17
Hisaaki Tabuchi, Bernhard Laback, Thibaud Necciari, Piotr Majdak
Peripheral compression is believed to play a major role in the masker phase effect (MPE). While compression is almost instantaneous, activation of the efferent system reduces compression in a temporally evolving manner. To study the role of efferent-controlled compression in the MPE, in experiment 1, simultaneous masking of a 30-ms 4-kHz tone by 40-ms Schroeder-phase harmonic complexes was measured with on- and off-frequency precursors as a function of masker phase curvature for two masker levels (60 and 90 dB sound pressure level)...
October 2016: Journal of the Acoustical Society of America
https://www.readbyqxmd.com/read/27791134/daptomycin-inhibits-cell-envelope-synthesis-by-interfering-with-fluid-membrane-microdomains
#18
Anna Müller, Michaela Wenzel, Henrik Strahl, Fabian Grein, Terrens N V Saaki, Bastian Kohl, Tjalling Siersma, Julia E Bandow, Hans-Georg Sahl, Tanja Schneider, Leendert W Hamoen
Daptomycin is a highly efficient last-resort antibiotic that targets the bacterial cell membrane. Despite its clinical importance, the exact mechanism by which daptomycin kills bacteria is not fully understood. Different experiments have led to different models, including (i) blockage of cell wall synthesis, (ii) membrane pore formation, and (iii) the generation of altered membrane curvature leading to aberrant recruitment of proteins. To determine which model is correct, we carried out a comprehensive mode-of-action study using the model organism Bacillus subtilis and different assays, including proteomics, ionomics, and fluorescence light microscopy...
October 24, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/27771858/curvature-correction-to-the-mobility-of-fluid-membrane-inclusions
#19
D R Daniels
Using rigorous low-Reynolds-number hydrodynamic theory on curved surfaces, we provide, via a Stokeslet-type approach, a general and concise expression for the leading-order curvature correction to the canonical, planar, Saffman-Delbrück value of the diffusion constant for a small inclusion embedded in an arbitrarily (albeit weakly) curved fluid membrane. In order to demonstrate the efficacy and utility of this general result, we apply our theory to the specific case of calculating the diffusion coefficient of a locally curvature inducing membrane inclusion...
October 2016: European Physical Journal. E, Soft Matter
https://www.readbyqxmd.com/read/27766858/solid-state-nmr-investigation-of-the-structural-topology-and-lipid-interactions-of-a-viral-fusion-protein-chimera-containing-the-fusion-peptide-and-transmembrane-domain
#20
Hongwei Yao, Myungwoon Lee, Shu Y Liao, Mei Hong
The fusion peptide (FP) and transmembrane domain (TMD) of viral fusion proteins play important roles during virus-cell membrane fusion, by inducing membrane curvature and transient dehydration. The structure of the water-soluble ectodomain of viral fusion proteins has been extensively studied crystallographically, but the structures of the FP and TMD bound to phospholipid membranes are not well understood. We recently investigated the conformations and lipid interactions of the separate FP and TMD peptides of the parainfluenza virus 5 (PIV5) fusion protein F using solid-state NMR...
October 21, 2016: Biochemistry
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