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membrane protein folding

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https://www.readbyqxmd.com/read/28102001/evaluation-of-the-hybrid-resolution-pace-model-for-the-study-of-folding-insertion-and-pore-formation-of-membrane-associated-peptides
#1
Michael D Ward, Shivangi Nangia, Eric R May
The PACE force field presents an attractive model for conducting molecular dynamics simulations of membrane-protein systems. PACE is a hybrid model, in which lipids and solvents are coarse-grained consistent with the MARTINI mapping, while proteins are described by a united atom model. However, given PACE is linked to MARTINI, which is widely used to study membranes, the behavior of proteins interacting with membranes has only been limitedly examined in PACE. In this study, PACE is used to examine the behavior of several peptides in membrane environments, namely WALP peptides, melittin and influenza hemagglutinin fusion peptide (HAfp)...
January 19, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/28097795/impaired-n-linked-glycosylation-of-uptake-and-efflux-transporters-in-human-nonalcoholic-fatty-liver-disease
#2
John D Clarke, Petr Novak, April D Lake, Rhiannon N Hardwick, Nathan J Cherrington
BACKGROUND & AIMS: N-linked glycosylation of proteins is critical for proper protein folding and trafficking to the plasma membrane. Drug transporters are one class of proteins that have reduced function when glycosylation is impaired. N-linked glycosylation of plasma proteins has also been investigated as a biomarker for several liver diseases, including non-alcoholic fatty liver disease (NAFLD). The purpose of this study was to assess the transcriptomic expression of genes involved in protein processing and glycosylation, and to determine the glycosylation status of key drug transporters during human NAFLD progression...
January 18, 2017: Liver International: Official Journal of the International Association for the Study of the Liver
https://www.readbyqxmd.com/read/28097727/energetics-kinetics-and-pathway-of-snare-folding-and-assembly-revealed-by-optical-tweezers
#3
REVIEW
Yongli Zhang
Soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs) are universal molecular engines that drive membrane fusion. Particularly, synaptic SNAREs mediate fast calcium-triggered fusion of neurotransmitter-containing vesicles with plasma membranes for synaptic transmission, the basis of all thought and action. During membrane fusion, complementary SNAREs located on two apposed membranes (often called t- and v-SNAREs) join together to assemble into a parallel four-helix bundle, releasing the energy to overcome the energy barrier for fusion...
January 18, 2017: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/28095524/combination-of-collagen-barrier-membrane-with-enamel-matrix-derivative-liquid-improves-osteoblast-adhesion-and-differentiation
#4
Richard J Miron, Masako Fujioka-Kobayashi, Daniel Buser, Yufeng Zhang, Dieter D Bosshardt, Anton Sculean
PURPOSE: Collagen barrier membranes were first introduced to regenerative periodontal and oral surgery to prevent fast ingrowing soft tissues (ie, epithelium and connective tissue) into the defect space. More recent attempts have aimed at combining collagen membranes with various biologics/growth factors to speed up the healing process and improve the quality of regenerated tissues. Recently, a new formulation of enamel matrix derivative in a liquid carrier system (Osteogain) has demonstrated improved physico-chemical properties for the adsorption of enamel matrix derivative to facilitate protein adsorption to biomaterials...
January 2017: International Journal of Oral & Maxillofacial Implants
https://www.readbyqxmd.com/read/28089452/co-folding-of-a-flif-flig-split-domain-forms-the-basis-of-the-ms-c-ring-interface-within-the-bacterial-flagellar-motor
#5
Michael J Lynch, Robert Levenson, Eun A Kim, Ria Sircar, David F Blair, Frederick W Dahlquist, Brian R Crane
The interface between the membrane (MS) and cytoplasmic (C) rings of the bacterial flagellar motor couples torque generation to rotation within the membrane. The structure of the C-terminal helices of the integral membrane protein FliF (FliFC) bound to the N terminal domain of the switch complex protein FliG (FliGN) reveals that FliGN folds around FliFC to produce a topology that closely resembles both the middle and C-terminal domains of FliG. The interface is consistent with solution-state nuclear magnetic resonance, small-angle X-ray scattering, in vivo interaction studies, and cellular motility assays...
December 31, 2016: Structure
https://www.readbyqxmd.com/read/28088573/heat-shock-proteins-and-cancer-how-can-nanomedicine-be-harnessed
#6
REVIEW
Félix Sauvage, Samir Messaoudi, Elias Fattal, Gillian Barratt, Juliette Vergnaud-Gauduchon
Heat shock protein (hsp90) is an interesting target for cancer therapy because it is involved in the folding and stabilization of numerous proteins, including many that contribute to the development of cancer. It is part of the chaperone machinery that includes other heat shock proteins (hsp70, hsp27, hsp40) and is mainly localized in the cytosol, although many analogues or isoforms can be found in mitochondrion, endoplasmic reticulum and the cell membrane. Many potential inhibitors of hsp90 have been tested for cancer therapy but their usefulness is limited by their poor solubility in water and their ability to reach the target cells and the correct intracellular compartment...
January 11, 2017: Journal of Controlled Release: Official Journal of the Controlled Release Society
https://www.readbyqxmd.com/read/28087757/alternative-transcription-of-sodium-bicarbonate-transporter-slc4a7-gene-enhanced-by-single-nucleotide-polymorphisms
#7
Hae Jeong Park, Soojung Lee, Eunji Ju, Jayre A Jones, Inyeong Choi
Genome-wide association studies have identified the single nucleotide polymorphism (SNP) rs3278 in the human SLC4A7 gene as one of the marker loci for addiction vulnerability. This marker is located in an intron of the gene, and its genomic role has been unknown. In this study, we examined rs3278 and three adjacent SNPs prevalent in alcoholics for their effects on an alternative promoter that would lead to the production of the N-terminally truncated protein NBCn1ΔN450, missing the first 450 amino acids. Analysis of the transcription start site database and a promoter prediction algorithm identified a cluster of three promoters in intron 7 and two short CpG-rich sites in intron 6...
January 13, 2017: Physiological Genomics
https://www.readbyqxmd.com/read/28077332/molecular-identification-of-star-and-3%C3%AE-hsd1-and-characterization-in-response-to-gnih-stimulation-in-protogynous-hermaphroditic-grouper-epinephelus-coioides
#8
Qingqing Wang, Xin Qi, Haipei Tang, Yin Guo, Shuisheng Li, Gaofei Li, Xiaoli Yang, Haifa Zhang, Xiaochun Liu, Haoran Lin
Gonadal steroids are critical factors in reproduction and sex reverse process. StAR (steroidogenic acute regulatory protein), transferring the cholesterol from the outer mitochondrial membrane to the inner membrane, is the rate-limiting factor of steroidogenesis. 3βHSD (3β-hydroxysteroid dehydrogenase/Δ5-Δ4 isomerase), converting Δ5-steroids into Δ4-steroids, is an important oxidoreductase in steroidogenesis. In the present study, StAR and 3βHSD1 were cloned and characterized from protogynous orange-spotted grouper...
January 8, 2017: Comparative Biochemistry and Physiology. Part B, Biochemistry & Molecular Biology
https://www.readbyqxmd.com/read/28075131/classical-galactosemia-insight-into-molecular-pathomechanisms-by-differential-membrane-proteomics-of-fibroblasts-under-galactose-stress
#9
Simon Staubach, Stefan Müller, Murat Pekmez, Franz-Georg Hanisch
Classical galactosemia, a hereditary metabolic disease caused by the deficiency of galactose-1-phosphate uridyltransferase (GALT; EC 2.7.712), results in an impaired galactose metabolism and serious long-term developmental affection of the CNS and ovaries, potentially related in part to endogenous galactose-induced protein dysglycosylation. In search for galactose-induced changes in membrane raft proteomes of GALT-deficient cells, we performed differential analyses of lipid rafts from patient-derived (Q) and sex- and age-matched control fibroblasts (H) in the presence or absence of the stressor...
January 11, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28073120/nano-pelargonidin-protects-hyperglycemic-induced-l6-cells-against-mitochondrial-dysfunction
#10
Asmita Samadder, Debojyoti Tarafdar, Suresh K Abraham, Kumaresh Ghosh, Anisur Rahman Khuda-Bukhsh
Nano-encapsulation of several natural products has become an important tool in enhancing the bioavailability of some modern drugs against many diseases. Pelargonidin is an anthocyanidin found in many fruits and vegetables. Pelargonidin is loaded with poly-lactide-co-glycolic-acid, a non-toxic biodegradable polymer, to produce nano-pelargonidin. Size, morphology, zeta potential, and planar uniformity of formulated nano-pelargonidin were determined by atomic force microscopy and dynamic light scattering. The time required for cellular entry, folds of nano-pelargonidin, and drug encapsulation efficiency of poly-lactide-co-glycolic-acid were also ascertained...
January 10, 2017: Planta Medica
https://www.readbyqxmd.com/read/28071645/integrating-mass-spectrometry-with-md-simulations-reveals-the-role-of-lipids-in-na-h-antiporters
#11
Michael Landreh, Erik G Marklund, Povilas Uzdavinys, Matteo T Degiacomi, Mathieu Coincon, Joseph Gault, Kallol Gupta, Idlir Liko, Justin L P Benesch, David Drew, Carol V Robinson
Na(+)/H(+) antiporters are found in all kingdoms of life and exhibit catalysis rates that are among the fastest of all known secondary-active transporters. Here we combine ion mobility mass spectrometry and molecular dynamics simulations to study the conformational stability and lipid-binding properties of the Na(+)/H(+) exchanger NapA from Thermus thermophilus and compare this to the prototypical antiporter NhaA from Escherichia coli and the human homologue NHA2. We find that NapA and NHA2, but not NhaA, form stable dimers and do not selectively retain membrane lipids...
January 10, 2017: Nature Communications
https://www.readbyqxmd.com/read/28069645/a-novel-phosphodiesterase-of-the-gdpp-family-modulates-cyclic-di-amp-levels-in-response-to-cell-membrane-stress-in-daptomycin-resistant-enterococci
#12
Xu Wang, Milya Davlieva, Jinnethe Reyes, Diana Panesso, Cesar A Arias, Yousif Shamoo
Substitutions in the LiaFSR membrane stress pathway are frequently associated with emergence of antimicrobial peptide resistance in both Enterococcus faecalis and Enterococcus faecium Cyclic di-AMP (c-di-AMP) is an important signal molecule that affects many aspects of bacterial physiology including stress response. We have identified previously a mutation in a gene (designated yybT) in E. faecalis that was associated with development of daptomycin resistance resulting in a change at position 440 in the predicted protein (yybT(I440S))...
January 9, 2017: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/28069414/peptides-derived-from-%C3%AE-lactalbumin-membrane-binding-helices-oligomerize-in-presence-of-lipids-and-disrupt-bilayers
#13
Øyvind Strømland, Ørjan S Handegård, Morten G Larsen, Hanzhen Wen, Øyvind Halskau
Helix A and -C of α-Lactalbumin, a loosely folded amphitropic protein, perturb lipid monolayers by the formation of amyloid pore-like structures. To investigate whether these helices are able to disrupt fully formed bilayers, we designed peptides comprised of Helix A and -C, and investigated their membrane-perturbing properties. The peptides, designated A-Cage-C and A-Lnk-C, were prepared with tryptophan sites in the helical and the spacer segments in order to monitor which part were involved in membrane association under given conditions...
January 6, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28067619/analyzing-native-membrane-protein-assembly-in-nanodiscs-by-combined-non-covalent-mass-spectrometry-and-synthetic-biology
#14
Erik Henrich, Oliver Peetz, Christopher Hein, Aisha Laguerre, Beate Hoffmann, Jan Hoffmann, Volker Dötsch, Frank Bernhard, Nina Morgner
Membrane proteins frequently assemble into higher order homo- or hetero-oligomers within their natural lipid environment. This complex formation can modulate their folding, activity as well as substrate selectivity. Non-disruptive methods avoiding critical steps such as membrane disintegration, transfer into artificial environments or chemical modifications are therefore essential to analyze molecular mechanisms of native membrane protein assemblies. The combination of cell-free synthetic biology, nanodisc-technology and non-covalent mass spectrometry provides excellent synergies for the analysis of membrane protein oligomerization within defined membranes...
January 9, 2017: ELife
https://www.readbyqxmd.com/read/28062948/low-levels-of-prohibitin-in-substantia-nigra-makes-dopaminergic-neurons-vulnerable-in-parkinson-s-disease
#15
Debashis Dutta, Nilufar Ali, Emili Banerjee, Raghavendra Singh, Amit Naskar, Ramesh Kumar Paidi, Kochupurackal P Mohanakumar
Since substantia nigra (SN) and ventral tegmental area (VTA) dopaminergic neurons are, respectively, susceptible or largely unaffected in Parkinson's disease (PD), we searched for protein(s) that regulates this differential sensitivity. Differentially, expressed proteins in SN and VTA were investigated employing two-directional gel electrophoresis- matrix-assisted laser desorption ionization time of flight (MALDI-TOF-TOF) analyses. Prohibitin, which is involved in mitochondrial integrity, was validated using immunoblot, qRT-PCR, and immunohistochemistry in normal mice as well as 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-model, PD postmortem human brains, and PD cybrids...
January 6, 2017: Molecular Neurobiology
https://www.readbyqxmd.com/read/28062807/junctional-adhesion-molecule-a-expression-in-the-murine-epididymal-tract-and-accessory-organs-and-acquisition-by-maturing-sperm
#16
Kathie Z Wu, Kun Li, Deni S Galileo, Patricia A Martin-DeLeon
STUDY QUESTION: Is junctional adhesion molecule A (JAM-A), a sperm protein essential for normal motility, expressed in the murine post-testicular pathway and involved in sperm maturation? SUMMARY ANSWER: JAM-A is present in the prostate and seminal vesicles and in all three regions of the epididymis where it is secreted in epididymosomes in the luminal fluid and can be delivered to sperm in vitro. WHAT IS KNOWN ALREADY: JAM-A shares with the plasma membrane Ca(2+)ATPase 4 (PMCA4, the major Ca(2+) efflux pump in murine sperm) a common interacting partner, CASK (Ca(2+)/CaM-dependent serine kinase)...
January 6, 2017: Molecular Human Reproduction
https://www.readbyqxmd.com/read/28062509/adam17-deficiency-promotes-atherosclerosis-by-enhanced-tnfr2-signaling-in-mice
#17
Alexandros Nicolaou, Zhen Zhao, Bernd H Northoff, Kristina Sass, Andreas Herbst, Alexander Kohlmaier, Athena Chalaris, Christian Wolfrum, Christian Weber, Sabine Steffens, Stefan Rose-John, Daniel Teupser, Lesca M Holdt
OBJECTIVE: ADAM17 (a disintegrin and metalloproteinase 17) is a sheddase releasing different types of membrane-bound proteins, including adhesion molecules, cytokines, and their receptors as well as inflammatory mediators. Because these substrates modulate important mechanisms of atherosclerosis, we hypothesized that ADAM17 might be involved in the pathogenesis of this frequent disease. APPROACH AND RESULTS: Because Adam17-knockout mice are not viable, we studied the effect of Adam17 deficiency on atherosclerosis in Adam17 hypomorphic mice (Adam17(ex/ex)), which have low residual Adam17 expression...
December 22, 2016: Arteriosclerosis, Thrombosis, and Vascular Biology
https://www.readbyqxmd.com/read/28062226/molecular-characterization-and-expression-analysis-of-three-subclasses-of-igt-in-rainbow-trout-oncorhynchus-mykiss
#18
Nu Zhang, Xu-Jie Zhang, Dan-Dan Chen, J Oriol Sunyer, Yong-An Zhang
As the teleost specific immunoglobulin, IgT plays important roles in systemic and mucosal immunity. In the current study, in rainbow trout, we have cloned the heavy chain (Igτ) genes of a secretory form of IgT2 as well as the membrane and secretory forms of a third IgT subclass, termed IgT3. Conserved cysteine and tryptophan residues that are crucial for the folding of the immunoglobulin domain as well as hydrophobic and hydrophilic residues within CART motif were identified in all IgT subclasses. Through analysis of the rainbow trout genome assembly, Igτ3 gene was found localized upstream of Igτ1 gene, while Igτ2 gene situated on another scaffold...
January 3, 2017: Developmental and Comparative Immunology
https://www.readbyqxmd.com/read/28060929/a-single-vector-platform-for-high-level-gene-transduction-of-central-neurons-adeno-associated-virus-vector-equipped-with-the-tet-off-system
#19
Jaerin Sohn, Megumu Takahashi, Shinichiro Okamoto, Yoko Ishida, Takahiro Furuta, Hiroyuki Hioki
Visualization of neurons is indispensable for the investigation of neuronal circuits in the central nervous system. Virus vectors have been widely used for labeling particular subsets of neurons, and the adeno-associated virus (AAV) vector has gained popularity as a tool for gene transfer. Here, we developed a single AAV vector Tet-Off platform, AAV-SynTetOff, to improve the gene-transduction efficiency, specifically in neurons. The platform is composed of regulator and response elements in a single AAV genome...
2017: PloS One
https://www.readbyqxmd.com/read/28058535/molecular-and-structural-characteristics-of-multidrug-resistance-associated-protein-7-in-chinese-liver-fluke-clonorchis-sinensis
#20
Fuhong Dai, Won Gi Yoo, Ji-Yun Lee, Yanyan Lu, Jhang Ho Pak, Woon-Mok Sohn, Sung-Jong Hong
Multidrug resistance-associated protein 7 (MRP7, ABCC10) is a C subfamily member of the ATP-binding cassette (ABC) superfamily. MRP7 is a lipophilic anion transporter that pumps endogenous and xenobiotic substrates from the cytoplasm to the extracellular milieu. Here, we cloned and characterized CsMRP7 as a novel ABC transporter from the Chinese liver fluke, Clonorchis sinensis. Full-length cDNA of CsMRP7 was 5174 nt, encoded 1636 amino acids (aa), and harbored a 147-bp 5'-untranslated region (5'-UTR) and 116-bp 3'-UTR...
January 5, 2017: Parasitology Research
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