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https://www.readbyqxmd.com/read/28732436/downregulation-of-aquaporin3-in-systemic-sclerosis-dermal-fibroblasts
#1
Bahman Yousefi, Mahdi Mahmoudi, Abdolfattah Sarafnejad, Elham Karimizadeh, Elham Farhadi, Ahmad Reza Jamshidi, Hoda Kavosi, Saeed Aslani, Farhad Gharibdoost
Skin dryness and thickening are hallmarks of systemic sclerosis (SSc) disease. Aquaporins (AQPs) are plasma membrane proteins that transport glycerol and water, resulting in water retention and skin hydration. Expression of AQPs has been evaluated in human normal skin. However, expression of these proteins in SSc dermal fibroblasts has not yet been reported. The aim of this study was to assess the expression profile of AQPs in dermal fibroblasts of SSc patients. Fibroblast cells were extracted from SSc and healthy skin biopsies and characterized using fibroblast surface protein antibody...
June 2017: Iranian Journal of Allergy, Asthma, and Immunology
https://www.readbyqxmd.com/read/28731091/developing-force-fields-when-experimental-data-is-sparse-amber-gaff-compatible-parameters-for-inorganic-and-alkyl-oxoanions
#2
Sadra Kashefolgheta, Ana Vila Verde
We present a set of Lennard-Jones parameters for classical, all-atom models of acetate and various alkylated and non-alkylated forms of sulfate, sulfonate and phosphate ions, optimized to reproduce their interactions with water and with the physiologically relevant sodium, ammonium and methylammonium cations. The parameters are internally consistent and are fully compatible with the Generalized Amber Force Field (GAFF), the AMBER force field for proteins, the accompanying TIP3P water model and the sodium model of Joung and Cheatham...
July 21, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28730525/identification-of-a-seed-coat-specific-promoter-fragment-from-the-arabidopsis-mucilage-modified4-gene
#3
Gillian H Dean, Zhaoqing Jin, Lin Shi, Elahe Esfandiari, Robert McGee, Kylie Nabata, Tiffany Lee, Ljerka Kunst, Tamara L Western, George W Haughn
The Arabidopsis seed coat-specific promoter fragment described is an important tool for basic and applied research in Brassicaceae species. During differentiation, the epidermal cells of the Arabidopsis seed coat produce and secrete large quantities of mucilage. On hydration of mature seeds, this mucilage becomes easily accessible as it is extruded to form a tightly attached halo at the seed surface. Mucilage is composed mainly of pectin, and also contains the key cell wall components cellulose, hemicellulose, and proteins, making it a valuable model for studying numerous aspects of cell wall biology...
July 20, 2017: Plant Molecular Biology
https://www.readbyqxmd.com/read/28729386/dormancy-in-embryos-insight-from-hydrated-encysted-embryos-of-an-aquatic-invertebrate
#4
Tamar Ziv, Vered Chalifa-Caspi, Nadav Denekamp, Inbar Plaschkes, Sylwiya Sylwia Kierszniowska, Idit Blais, Arie Admon, Esther Lubzens
Numerous aquatic invertebrates remain dormant for decades in a hydrated state as encysted embryos. In search for functional pathways associated with this form of dormancy, we used label-free quantitative proteomics to compare the proteomes of hydrated encysted dormant embryos (resting eggs; RE) with non-dormant embryos (amictic eggs; AM) of the rotifer Brachionus plicatilis</p> <p>A total of 2,631 proteins were identified in rotifer eggs. About 62% proteins showed higher abundance in AM relative to RE (Fold Change>3; p=0...
July 20, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28728032/tunable-fluorescence-quenching-near-the-graphene-aqueous-interface
#5
Aaron W Chen, Alejandro L Briseno, Maria M Santore
With increased interest in graphene-based sensors for biomolecules and other targets, we investigated the impact of ionic strength on the steady-state emissions from fluorescein labels on proteins adsorbing on pristine CVD (chemical vapor deposited)-graphene on a silica support. Using the model system of fluorescein-tagged fibrinogen we demonstrated that, for fluorescein tags on adsorbed fibrinogen, emission intensity was very sensitive to the salt concentration. This behavior was not seen for fluorescein-tagged fibrinogen in solution...
July 6, 2017: Journal of Colloid and Interface Science
https://www.readbyqxmd.com/read/28723250/application-of-molecular-dynamic-simulation-to-study-food-proteins-a-review
#6
Ashutosh Singh, Sai Kranthi Vanga, Valerie Orsat, Vijaya Raghavan
This review presents an overview of the application of molecular dynamic simulation to study food proteins. Processing of food using thermal, chemical, radiation, electromagnetic and mechanical techniques subject its macromolecular bio-components such as carbohydrates and proteins to extreme heat, ionic strength, pH and mechanical deformation. These processing factors affect protein's functional properties such as emulsification, dough formation, gelation, etc. which are associated with changes in their structure...
July 19, 2017: Critical Reviews in Food Science and Nutrition
https://www.readbyqxmd.com/read/28723223/free-energy-of-binding-and-mechanism-of-interaction-for-the-meevd-tpr2a-peptide-protein-complex
#7
Mauro Lapelosa
The association between the MEEVD C-terminal peptide from the heat shock protein 90 (Hsp90) and tetratricopeptide repeat A (TPR2A) domain of the heat shock organizing protein (Hop) is a useful prototype to study the fundamental molecular details about the Hop-Hsp90 interaction. We study here the mechanism of binding/unbinding, and compute the standard binding free energy and potential of mean force for the association of the MEEVD peptide to the TPR2A domain using the Adaptive Biasing Force (ABF) methodology...
July 19, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28721631/1-trichloromethyl-1-2-3-4-tetrahydro-beta-carboline-taclo-alters-cell-cycle-progression-in-human-neuroblastoma-cell-lines
#8
Rakesh Kumar Sharma, Eduardo Candelario-Jalil, Doris Feineis, Gerhard Bringmann, Bernd L Fiebich, Ravi Shankar Akundi
1-Trichloromethyl-1,2,3,4-tetrahydro-β-carboline, abbreviated as TaClo, is an endogenous neurotoxin capable of formation in the brain through the condensation of neuronal tryptamine with ingested exogenous toxins such as trichloroethylene or chloral hydrate. Due to its structural resemblance to 1-methyl-4-phenyl-1,2,5,6-tetrahydropyridine (MPTP), and similar ability to inhibit mitochondrial complex I, TaClo has been implicated in the etiology of Parkinson's disease. Previous studies have shown the cytotoxicity of TaClo in various cell culture models...
July 18, 2017: Neurotoxicity Research
https://www.readbyqxmd.com/read/28716860/novel-mechanisms-of-piezo1-dysfunction-in-hereditary-xerocytosis
#9
Edyta Glogowska, Eve R Schneider, Yelena Maksimova, Vincent P Schulz, Kimberly Lezon-Geyda, John Wu, Kottayam Radhakrishnan, Siobán B Keel, Donald Mahoney, Alison M Freidmann, Rachel A Altura, Elena O Gracheva, Sviatoslav N Bagriantsev, Theodosia A Kalfa, Patrick G Gallagher
Mutations in PIEZO1 are the primary cause of hereditary xerocytosis, a clinically heterogeneous, dominantly inherited disorder of erythrocyte dehydration. We utilized next generation sequencing-based techniques to identify PIEZO1 mutations in individuals from 9 kindreds referred with suspected HX and/or undiagnosed congenital hemolytic anemia. Mutations were primarily found in the highly conserved, COOH-terminal pore region domain. Several mutations were novel and demonstrated ethnic specificity. We characterized these mutations using genomic, bioinformatic, cell biology, and physiology-based functional assays...
July 17, 2017: Blood
https://www.readbyqxmd.com/read/28713996/downregulation-of-aqp2-in-the-anterior-vaginal-wall-is-associated-with-the-pathogenesis-of-female-stress-urinary-incontinence
#10
Zujuan Zhang, Pan Xu, Zhenwei Xie, Fengxian Shen, Ning Chen, Liming Yu, Ronghuan He
The pathogenesis of stress urinary incontinence (SUI) is unclear. Aquaporins (AQPs) are a family of transmembrane proteins that transport water and small solutes, including glycerol, across cell membranes. AQPs have been demonstrated to serve a role in skin hydration, cellular proliferation, migration, immunity, wound healing and vascular remodeling in multiple organs. Furthermore, studies have confirmed that abnormal synthesis and degradation of collagens in extracellular matrix (ECM) remodeling contributes to SUI, by altering normal tissue architecture and mechanical properties...
July 15, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28711050/distinguishing-dynamical-features-of-water-inside-protein-hydration-layer-distribution-reveals-what-is-hidden-behind-the-average
#11
Saumyak Mukherjee, Sayantan Mondal, Biman Bagchi
Since the pioneering works of Pethig, Grant, and Wüthrich on a protein hydration layer, many studies have been devoted to find out if there are any "general and universal" characteristic features that can distinguish water molecules inside the protein hydration layer from bulk. Given that the surface itself varies from protein to protein, and that each surface facing the water is heterogeneous, search for universal features has been elusive. Here, we perform an atomistic molecular dynamics simulation in order to propose and demonstrate that such defining characteristics can emerge if we look not at average properties but the distribution of relaxation times...
July 14, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28710385/electron-transfer-chain-in-respiratory-complex-i
#12
Daniel R Martin, Dmitry V Matyushov
Complex I is a part of the respiration energy chain converting the redox energy into the cross-membrane proton gradient. The electron-transfer chain of iron-sulfur cofactors within the water-soluble peripheral part of the complex is responsible for the delivery of electrons to the proton pumping subunit. The protein is porous to water penetration and the hydration level of the cofactors changes when the electron is transferred along the chain. High reaction barriers and trapping of the electrons at the iron-sulfur cofactors are prevented by the combination of intense electrostatic noise produced by the protein-water interface with the high density of quantum states in the iron-sulfur clusters caused by spin interactions between paramagnetic iron atoms...
July 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28705698/receptor-activity-modifying-protein-dependent-and-independent-activation-mechanisms-in-the-coupling-of-calcitonin-gene-related-peptide-and-adrenomedullin-receptors-to-gs
#13
Michael J Woolley, Christopher A Reynolds, John Simms, Christopher S Walker, Juan Carlos Mobarec, Michael L Garelja, Alex C Conner, David R Poyner, Debbie L Hay
Calcitonin gene-related peptide (CGRP) or adrenomedullin (AM) receptors are heteromers of the calcitonin receptor-like receptor (CLR), a class B G protein-coupled receptor, and one of three receptor activity-modifying proteins (RAMPs). How CGRP and AM activate CLR and how this process is modulated by RAMPs is unclear. We have defined how CGRP and AM induce Gs-coupling in CLR-RAMP heteromers by measuring the effect of targeted mutagenesis in the CLR transmembrane domain on cAMP production, modeling the active state conformations of CGRP and AM receptors in complex with the Gs C-terminus and conducting molecular dynamics simulations in an explicitly hydrated lipidic bilayer...
July 10, 2017: Biochemical Pharmacology
https://www.readbyqxmd.com/read/28700755/the-dead-seed-coat-functions-as-a-long-term-storage-for-active-hydrolytic-enzymes
#14
Buzi Raviv, Lusine Aghajanyan, Gila Granot, Vardit Makover, Omer Frenkel, Yitzchak Gutterman, Gideon Grafi
Seed development culminates in programmed cell death (PCD) and hardening of organs enclosing the embryo (e.g., pericarp, seed coat) providing essentially a physical shield for protection during storage in the soil. We examined the proposal that dead organs enclosing embryos are unique entities that store and release upon hydration active proteins that might increase seed persistence in soil, germination and seedling establishment. Proteome analyses of dead seed coats of Brassicaceae species revealed hundreds of proteins being stored in the seed coat and released upon hydration, many are stress-associated proteins such as nucleases, proteases and chitinases...
2017: PloS One
https://www.readbyqxmd.com/read/28699757/solvent-driven-dynamical-crossover-in-the-phenylalanine-side-chain-from-the-hydrophobic-core-of-amyloid-fibrils-detected-by-2-h-nmr-relaxation
#15
Liliya Vugmeyster, Dmitry Ostrovsky, Gina L Hoatson, Wei Qiang, Isaac B Falconer
Aromatic residues are important markers of dynamical changes in proteins' hydrophobic cores. In this work we investigated the dynamics of the F19 side-chain in the core of amyloid fibrils across a wide temperature range of 300 to 140 K. We utilized solid-state (2)H NMR relaxation to demonstrate the presence of a solvent-driven dynamical crossover between different motional regimes, often also referred to as the dynamical transition. In particular, the dynamics are dominated by small-angle fluctuations at low temperatures and by π-flips of the aromatic ring at high temperatures...
July 21, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28690066/experimental-evidence-for-previously-unclassified-calcium-phosphate-structures-in-the-casein-micelle
#16
J P Hindmarsh, P Watkinson
(1)H-(31)P Cross-polarization magic angle spinning (CP-MAS) measurements of 40-d-old Mozzarella cheese and 20 mM EDTA-treated casein micelles revealed that each sample had immobile phosphorus with the same spectral pattern, which did not match that of native casein micelles. To identify the immobile phosphorus bodies, (1)H-(31)P CP-MAS spectra and cross-polarization kinetics measurements were undertaken on native casein micelles, EDTA-chelated casein micelles, and reference samples of β-casein and hydroxyapatite...
July 6, 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/28686451/revival-of-the-intermolecular-nuclear-overhauser-effect-for-mapping-local-protein-hydration-dynamics
#17
Daniel Braun, Michael Schmollngruber, Othmar Steinhauser
The highly heterogeneous hydration dynamics of protein-water interfaces is considered important for protein stability and dynamics, protein folding, enzymatic activity, and even drug design. The nuclear Overhauser effect (NOE) between protein and water protons is the only experimental observable which, in principle, can provide a map of locally resolved hydration dynamics. However, its utility was questioned in various theoretical studies that emphasized the contributions of long-range NOE interactions. We show by a detailed analysis based on molecular dynamics simulations that, contrary to recent claims, the protein-water NOE is an excellent observable to map local hydration dynamics at the protein surface...
July 12, 2017: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/28678508/dehydration-as-a-universal-mechanism-for-ion-selectivity-in-graphene-and-other-atomically-thin-pores
#18
Subin Sahu, Massimiliano Di Ventra, Michael Zwolak
Ion channels play a key role in regulating cell behavior and in electrical signaling. In these settings, polar and charged functional groups - as well as protein response - compensate for dehydration in an ion-dependent way, giving rise to the ion selective transport critical to the operation of cells. Dehydration, though, yields ion-dependent free-energy barriers and thus is predicted to give rise to selectivity by itself. However, these barriers are typically so large that they will suppress the ion currents to undetectable levels...
July 5, 2017: Nano Letters
https://www.readbyqxmd.com/read/28669631/structure-and-cooperativity-of-the-cytosolic-domain-of-the-cora-mg-2-channel-from-escherichia-coli
#19
Michael Lerche, Hena Sandhu, Lukas Flöckner, Martin Högbom, Mikaela Rapp
Structures of the Mg(2+) bound (closed) and apo (open) states of CorA suggests that channel gating is accomplished by rigid-body motions between symmetric and asymmetric assemblies of the cytosolic portions of the five subunits in response to ligand (Mg(2+)) binding/unbinding at interfacial sites. Here, we structurally and biochemically characterize the isolated cytosolic domain from Escherichia coli CorA. The data reveal an Mg(2+)-ligand binding site located in a novel position between each of the five subunits and two Mg(2+) ions trapped inside the pore...
June 19, 2017: Structure
https://www.readbyqxmd.com/read/28664960/the-influence-of-polyanion-molecular-weight-on-polyelectrolyte-multilayers-at-surfaces-protein-adsorption-and-protein-polysaccharide-complexation-stripping-on-natural-polysaccharide-films-on-solid-supports
#20
Natalie L Benbow, Jessie L Webber, Sam Karpiniec, Marta Krasowska, James K Ferri, David A Beattie
Two different fucoidan polymers (unfractionated Fucus vesiculosus fucoidan, and fractionated low molecular weight Fucus vesiculosus fucoidan) have been used to create substrates for protein adsorption studies. Polyelectrolyte multilayers were formed using the fucoidans (polyanions) with chitosan as the corresponding polycation. Multilayer formation was studied using zeta potential measurements, quartz crystal microbalance with dissipation monitoring (QCM-D) and attenuated total reflectance (ATR) FTIR spectroscopy...
June 30, 2017: Physical Chemistry Chemical Physics: PCCP
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