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protein hydration

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https://www.readbyqxmd.com/read/28094985/beyond-the-hofmeister-series-ion-specific-effects-on-proteins-and-their-biological-functions
#1
Halil I Okur, Jana Hladílková, Kelvin B Rembert, Younhee Cho, Jan Heyda, Joachim Dzubiella, Paul S Cremer, Pavel Jungwirth
Ions differ in their ability to salt out proteins from solution as expressed in the lyotropic or Hofmeister series of cations and anions. Since its first formulation in 1888, this series has been invoked in a plethora of effects, going beyond the original salting-out/salting-in idea to include enzyme activities and the crystallization of proteins, as well as to processes not involving proteins like ion exchange, the surface tension of electrolytes, or bubble coalescence. Although it has been clear that the Hofmeister series is intimately connected to ion hydration in homogeneous and heterogeneous environments and to ion pairing, its molecular origin has not been fully understood...
January 17, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28093583/interaction-of-organic-ions-with-proteins
#2
Leonor Pérez-Fuentes, Carlos Drummond, Jordi Faraudo, Delfi Bastos-González
In this study we have investigated how different proteins interact with big organic ions. Two ions that are similar in size and chemical structure (Ph4B(-) anion and Ph4As(+) cation) were studied. The proteins chosen are the two major allergenic proteins of cow's milk, β-lactoglobulin and β-casein, and bovine serum albumin, BSA, as the reference protein. First, a quantitative study to determine the hydrophobic degree of the proteins was performed. Then, electrokinetic and stability measurements on protein-coated polystyrene (PS) microspheres as a function of the tetraphenyl ion concentration were carried out...
January 17, 2017: Soft Matter
https://www.readbyqxmd.com/read/28076803/drunken-membranes-short-chain-alcohols-alter-fusion-of-liposomes-to-planar-lipid-bilayers
#3
Jason Paxman, Brady Hunt, David Hallan, Samuel R Zarbock, Dixon J Woodbury
Although the effects of ethanol on protein receptors and lipid membranes have been studied extensively, ethanol's effect on vesicles fusing to lipid bilayers is not known. To determine the effect of alcohols on fusion rates, we utilized the nystatin/ergosterol fusion assay to measure fusion of liposomes to a planar lipid bilayer (BLM). The addition of ethanol excited fusion when applied on the cis (vesicle) side, and inhibited fusion on the trans side. Other short-chain alcohols followed a similar pattern. In general, the inhibitory effect of alcohols (trans) occurs at lower doses than the excitatory (cis) effect, with a decrease of 29% in fusion rates at the legal driving limit of 0...
January 10, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28076665/carbohydrate-lectin-interactions-an-unexpected-contribution-to-affinity
#4
Giulio Navarra, Pascal Zihlmann, Roman P Jakob, Katia Stangier, Roland C Preston, Said Rabbani, Martin Smiesko, Bea Wagner, Timm Maier, Beat Ernst
Uropathogenic E. coli exploit the PapG-II adhesin for infecting host cells of the kidney; moreover, the expression of PapG-II located at the tip of bacterial pili has been correlated with the onset of pyelonephritis in humans, a potentially life-threatening condition. It was envisaged that the blocking of PapG-II, and thus bacterial adhesion, embodies a viable therapeutic alternative to conventional antibiotic treatment. Within our search for potent PapG-II antagonists, we observed an increase in affinity when tetrasaccharide 1, the natural ligand of PapG-II in human kidneys, was elongated to hexasaccharide 2, although the additional Siaα(2-3)Gal extension is not in direct contact with the lectin...
January 11, 2017: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/28074088/accurate-optimization-of-amino-acid-form-factors-for-computing-small-angle-x-ray-scattering-intensity-of-atomistic-protein-structures
#5
Dudu Tong, Sichun Yang, Lanyuan Lu
Structure modelling via small-angle X-ray scattering (SAXS) data generally requires intensive computations of scattering intensity from any given biomolecular structure, where the accurate evaluation of SAXS profiles using coarse-grained (CG) methods is vital to improve computational efficiency. To date, most CG SAXS computing methods have been based on a single-bead-per-residue approximation but have neglected structural correlations between amino acids. To improve the accuracy of scattering calculations, accurate CG form factors of amino acids are now derived using a rigorous optimization strategy, termed electron-density matching (EDM), to best fit electron-density distributions of protein structures...
August 1, 2016: Journal of Applied Crystallography
https://www.readbyqxmd.com/read/28071938/tailoring-structure-and-technological-properties-of-plant-proteins-using-high-hydrostatic-pressure
#6
Rui P Queirós, Jorge A Saraiva, José A Lopes da Silva
The demand for proteins is rising and alternatives to meat proteins are necessary since animal husbandry is expensive and intensive to the environment. Plant proteins appear as an alternative; however, their techno-functional properties need improvement. High-pressure processing (HPP) is a non-thermal technology that has several applications including the modification of proteins. The application of pressure allows modifying proteins' structure hence allowing to change several of their properties, such as hydration, hydrophobicity, and hydrophilicity...
January 10, 2017: Critical Reviews in Food Science and Nutrition
https://www.readbyqxmd.com/read/28069412/influence-of-glutamic-acid-residues-and-ph-on-the-properties-of-transmembrane-helices
#7
Venkatesan Rajagopalan, Denise V Greathouse, Roger E Koeppe
Negatively charged side chains are important for the function of particular ion channels and certain other membrane proteins. To investigate the influence of single glutamic acid side chains on helices that span lipid-bilayer membranes, we have employed GWALP23 (acetyl-GGALW(5)LALALALALALALW(19)LAGA-amide) as a favorable host peptide framework. We substituted individual Leu residues with Glu residues (L12E or L14E or L16E) and incorporated specific (2)H-labeled alanine residues within the core helical region or near the ends of the sequence...
January 7, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28067047/solvatochromic-and-fluorogenic-dyes-as-environment-sensitive-probes-design-and-biological-applications
#8
Andrey S Klymchenko
Fluorescent environment-sensitive probes are specially designed dyes that change their fluorescence intensity (fluorogenic dyes) or color (e.g., solvatochromic dyes) in response to change in their microenvironment polarity, viscosity, and molecular order. The studies of the past decade, including those of our group, have shown that these molecules become universal tools in fluorescence sensing and imaging. In fact, any biomolecular interaction or change in biomolecular organization results in modification of the local microenvironment, which can be directly monitored by these types of probes...
January 9, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28064081/accuracy-comparison-of-several-common-implicit-solvent-models-and-their-implementations-in-the-context-of-protein-ligand-binding
#9
E V Katkova, A V Onufriev, B Aguilar, V B Sulimov
In this study several commonly used implicit solvent models are compared with respect to their accuracy of estimating solvation energies of small molecules and proteins, as well as desolvation penalty in protein-ligand binding. The test set consists of 19 small proteins, 104 small molecules, and 15 protein-ligand complexes. We compared predicted hydration energies of small molecules with their experimental values; the results of the solvation and desolvation energy calculations for small molecules, proteins and protein-ligand complexes in water were also compared with Thermodynamic Integration calculations based on TIP3P water model and Amber12 force field...
December 21, 2016: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28063289/surface-charge-bias-impact-of-amine-contained-pseudozwitterionic-biointerfaces-on-the-human-blood-compatibility
#10
Antoine Venault, Ko-Jen Hsu, Lu-Chen Yeh, Arunachalam Chinnathambi, Hsin-Tsung Ho, Yung Chang
This work discusses the impact of the charge bias and the hydrophilicity on the human blood compatibility of pseudozwitterionic biomaterial gels. Four series of hydrogels were prepared, all containing negatively-charged 3-sulfopropyl methacrylate (SA), and either acrylamide, N-isopropylacrylamide, 2-dimethylaminoethyl methacrylate (DMAEMA) or [2-(methacryloyloxy)ethyl]trimethylammonium (TMA), to form SnAm, SnNm, SnDm or SnTm hydrogels, respectively. An XPS analysis proved that the polymerization was well controlled from the initial monomer ratios...
December 29, 2016: Colloids and Surfaces. B, Biointerfaces
https://www.readbyqxmd.com/read/28059510/the-multiple-roles-of-waters-in-protein-solvation
#11
Adam Hospital, Michela Candotti, Josep Lluis Gelpi, Modesto Orozco
Extensive molecular dynamics (MD) simulations have been used to characterize the multiple roles of water in solvating different types of proteins under different environmental conditions. We analyzed a small set of proteins, representative of the most prevalent meta-folds under native conditions, in the presence of crowding agents, and at high temperature with or without high concentration of urea. We considered also a protein in the unfolded state as characterized by NMR and atomistic MD simulations. Our results outline the main characteristics of the hydration environment of proteins and illustrate the dramatic plasticity of water, and its chameleonic ability to stabilize proteins under a variety of conditions...
January 6, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28059422/direct-electron-irradiation-of-dna-in-a-fully-aqueous-environment-damage-determination-in-combination-with-monte-carlo-simulations
#12
Marc Benjamin Hahn, Susann Meyer, Maria-Astrid Schröter, Harald Seitz, Hans-Jörg Kunte, Tihomir Solomun, Heinz Sturm
We report on a study in which plasmid DNA in water was irradiated with 30 keV electrons generated by a scanning electron microscope and passed through a 100 nm thick Si3N4 membrane. The corresponding Monte Carlo simulations suggest that the kinetic energy spectrum of the electrons throughout the water is dominated by low energy electrons (<100 eV). The DNA radiation damage, single-strand breaks (SSBs) and double-strand breaks (DSBs), was determined by gel electrophoresis. The median lethal dose of D1/2 = 1...
January 18, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28059145/a-markov-state-based-quantitative-kinetic-model-of-sodium-release-from-the-dopamine-transporter
#13
Asghar M Razavi, George Khelashvili, Harel Weinstein
The dopamine transporter (DAT) belongs to the neurotransmitter:sodium symporter (NSS) family of membrane proteins that are responsible for reuptake of neurotransmitters from the synaptic cleft to terminate a neuronal signal and enable subsequent neurotransmitter release from the presynaptic neuron. The release of one sodium ion from the crystallographically determined sodium binding site Na2 had been identified as an initial step in the transport cycle which prepares the transporter for substrate translocation by stabilizing an inward-open conformation...
January 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28056548/l-carnitine-contributes-to-enhancement-of-neurogenesis-from-mesenchymal-stem-cells-through-wnt-%C3%AE-catenin-and-pka-pathway
#14
Ezzatollah Fathi, Raheleh Farahzadi, Hojjatollah N Charoudeh
The identification of factors capable of enhancing neurogenesis has great potential for cellular therapies in neurodegenerative diseases. Multiple studies have shown the neuroprotective effects of L-carnitine (LC). This study determined whether neuronal differentiation of rat adipose tissue-derived mesenchymal stem cells (ADSCs) can be activated by LC. In this study, protein kinase A (PKA) and Wnt/β-catenin pathways were detected to show if this activation was due to these pathways. The expression of LC-induced neurogenesis markers in ADSCs was characterized using real-time PCR...
January 1, 2017: Experimental Biology and Medicine
https://www.readbyqxmd.com/read/28054487/guanidinium-can-both-cause-and-prevent-the-hydrophobic-collapse-of-biomacromolecules
#15
Jan Heyda, Halil I Okur, Jana Hladílková, Kelvin B Rembert, William Hunn, Tinglu Yang, Joachim Dzubiella, Pavel Jungwirth, Paul S Cremer
A combination of Fourier transform infrared and phase transition measurements as well as molecular computer simulations, and thermodynamic modeling were performed to probe the mechanisms by which guanidinium (Gnd(+)) salts influence the stability of the collapsed versus uncollapsed state of an elastin-like polypeptide (ELP), an uncharged thermoresponsive polymer. We found that the cation's action was highly dependent upon the counteranion with which it was paired. Specifically, Gnd(+) was depleted from the ELP/water interface and was found to stabilize the collapsed state of the macromolecule when paired with well-hydrated anions such as SO4(2-)...
January 18, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28030769/polarizable-multipole-based-force-field-for-aromatic-molecules-and-nucleobases
#16
Changsheng Zhang, David Bell, Matthew Harger, Pengyu Ren
Aromatic molecules with π electrons are commonly involved in chemical and biological recognitions. For example, nucleobases play central roles in DNA/RNA structure and their interactions with proteins. The delocalization of the π electrons is responsible for the high polarizability of aromatic molecules. In this work, the AMOEBA force field has been developed and applied to 5 regular nucleobases and 12 aromatic molecules. The permanent electrostatic energy is expressed as atomic multipole interactions between atom pairs, and many-body polarization is accounted for by mutually induced atomic dipoles...
January 13, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28028244/origin-of-hydrophobicity-and-enhanced-water-hydrogen-bond-strength-near-purely-hydrophobic-solutes
#17
Joze Grdadolnik, Franci Merzel, Franc Avbelj
Hydrophobicity plays an important role in numerous physicochemical processes from the process of dissolution in water to protein folding, but its origin at the fundamental level is still unclear. The classical view of hydrophobic hydration is that, in the presence of a hydrophobic solute, water forms transient microscopic "icebergs" arising from strengthened water hydrogen bonding, but there is no experimental evidence for enhanced hydrogen bonding and/or icebergs in such solutions. Here, we have used the redshifts and line shapes of the isotopically decoupled IR oxygen-deuterium (O-D) stretching mode of HDO water near small purely hydrophobic solutes (methane, ethane, krypton, and xenon) to study hydrophobicity at the most fundamental level...
December 27, 2016: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28026092/dipolar-relaxation-dynamics-at-the-active-site-of-an-atpase-regulated-by-membrane-lateral-pressure
#18
Elisabeth Fischermeier, Petr Pospíšil, Ahmed Sayed, Martin Hof, Marc Solioz, Karim Fahmy
The active transport of ions across biological membranes requires their hydration shell to interact with the interior of membrane proteins. However, the influence of the external lipid phase on internal dielectric dynamics is hard to access by experiment. Using the octahelical transmembrane architecture of the copper-transporting P1B -type ATPase from Legionella pneumophila as a model structure, we have established the site-specific labeling of internal cysteines with a polarity-sensitive fluorophore. This enabled dipolar relaxation studies in a solubilized form of the protein and in its lipid-embedded state in nanodiscs...
December 27, 2016: Angewandte Chemie
https://www.readbyqxmd.com/read/28013170/proteomic-analysis-of-common-bean-stem-under-drought-stress-using-in-gel-stable-isotope-labeling
#19
Tanja Zadražnik, Wolfgang Egge-Jacobsen, Vladimir Meglič, Jelka Šuštar-Vozlič
Drought is an abiotic stress that strongly influences plant growth, development and productivity. Proteome changes in the stem of the drought-tolerant common bean (Phaseolus vulgaris L.) cultivar Tiber have were when the plants were exposed to drought. Five-week-old plants were subjected to water deficit by withholding irrigation for 7, 12 and 17days, whereas control plants were regularly irrigated. Relative water content (RWC) of leaves, as an indicator of the degree of cell and tissue hydration, showed the highest statistically significant differences between control and drought-stressed plants after 17days of treatment, where RWC remained at 90% for control and declined to 45% for stressed plants...
December 5, 2016: Journal of Plant Physiology
https://www.readbyqxmd.com/read/28009501/charges-in-hydrophobic-environments-a-strategy-for-identifying-alternative-states-in-proteins
#20
Aaron C Robinson, Ananya Majumdar, Jamie L Schlessman, Bertrand García-Moreno E
In the V23E variant of staphylococcal nuclease, Glu-23 has a pKa of 7.5. At low pH, Glu-23 is neutral and buried in the hydrophobic interior of the protein. Crystal structures and NMR spectroscopy experiments show that when Glu-23 becomes charged, the protein switches into an open state in which strands β1 and β2 separate from the β-barrel; the remaining structure is unaffected. In the open state the hydrophobic interior of the protein is exposed to bulk water, allowing Glu-23 to become hydrated. This illustrates several key aspects of protein electrostatics: (1) The apparent pKa of an internal ionizable group can reflect the average of the very different pKa values (open ≈4...
December 23, 2016: Biochemistry
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