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protein hydration

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https://www.readbyqxmd.com/read/28636363/distinct-protein-hydration-water-species-defined-by-spatially-resolved-spectra-of-intermolecular-vibrations
#1
Viren Sureshkumar Pattni, Tatiana Vasilevskaya, Walter Thiel, Matthias Heyden
In this molecular dynamics simulation study, we analyze intermolecular vibrations in the hydration shell of a solvated enyzme, the membrane type 1--matrix metalloproteinase, with high spatial resolution. Our approach allows us to characterize vibrational signatures of the local hydrogen bond network, the translational mobility of water molecules, as well as the molecular entropy, in specific local environments. Our study demonstrates the heterogeneity of water properties within the hydration shell of a complex biomolecule...
June 21, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28636077/arabidopsis-shaker-pollen-inward-k-channel-spik-functions-in-snrk1-complex-regulated-pollen-hydration-on-the-stigma
#2
Dan-Dan Li, Huan Guan, Fei Li, Chang-Zhen Liu, Yu-Xiu Dong, Xian-Sheng Zhang, Xin-Qi Gao
Pollen hydration is a critical step that determines pollen germination on stigma. KINβγ is a plant-specific subunit of the SNF1-related protein kinase 1 complex (SnRK1 complex). In pollen of the Arabidopsis kinβγ mutant, the levels of reactive oxygen species (ROS) were decreased which lead to compromised hydration of the mutant pollen on stigma. In this study, we analyzed gene expression in kinβγ mutant pollen by RNA-seq and found the expression of inward shaker K(+) channel SPIK was down-regulated in the kinβγ pollen...
June 21, 2017: Journal of Integrative Plant Biology
https://www.readbyqxmd.com/read/28636001/wataa-atlas-of-protein-hydration-exploring-synergies-between-data-mining-and-ab-initio-calculations
#3
Jiří Černý, Bohdan Schneider, Lada Biedermannová
Water molecules represent an integral part of proteins and a key determinant of protein structure, dynamics and function. WatAA is a newly developed, web-based atlas of amino-acid hydration in proteins. The atlas provides information about the ordered first hydration shell of the most populated amino-acid conformers in proteins. The data presented in the atlas are drawn from two sources: experimental data and ab initio quantum-mechanics calculations. The experimental part is based on a data-mining study of a large set of high-resolution protein crystal structures...
June 21, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28635287/configurational-disorder-of-water-hydrogen-bond-network-at-the-protein-dynamical-transition
#4
Obaidur Rahaman, Maria Kalimeri, Marina Katava, Alessandro Paciaroni, Fabio Sterpone
We introduce a novel strategy to quantify the disorder of extended water-water hydrogen-bond (HB) networks sampled in particle-based computer simulations. The method relies on the conformational clustering of the HB connectivity states. We successfully applied it to unveil the fine relationship among the protein dynamical transition in hydrated powder, which marks the activation of protein flexibility at Td∽240 K, and the sudden increase of the configurational disorder of the water HB network enveloping the proteins...
June 21, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28627579/correlation-analysis-of-protein-quality-characteristics-with-gluten-free-bread-properties
#5
S W Horstmann, M Foschia, E K Arendt
The interest in gluten-free cereal products has increased significantly over the last number of years and there is still a high demand for high quality products. This study aims to establish possible connections between protein properties and dough and bread quality which could advance the knowledge for gluten-free product development. The objective of the present study was to correlate protein properties with bread characteristics. Therefore, a wide range of tests (solubility, emulsifying, foaming, water hydration properties) was performed to characterize a range of food proteins (potato, pea, carob, lupin and soy)...
June 19, 2017: Food & Function
https://www.readbyqxmd.com/read/28622579/evidence-of-promising-biological-pharmacological-activities-of-the-sertraline-based-copper-complex-serh2-2-cucl4
#6
Nancy Martini, Juliana E Parente, Maria Eugenia Toledo, Graciela E Escudero, Carlos H Laino, Juan José Martínez Medina, Gustavo A Echeverría, Oscar E Piro, Luis Lezama, Patricia A M Williams, Evelina G Ferrer
In the current study the ability of copper complex to exert multiple biological activities is combined with the pharmacological action of sertraline (SerH2Cl, antidepressant drug). The hydrated and anhydrous forms of the tetrachlorocuprate(II) salts, namely (SerH2)2[CuCl4]·½H2O and (SerH2)2[CuCl4], were synthesized and characterized by physicochemical methods. The crystal structures were determined by X-ray diffraction methods. The hydrate complex crystallizes in the monoclinic P21 space group with a=8.0807(2) Å, b=36...
June 1, 2017: Journal of Inorganic Biochemistry
https://www.readbyqxmd.com/read/28617190/experimental-and-theoretical-studies-of-cadmium-ions-absorption-by-a-new-reduced-recombinant-defensin
#7
Karim Mahnam, Samira Foruzandeh, Neda Mirakhorli, Behnaz Saffar
Heavy metal pollutants such as Cd, Hg, Pb, As and Se are considered as both a global problem and a growing threat to the humanity. Being strongly poisonous to the metal-sensitive enzymes and leading to the growth inhibition and death of organisms, these metals have a toxic impact on the plants and animals. Inducing the metal-binding cysteine-rich peptides such as metallothioneins, phytochelatins, and defensins, higher organisms like plants and animals usually react to the heavy metal stress. In this study, a recombinant defensin protein was expressed in bean and its ability in the cadmium absorption was determined...
June 15, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28616992/coherent-experimental-and-simulation-approach-to-explore-the-underlying-mechanism-of-denaturation-of-stem-bromelain-in-osmolytes
#8
Anjeeta Rani, Mohamed Taha, Pannuru Venkatesu, Ming-Jer Lee
Characterization of a protein in the context of its environment is of crucial importance for a complete understanding of its function. Although biophysical techniques provide powerful tools for studying the stability and activity of the enzyme in the presence of various cosolvents, an approach of combining both experimental techniques and molecular dynamic (MD) simulations may lead to the mechanistic insight into the interactions governing the stability of an enzyme. The knowledge of these interactions can be further utilized for range of modifications in the wild form of an enzyme for various pharmaceutical applications...
June 15, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28614812/the-discovery-of-water-channels-aquaporins
#9
Dennis Brown
The movement of water into and out of cells is a fundamental biological process that is essential for life. Such water movement not only regulates the activity of individual cells but also is responsible for the functioning of many organ systems and for maintaining whole body water balance. It had long been suspected that water movement across biological cell membranes was in some way enhanced or facilitated by pores or channels, but the search to identify these channels was long and tedious. As is often the case in science, the secret of the water channel was eventually discovered by chance in 1992 by Peter Agre and his colleagues at the Johns Hopkins University in Baltimore, who were working on red blood cell membrane proteins...
2017: Annals of Nutrition & Metabolism
https://www.readbyqxmd.com/read/28613875/modeling-of-polarization-transfer-kinetics-in-protein-hydration-using-hyperpolarized-water
#10
Jihyun Kim, Mengxiao Liu, Christian Hilty
Water-protein interactions play a central role in protein structure, dynamics, and function. These interactions, traditionally, have been studied using nuclear magnetic resonance (NMR) by measuring chemical exchange and nuclear Overhauser effect (NOE). Polarization transferred from hyperpolarized water can result in substantial transient signal enhancements of protein resonances due to these processes. Here, we use dissolution dynamic nuclear polarization and flow-NMR for measuring the pH dependence of transferred signals to the protein trypsin...
June 14, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28612358/%C3%AE-chymotrypsin-in-water-acetone-and-water-dimethyl-sulfoxide-mixtures-effect-of-preferential-solvation-and-hydration
#11
Vladimir A Sirotkin, Alexandra A Kuchierskaya
We investigated water/organic solvent sorption and residual enzyme activity to simultaneously monitor preferential solvation/hydration of protein macromolecules in the entire range of water content at 25°C. We applied this approach to estimate protein destabilization/stabilization due to the preferential interactions of bovine pancreatic α-chymotrypsin with water-acetone (moderate-strength H-bond acceptor) and water-DMSO (strong H-bond acceptor) mixtures. There are three concentration regimes for the dried α-chymotrypsin...
June 13, 2017: Proteins
https://www.readbyqxmd.com/read/28610447/significance-of-heat-moisture-treatment-conditions-on-the-pasting-and-gelling-behaviour-of-various-starch-rich-cereal-and-pseudocereal-flours
#12
Concha Collar
The impact of heat-moisture treatment processing conditions (15%, 25%, and 35% moisture content; 1, 3, and 5 h heating time at 120 ℃) on the viscosity pasting and gelling profiles of different grain flours matrices (barley, buckwheat, sorghum, high β-glucan barley, and wheat) was investigated by applying successive cooking and cooling cycles to rapid visco analyser canisters with highly hydrated samples (3.5:25, w:w). At a milder heat-moisture treatment conditions (15% moisture content, 1 h heating time), except for sorghum, heat-moisture treatment flours reached much higher viscosity values during earlier pasting and subsequent gelling than the corresponding native counterparts...
January 1, 2017: Food Science and Technology International, Ciencia y Tecnología de Los Alimentos Internacional
https://www.readbyqxmd.com/read/28605584/statistical-analysis-investigation-and-prediction-of-the-water-positions-in-the-binding-sites-of-proteins
#13
Wei Xiao, Zenghui He, Meijian Sun, Shiliang Li, Honglin Li
Water molecules play a crucial role in biomolecular associations by mediating a hydrogen bond network or filling spaces with van der Waals interactions. Although current drug design technologies have taken water molecule interactions into account, their applications are still limited to their reliance on either excessive computer resources or a particular potential energy model. Here, we introduce a statistical method that is based on experimentally-determined water molecules in the binding sites of high-resolution X-ray crystal structures to predict the potential hydration sites in the binding sites of a crystal structures of interest...
June 12, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28603906/atopic-skin-in-vivo-raman-identification-of-global-molecular-signature-a-comparative-study-with-healthy-skin
#14
L Verzeaux, R Vyumvuhore, D Boudier, M Le Guillou, S Bordes, M Essendoubi, M Manfait, B Closs
Atopic dermatitis (AD) is the most common skin inflammatory disease, affecting up to 3% of adults and 20% of children. Skin barrier impairment is thought to be the primary factor in this disease. Currently, there is no method proposed to monitor non-invasively the different molecular disorders involved in the upper layer of AD skin. Raman microspectroscopy has proved to be a powerful tool to characterize some AD molecular descriptors such as lipid content, global hydration level, filaggrin and its derivatives...
June 11, 2017: Experimental Dermatology
https://www.readbyqxmd.com/read/28603672/chemical-composition-and-the-potential-for-proteomic-transformation-in-cancer-hypoxia-and-hyperosmotic-stress
#15
Jeffrey M Dick
The changes of protein expression that are monitored in proteomic experiments are a type of biological transformation that also involves changes in chemical composition. Accompanying the myriad molecular-level interactions that underlie any proteomic transformation, there is an overall thermodynamic potential that is sensitive to microenvironmental conditions, including local oxidation and hydration potential. Here, up- and down-expressed proteins identified in 71 comparative proteomics studies were analyzed using the average oxidation state of carbon (ZC) and water demand per residue ([Formula: see text]), calculated using elemental abundances and stoichiometric reactions to form proteins from basis species...
2017: PeerJ
https://www.readbyqxmd.com/read/28595095/differential-expression-between-dsp-only-and-dsp-pp523-transcripts-in-rat-molar-teeth
#16
Ya-Qin Zhu, Ryan M Song, Helena H Ritchie
OBJECTIVE: To compare the expression patterns of two multiple transcripts derived from DSP-PP gene during tooth development. One is DSP-only transcript (i.e. does not encode PP) and the other is DSP-PP523 transcript, a main DSP-PP transcript. DESIGN: Unique antisense and sense riboprobes were generated from DSP-only and DSPPP523 cDNAs for in situ studies to examine DSP-only and DSP-PP523 transcript expression in developing molars. Paraffin-embedded sections (5-7μ m) from embryonic 20day, postnatal 2, 3 and 6days were deparaffined and hydrated...
May 31, 2017: Archives of Oral Biology
https://www.readbyqxmd.com/read/28592843/pluronic-f127-and-d-%C3%AE-tocopheryl-polyethylene-glycol-succinate-tpgs-mixed-micelles-for-targeting-drug-delivery-across-the-blood-brain-barrier
#17
Xin Meng, Jiansheng Liu, Xiangrong Yu, Jiajia Li, Xiaotong Lu, Teng Shen
A novel polymeric mixed micelle composed of Pluronic F127 and D-α-tocopheryl polyethylene glycol succinate (TPGS) was developed to improve the delivery of fluorescent dyes and protein across the blood brain barrier (BBB). Rhodamine 123 (Rho123) and DiR loaded mixed micelles, composed of Pluronic F127 and TPGS with proportion of 4:1 (FT), were prepared by thin-film hydration, and β-galactosidase (β-Gal) loaded FT mixed micelles were prepared by self-assembly. The brain-targeted capability of FT mixed micelles were evaluated both in vitro and in vivo...
June 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28590130/paying-the-price-of-desolvation-in-solvent-exposed-protein-pockets-impact-of-distal-solubilizing-groups-on-affinity-and-binding-thermodynamics-in-a-series-of-thermolysin-inhibitors
#18
Jonathan Cramer, Stefan G Krimmer, Andreas Heine, Gerhard Klebe
In medicinal-chemistry lead optimization programs open, solvent-exposed protein pockets are often disregarded as prospective binding sites. Due to the proximity of the bulk solvent, many researchers are instead enticed to attach charged and polar groups to a respective position of an inhibitor scaffold in order to improve solubility and pharmacokinetic properties of a lead candidate. It is rarely considered that solvent effects from the organization of water molecules in the first hydration shell of a protein-ligand complex can take significant impact on the thermodynamics of binding...
June 7, 2017: Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28589200/protein-hydration-in-living-cells-probed-by-fourier-transform-infrared-ft-ir-spectroscopic-imaging
#19
H Shinzawa, B Turner, J Mizukado, S G Kazarian
An application of disrelation mapping to Fourier transform infrared (FT-IR) spectroscopic imaging datasets is provided to reveal different H-bonded water species within a mammalian cell. 2D correlation analysis revealed a disrelation peak at (3420 cm(-1), 3220 cm(-1)), showing the existence of a specific water band at around 3220 cm(-1) whose variation of absorbance did not follow the trend of water molecules with a well-coordinated H-bonding network. Disrelation maps constructed with disrelation intensities between (3420 cm(-1), 3220 cm(-1)) and (3420 cm(-1), 1540 cm(-1)) reveal that the disruption of the water network occurs around the interfacial regions between the cell and media, indicating the disintegration of the H-bonding network of bulk water due to the entrapment of water by the protein inside the cell...
June 7, 2017: Analyst
https://www.readbyqxmd.com/read/28586107/are-energy-and-protein-requirements-met-in-hospital
#20
K Pullen, R Collins, T Stone, H Carter, H Sadler, A Collinson
BACKGROUND: Malnutrition is a problem within hospitals, which impacts upon clinical outcomes. The present audit assesses whether a hospital menu meets the energy and protein standards recommended by the British Dietetic Association's (BDA) Nutrition and Hydration Digest and determines the contribution of oral nutrition supplements (ONS) and additional snacks. METHODS: Patients in a UK South West hospital were categorised as 'nutritionally well' or 'nutritionally vulnerable' in accordance with their Malnutrition Universal Screening Tool score...
June 6, 2017: Journal of Human Nutrition and Dietetics: the Official Journal of the British Dietetic Association
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