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https://www.readbyqxmd.com/read/27905589/hydrogen-bond-dynamics-at-the-bio-water-interface-in-hydrated-proteins-a-molecular-dynamics-study
#1
Prithwish K Nandi, Niall J English, Zdenek Futera, Antonio Benedetto
Water is fundamental to the biochemistry of enzymes. It is well known that without a minimum amount of water, enzymes are not biologically active. Bare minimal solvation for biological function corresponds to about a single layer of water covering enzymes' surfaces. Many contradictory studies on protein-hydration-water-coupled dynamics have been published in recent decades. Following prevailing wisdom, a dynamical crossover in hydration water (at around 220 K for hydrated lysozymes) can trigger larger-amplitude motions of the protein, activating, in turn, biological functions...
December 1, 2016: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/27904702/ethanol-extracts-from-portulaca-oleracea-l-attenuated-ischemia-reperfusion-induced-rat-neural-injury-through-inhibition-of-hmgb1-induced-inflammation
#2
Chenggang Zheng, Chen Liu, Wanyin Wang, Gusheng Tang, Liwei Dong, Juan Zhou, Zhengrong Zhong
It is well demonstrated that the high mobility group box 1 (HMGB1) mediated inflammation has been implicated as one of the important causes for brain damage induced by cerebral ischemia/reperfusion (I/R). In the present study, we assessed the neuro-protective and anti-inflammation effects of the ethanol extracts from Portulaca oleracea L. (EEPO) against cerebral I/R injury in the rat transient middle cerebral artery occlusion (tMCAO) model. Rats were administrated with their respective treatment for 7 days before the MCA occlusion...
2016: American Journal of Translational Research
https://www.readbyqxmd.com/read/27894842/energetic-basis-on-interactions-between-ferredoxin-and-ferredoxin-nadp-reductase-at-varying-physiological-conditions
#3
Misaki Kinoshita, Ju Yaen Kim, Satoshi Kume, Yuxi Lin, K Hun Mok, Yosky Kataoka, Koichiro Ishimori, Natalia Markova, Genji Kurisu, Toshiharu Hase, Young-Ho Lee
In spite of a number of studies to characterize ferredoxin (Fd):ferredoxin NADP(+) reductase (FNR) interactions at limited conditions, detailed energetic investigation on how these proteins interact under near physiological conditions and its linkage to FNR activity are still lacking. We herein performed systematic Fd:FNR binding thermodynamics using isothermal titration calorimetry (ITC) at distinct pH (6.0 and 8.0), NaCl concentrations (0-200 mM), and temperatures (19-28 °C) for mimicking physiological conditions in chloroplasts...
November 25, 2016: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/27894244/umbelliferone-decreases-intracellular-ph-and-sensitizes-melanoma-cell-line-a375-to-dacarbazin-comparison-with-acetazolamide
#4
Clémentine Puech, Morgane Chatard, Delphine Felder-Flesch, Nathalie Prevot, Nathalie Perek
The high degree of malignancy of tumour cells is linked to alterations of many physiological parameters like the intracellular pH (pHi). The pHi in cancer cell line is regulated by the anhydrase carbonique IX (CA IX). The main enzymatic function of the CA IX protein is to catalyze the hydration of carbon dioxide into bicarbonate ions and protons. Inhibiton of transmembrane tumor associated isozyme carbonic anhydrase IX (CA IX) with specific inhibitors is a promising and expanding field as CA IX is involved in tumor progression...
November 28, 2016: Current Molecular Pharmacology
https://www.readbyqxmd.com/read/27892923/origin-and-function-of-stomata-in-the-moss-physcomitrella-patens
#5
Caspar C Chater, Robert S Caine, Marta Tomek, Simon Wallace, Yasuko Kamisugi, Andrew C Cuming, Daniel Lang, Cora A MacAlister, Stuart Casson, Dominique C Bergmann, Eva L Decker, Wolfgang Frank, Julie E Gray, Andrew Fleming, Ralf Reski, David J Beerling
Stomata are microscopic valves on plant surfaces that originated over 400 million years (Myr) ago and facilitated the greening of Earth's continents by permitting efficient shoot-atmosphere gas exchange and plant hydration(1). However, the core genetic machinery regulating stomatal development in non-vascular land plants is poorly understood(2-4) and their function has remained a matter of debate for a century(5). Here, we show that genes encoding the two basic helix-loop-helix proteins PpSMF1 (SPEECH, MUTE and FAMA-like) and PpSCREAM1 (SCRM1) in the moss Physcomitrella patens are orthologous to transcriptional regulators of stomatal development in the flowering plant Arabidopsis thaliana and essential for stomata formation in moss...
November 28, 2016: Nature Plants
https://www.readbyqxmd.com/read/27886662/osteoblast-response-to-the-surface-topography-of-hydroxyapatite-two-dimensional-films
#6
Gai Yang, Zili Liu, Yuming Guo, Jie Zhang, Han Li, Weike Shi, Jing Feng, Kui Wang, Lin Yang
In the current study, three hydroxyapatite two-dimensional films with similar wettability but different topological roughness have been prepared through a facile one-step method using hydrated polylactic acid discs as substrates. The results indicated that the protein adsorption capabilities of the hydroxyapatite two-dimensional films and the proliferation of osteoblast cells on the as-prepared films increased obviously with the increase of the films' roughness. These reveal that the cellular responses to two-dimensional materials can be efficiently tuned by easily adjusting the topological roughness...
November 25, 2016: Journal of Biomedical Materials Research. Part A
https://www.readbyqxmd.com/read/27882844/effect-of-glycosylation-on-hydration-behavior-at-the-ice-binding-surface-of-the-oceanpout-type-iii-antifreeze-protein-a-molecular-dynamics-simulation
#7
Swagata Halder, Chaitali Mukhopadhyay
Antifreeze proteins (AFPs), found in certain vertebrates, plants, fungi and bacteria have the ability to permit their survival in subzero environments by thermal hysteresis mechanism. However, the exact mechanism of ice growth inhibition is still not clearly understood. Here four long explicit molecular dynamics (MD) simulations have been carried out at two different temperatures (277K and 298 K)with and without glycan to study the conformational rigidity of the Ocean pout type III antifreeze protein in aqueous medium and the structural arrangements of water molecules hydrating its ice binding surface...
November 24, 2016: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/27881985/pollen-aquaporins-the-solute-factor
#8
REVIEW
Juliana A Pérez Di Giorgio, Gabriela C Soto, Jorge P Muschietti, Gabriela Amodeo
In the recent years, the biophysical properties and presumed physiological role of aquaporins (AQPs) have been expanded to specialized cells where water and solute exchange are crucial traits. Complex but unique processes such as stomatal movement or pollen hydration and germination have been addressed not only by identifying the specific AQP involved but also by studying how these proteins integrate and coordinate cellular activities and functions. In this review, we referred specifically to pollen-specific AQPs and analyzed what has been assumed in terms of transport properties and what has been found in terms of their physiological role...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27878168/comparison-of-hydration-behavior-and-conformational-preferences-of-the-trp-cage-mini-protein-in-different-rigid-body-water-models
#9
Madhulika Gupta, Divya Nayar, Charusita Chakravarty, Sanjoy Bandyopadhyay
The secondary structure conformational properties and hydration shell metrics of the Trp-cage mini-protein are examined in the folded and unfolded ensembles in mTIP3P, TIP4P, and TIP4P-Ew water models with the CHARMM22 force-field using molecular dynamics simulations at 250 K. Upon changing the water model, the conformational order metrics of the peptide show significant differences in the unfolded rather than in the folded ensemble. The unfolding temperatures for Trp-cage are observed to be around 460, 470, and 430 K in mTIP3P, TIP4P, and TIP4P-Ew, respectively...
November 23, 2016: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/27871369/co2-reduction-and-organic-compounds-production-by-photosynthetic-bacteria-with-surface-displayed-carbonic-anhydrase-and-inducible-expression-of-phosphoenolpyruvate-carboxylase
#10
Ju-Yong Park, Yang-Hoon Kim, Jiho Min
In Rhodobacter sphaeroides, carbonic anhydrase (CA; EC 4.2.1.1) is a zinc-containing metalloenzyme that catalyzes the reversible hydration of CO2 to HCO3(-) while phosphoenolpyruvate carboxylase (PEPC; 4.1.1.31), an enzyme involved in the carbon metabolism that catalyzed the fixation of CO2 to PEP, is a key factor for biological fixation of CO2 and enhances the production of organic compounds. In this study, the recombinant R. sphaeroides with highly-expressed CA was developed based on a surface displayed system of CA (pJY-OmpCA) on the outer membrane of R...
January 2017: Enzyme and Microbial Technology
https://www.readbyqxmd.com/read/27869262/statistical-thermodynamics-of-aromatic-aromatic-interactions-in-aqueous-solution
#11
Tomohiko Hayashi, Masahiro Kinoshita
To elucidate the interactions between aromatic rings, which are believed to play essential roles in a variety of biological processes, we analyze the water-mediated interactions between toluene molecules along face-to-face stacked (FF) and point-to-face T-shaped (TS) paths using a statistical-mechanical theory of liquids combined with a molecular model for water. The theory enables us to decompose each interaction into physically insightful components, revealing detailed hydration effects. The dimers (i.e., molecules in contact with each other) formed in the FF and TS paths, which are referred to as "FF stacking" and "TS contact", respectively, share almost the same stability in vacuum...
November 30, 2016: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/27859392/developing-multisite-empirical-force-field-models-for-pt-ii-and-cisplatin
#12
John P Cvitkovic, George A Kaminski
We have developed empirical force field parameters for Pt(II) and cisplatin. Two force field frameworks were used-modified OPLS-AA and our second-order polarizable POSSIM. A seven-site model was used for the Pt(II) ion. The goal was to create transferable parameter sets compatible with the force field models for proteins and general organic compounds. A number of properties of the Pt(II) ion and its coordination compounds have been considered, including geometries and energies of the complexes, hydration free energy, and radial distribution functions in water...
November 11, 2016: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/27851938/fast-motions-of-key-methyl-groups-in-amyloid-%C3%AE-fibrils
#13
Liliya Vugmeyster, Dmitry Ostrovsky, Matthew A Clark, Isaac B Falconer, Gina L Hoatson, Wei Qiang
Amyloid-β (Aβ) peptide is the major component of plaques found in Alzheimer's disease patients. Using solid-state (2)H NMR relaxation performed on selectively deuterated methyl groups, we probed the dynamics in the threefold symmetric and twofold symmetric polymorphs of native Aβ as well as the protofibrils of the D23N mutant. Specifically, we investigated the methyl groups of two leucine residues that belong to the hydrophobic core (L17 and L34) as well as M35 residues belonging to the hydrophobic interface between the cross-β subunits, which has been previously found to be water-accessible...
November 15, 2016: Biophysical Journal
https://www.readbyqxmd.com/read/27849309/activation-of-rac1-and-rhoa-preserve-corneal-endothelial-barrier-function
#14
María C Ortega, Diana Santander-García, Beatriz Marcos-Ramiro, Susana Barroso, Susan Cox, Ignacio Jiménez-Alfaro, Jaime Millán
Purpose: The corneal endothelium is responsible for the correct hydration of the corneal stroma. Corneal endothelial cells have a low proliferative capacity, so preserving their barrier function under suboptimal conditions that cause osmotic imbalance, such as those arising from corneal pathologies, age, cryopreservation, and transplantation, is essential for maintaining corneal transparency. We have investigated the signaling induced by hyperosmotic shock that reversibly disrupts corneal endothelial barriers in human endothelial cells and in murine corneas...
November 1, 2016: Investigative Ophthalmology & Visual Science
https://www.readbyqxmd.com/read/27837534/elastic-liposomes-for-topical-and-transdermal-drug-delivery
#15
Heather A E Benson
Elastic liposomes have been developed and evaluated as novel topical and transdermal delivery systems. They share some similarities to conventional liposomes but their composition is designed to confer flexibility and elasticity in the lipid bilayer structure. Elastic liposomes are applied non-occluded to the skin and are reported to permeate through the stratum corneum lipid lamellar regions as a result of the hydration or osmotic force in the skin. They have been investigated as drug carriers for a range of small molecules, peptides, proteins, and vaccines, both in vitro and in vivo...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27828771/how-does-chronic-cigarette-smoke-exposure-affect-human-skin-a-global-proteomics-study-in-primary-human-keratinocytes
#16
Pavithra Rajagopalan, Vishalakshi Nanjappa, Remya Raja, Ankit P Jain, Kiran K Mangalaparthi, Gajanan J Sathe, Niraj Babu, Krishna Patel, Nükhet Cavusoglu, Jeremie Soeur, Akhilesh Pandey, Nita Roy, Lionel Breton, Aditi Chatterjee, Namita Misra, Harsha Gowda
Cigarette smoking has been associated with multiple negative effects on human skin. Long-term physiological effects of cigarette smoke are through chronic and not acute exposure. Molecular alterations due to chronic exposure to cigarette smoke remain unclear. Primary human skin keratinocytes chronically exposed to cigarette smoke condensate (CSC) showed a decreased wound-healing capacity with an increased expression of NRF2 and MMP9. Using quantitative proteomics, we identified 4728 proteins, of which 105 proteins were overexpressed (≥2-fold) and 41 proteins were downregulated (≤2-fold) in primary skin keratinocytes chronically exposed to CSC...
November 2016: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/27816280/exploring-the-effects-of-temperature-and-pressure-on-the-structure-and-stability-of-a-small-rna-hairpin
#17
Caroline Schuabb, Salome Pataraia, Melanie Berghaus, Roland Winter
RNAs perform multiple vital roles within cells, including catalyzing biological reactions and expression of proteins. Small RNA hairpins (sRNAh) are the smallest functional entities of nucleic acids and are involved in various important biological functions such as ligand binding and tertiary folding initiation of proteins. We investigated the conformational and free energy landscape of the sRNAh gcUUCGgc over a wide range of temperatures and pressures using fluorescence resonance energy transfer, Fourier-transform infrared and UV/Vis spectroscopy as well as small-angle X-ray scattering on the unlabeled and/or fluorescently labeled sRNAh...
October 31, 2016: Biophysical Chemistry
https://www.readbyqxmd.com/read/27813296/simple-method-to-introduce-an-ester-infrared-probe-into-proteins
#18
Ismail A Ahmed, Feng Gai
The ester carbonyl stretching vibration has recently been shown to be a sensitive and convenient infrared (IR) probe of protein electrostatics due to the linear dependence of its frequency on local electric field. While an ester moiety can be easily incorporated into peptides via solid-phase synthesis, currently there is no method available to site-specifically incorporate it into a large protein. Herein, we show that it is possible to use a cysteine alkylation reaction to achieve this goal and demonstrate the feasibility of this simple method by successfully incorporating a methyl ester group (-CH2 COOCH3 ) into a model peptide (YGGCGG), two amyloid-forming peptides derived from the insulin B chain and Aβ, and bovine serum albumin (BSA)...
November 4, 2016: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/27813264/protein-charge-determination-and-implications-for-interactions-in-cell-extracts
#19
Ciara Kyne, Kiara Jordon, Dana I Filoti, Thomas M Laue, Peter B Crowley
Decades of dilute-solution studies have revealed the influence of charged residues on protein stability, solubility and stickiness. Similar characterizations are now required in physiological solutions to understand the effect of charge on protein behaviour under native conditions. Toward this end, we used free boundary and native gel electrophoresis to explore the charge of cytochrome c in buffer and in Escherichia coli extracts. We find that the charge of cytochrome c was ∼2-fold lower than predicted from primary structure analysis...
November 4, 2016: Protein Science: a Publication of the Protein Society
https://www.readbyqxmd.com/read/27811004/biomechanical-biochemical-and-morphological-mechanisms-of-heat-shock-mediated-germination-in-carica-papaya-seed
#20
Rachel E Webster, Wanda M Waterworth, Wolfgang Stuppy, Christopher E West, Roland Ennos, Clifford M Bray, Hugh W Pritchard
Carica papaya (papaya) seed germinate readily fresh from the fruit, but desiccation induces a dormant state. Dormancy can be released by exposure of the hydrated seed to a pulse of elevated temperature, typical of that encountered in its tropical habitat. Carica papaya is one of only a few species known to germinate in response to heat shock (HS) and we know little of the mechanisms that control germination in tropical ecosystems. Here we investigate the mechanisms that mediate HS-induced stimulation of germination in pre-dried and re-imbibed papaya seed...
November 2, 2016: Journal of Experimental Botany
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