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protein hydration

Suzanne M Mithieux, Behnaz Aghaei-Ghareh-Bolagh, Leping Yan, Kekini V Kuppan, Yiwei Wang, Francia Garces-Suarez, Zhe Li, Peter K Maitz, Elizabeth A Carter, Christina Limantoro, Wojciech Chrzanowski, David Cookson, Alan Riboldi-Tunnicliffe, Clair Baldock, Kosuke Ohgo, Kristin K Kumashiro, Glenn Edwards, Anthony S Weiss
A novel, pure, synthetic material is presented that promotes the repair of full-thickness skin wounds. The active component is tropoelastin and leverages its ability to promote new blood vessel formation and its cell recruiting properties to accelerate wound repair. Key to the technology is the use of a novel heat-based, stabilized form of human tropoelastin which allows for tunable resorption. This implantable material contributes a tailored insert that can be shaped to the wound bed, where it hydrates to form a conformable protein hydrogel...
February 16, 2018: Advanced Healthcare Materials
Se Yeong Lee, Yunki Lee, Phuong Le Thi, Dong Hwan Oh, Ki Dong Park
Background: Zwitterionic molecules have been widely studied as coating materials for preparing anti-fouling surfaces because they possess strong hydration properties that can resist non-specific protein adsorption. Numerous studies on surface modification using zwitterionic molecules have been investigated, such as electrochemically mediated and photoinitiated radical polymerization. However, these methods have some limitations, including multi-step process, difficulties in producing thick and dense layers as well as the requirement of extra facilities...
2018: Biomaterials Research
Kevin R DeMarco, Slava Bekker, Colleen E Clancy, Sergei Y Noskov, Igor Vorobyov
Interactions of drug molecules with lipid membranes play crucial role in their accessibility of cellular targets and can be an important predictor of their therapeutic and safety profiles. Very little is known about spatial localization of various drugs in the lipid bilayers, their active form (ionization state) or translocation rates and therefore potency to bind to different sites in membrane proteins. All-atom molecular simulations may help to map drug partitioning kinetics and thermodynamics, thus providing in-depth assessment of drug lipophilicity...
2018: Frontiers in Pharmacology
Todor Dudev, Diana Cheshmedzhieva, Lyudmila Doudeva
Abiogenic aluminum has been implicated in some health disorders in humans. Protein binding sites containing essential metals (mostly magnesium) have been detected as targets for the "alien" Al 3+ . However, the acute toxicity of aluminum is very low. Although a substantial body of information has been accumulated on the biochemistry of aluminum, the underlying mechanisms of its toxicity are still not fully understood. Several outstanding questions remain unanswered: (1) Why is the toxicity of aluminum, unlike that of other "alien" metal cations, relatively low? (2) Apart from Mg 2+ active centers in proteins, how vulnerable are other essential metal binding sites to Al 3+ attack? (3) Generally, what factors do govern the competition between 'alien" Al 3+ and cognate divalent metal cations in metalloproteins under physiologically relevant conditions? Here, we endeavor to answer these questions by studying the thermodynamic outcome of the competition between Al 3+ and a series of biogenic metal cations, such as Mg 2+ , Fe 2+ and Zn 2+ , in model protein binding sites of various structures, compositions, solvent exposure and charge states...
February 14, 2018: Journal of Molecular Modeling
Mylène Da Silva, Clara Dombre, Aurélien Brionne, Philippe Monget, Magali Chessé, Marion De Pauw, Maryse Mills, Lucie Combes-Soia, Valérie Labas, Nicolas Guyot, Yves Nys, Sophie Rehault-Godbert
In many amniotes, the amniotic fluid is depicted as a dynamic milieu that participates in the protection of the embryo (cushioning, hydration, and immunity). However, in birds, the protein profile of the amniotic fluid remains unexplored, even though its proteomic signature is predicted to differ compared to human's. In fact, unlike humans, chicken amniotic fluid does not collect excretory products and its protein composition strikingly changes at mid-development due to the massive inflow of egg white proteins, which are thereafter swallowed by the embryo to support its growth...
February 14, 2018: Molecular & Cellular Proteomics: MCP
Divya Nayar, Nico F A van der Vegt
Water-mediated hydrophobic interactions play an important role in self-assembly processes, aqueous polymer solubility, and protein folding, to name a few. Cosolvents affect these interactions however the implications for hydrophobic polymer collapse and protein folding equilibria are not well-understood. This study examines cosolvent effects on the hydrophobic collapse equilibrium of a generic 32-mer hydrophobic polymer in urea, trimethylamine-N-oxide (TMAO), and acetone aqueous solutions using molecular dynamics simulations...
February 14, 2018: Journal of Physical Chemistry. B
Julija Zavadlav, Siewert J Marrink, Matej Praprotnik
To perform computationally efficient concurrent multiscale simulations of biological macromolecules in solution, where the all-atom (AT) models are coupled to supramolecular coarse-grained (SCG) solvent models, previous studies resorted to a modified AT water models, such as the bundled-SPC models, that use semi-harmonic springs to restrict the relative movement of water molecules within a cluster. Those models can have a significant impact on the simulated biomolecules and can lead, for example, to a partial unfolding of a protein...
February 13, 2018: Journal of Chemical Theory and Computation
Bowen Li, Shaoyi Jiang, Jingyi Xie, Zhefan Yuan, Priyesh Jain, Xiaojie Lin, Kan Wu
While hydrophobic nanoparticles (NPs) have been long recognized to boost the immune activation, whether hydrophilic NPs modulate an immune system challenged by immune stimulators and how their hydrophilic properties may affect the immune response is still unclear. To answer this question, three polymers, poly(ethylene glycol)(PEG), poly(sulfobetaine)(PSB) and poly(carboxybetaine)(PCB) are studied. For fair comparison, nanogels with uniform size and pure surface functionalities were made from these polymers...
February 12, 2018: Angewandte Chemie
Tahereh Ghane, Rene F Gorriz, Sandro Wrzalek, Senta Volkenandt, Ferand Dalatieh, Marco Reidelbach, Petra Imhof
Proton transfer in cytochrome c oxidase (CcO) from the cellular inside to the binuclear redox centre as well as proton pumping through the membrane takes place through proton entrance via two distinct pathways, the D- and K-channel. Both channels show a dependence of their hydration level on the protonation states of their key residues, K362 for the K-channel, and E286 or D132 for the D-channel. In the oxidative half of CcO's catalytic cycle the D-channel is the proton-conducting path. For this channel, an interplay of protonation state of the D-channel residues with the water and hydrogen-bond dynamics has been observed in molecular dynamics simulations of the CcO protein, embedded in a lipid bi-layer, modelled in different protonation states...
February 12, 2018: Journal of Membrane Biology
Filipa Mota, Constantina Fotinou, Rohini Rhana, A W Edith Chan, Tamas Yelland, Mohamed T Arooz, Andrew P O'Leary, Jennie Hutton, Paul Frankel, Ian Zachary, David Selwood, Snezana Djordjevic
Neuropilin-1 (NRP1) is a transmembrane co-receptor involved in binding interactions with variety of ligands and receptors, including receptor tyrosine kinases. Expression of NRP1 in several cancers correlates with cancer stages and poor prognosis. Thus, NRP1 has been considered a therapeutic target and is the focus of multiple drug discovery initiatives. Vascular endothelial growth factor (VEGF) binds to the b1 domain of NRP1 through interactions between the C-terminal arginine of VEGF and residues in the NRP1 binding site including Tyr297, Tyr353, Asp320, Ser346, and Thr349...
February 12, 2018: FEBS Journal
Javier Lopez-Garrido, Nikola Ojkic, Kanika Khanna, Felix R Wagner, Elizabeth Villa, Robert G Endres, Kit Pogliano
The means by which the physicochemical properties of different cellular components together determine bacterial cell shape remain poorly understood. Here, we investigate a programmed cell-shape change during Bacillus subtilis sporulation, when a rod-shaped vegetative cell is transformed to an ovoid spore. Asymmetric cell division generates a bigger mother cell and a smaller, hemispherical forespore. The septum traps the forespore chromosome, which is translocated to the forespore by SpoIIIE. Simultaneously, forespore size increases as it is reshaped into an ovoid...
February 8, 2018: Cell
Alexandru Zabara, Josephine Tse Yin Chong, Isabelle Martiel, Laura Stark, Brett A Cromer, Chiara Speziale, Calum John Drummond, Raffaele Mezzenga
In meso crystallization of membrane proteins from lipidic mesophases is central to protein structural biology but limited to membrane proteins with small extracellular domains (ECDs), comparable to the water channels (3-5 nm) of the mesophase. Here we present a strategy expanding the scope of in meso crystallization to membrane proteins with very large ECDs. We combine monoacylglycerols and phospholipids to design thermodynamically stable ultra-swollen bicontinuous cubic phases of double-gyroid (Ia3d), double-diamond (Pn3m), and double-primitive (Im3m) space groups, with water channels five times larger than traditional lipidic mesophases, and showing re-entrant behavior upon increasing hydration, of sequences Ia3d→Pn3m→Ia3d and Pn3m→Im3m→Pn3m, unknown in lipid self-assembly...
February 7, 2018: Nature Communications
Madina Sifi, Roza Benabdesselam, Sabrina Souttou, Tiziana Annese, Alvaro Rendon, Beatrice Nico, Latifa Dorbani-Mamine
Dystrophin (Dp) is a multidomain protein that links the actin cytoskeleton to the extracellular matrix through the dystrophin associated proteins complex (DAPC). Dp of 71 kDa (Dp71), corresponding to the COOH-terminal domain of dystrophin, and α1-syntrophin (α1Syn) as the principal component of the DAPC, are strongly expressed in the brain. To clarify their involvement in the central control of osmotic homeostasis, we investigated the effect of 14 days of salt loading (with drinking water containing 2% NaCl) and then reversibly to 30 days of normal hydration (with drinking water without salt), first on the expression by western-blotting and the distribution by immunochemistry of Dp71 and α1Syn in the SON of the rat and, second, on the level of some physiological parameters, as the plasma osmolality, natremia and hematocrit...
January 26, 2018: Acta Histochemica
Richard C Remsing, Erte Xi, Amish Jagdish Patel
The solubility of proteins and other macromolecular solutes plays an important role in numerous biological, chemical, and medicinal processes. An important determinant of protein solubility is the solvation free energy of the protein, which quantifies the overall strength of the interactions between the protein and the aqueous solution that surrounds it. Here we present an all-atom explicit-solvent computational framework for the rapid estimation of protein solvation free energies. Using this framework, we estimate the hydration free energy of Hydrophobin II, an amphiphilic fungal protein, in a computationally efficient manner...
February 2, 2018: Journal of Physical Chemistry. B
Peng Luo, Dong-Ping He
Liposomal angiotensin-I-converting enzyme inhibitory (ACEI) peptides were prepared from sunflower protein hydrolysates by the thin‑film ultrasonic method. Response surface methodology (RSM), in combination with fractional factorial designs and central composite design methods were utilized to optimize entrapment efficiency and balance the drug release. We found that the ratio of phospholipids to cholesterol, ultrasound time and the ratio of phospholipids to ACEI peptides were significant factors affecting entrapment efficiency (P<0...
January 24, 2018: Molecular Medicine Reports
Li-En Lin, Pin-Rui Su, Hsin-Yi Wu, Cheng-Chih Hsu
Proper matrix application is crucial in obtaining high quality matrix-assisted laser desorption ionization (MALDI) mass spectrometry imaging (MSI). Solvent-free sublimation was essentially introduced as an approach of homogeneous coating that gives small crystal size of the organic matrix. However, sublimation has lower extraction efficiency of analytes. Here, we present that a simple sonication step after the hydration in standard sublimation protocol significantly enhances the sensitivity of MALDI MSI. This modified procedure uses a common laboratory ultrasonicator to immobilize the analytes from tissue sections without noticeable delocalization...
February 1, 2018: Journal of the American Society for Mass Spectrometry
Upasana Yadav, Narpinder Singh, Amritpal Kaur, Sheetal Thakur
Physico-chemical, hydration, cooking, textural and pasting properties of thirteen adzuki bean (Vigna angularis) accessions were studied. Protein and ash content ranged from 18.82 to 24.52% and 2.02 to 7.03%, respectively. Bulk density and seed weight of the adzuki seed ranged from 0.76 to 1.00 g/mL and 74.87 to 148.20 g/1000 seeds, respectively. Hydration capacity, swelling capacity and cooking time ranged from 0.05 to 0.12 g/seed, 0.04 to 0.15 mL/seed and 48.67 to 74.33 min, respectively. Different accessions showed significant variations in their physicochemical, cooking, hydration and texture properties...
February 2018: Journal of Food Science and Technology
Majid Jafari, Faramarz Mehrnejad, Fereshteh Rahimi, S Mohsen Asghari
To investigate the molecular interactions of sodium dodecyl sulfate (SDS) with human ubiquitin and its unfolding mechanisms, a comparative study was conducted on the interactions of the protein in the presence and absence of SDS at different temperatures using six independent 500 ns atomistic molecular dynamics (MD) simulations. Moreover, the effects of partial atomic charges on SDS aggregation and micellar structures were investigated at high SDS concentrations. The results demonstrated that human ubiquitin retains its native-like structure in the presence of SDS and pure water at 300 K, while the conformation adopts an unfolded state at a high temperature...
February 1, 2018: Scientific Reports
Sudipta Samanta, Sanchita Mukherjee
The first hydration shell of a protein exhibits heterogeneous behavior owing to several attributes, majorly local polarity and structural flexibility as revealed by solvation dynamics of secondary structural elements. We attempt to recognize the change in complex water counteraction generated due to substantial alteration in flexibility during protein complex formation. The investigation is carried out with the signaling lymphocytic activation molecule (SLAM) family of receptors, expressed by an array of immune cells, and interacting with SLAM-associated protein (SAP), composed of one SH2 domain...
January 28, 2018: Journal of Chemical Physics
Alaganandam Kumaran, Cheng Chang Ho, Lucy Sun Hwang
Alzheimer's disease (AD) is the most common cause of dementia in the elderly. β-Amyloid (Aβ) has been proposed to play a role in the pathogenesis of AD. Deposits of insoluble Aβ are found in the brains of patients with AD and are one of the pathological hallmarks of the disease, but the underlying signaling pathways are poorly understood. In order to develop antidementia agents with potential therapeutic value, we examined the inhibitory effect of the Nelumbo nucifera seed embryo extracts on to the aggregated amyloid β peptide (agg Aβ1-40)-induced damage of differentiated PC-12 cells (dPC-12), a well-known cell model for AD...
January 2018: Journal of Food and Drug Analysis
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