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protein hydration

Lucas R Smith, Sangkyun Cho, Dennis E Discher
Stem cells mechanosense the stiffness of their microenvironment, which impacts differentiation. Although tissue hydration anti-correlates with stiffness, extracellular matrix (ECM) stiffness is clearly transduced into gene expression via adhesion and cytoskeleton proteins that tune fates. Cytoskeletal reorganization of ECM can create heterogeneity and influence fates, with fibrosis being one extreme.
January 1, 2018: Physiology
Dario Fassini, Ana Rita C Duarte, Rui L Reis, Tiago H Silva
Collagen is a natural and abundant polymer that serves multiple functions in both invertebrates and vertebrates. As collagen is the natural scaffolding for cells, collagen-based hydrogels are regarded as ideal materials for tissue engineering applications since they can mimic the natural cellular microenvironment. Chondrosia reniformis is a marine demosponge particularly rich in collagen, characterized by the presence of labile interfibrillar crosslinks similarly to those described in the mutable collagenous tissues (MCTs) of echinoderms...
December 4, 2017: Marine Drugs
Rajib Biswas, Biman Bagchi
In nature, water is often found in contact with surfaces that are extended on the scale of molecule size but small on a macroscopic scale. Examples include lipid bilayers and reverse micelles as well as biomolecules like proteins, DNA and zeolites, to name a few. While the presence of surfaces and interfaces interrupts the continuous hydrogen bond network of liquid water, confinement on a mesoscopic scale introduces new features. Even when extended on a molecular scale, natural and biological surfaces often have features (like charge, hydrophobicity) that vary on the scale of the molecular diameter of water...
December 5, 2017: Journal of Physics. Condensed Matter: An Institute of Physics Journal
Reiko Urade, Nobuhiro Sato, Masaaki Sugiyama
Gliadins are well-known wheat grain proteins, particularly important in food science. They were studied as early as the 1700s. Despite their long history, it has been difficult to identify their higher-order structure as they aggregate in aqueous solution. Consequently, most studies have been performed by extracting the proteins in 70% ethanol or dilute acidic solutions. The carboxy-terminal half of α- and γ-gliadins have α-helix-rich secondary structures stabilized with intramolecular disulfide bonds, which are present in either aqueous ethanol or pure water...
December 4, 2017: Biophysical Reviews
Ahmed I Gomaa, Cynthia Martinent, Riadh Hammami, Ismail Fliss, Muriel Subirade
Antimicrobial peptides have been proposed as a potential biopreservatives in pharmaceutical research and agribusiness. However, many limitations hinder their utilization, such as their vulnerability to proteolytic digestion and their potential interaction with other food ingredients in complex food systems. One approach to overcome such problems is developing formulations entrapping and thereby protecting the antimicrobial peptides. Liposome encapsulation is a strategy that could be implemented to combine protection of the antimicrobial activity of the peptides from proteolytic enzymes and the controlled release of the encapsulated active ingredients...
2017: Frontiers in Chemistry
Suresh Gorle, Yangang Pan, Zhiqiang Sun, Luda S Shlyakhtenko, Reuben S Harris, Yuri L Lyubchenko, Lela Vuković
APOBEC3G (A3G) is a restriction factor that provides innate immunity against HIV-1 in the absence of viral infectivity factor (Vif) protein. However, structural information about A3G, which can aid in unraveling the mechanisms that govern its interactions and define its antiviral activity, remains unknown. Here, we built a computer model of a full-length A3G using docking approaches and molecular dynamics simulations, based on the available X-ray and NMR structural data for the two protein domains. The model revealed a large-scale dynamics of the A3G monomer, as the two A3G domains can assume compact forms or extended dumbbell type forms with domains visibly separated from each other...
November 22, 2017: ACS Central Science
Palak Patel, Krupali Parmar, Mili Das
We report here the inhibition of amyloid fibrillation of human insulin in vitro by Morin hydrate, a naturally occurring small molecule. Using spectroscopic assays and transmission electron microscopy, we found that Morin hydrate effectively inhibits insulin amyloid fibrillation in a dose dependent manner with more than 80% inhibition occurring even at only a 1:1 concentration. As suggested by fluorescence spectroscopic titration studies, Morin hydrate binds to insulin with a fairly strong affinity of -26.436kJmol-1...
November 29, 2017: International Journal of Biological Macromolecules
Alberto Cuzzolin, Giuseppe Deganutti, Veronica Salmaso, Mattia Sturlese, Stefano Moro
Unquestionably water appears to be an active player in noncovalent protein-ligand association processes, as it can either bridge interactions between protein and ligand or can be replaced by the bound ligand. Accordingly, in the last decade, alternative computational methodologies have been sought, that guess the position and thermodynamic profile of water molecules (i.e., hydration sites) in the binding site using either the ligand-bound or ligand-free protein conformation. Herein, we present an alternative approach, named AquaMMapS, that provides a three-dimensional sampling of putative hydration sites...
November 29, 2017: ChemMedChem
Shivangi Sharma, Parbati Biswas
A stochastic noise-driven dynamic model is proposed to study the diffusion of water molecules around the protein surface, under the effect of thermal fluctuations that arises due to the collisions of water molecules with the surrounding environment. The underlying dynamics of such a system may be described in the framework of generalized Langevin equation, where the thermal fluctuations are assumed to be algebraically correlated in time, which governs the non-Markovian behavior of the system...
December 1, 2017: Journal of Physics. Condensed Matter: An Institute of Physics Journal
Hajime Torii
For better understanding and more efficient use of the spectroscopic probes (vibrational and NMR) of the local electrostatic situations inside proteins, appropriate modeling of the properties of those probes is essential. The present study is devoted to examining the strategy for constructing such models. A more well-founded derivation than the ones in previous studies is given in constructing the models. Theoretical analyses are conducted on two representative example cases related to proteins, i.e., the peptide group of the main chains and the CO and NO ligands to the Fe2+ ion of heme, with careful treatment of the behavior of electrons in the electrostatic responses and with verification of consistency with observable quantities...
December 1, 2017: Journal of Physical Chemistry. B
Leixiao Yu, Yong Hou, Chong Cheng, Christoph Schlaich, Paul-Ludwig Michael Noeske, Qiang Wei, Rainer Haag
A new "adsorption - crosslinking" technology is presented to generate a highly dense polymer brush coating on various nonpolar substrates, including the most inert and low-energy surfaces of polydimethylsiloxane (PDMS) and polytetrafluoroethylene (PTFE). This prospective surface modification strategy is based on a tailored bifunctional amphiphilic block copolymer with benzophenone units as the hydrophobic anchor/chemical cross-linker and terminal azide groups for in situ post modification. The resulting polymer brushes exhibited long-term and ultra-low protein adsorption and cell adhesion benefiting from the high density and high hydration ability of polyglycerol blocks...
November 30, 2017: ACS Applied Materials & Interfaces
Hamid Nurrohman, Karina M M Carneiro, John Hellgeth, Kuniko Saeki, Sally J Marshall, Grayson W Marshall, Stefan Habelitz
Mineralized and sound dentin matrices contain inactive preforms of proteolytic enzymes that may be activated during the demineralization cycle. In this study, we tested the hypothesis that protease inhibitors (PI) preserve demineralized collagen fibrils and other constituents of the dentin matrix and thereby affect the potential for remineralization. Artificial carious lesions with lesion depths of 140 μm were created with acetate buffer (pH = 5.0, 66 hours), and remineralized using a polymer-induced-liquid-precursor (PILP) process (pH = 7...
2017: PloS One
Céline Houriez, Michael Mautner, Michel Masella
We report simulation results regarding the hydration process of the guanidinium cation in water droplets and in bulk liquid water, at a low concentration of 0.03 M, performed using a polarizable approach to model both water/water and ion/water interactions. In line with earlier theoretical studies, our simulations show a preferential orientation of guanidinium at water/vacuum interfaces, i.e. a parallel orientation of the guanidinium plane to the aqueous surface. In an apparent contradiction with earlier simulation studies, we show also that guanidinium has a stronger propensity for the cores of aqueous systems than the ammonium cation...
November 28, 2017: Journal of Physical Chemistry. B
Aurora Garre, Gemma Martinez-Masana, Jaime Piquero-Casals, Corinne Granger
Background: Skin aging is accelerated by multiple extrinsic factors: ultraviolet radiation, smoking and pollution increase oxidative activity, damaging cellular and extracellular components such as DNA, proteins, and lipids. With age, collagen and hyaluronic acid levels decline, resulting in loss of elasticity and moisture of the skin. Over time this damage leads to characteristic signs that make the skin look older: altered facial contour, sagging skin, wrinkles, and an uneven complexion...
2017: Clinical, Cosmetic and Investigational Dermatology
Mary K Cowman
The glycosaminoglycan hyaluronan (HA) is a key component of the microenvironment surrounding cells. In healthy tissues, HA molecules have extremely high molecular mass and consequently large hydrodynamic volumes. Tethered to the cell surface by clustered receptor proteins, HA molecules crowd each other, as well as other macromolecular species. This leads to severe nonideality in physical properties of the biomatrix, because steric exclusion leads to an increase in effective concentration of the macromolecules...
2017: Advances in Carbohydrate Chemistry and Biochemistry
Pratap Parida, Raj Narain Singh Yadav, Budheswar Dehury, Debosree Ghosh, Namita Mahapatra, Tapan Kumar Mohanta
BACKGROUND: The ligand PKP10 having substitution of Cl- at R2 and R3 positions of ring A of Panduratin A i.e.,((1R,2S,5S)-5-(2,3-dichlorophenyl)-3-methyl-2-(3-methylbut-2-nyl)cyclohex-3-enyl)(2,6-dihydroxy-4-methylphenyl)methanone hydrate) has been observed to block the Nuclear Receptor Binding Protein binding site of Non Structural protein 3 in all dengue serotypes. In continuation with our earlier study, we have reported sixty novel Panduratin A derivatives compounds where substitution was done in positions 2 and 3 position of the benzyl ring A of Panduratin A with various substituents...
November 22, 2017: Current Pharmaceutical Biotechnology
Emery Smith, Kenneth A Giuliano, Justin Shumate, Pierre Baillargeon, Brigid McEwan, Matthew D Cullen, John P Miller, Lawrence Drew, Louis Scampavia, Timothy P Spicer
Cystic fibrosis (CF), an inherited genetic disease, is caused by mutation of the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) gene, which encodes an ion channel involved in hydration maintenance by anion homeostasis. Ninety percent of CF patients possess one or more copies of the F508del CFTR mutation. This mutation disrupts trafficking of the protein to the plasma membrane and diminishes function of mature CFTR. Identifying small molecule modulators of mutant CFTR activity or biosynthesis may yield new tools for discovering novel CF treatments...
November 27, 2017: Assay and Drug Development Technologies
Adam K Sieradzan, Agnieszka G Lipska, Emilia A Lubecka
One of the most important interactions responsible for protein folding and stability are hydrogen bonds between peptide groups. There is a constant competition between the water molecules and peptide groups in a hydrogen bond formation. Also side-chains take part in this process by reducing hydration of peptide group (shielding effect) that promotes the protein folding. In this paper, a new approach to take into account a shielding effect is presented. A modification of the energy function is derived and incorporated into the UNited RESidue (UNRES) force field...
November 1, 2017: Journal of Molecular Graphics & Modelling
Fengyu Yang, Yonglan Liu, Yanxian Zhang, Baiping Ren, Jianxiong Xu, Jie Zheng
Rational design of biomaterials with antifouling properties still remains a challenge, but is important for many bench-to-bedside applications for biomedical implants, drug delivery carriers, and marine coatings. Herein we synthesized and characterized poly(N-acryloylglycinamide) (polyNAGA) and then grafted poly(NAGA) onto Au substrate to form polymer brushes with well controlled film stability, wettability and thickness using the surface-initiated atom transfer radical polymerization (SI-ATRP). The NAGA monomer integrates two hydrophilic amides on the side chain to enhance surface hydration, which is thought as a critical contributor to antifouling property...
November 21, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
Tomotaka Oroguchi, Masayoshi Nakasako
The influence of lone-pair electrons on the directionality of hydrogen bonds that are formed by oxygen and nitrogen atoms in the side chains of nine hydrophilic was investigated using molecular dynamics simulations. The simulations were conducted using two types of force fields; one incorporated lone-pair electrons placed at off-atom sites and the other did not. The density distributions of the hydration water molecules around the oxygen and nitrogen atoms were calculated from the simulation trajectories, and were compared with the empirical hydration distribution functions, which were constructed from a large number of hydration water molecules found in the crystal structures of proteins...
November 20, 2017: Scientific Reports
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