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protein hydration

Erik Frotscher, Georg Krainer, Michael Schlierf, Sandro Keller
The structural dynamics of proteins on the nanosecond timescale can be probed with dipolar relaxation in response to photoexcitation of intrinsic tryptophan (Trp) residues. For membrane proteins, however, the complexity due to overlapping contributions from the protein itself, the membrane mimic, and the aqueous solvent impairs detailed analysis and interpretation. To disentangle these contributions, we measured time-resolved emission spectra of Trp in the protein Mistic in detergent micelles of various polarities...
April 13, 2018: Journal of Physical Chemistry Letters
Kanta Yanagi, Norifumi L Yamada, Kazuaki Kato, Kohzo Ito, Hideaki Yokoyama
Dense polymer brushes with closely packed rotaxane structures were formed at the interface of water and a styrene-butadiene elastomer by spontaneous segregation of an amphiphilic polyrotaxane (PR), a mechanically interlocked polymer consisting of hydrophobic polybutadiene threading through multiple hydrophilic γ-cyclodextrin (γ-CD) derivatives. Segrega-tion of PR at the water/elastomer interface was suggested by X-ray photoelectron spectroscopy. The polymer brush structure at the water interface was investigated using neutron reflectometry...
April 13, 2018: Langmuir: the ACS Journal of Surfaces and Colloids
Hakan Atakisi, David W Moreau, Robert E Thorne
The modulation of main-chain and side-chain conformational heterogeneity and solvent structure in monoclinic lysozyme crystals by dehydration (related to water activity) and temperature is examined. Decreasing the relative humidity (from 99 to 11%) and decreasing the temperature both lead to contraction of the unit cell, to an increased area of crystal contacts and to remodeling of primarily contact and solvent-exposed residues. Both lead to the depopulation of some minor side-chain conformers and to the generation of new conformations...
April 1, 2018: Acta Crystallographica. Section D, Structural Biology
Yuuki Inoue, Yuya Onodera, Kazuhiko Ishihara
Dynamic changes in the properties of adsorbed protein layers at material surfaces make it difficult to analyze a cell adhesion behavior. Adhesion is affected by the ligand molecules in the adsorbed protein layers on the material's surface. This study aimed to quantitatively analyze the initial cell adhesion onto a polymeric surface modified with immobilized cell adhesion molecules with a well-defined structure. Peptides containing an arginine-glycine-aspartic acid (RGD) sequence were introduced at almost all the termini of the grafted poly(2-methacryloyloxyethyl phosphorylcholine) (poly(MPC)) chains using a click reaction at a highly protein-resistant poly(MPC) brush layer...
April 13, 2018: ACS Applied Materials & Interfaces
Haiyang Zhang, Chunhua Yin, Yang Jiang, David van der Spoel
Thermodynamic and kinetic properties are of critical importance for the applicability of computational models to biomolecules such as proteins. Here we present an extensive evaluation of the Amber ff99SB-ILDN force field for modeling hydration and diffusion of amino acids with three-site (SPC, SPC/E, SPC/Eb, and TIP3P), four-site (TIP4P, TIP4P-Ew, and TIP4P/2005), and five-site (TIP5P and TIP5P-Ew) water models. Hydration free energies (HFEs) of neutral amino acid side chain analogues have little dependence on the water models with a root-mean-square error (RMSE) of ~1 kcal/mol from experimental observations...
April 12, 2018: Journal of Chemical Information and Modeling
Muhammad Khattab, Feng Wang, Andrew Harry A Clayton
To understand drug-protein dynamics, it is necessary to account for drug molecular flexibility and binding site plasticity. Herein, we exploit fluorescence from a tyrosine kinase inhibitor, AG1478, as a reporter of its conformation and binding-site environment when complexed with its cognate kinase. Water-soluble kinases, aminoglycoside phosphotransferase APH(3`)-Ia and mitogen activated protein kinase 14 (MAPK 14), were chosen for this study. Based on our prior work, the AG1478 conformation (planar or twisted) was inferred from the fluorescence excitation spectrum, the polarity of the AG1478 binding site was deduced from the fluorescence emission spectrum, while red-edge excitation shift (REES) probed the heterogeneity of the binding site (protein conformation and hydration) distributions in the protein conformational ensemble...
April 9, 2018: Journal of Physical Chemistry. B
Zhikun Cai, Yang Zhang
Understanding the interaction between proteins and graphene not only helps elucidate the behaviors of proteins in confined geometries, but is also imperative to the development of a plethora of graphene-based biotechnologies, such as the graphene liquid cell transmission electron microscopy. To discuss the overall geometrical-thermal effects on proteins, we performed molecular dynamics simulations of hydrated Trp-cage miniprotein sandwiched between two graphene sheets and in the bulk environment at the temperatures below and above its unfolding temperature...
March 27, 2018: Colloids and Surfaces. B, Biointerfaces
Eva Meirovitch, Zhichun Liang, Jack H Freed
The microscopic-order-macroscopic-disorder (MOMD) approach for2 H NMR lineshape analysis is applied to dry and hydrated 3-fold-, and 2-fold-symmetric amyloid-Aβ40 fibrils, and protofibrils of the D23N mutant. The methyl-moieties of L17, L34, V36 (C-CD3 ) and M35 (S-CD3 ) serve as probes. Experimental2 H spectra acquired previously in the 147-310 K range are used. MOMD describes local probe motion as axial diffusion ( R-tensor) in the presence of a potential, u, which represents the spatial restrictions exerted by the molecular surroundings...
April 6, 2018: Journal of Physical Chemistry. B
Michel Leandro Campos, Leticia Bonancio Cerqueira, Bruna Cristina Ulian Silva, Taisa Busaranho Franchin, Marina Rocha Galdino-Pitta, Ivan Rocha Pitta, Rosangela Goncalves Peccinini, Roberto Pontarolo
Thiazolidinediones are drugs used to treat type 2 diabetes mellitus; however, there remain several safety concerns regarding the available drugs in this class. Therefore, the search for new thiazolidinedione candidates is still ongoing; metabolism studies play a crucial step in the development of new candidates. Pioglitazone, which is one of the most commonly used thiazolidinediones, and GQ-11, a new N-substituted thiazolidinedione, were investigated in terms of their metabolic activity in rat and human liver microsomes, in order to assess their metabolic stability and to investigate their metabolites...
April 4, 2018: Drug Metabolism and Disposition: the Biological Fate of Chemicals
Orly B Tarun, Christof Hannesschläger, Peter Pohl, Sylvie Roke
Biological membranes are highly dynamic and complex lipid bilayers, responsible for the fate of living cells. To achieve this function, the hydrating environment is crucial. However, membrane imaging typically neglects water, focusing on the insertion of probes, resonant responses of lipids, or the hydrophobic core. Owing to a recent improvement of second-harmonic (SH) imaging throughput by three orders of magnitude, we show here that we can use SH microscopy to follow membrane hydration of freestanding lipid bilayers on millisecond time scales...
April 2, 2018: Proceedings of the National Academy of Sciences of the United States of America
Ana Campuzano, Cristina M Rosell, Fabiola Cornejo
Banana flour has been recognized as functional ingredient, owing to its healthy nutritional pattern. Nevertheless, unripe and ripe banana flours show different characteristics and scarce information is available about changes undergone during banana ripening. This study evaluates the changes on physiochemical (chemical composition, hydration properties, rheological properties and structural characteristic) and nutritional (resistant starch content, phenolic compound and antioxidant activity) characteristics of banana flour at the initial four ripening stages...
August 1, 2018: Food Chemistry
Louie D Henderson, Morgan Beeby
Electron cryo-tomography and subtomogram averaging enable visualization of protein complexes in situ, in three dimensions, in a near-native frozen-hydrated state to nanometer resolutions. To achieve this, intact cells are vitrified and imaged over a range of tilts within an electron microscope. These images can subsequently be reconstructed into a three-dimensional volume representation of the sample cell. Because complexes are visualized in situ, crucial insights into their mechanism, assembly process, and dynamic interactions with other proteins become possible...
2018: Methods in Molecular Biology
Yoshihiko Tokunaga, Yu Yamamori, Nobuyuki Matubayasi
Toward identifying the driving force of protein folding, energetics was analyzed in water for Trp-cage (20 residues), protein G (56 residues), and ubiquitin (76 residues) at their native (folded) and heat-denatured (unfolded) states. All-atom molecular dynamics simulation was conducted, and the hydration effect was quantified by the solvation free energy. The free-energy calculation was done by employing the solution theory in the energy representation, and it was seen that the sum of the protein intramolecular (structural) energy and the solvation free energy is more favorable for a folded structure than for an unfolded one generated by heat...
March 28, 2018: Journal of Chemical Physics
Geng Chen, Naoji Matsuhisa, Zhiyuan Liu, Dianpeng Qi, Pingqiang Cai, Ying Jiang, Changjin Wan, Yajing Cui, Wan Ru Leow, Zhuangjian Liu, Suxuan Gong, Ke-Qin Zhang, Yuan Cheng, Xiaodong Chen
Soft and stretchable electronic devices are important in wearable and implantable applications because of the high skin conformability. Due to the natural biocompatibility and biodegradability, silk protein is one of the ideal platforms for wearable electronic devices. However, the realization of skin-conformable electronic devices based on silk has been limited by the mechanical mismatch with skin, and the difficulty in integrating stretchable electronics. Here, silk protein is used as the substrate for soft and stretchable on-skin electronics...
March 30, 2018: Advanced Materials
Qiongying Xu, Qiandi Wang, Weijun Zhang, Peng Yang, Youjing Du, Dongsheng Wang
Proteins are the dominant organic component of extracellular polymeric substances (EPS) in waste activated sludge (WAS), and play an important role during sludge dewatering processes. Methanol is a polar hydrophilic reagent and can denature proteins, which suggested to us that the modification of protein configurations with methanol could improve sludge dewatering performance. In this study, methanol was used to precondition WAS prior to adding inorganic coagulants for dewatering enhancement. The morphology and EPS properties (especially of proteins) were investigated to analyze and explain the effects of methanol in the sludge conditioning process...
March 16, 2018: Water Research
Ying Yang, Amr H A Abdallah, Markus A Lill
Water molecules in the binding site of a protein significantly influence protein structure and function, for example, by mediating protein-ligand interactions or in form of desolvation as driving force for ligand binding. The knowledge about location and thermodynamic properties of water molecules in the binding site is crucial to the understanding of protein function. This chapter describes the method of calculating the location and thermodynamic properties of bound water molecules from molecular dynamics (MD) simulation trajectories...
2018: Methods in Molecular Biology
Tao Yu, Shi-Jie Chen
The interaction between metal ions, especially Mg2+ ions, and RNA plays a critical role in RNA folding. Upon binding to RNA, a metal ion that is fully hydrated in bulk solvent can become dehydrated. Here we use molecular dynamics simulation to investigate the dehydration of bound hexahydrated Mg2+ ions. We find that a hydrated Mg2+ ion in the RNA groove region can involve significant dehydration in the outer hydration shell. The first or innermost hydration shell of the Mg2+ ion, however, is retained during the simulation because of the strong ion-water electrostatic attraction...
March 27, 2018: Biophysical Journal
Elzinandes Leal Azeredo, Flavia Barreto Dos Santos, Luciana Santos Barbosa, Thiara Manuele Alves Souza, Jessica Badolato-Corrêa, Juan Camilo Sánchez-Arcila, Priscila Conrado Guerra Nunes, Luzia Maria de-Oliveira-Pinto, Ana Maria de Filippis, Márcia Dal Fabbro, Izilyanne Hoscher Romanholi, Rivaldo Venancio da Cunha
BACKGROUND: The current triple epidemic caused by dengue, zika and chikungunya constitutes a serious health problem in Brazil. The aim of this study was to investigate acute samples (up to the 7 days of symptoms) from patients presenting acute fever syndrome suspected as arboviral infection and characterize the clinical and laboratorial profile during the co-circulation of dengue, zika and chikungunya in Campo Grande, Mato Grosso do Sul (MS), midwest region of Brazil. METHODS: All suspected cases (n=134) were tested by using serological and molecular diagnostic tests including DENV, ZIKV and CHIKV RT-PCR, Dengue nonstructural protein 1 (NS1) antigen capture ELISA, anti- DENV IgM ELISA and anti-CHIKV IgM ELISA...
February 15, 2018: PLoS Currents
Patricia S Hegger, Julia Kupka, Burcu Baykal Minsky, Sabine Laschat, Heike Boehm
The extracellular matrix (ECM) represents a highly charged and hydrated network in which different cells in vertebrate tissues are embedded. Hydrogels as minimal ECM mimetics with a controlled chemistry offer the opportunity to vary material properties by varying the negative network charge. In this paper, a synthetic biology model of the ECM based on natural and highly negatively charged polyelectrolyte hyaluronic acid (HA) is characterized with specific emphasis on its charge-related bioactivity. Therefore, the thiol-Michael addition click reaction is used to produce HA hydrogels with defined network structure and charge density...
March 27, 2018: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
Ysaias J Alvarado, Atilio Ferrebuz, Jose Luis Paz, Patricia Rodriguez-Lugo, Jelem Restrepo, Freddy Romero, Jaqueline Fernández-Acuña, Yhan Williams, Jhoan Toro-Mendoza
The effect of the presence of glucose and sucrose on the non-intrinsic contribution to partial molar volume hini of Bovine Serum Albumin (BSA) is determined by means of static and dynamic electronic polarizability measurements. For that aim, a combined strategy based on high-resolution refractometry, high exactitude densitometry, and synchronous uorescence spectroscopy is applied. Both static and dynamic mean electronic molecular polarizability values are found to be sensitive to the presence of glucose. In the case of sucrose, the polarizability of BSA is not appreciably affected...
March 27, 2018: Journal of Physical Chemistry. B
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