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https://www.readbyqxmd.com/read/29054096/simplified-autodock-force-field-for-hydrated-binding-sites
#1
Marek Wojciechowski
A set of high quality structures of protein-ligand complexes with experimentally determined binding affinities has been extracted from the Protein Data Bank and used to test and recalibrate AutoDock force field. Since for some binding sites water molecules are crucial for bridging the receptor-ligand interactions, they have to be included in the analysis. To simplify the process of incorporating water molecules into the binding sites and make it less ambiguous, new simple water model was created. After recalibration of the force field on the new dataset much better correlation between the computed and experimentally determined binding affinities was achieved and the quality of pose prediction improved even more...
September 23, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/29052335/a-comparative-study-on-intrinsic-fluorescence-of-bsa-and-lysozyme-proteins-in-presence-of-different-divalent-ions-from-their-solution-and-thin-film-conformations
#2
Ashim Chandra Bhowal, Sarathi Kundu
Optical emission behaviours of lysozyme and bovine serum albumin, from bulk and thin film geometry, were studied in the presence of three different divalent ions (Mg(2+) , Ca(2+) or Ba(2+) ) using different spectroscopic [steady-state fluorescence, UV-Vis and Fourier transform infra-red (FTIR)] techniques. Additionally, protein thin films on silicon surfaces were prepared and morphological studies were carried out using atomic force microscopy. Dynamic quenching was mainly identified for both proteins in the presence of Mg(2+) , Ca(2+) and Ba(2+) ions...
October 20, 2017: Luminescence: the Journal of Biological and Chemical Luminescence
https://www.readbyqxmd.com/read/29051181/disorders-of-erythrocyte-hydration
#3
Patrick G Gallagher
The erythrocyte contains a network of pathways that regulate salt and water content in the face of extracellular and intracellular osmotic perturbations. This allows the erythrocyte to maintain a narrow range of cell hemoglobin concentration, a process critical for normal red blood cell function and survival. Primary disorders that perturb volume homeostasis jeopardize the erythrocyte and may lead to its premature destruction. These disorders are marked by clinical, laboratory, and physiologic heterogeneity...
October 19, 2017: Blood
https://www.readbyqxmd.com/read/29043510/taurine-as-a-water-structure-breaker-and-protein-stabilizer
#4
P Bruździak, A Panuszko, E Kaczkowska, B Piotrowski, A Daghir, S Demkowicz, J Stangret
The enhancing effect on the water structure has been confirmed for most of the osmolytes exhibiting both stabilizing and destabilizing properties in regard to proteins. The presented work concerns osmolytes, which should be classified as "structure breaking" solutes: taurine and N,N,N-trimethyltaurine (TMT). Here, we combine FTIR spectroscopy, DSC calorimetry and DFT calculations to gain an insight into the interactions between osmolytes and two proteins: lysozyme and ubiquitin. Despite high structural similarity, both osmolytes exert different influence on protein stability: taurine is a stabilizer, TMT is a denaturant...
October 17, 2017: Amino Acids
https://www.readbyqxmd.com/read/29043368/self-coacervation-of-modular-squid-beak-proteins-a-comparative-study
#5
Hao Cai, Bartosz Gabryelczyk, Malathy S S Manimekalai, Gerhard Grüber, Stefan Salentinig, Ali Miserez
The beak of the Humboldt squid is a biocomposite material made solely of organic components - chitin and proteins - which exhibits 200-fold stiffness and hardness gradients from the soft base to the exceptionally hard tip (rostrum). The outstanding mechanical properties of the squid beak are achieved via controlled hydration and impregnation of the chitin-based scaffold by protein coacervates. Molecular-based understanding of these proteins is essential to mimic the natural beak material. Here, we present detailed studies of two histidine-rich beak proteins (HBP-1 and -2) that play central roles during beak bio-fabrication...
October 18, 2017: Soft Matter
https://www.readbyqxmd.com/read/29043324/privileged-hydration-sites-in-aromatic-side-chains-effect-on-conformational-equilibrium
#6
Belén Hernández, Fernando Pflüger, Manuel Dauchez, Mahmoud Ghomi
Water interaction with peptide chains is one of the key structure stabilizing factors in an aqueous environment. Because of its strong polar character, water can bind to both anionic and cationic sites via electrostatic interactions. It can also act as a hydrogen-bond donor or acceptor according to its interactions with different polar groups in the backbone and side chains of peptides and proteins. Based on density functional theory calculations, the present report aims at illustrating the most energetically favorable interaction sites of aromatic side chains of phenylalanine, tyrosine, tryptophan, and histidine (neutral and protonated species) with surrounding water molecules...
October 18, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/29036437/fimbrins-4-and-5-act-synergistically-during-polarized-pollen-tube-growth-to-ensure-fertility-in-arabidopsis
#7
Hui Su, Hualing Feng, Xiaoting Chao, Xia Ding, Qiong Nan, Chenxi Wen, Huidong Liu, Sinuo Liu, Yun Xiang, Wenzhe Liu
The germination and polar growth of pollen are prerequisite for double fertilization in plants. The actin cytoskeleton and its binding proteins play pivotal roles in pollen germination and pollen-tube growth. Two homologs of the actin-bundling protein fimbrin, AtFIM4 and AtFIM5, are highly expressed in pollen in Arabidopsis and can form distinct actin architectures in vitro, but how they cooperatively regulate pollen germination and pollen-tube growth in vivo is largely unknown. In this study, we explored their functions during pollen germination and polar growth...
September 29, 2017: Plant & Cell Physiology
https://www.readbyqxmd.com/read/29036376/the-mechanism-and-high-free-energy-transition-state-of-lac-repressor-lac-operator-interaction
#8
Rituparna Sengupta, Michael W Capp, Irina A Shkel, M Thomas Record
Significant, otherwise-unavailable information about mechanisms and transition states (TS) of protein folding and binding is obtained from solute effects on rate constants. Here we characterize TS for lac repressor(R)-lac operator(O) binding by analyzing effects of RO-stabilizing and RO-destabilizing solutes on association (ka) and dissociation (kd) rate constants. RO-destabilizing solutes (urea, KCl) reduce ka comparably (urea) or more than (KCl) they increase kd, demonstrating that they destabilize TS relative to reactants and RO, and that TS exhibits most of the Coulombic interactions between R and O...
October 3, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29034914/local-water-sensing-water-exchange-in-bacterial-photosynthetic-reaction-centers-embedded-in-a-trehalose-glass-studied-using-multiresonance-epr
#9
Anna Nalepa, Marco Malferrari, Wolfgang Lubitz, Giovanni Venturoli, Klaus Möbius, Anton Savitsky
Using isotope labeled water (D2O and H2(17)O) and pulsed W-band (94 GHz) high-field multiresonance EPR spectroscopies, such as ELDOR-detected NMR and ENDOR, the biologically important question of detection and quantification of local water in proteins is addressed. A bacterial reaction center (bRC) from Rhodobacter sphaeroides R26 embedded into a trehalose glass matrix is used as a model system. The bRC hosts the two native radical cofactor ions (primary electron donor) and (primary electron acceptor) as well as an artificial nitroxide spin label site-specifically attached to the surface of the H-protein domain...
October 16, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/29032199/affinity-and-path-of-binding-xylopyranose-unto-e-%C3%A2-coli-xylose-permease
#10
Thierry O Wambo, Liao Y Chen, Clyde Phelix, George Perry
Glucose transporters (GLUTs), expressed in all types of human cells, are responsible for the uptake of sugars as the primary energy source for the normal functions of good cells and for the abnormal growth of cancer cells. The E. coli xylose permease (XylE), a homologue of human GLUTs, has been investigated more thoroughly than other major facilitator proteins in the current literature. In this paper, we present a molecular dynamics (MD) study of an all-atom model system to elucidate the atomistic details and the free-energy landscape along the path of binding a xylopyranose (XYP) from the extracellular space to the inside of the transporter protein XylE...
October 12, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29024903/bacteria-mould-and-yeast-spore-inactivation-studies-by-scanning-electron-microscope-observations
#11
Siti N M Rozali, Elham A Milani, Rebecca C Deed, Filipa V M Silva
Spores are the most resistant form of microbial cells, thus difficult to inactivate. The pathogenic or food spoilage effects of certain spore-forming microorganisms have been the primary basis of sterilization and pasteurization processes. Thermal sterilization is the most common method to inactivate spores present on medical equipment and foods. High pressure processing (HPP) is an emerging and commercial non-thermal food pasteurization technique. Although previous studies demonstrated the effectiveness of thermal and non-thermal spore inactivation, the in-depth mechanisms of spore inactivation are as yet unclear...
October 4, 2017: International Journal of Food Microbiology
https://www.readbyqxmd.com/read/29021160/off-axis-electron-holography-of-bacterial-cells-and-magnetic-nanoparticles-in-liquid
#12
Tanya Prozorov, Trevor P Almeida, András Kovács, Rafal E Dunin-Borkowski
The mapping of electrostatic potentials and magnetic fields in liquids using electron holography has been considered to be unrealistic. Here, we show that hydrated cells of Magnetospirillum magneticum strain AMB-1 and assemblies of magnetic nanoparticles can be studied using off-axis electron holography in a fluid cell specimen holder within the transmission electron microscope. Considering that the holographic object and reference wave both pass through liquid, the recorded electron holograms show sufficient interference fringe contrast to permit reconstruction of the phase shift of the electron wave and mapping of the magnetic induction from bacterial magnetite nanocrystals...
October 2017: Journal of the Royal Society, Interface
https://www.readbyqxmd.com/read/29020453/small-angle-neutron-scattering-sans-studies-on-r67-dihydrofolate-reductase-a-tetrameric-protein-with-intrinsically-disordered-n-termini
#13
Purva P Bhojane, Michael R Duff, Khushboo Bafna, Pratul K Agarwal, Christopher B Stanley, Elizabeth E Howell
R67 dihydrofolate reductase (DHFR) is a homo-tetramer with a single active site pore and no sequence or structural homology with chromosomal DHFRs. The R67 enzyme provides resistance to trimethoprim, an active site directed inhibitor of E. coli DHFR. 16-20 N-terminal amino acids are intrinsically disordered in the R67 dimer crystal structure. Chymotrypsin cleavage of 16 N-terminal residues results in an active enzyme with lowered stability. The space sampled by the disordered N-termini of R67 DHFR was investigated using small angle neutron scattering...
October 11, 2017: Biochemistry
https://www.readbyqxmd.com/read/29017796/anti-inflammatory-effect-of-collagen-tripeptide-in-atopic-dermatitis
#14
Amiko Hakuta, Yukie Yamaguchi, Tomoko Okawa, Shoko Yamamoto, Yasuo Sakai, Michiko Aihara
BACKGROUND: Atopic dermatitis (AD) is a chronic, pruritic inflammatory skin disease in which type 2 allergic inflammation plays an important role. Collagen tripeptide (CTP) is a functional collagen fraction with a high content of Gly-X-Y tripeptides. OBJECTIVE: To examine the effect of CTP on inflammation in AD. METHODS: Levels of inflammatory cytokines and chemokines, such as thymus- and activation-regulated chemokine (TARC), macrophage-derived chemokine, and thymic stromal lymphopoietin (TSLP), were examined in human keratinocytes supplemented with or without CTP under AD-like inflammation...
September 28, 2017: Journal of Dermatological Science
https://www.readbyqxmd.com/read/28994836/confined-water-dynamics-in-a-hydrated-photosynthetic-pigment-protein-complex
#15
Yael Kurzweil-Segev, Ivan Popov, Ido Eisenberg, Shira Yochelis, Nir Keren, Yossi Paltiel, Yuri Feldman
Water is of fundamental importance for life. It plays a critical role in all biological systems. In phycocyanin, a pigment-protein complex, the hydration level influences its absorption spectrum. However, there is currently a gap in the understanding of how protein interfaces affect water's structure and properties. This work presents combined dielectric and calorimetric measurements of hydrated phycocyanin with different levels of hydration in a broad temperature interval. Based on the dielectric and calorimetric tests, it was shown that two types of water exist in the phycocyanin hydration shell...
October 10, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28993927/rhodium-ii-complex-with-2-benzoylpyridine-a-novel-potential-chemotherapeutic-drug-induces-cell-cycle-arrest-and-apoptosis-in-hepg2-cells
#16
Xuehong Wang, Yulan Li, Minglin Lin, Junfei Jin, Zhaoquan Huang
Rhodium (II) complex with 2-benzoylpyridine (Rh(L)2Cl2) is a new, synthetic, active metal-complex, which is produced by the reaction of 2-benzoylpyridine (L) with rhodium chloride hydrate (RhCl3·nH2O). The crystal structure was determined by X-ray diffraction which is mono-nuclear. In order to explore the biological properties of the novel complex, a series of studies were performed. The results showed that Rh(L)2Cl2 had the anti-tumor activity in HepG2 and other cell lines and has been shown to induce G1 cell cycle arrest and apoptosis in HepG2 cells...
October 9, 2017: Biometals: An International Journal on the Role of Metal Ions in Biology, Biochemistry, and Medicine
https://www.readbyqxmd.com/read/28992702/open-boundary-simulations-of-proteins-and-their-hydration-shells-by-hamiltonian-adaptive-resolution-scheme
#17
Thomas Tarenzi, Vania Calandrini, Raffaello Potestio, Alejandro Giorgetti, Paolo Carloni
The recently proposed Hamiltonian Adaptive Resolution Scheme (H-AdResS) allows to perform molecular simulations in an open boundary framework. It allows to change on the fly the resolution of specific subset of molecules (usually the solvent), which are free to diffuse between the atomistic region and the coarse-grained reservoir. So far, the method has been successfully applied to pure liquids. Coupling the H-AdResS methodology to hybrid models of proteins, such as the Molecular Mechanics/Coarse-Grained (MM/CG) scheme, is a promising approach for rigorous calculations of ligand binding free energies in low-resolution protein models...
October 9, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28988529/effect-of-anesthetics-on-efficiency-of-remote-ischemic-preconditioning
#18
D N Silachev, E A Usatikova, I B Pevzner, L D Zorova, V A Babenko, M V Gulyaev, Yu A Pirogov, E Yu Plotnikov, D B Zorov
Remote ischemic preconditioning of hind limbs (RIPC) is an effective method for preventing brain injury resulting from ischemia. However, in numerous studies RIPC has been used on the background of administered anesthetics, which also could exhibit neuroprotective properties. Therefore, investigation of the signaling pathways triggered by RIPC and the effect of anesthetics is important. In this study, we explored the effect of anesthetics (chloral hydrate and Zoletil) on the ability of RIPC to protect the brain from injury caused by ischemia and reperfusion...
September 2017: Biochemistry. Biokhimii︠a︡
https://www.readbyqxmd.com/read/28987986/morphology-composition-and-aggregation-mechanisms-of-soft-bioflocs-in-marine-snow-and-activated-sludge-a-comparative-review
#19
REVIEW
Berrin Tansel
Conditions that lead to marine snow formation and aggregates that constitute the marine snow have similarities with the soft bioflocs that form during wastewater treatment by activated sludge process. Analysis of the conditions and similarities of the soft bioflocs in these two aquatic environments provide insight for the processes that lead to formation and growth of hydrated aggregates consisting of both living and nonliving particles, their chemical and biolocial composition, settling/suspension behavior, and contributing factors for their structure and morphology...
October 5, 2017: Journal of Environmental Management
https://www.readbyqxmd.com/read/28986788/microscale-thermophoresis-a-rapid-and-precise-method-to-quantify-protein-nucleic-acid-interactions-in-solution
#20
Adrian Michael Mueller, Dennis Breitsprecher, Stefan Duhr, Philipp Baaske, Thomas Schubert, Gernot Längst
Interactions between nucleic acids and proteins are driving gene expression programs and regulating the development of organisms. The binding affinities of transcription factors to their target sites are essential parameters to reveal their binding site occupancy and function in vivo. Microscale Thermophoresis (MST) is a rapid and precise method allowing for quantitative analysis of molecular interactions in solution on a microliter scale. The technique is based on the movement of molecules in temperature gradients, which is referred to as thermophoresis, and depends on molecule size, charge, and hydration shell...
2017: Methods in Molecular Biology
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