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https://www.readbyqxmd.com/read/28636952/human-leukocyte-antigen-f-presents-peptides-and-regulates-immunity-through-interactions-with-nk-cell-receptors
#1
Charles L Dulberger, Curtis P McMurtrey, Angelique Hölzemer, Karlynn E Neu, Victor Liu, Adriana M Steinbach, Wilfredo F Garcia-Beltran, Michael Sulak, Bana Jabri, Vincent J Lynch, Marcus Altfeld, William H Hildebrand, Erin J Adams
Evidence is mounting that the major histocompatibility complex (MHC) molecule HLA-F (human leukocyte antigen F) regulates the immune system in pregnancy, infection, and autoimmunity by signaling through NK cell receptors (NKRs). We present structural, biochemical, and evolutionary analyses demonstrating that HLA-F presents peptides of unconventional length dictated by a newly arisen mutation (R62W) that has produced an open-ended groove accommodating particularly long peptides. Compared to empty HLA-F open conformers (OCs), HLA-F tetramers bound with human-derived peptides differentially stained leukocytes, suggesting peptide-dependent engagement...
June 20, 2017: Immunity
https://www.readbyqxmd.com/read/28636915/probing-the-structural-dynamics-of-the-nmda-receptor-activation-by-coarse-grained-modeling
#2
Wenjun Zheng, Han Wen, Gary J Iacobucci, Gabriela K Popescu
N-Methyl-D-aspartate (NMDA) receptors are glutamate-gated excitatory channels that play essential roles in brain functions. High-resolution structures have been solved for an allosterically inhibited and agonist-bound form of a functional NMDA receptor; however, other key functional states (particularly the active open-channel state) were only resolved at moderate resolutions by cryo-electron microscopy (cryo-EM). To decrypt the mechanism of the NMDA receptor activation, structural modeling is essential to provide presently missing information about structural dynamics...
June 20, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28636911/direct-conversion-of-an-enzyme-from-native-like-to-amyloid-like-aggregates-within-inclusion-bodies
#3
Francesco Elia, Francesca Cantini, Fabrizio Chiti, Christopher Martin Dobson, Francesco Bemporad
The acylphosphatase from Sulfolobus solfataricus (Sso AcP) is a globular protein able to aggregate in vitro from a native-like conformational ensemble without the need for a transition across the major unfolding energy barrier. This process leads to the formation of assemblies in which the protein retains its native-like structure, which subsequently convert into amyloid-like aggregates. Here, we investigate the mechanism by which Sso AcP aggregates in vivo to form bacterial inclusion bodies after expression in E...
June 20, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28636909/electric-field-induced-protein-translocation-via-a-conformational-transition-in-secdf-an-md-study
#4
Emel Ficici, Daun Jeong, Ioan Andricioaei
SecDF is an important component of the Sec protein translocation machinery embedded in the bacterial membrane, which is associated with many functions, such as stabilizing other Sec translocon components within the membrane, maintaining the transmembrane (TM) potential, and facilitating the ATP-independent stage of the translocation mechanism. Related studies suggest that SecDF undergoes functionally important conformational changes that involve mainly its P1-head domain and that these changes are coupled with the proton motive force (Δp)...
June 20, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28636907/epr-spectroscopy-targets-structural-changes-in-the-e-%C3%A2-coli-membrane-fusion-cusb-upon-cu-i-binding
#5
Aviv Meir, Ahmad Abdelhai, Yoni Moskovitz, Sharon Ruthstein
Bacterial cells have developed sophisticated systems to deal with the toxicity of metal ions. Escherichia coli CusCFBA is a complex efflux system, responsible for transferring Cu(I) and Ag(I) ions; this system, located in the periplasm, involves four proteins, CusA, CusB, CusC, and CusF. CusA, CusB, and CusC are connected to one another in an oligomerization ratio of 3:6:3 CusA/CusB/CusC to form the CusCBA periplasm membrane transporter. CusB is an adaptor protein that connects the two membrane proteins CusA (inner membrane) and CusC (outer membrane)...
June 20, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/28636788/role-of-positively-charged-residues-on-the-polar-and-non-polar-faces-of-amphipathic-%C3%AE-helical-antimicrobial-peptides-amps-on-specificity-and-selectivity-for-gram-negative-pathogens
#6
Ziqing Jiang, Colin T Mant, Michael Vasil, Robert S Hodges
We have designed de novo and synthesized eight 26-residue all D-conformation amphipathic α-helical cationic antimicrobial peptides (AMPs), four with "specificity determinants" which provide specificity for prokaryotic cells over eukaryotic cells and four AMPs without specificity determinants. The eight AMPs contain six positively charged Lys residues on the polar face in four different arrangements to understand the role of these residues have on antimicrobial activity against 14 Acinetobacter baumannii strains, 7 of which were resistant to polymyxin B and colistin; 6 diverse Pseudomonas aeruginosa strains and 17 Staphylococcus aureus strains, 9 of which were Methicillin-sensitive (MSSA) and 8 of which were Methicillin-resistant (MRSA)...
June 21, 2017: Chemical Biology & Drug Design
https://www.readbyqxmd.com/read/28636681/thermally-induced-conformational-changes-and-protein-protein-interactions-of-bovine-serum-albumin-in-aqueous-solution-under-different-ph-and-ionic-strengths-as-revealed-by-saxs-measurements
#7
Dmitry Molodenskiy, Evgeny Shirshin, Tatiana Tikhonova, Andrey Gruzinov, Georgy Peters, Francesco Spinozzi
Thermal-induced conformational changes and protein-protein interactions of bovine serum albumin (BSA) in aqueous solution are assessed by small angle X-ray scattering (SAXS) at two pH values (7.4 and 9.0) and two ionic strengths (0.1 and 0.5). We demonstrate that Guinier analysis in two ranges of the modulus of the scattering vector allows protein melting and aggregation to be monitored simultaneously, thus providing insights into the mechanism of thermal-induced BSA aggregation. Results of the analysis suggest that at room temperature monomeric and dimeric BSA fractions are present in solution...
June 21, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28636680/unifying-the-microscopic-picture-of-his-containing-turns-from-gas-phase-model-peptides-to-crystallized-proteins
#8
Woon Yong Sohn, Sana Habka, Eric Gloaguen, Michel Mons
The presence in crystallized proteins of a local anchoring between the side chain of a His residue, located in the central position of a γ- or β-turn, and its local main chain environment, was assessed by the comparison of protein structures with relevant isolated model peptides. Gas phase laser spectroscopy, combined with relevant quantum chemistry methods, was used to characterize the γ- and β-turn structures in these model peptides. A conformer-selective NH stretch infrared study provided evidence for the formation in vacuo of two types of short-range H-bonded motifs, labelled ε-6(δ) and δ-(δ)7/π(H), bridging the His side chain (in its gauche+ rotamer) to the neighbouring NH(i) and CO(i) sites of the backbone; each side chain-backbone motif was found to be specific of the tautomer (ε or δ) adopted by the His side chain in its neutral form...
June 21, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28636462/are-commercial-complementary-food-distributions-to-refugees-and-migrants-in-europe-conforming-to-international-policies-and-guidelines-on-infant-and-young-child-feeding-in-emergencies
#9
Melissa Ann Theurich, Veit Grote
In 2015, more than one million migrants and refugees arrived in Europe. Commercial complementary foods, processed foods marketed for infants and young children 6-23 months of age, were distributed by various humanitarian actors along migrant routes and in European refugee camps. Unsolicited donations and distributions of commercial complementary food products were problematic and divergent from international policies on infant and young child feeding during humanitarian emergencies. Interim guidance regarding commercial complementary foods was published during the peak of the emergency but implemented differently by various humanitarian actors...
June 1, 2017: Journal of Human Lactation: Official Journal of International Lactation Consultant Association
https://www.readbyqxmd.com/read/28636397/a-comparison-of-the-structural-response-to-pressure-of-ils-with-ether-and-alkyl-functionalities
#10
Kamal B Dhungana, Claudio Javier Margulis
The response of ionic liquids to external perturbations including elevated pressure is a topic of current interest for applications such as tribology. Ionic liquids come in many classes, including those that are amphiphilic and some that are mostly polar having either cationic or anionic tails that are functionalized. The current study compares the effect of elevated pressure on two ionic liquids with different types of cationic tail. 1-decyl-3-methylimidazolium bis(trifluoromethylsulfonyl)amide (C10mim+/NTf2-) is amphiphilic whereas isoelectronic ether-functionalized 1-(2-(2-(2-methoxyethoxy)ethoxy)ethyl)-3-methylimidazolium bis(trifluoromethylsulfonyl)amide (C7O3mim+/NTf2-) has cationic tails that are more polar and conformationally different...
June 21, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28636345/levels-of-organochlorine-pesticides-are-associated-with-amyloid-aggregation-in-apex-avian-brains
#11
Kelly A Heys, Richard F Shore, M Gloria Pereira, Francis Luke Martin
Organochlorine (OC) pesticides pose a significant environmental risk to wildlife and humans and have been associated with Alzheimer's disease (AD). This study aims to spectroscopically analyse brains from free-flying birds and link the results to OC exposure and consequent amyloid aggregation. As long-lived apex predators, predatory birds represent a sentinel species similar to humans. Therefore, the results have implications for both species and may also add to our understanding of the role OC pesticides play in the development of AD...
June 21, 2017: Environmental Science & Technology
https://www.readbyqxmd.com/read/28636340/three-dimensional-modeling-of-quasicrystal-structures-from-x-ray-diffraction-an-icosahedral-al-cu-fe-alloy
#12
Seung-Tae Hong
Quasicrystals (QCs) are well-ordered but aperiodic crystals with classically forbidden symmetries (such as 5-fold). High-dimensional (HD) crystallography is a standard method to locate atom positions explicitly. However, in practice, it is still challenging because of its complexity. Here, we report a new simple approach to three-dimensional (3D) atomic modeling derived from X-ray diffraction data, and apply it to the icosahedral QC Al0.63Cu0.25Fe0.12. Electron density maps were calculated directly from 3D diffraction data indexed with noninteger (fractional) numbers as measured, with proper phases; each of 2(5) = 32 possible phase assignments for the five strongest reflections was used for Fourier synthesis...
June 21, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/28636317/downsizing-proto-oncogene-cfos-to-short-helix-constrained-peptides-that-bind-jun
#13
Daniel Baxter, Samuel R Perry, Timothy A Hill, W Mei Kok, Nathan R Zaccai, R Leo Brady, David P Fairlie, Jody M Mason
The oncogenic transcription factor activator protein-1 (AP-1) is a DNA-binding protein that assembles through dimerization of Fos and Jun protein subunits, their leucine-rich helical sequences entwining into a coiled-coil structure. This study reports on downsizing the proto-oncogene cFos protein (380 residues) to shorter peptides (37-25 residues) modified with helix-inducing constraints to enhance binding to Jun. A crystal structure is reported for a 37-residue Fos-derived peptide (FosW) bound to Jun. This guided iterative downsizing of FosW to shorter peptide sequences that were constrained into stable water-soluble α-helices by connecting amino acid side chains to form cyclic pentapeptide components...
June 21, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/28636310/sensing-mechanisms-in-the-redox-regulated-2fe-2s-cluster-containing-bacterial-transcriptional-factor-soxr
#14
Kazuo Kobayashi
Bacteria possess molecular biosensors that enable responses to a variety of stressful conditions, including oxidative stress, toxic compounds, and interactions with other organisms, through elaborately coordinated regulation of gene expression. In Escherichia coli and related bacteria, the transcription factor SoxR functions as a sensor of oxidative stress and nitric oxide (NO). SoxR protein contains a [2Fe-2S] cluster essential for its transcription-enhancing activity, which is regulated by redox changes in the [2Fe-2S] cluster...
June 21, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28636238/segmental-domain-selective-perdeuteration-and-small-angle-neutron-scattering-for-structural-analysis-of-multi-domain-proteins
#15
Miriam Sonntag, Pravin Jagtap, Bernd Simon, Marie-Sousai Appavou, Arie Geerlof, Ralf Stehle, Frank Gabel, Janosch Hennig, Michael Sattler
Multi-domain proteins play critical roles in fine-tuning essential processes in cellular signaling and gene regulation. Typically, multiple globular domains that are connected by flexible linkers undergo dynamic re-arrangements upon binding to protein, DNA or RNA ligands. RNA binding proteins (RBPs) represent an important class of multi-domain proteins, which regulate gene expression by recognizing linear or structured RNA sequence motifs. Here, we employ segmental perdeuteration of the three RNA recognition motif (RRM) domains in the RBP TIA-1 using Sortase A-mediated protein ligation...
June 21, 2017: Angewandte Chemie
https://www.readbyqxmd.com/read/28636001/wataa-atlas-of-protein-hydration-exploring-synergies-between-data-mining-and-ab-initio-calculations
#16
Jiří Černý, Bohdan Schneider, Lada Biedermannová
Water molecules represent an integral part of proteins and a key determinant of protein structure, dynamics and function. WatAA is a newly developed, web-based atlas of amino-acid hydration in proteins. The atlas provides information about the ordered first hydration shell of the most populated amino-acid conformers in proteins. The data presented in the atlas are drawn from two sources: experimental data and ab initio quantum-mechanics calculations. The experimental part is based on a data-mining study of a large set of high-resolution protein crystal structures...
June 21, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28635645/cembrene-diterpenoids-with-ether-linkages-from-sarcophyton-ehrenbergi-an-anti-proliferation-and-molecular-docking-assessment
#17
Mohamed-Elamir F Hegazy, Abdelsamed I Elshamy, Tarik A Mohamed, Ahmed R Hamed, Mahmoud A A Ibrahim, Shinji Ohta, Paul W Paré
Three new cembrene diterpenoids, sarcoehrenbergilid A-C (1-3), along with four known diterpenoids, sarcophine (4), (+)-7α,8β-dihydroxydeepoxysarcophine (5), sinulolide A (6), and sinulolide B (7), and one steroid, sardisterol (8), were isolated and characterized from a solvent extract of the Red Sea soft coral Sarcophyton ehrenbergi. Chemical structures were elucidated by NMR and MS analyses with absolute stereochemistry determined by X-ray analysis. Since these isolated cembrene diterpenes contained 10 or more carbons in a large flexible ring, conformer stabilities were examined based on density functional theory calculations...
June 21, 2017: Marine Drugs
https://www.readbyqxmd.com/read/28635293/probing-the-importance-of-charge-flux-in-force-field-modelling
#18
Elaheh Sedghamiz, Balazs Nagy, Frank Jensen
We analyze the conformational dependence of atomic charges and molecular dipole moments for a selection of ~900 conformations of peptide models of the 20 neutral amino acids. Based on a set of reference density functional theory calculations, we partition the changes into effects due to changes in bond distances, bond angles and torsional angles, and into geometry and charge flux contributions. This allows an assessment of the limitations of fixed charge force fields, and indications for how to design improved force fields...
June 21, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28635287/configurational-disorder-of-water-hydrogen-bond-network-at-the-protein-dynamical-transition
#19
Obaidur Rahaman, Maria Kalimeri, Marina Katava, Alessandro Paciaroni, Fabio Sterpone
We introduce a novel strategy to quantify the disorder of extended water-water hydrogen-bond (HB) networks sampled in particle-based computer simulations. The method relies on the conformational clustering of the HB connectivity states. We successfully applied it to unveil the fine relationship among the protein dynamical transition in hydrated powder, which marks the activation of protein flexibility at Td∽240 K, and the sudden increase of the configurational disorder of the water HB network enveloping the proteins...
June 21, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28635174/flash-light-millisecond-self-assembly-of-high-%C3%AF-block-copolymers-for-wafer-scale-sub-10-nm-nanopatterning
#20
Hyeong Min Jin, Dae Yong Park, Seong-Jun Jeong, Gil Yong Lee, Ju Young Kim, Jeong Ho Mun, Seung Keun Cha, Joonwon Lim, Jun Soo Kim, Kwang Ho Kim, Keon Jae Lee, Sang Ouk Kim
One of the fundamental challenges encountered in successful incorporation of directed self-assembly in sub-10 nm scale practical nanolithography is the process compatibility of block copolymers with a high Flory-Huggins interaction parameter (χ). Herein, reliable, fab-compatible, and ultrafast directed self-assembly of high-χ block copolymers is achieved with intense flash light. The instantaneous heating/quenching process over an extremely high temperature (over 600 °C) by flash light irradiation enables large grain growth of sub-10 nm scale self-assembled nanopatterns without thermal degradation or dewetting in a millisecond time scale...
June 21, 2017: Advanced Materials
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