Equivalent Sites Research Articles

Common Anesthetic-binding Site for Inhibition of Pentameric Ligand-gated Ion Channels.

Identifying functionally relevant anesthetic-binding sites in pentameric ligand-gated ion channels (pLGICs) is an important step toward understanding the molecular mechanisms underlying anesthetic action. The anesthetic propofol is known to inhibit cation-conducting pLGICs, including a prokaryotic pLGIC from Erwinia chrysanthemi (ELIC), but the sites responsible for functional inhibition remain undetermined. We photolabeled ELIC with a light-activated derivative of propofol (AziPm) and performed fluorine-19 nuclear magnetic resonance experiments to support propofol binding to a transmembrane domain (TMD) intrasubunit pocket. To differentiate sites responsible for propofol inhibition from those that are functionally irrelevant, we made an ELIC-γ-aminobutyric acid receptor (GABAAR) chimera that replaced the ELIC-TMD with the α1β3GABAAR-TMD and compared functional responses of ELIC-GABAAR and ELIC with propofol modulations. Photolabeling showed multiple AziPm-binding sites in the extracellular domain (ECD) but only one site in the TMD with labeled residues M265 and F308 in the resting state of ELIC. Notably, this TMD site is an intrasubunit pocket that overlaps with binding sites for anesthetics, including propofol, found previously in other pLGICs. Fluorine-19 nuclear magnetic resonance experiments supported propofol binding to this TMD intrasubunit pocket only in the absence of agonist. Functional measurements of ELIC-GABAAR showed propofol potentiation of the agonist-elicited current instead of inhibition observed on ELIC. The distinctly different responses of ELIC and ELIC-GABAAR to propofol support the functional relevance of propofol binding to the TMD. Combining the newly identified TMD intrasubunit pocket in ELIC with equivalent TMD anesthetic sites found previously in other cationic pLGICs, we propose this TMD pocket as a common site for anesthetic inhibition of pLGICs.

Effect of SLC26 anion transporter disease-causing mutations on the stability of the homologous STAS domain of E. coli DauA (YchM).

The human solute carrier 26 (SLC26) family of anion transporters consists of ten members that are found in various organs in the body including the stomach, intestine, kidney, thyroid and ear where they transport anions including bicarbonate, chloride and sulfate, typically in an exchange mode. Mutations in these genes cause a plethora of diseases such as diastrophic dysplasia affecting sulfate uptake into chondrocytes (SLC26A2), congenital chloride-losing diarrhoea (SLC26A3) affecting chloride secretion in the intestine and Pendred's syndrome (SLC26A4) resulting in hearing loss. To understand how these mutations affect the structures of the SLC26 membrane proteins and their ability to function properly, 12 human disease-causing mutants from SLC26A2, SLC26A3 and SLC26A4 were introduced into the equivalent sites of the sulfate transporter anti-sigma factor antagonist (STAS) domain of a bacterial homologue SLC26 protein DauA (YchM). Biophysical analyses including size-exclusion chromatography, circular dichroism (CD), differential scanning fluorimetry (DSF) and tryptophan fluorescence revealed that most mutations caused protein instability and aggregation. The mutation A463K, equivalent to N558K in human SLC26A4, which is located within α-helix 1 of the DauA STAS domain, stabilized the protein. CD measurements showed that most disease-related mutants had a mildly reduced helix content, but were more sensitive to thermal denaturation. Fluorescence spectroscopy showed that the mutants had more open structures and were more readily denatured by urea, whereas DSF indicated more labile folds. Overall, we conclude that the disease-associated mutations destabilized the STAS domain resulting in an increased propensity to misfold and aggregate.

The Drabo corymbosae-Papaveretea dahliani − a new vegetation class of the High Arctic polar deserts

Abstract A new class and a new order (Drabo corymbosae-Papaveretea dahliani and Saxifrago oppositifoliae-Papaveretalia dahliani) have been described, and the Papaverion dahliani validated. This is vegetation of zonal habitats in lowlands of the High Arctic subzone A (or Arctic herb, cushion forb or polar desert subzone) and of ecologically equivalent sites at high altitudes on the mountain plateaus of the High Arctic. The new class spans three continents – North America (Canadian Arctic Archipelago and Greenland), Europe (parts of Svalbard and Franz Josef Land), and Asia, including northern regions of Chelyuskin Peninsula (Taymir Peninsula), Severnaya Zemlya Archipelago and De Longa Islands.

Fundamental Constants for Activation of Human Endplate Receptors

Receptors have a low probability of being active in the absence of agonists (equilibrium constant E0). Agonists increase this probability because they bind with a higher affinity to active (Jd) vs. resting (Kd) receptors. For a receptor with n equivalent agonist binding sites, En=E0(Kd/Jd)∧n. Some mutations that cause congenital myaesthenic syndromes do nothing more than increase E0 above the WT level. We estimated E0 in adult human endplate AChRs by adding background mutations that increase this constant to known extents, and then extrapolating to the zero-effect intercept (−100 mV). The provisional result is E0(WT)∼8.7E-7 or +8.2 kcal/mol (7.4E-7 or 8.3 kcal/mol in adult mouse AChRs). The effects of mutations in mouse and human AChRs were comparable. For many agonists of mouse endplate AChRs, the resting and active affinities have an exponential relationship, Jd=Kd∧M, where M=1.92 (Jadey and Auerbach 2012, JGP 140:17). Hence, log efficacy and log resting affinity are correlated linearly: log(En)=log (E0)+n(1-M)log(Kd). We are also estimating E0 and M for human endplate AChRs from a linear fit of a log-affinity vs. log-efficacy plot, for different agonists. E0 and M are the fundamental, receptor-specific and agonist-independent parameters that shape the dose-response profile.

Subunit stoichiometry and arrangement in a heteromeric glutamate-gated chloride channel

The invertebrate glutamate-gated chloride-selective receptors (GluClRs) are ion channels serving as targets for ivermectin (IVM), a broad-spectrum anthelmintic drug used to treat human parasitic diseases like river blindness and lymphatic filariasis. The native GluClR is a heteropentamer consisting of α and β subunit types, with yet unknown subunit stoichiometry and arrangement. Based on the recent crystal structure of a homomeric GluClαR, we introduced mutations at the intersubunit interfaces where Glu (the neurotransmitter) binds. By electrophysiological characterization of these mutants, we found heteromeric assemblies with two equivalent Glu-binding sites at β/α intersubunit interfaces, where the GluClβ and GluClα subunits, respectively, contribute the "principal" and "complementary" components of the putative Glu-binding pockets. We identified a mutation in the IVM-binding site (far away from the Glu-binding sites), which significantly increased the sensitivity of the heteromeric mutant receptor to both Glu and IVM, and improved the receptor subunits' cooperativity. We further characterized this heteromeric GluClR mutant as a receptor having a third Glu-binding site at an α/α intersubunit interface. Altogether, our data unveil heteromeric GluClR assemblies having three α and two β subunits arranged in a counterclockwise β-α-β-α-α fashion, as viewed from the extracellular side, with either two or three Glu-binding site interfaces.

Crystal structure and conformational analysis of 2-hy-droxy-3-(2-methyl-prop-1-en-1-yl)naphthalene-1,4-dione.

In the structure of the title compound, C14H12O3, the substituent side chain, in which the H atoms of both methyl groups are disordered over six equivalent sites, lies outside of the plane of the naphthalene-dione ring. The ring-to-chain C-C-C-C torsion angles are 50.7 (3), -176.6 (2) and 4.9 (4)°. An intra-molecular meth-yl-hy-droxy C-H⋯O hydrogen bond is present. In the crystal, mol-ecules are primarily connected by inter-molecular O-H⋯O hydrogen bonds, forming a centrosymmetric cyclic dimer motif [graph set R 2 (2)(10)]. Also present is a weak inter-molecular C-H⋯O hydrogen bond linking the dimers and a weak π-π ring inter-action [ring centroid separation = 3.7862 (13) Å], giving layers parallel to (10-3).

A New Mononuclear Complex: Structure, Vibrational (FT-IR and Raman), Hirshfeld Surfaces Analysis, Electrical Properties and Equivalent Circuit

The present paper aims to develop the synthesis, crystal structure, and properties of Zn(C7H5NO4)Cl2.H2O compound investigated by vibrational study, thermal analysis and dielectric measurements. The single crystal X-ray diffraction investigation reveals that the studied compound crystallizes in the orthorhombic system with space group Pnna according to the following lattice parameters: a=13.8816(4) A, b=10.3602(3) A, c=7.8967(2) A and Z=4. The presence of the key functional groups in the molecule has already been confirmed by Fourier transform infrared (FT-IR) analysis. Thermal behaviour of this sample, studied by TGA and DSC exhibit two anomalies at 345 and 386K. The hydrogen bonding plays a significant role in the stabilization of the structure. Such a parallel displaced structure has also a contribution from π-σ non-covalent interactions (C-H…π and C-O…π stacking between the C-H groups and C-O groups with the benzene rings). The dipicolonic acid (2,6-pyridinedicarboxylic acid) ligand coordinated to the Zn(II) ions through a nitrogen atom of pyridine ring, two oxygen atom of carboxylic group and two chloride atoms as a tridentate ligand. Hirshfeld surface analysis of the intermolecular interactions in crystal structures have been used to scrutinize molecular shapes. The characteristic features of 13C solid state CP/MAS-NMR applications showed five isotropic resonances, confirming the structure determined by XRD. Its dielectric properties as a function of temperature and frequency in the ranges 298-418 K and 209 Hz-5 MHz are measured. The Cole-Cole (Z’ versus Z’’) plots are analyzed by fitting to an equivalent electrical circuit model, consisting of a circuit elements; grain, grain boundary, electrode-solid interface polarization and Warburg resistance. Each circuit elements is formed by a parallel combination resistance (R) and constant phase elements (CPE). The grain conductivity as well as the activation energy depending to of temperature, via impedance technique, besides the activation energy due to relaxation time as function of temperature, have been studied showing two anomalies, which are also detected by the TGA and DSC. They could be explained by not only a phase transition and reorientation hopping between equivalent sites at 343K but also the disappearance of the water molecule of the structure at 388K.

Changes in Choroidal Thickness in Branch Retinal Vein Occlusion

Purpose: To compare the choroidal thickness of a branch retinal vein occlusion (BRVO) lesion and that of other areas in the eyes. Methods: Patients who visited the Ophthalmologic Clinic of Inje University Sanggye Paik Hospital for BRVO between March 2015 and October 2015 were reviewed retrospectively. We performed basic ophthalmologic exam and enhanced depth imaging optical coherence tomography in 48 eyes of 24 patients with BRVO. The choroidal thickness was compared in a total of 4 places, the branch retinal vein occlusion lesion, the symmetric site in the same eye, and the equivalent sites in the fellow eye by paired t-test. All measurements were performed by 2 independent observers. Results: Choroidal thickness had strong inter-observer correlation. Choroidal thickness of the BRVO lesion was significantly thicker than that in the symmetric site of same eye, the equivalent site of lesion, and the equivalent site of the symmetric site to lesion in the fellow eye. Conclusions: Choroidal thickness in acute BRVO lesions was thicker than choroidal thickness in other areas of the eyes. It is thought that both hydrostatic pressure and the effects of vascular endothelial growth factor influence choroidal thickness in the acute phase of BRVO. J Korean Ophthalmol Soc 2016;57(8):1222-1227

School leadership and the knowledge of teacher-student interaction on Facebook: a study of a lower secondary school in Norway

The use of various social media sites is one of the most common activities of today's adolescents. A content analysis of printouts of teacher-student dialogue from a 10th grade Facebook group throughout a school year suggests that teacher and school leaders' personal involvement in social media is of importance in a 'new era' of learning contexts. By lending perspectives from distributed leadership theories, the article investigates how teachers and students in a Norwegian lower secondary school jointly participate in Facebook interaction. It is important for school leaders to be present in the forceful and ephemeral nature of the social network sites students' use at any given time. The findings show that teachers and school leaders may profit from gaining knowledge about Facebook and equivalent sites for the benefit of leading instruction and managing schools. The implications for teachers and school leaders are thus discussed in this paper.

Barrel-shaped ClpP Proteases Display Attenuated Cleavage Specificities.

ClpP is a self-compartmentalizing protease with crucial roles in bacterial and mitochondrial protein quality control. Although the ClpP homocomplex is composed of 14 equivalent active sites, it degrades a multitude of substrates to small peptides, demonstrating its capability to carry out diverse cleavage reactions. Here, we show that ClpP proteases from E. coli, S. aureus, and human mitochondria exhibit preferences for certain amino acids in the P1, P2, and P3 positions using a tailored fluorogenic substrate library. However, this high specificity is not retained during proteolysis of endogenous substrates as shown by mass spectrometric analysis of peptides produced in ClpXP-mediated degradation reactions. Our data suggest a mechanism that implicates the barrel-shaped architecture of ClpP not only in shielding the active sites to prevent uncontrolled proteolysis but also in providing high local substrate concentrations to enable efficient proteolytic processing. Furthermore, we introduce customized fluorogenic substrates with unnatural amino acids that greatly surpass the sensitivity of previously used tools. We used these to profile the activity of cancer-patient- and Perrault-syndrome-derived ClpP mutant proteins.

Guidelines for the Appropriate Use of Bedside General and Cardiac Ultrasonography in the Evaluation of Critically Ill Patients-Part I: General Ultrasonography.

To establish evidence-based guidelines for the use of bedside ultrasound by intensivists and specialists in the ICU and equivalent care sites for diagnostic and therapeutic purposes for organs of the chest, abdomen, pelvis, neck, and extremities. The Grading of Recommendations, Assessment, Development and Evaluation system was used to determine the strength of recommendations as either strong or conditional/weak and to rank the "levels" of quality of evidence into high (A), moderate (B), or low (C) and thus generating six "grades" of recommendation (1A-1B-1C-2A-2B-2C). Grading of Recommendations, Assessment, Development and Evaluation (GRADE) was used for all questions with clinically relevant outcomes. RAND appropriateness method, incorporating modified Delphi technique, was used in steps of GRADE that required panel judgment and for those based purely on expert consensus. The process was conducted by teleconference and electronic-based discussion, following clear rules for establishing consensus and agreement/disagreement. Individual panel members provided full disclosure and were judged to be free of any commercial bias. The process was conducted independent of industry funding. Twenty-four statements regarding the use of ultrasound were considered-three did not achieve agreement and nine were approved as conditional recommendations (strength class 2). The remaining 12 statements were approved as strong recommendations (strength class 1). Each recommendation was also linked to its level of quality of evidence. Key strong recommendations included the use of ultrasonography for ruling-in pleural effusion and assisting its drainage, ascites drainage, ruling-in pneumothorax, central venous cannulation, particularly for internal jugular and femoral sites, and for diagnosis of deep venous thrombosis. Conditional recommendations were given to the use of ultrasound by the intensivist for diagnosis of acalculous cholecystitis, renal failure, and interstitial and parenchymal lung diseases. No recommendations were made regarding static (vs dynamic) ultrasound guidance of vascular access or the use of needle guide devices. There was strong agreement among a large cohort of international experts regarding several recommendations for the use of ultrasound in the ICU. Evidence-based recommendations regarding the appropriate use of this technology are a step toward improving patient outcomes in relevant patients.

Preparation and characterization of bio-organoclays using nonionic surfactant

The present study was aimed at the preparation and characterization of tailor made hybrid materials, whose peculiar hosting capability could be exploited in biotechnological applications. With this purpose, the modification of K10 montmorillonite by intercalation of Tween 20 surfactant, was accomplished. The influence of two internal parameters, namely pH and surfactant/clay ratio, on the surfactant uptake ability by clay was investigated. The adsorption mechanism was elucidated on the basis of complementary kinetic and equilibrium studies and, then, corroborated by the useful information provided by the FT-IR, TGA and XRD characterization. The gathered results allow to draw the conclusion that the whole surfactant uptake is the result of two contributions: a site-limiting component, governed by negative cooperative interactions, which takes into account for the Tween 20 adsorption onto the pristine clay, and a non-specific linear partitioning component, related to the adsorption of the surfactant onto the in situ prepared organo-clay. Moreover, at strongly acidic pH, a mechanism consisting of two-steps pathways involving two non-energetically equivalent binding sites of the clay surfaces, was proposed, while, on increasing the pH, the clay interlayer becomes the sole available site for the surfactant uptake. In the light of the interesting results obtained, among the plethora of potential biotechnological applications, the present paper suggests the exploitation of the prepared organo-clays to improve the performance of either hydrophilic or hydrophobic drug carriers systems.

Attachment of norovirus to histo blood group antigens: a cooperative multistep process.

Human noroviruses recognize histo blood group antigens (HBGAs) as cellular attachment factors. Recently, it has been discovered that norovirus infection can be significantly enhanced by HBGA binding. Yet the attachment process and how it promotes host-cell entry is only poorly understood. The binding of a norovirus protruding (P) domain of a predominant GII.4 Saga strain to HBGAs at atomic resolution was studied. So far, independent and equivalent multiple binding sites were held responsible for attachment. Using NMR experiments we show that norovirus-HBGA binding is a cooperative multi-step process, and native mass spectrometry reveals four instead of two HBGA binding sites per P-dimer. An accompanying crystallographic study has disclosed four instead of two L-fucose binding sites per P-dimer of a related GII.10 strain1 further supporting our findings. We have uncovered a novel paradigm for norovirus-HBGA recognition that will inspire further studies into norovirus-host interactions.

Attachment of Norovirus to Histo Blood Group Antigens: A Cooperative Multistep Process

AbstractHuman noroviruses recognize histo blood group antigens (HBGAs) as cellular attachment factors. Recently, it has been discovered that norovirus infection can be significantly enhanced by HBGA binding. Yet the attachment process and how it promotes host‐cell entry is only poorly understood. The binding of a norovirus protruding (P) domain of a predominant GII.4 Saga strain to HBGAs at atomic resolution was studied. So far, independent and equivalent multiple binding sites were held responsible for attachment. Using NMR experiments we show that norovirus‐HBGA binding is a cooperative multi‐step process, and native mass spectrometry reveals four instead of two HBGA binding sites per P‐dimer. An accompanying crystallographic study has disclosed four instead of two L‐fucose binding sites per P‐dimer of a related GII.10 strain1 further supporting our findings. We have uncovered a novel paradigm for norovirus‐HBGA recognition that will inspire further studies into norovirus–host interactions.

EMS study of vibrational effects on electron momentum distributions of C2H4 and CH2F2

SynopsisWe report an electron momentum spectroscopy study of vibrational effects on the electron momentum distributions for the outer valence orbitals of C2H4 and CH2F2. The symmetric noncoplanar (e,2e) experiment has been conducted at impact energy of 1.2 keV. Furthermore, a theoretical method of calculating electron momentum distributions has been developed with vibrational effects being involved. The experimental and theoretical results for these molecules strongly suggest that vibrational effects on electron momentum distributions tend to be appreciable for non-total symmetry molecular orbitals delocalized over some equivalent CH-bond sites.

Thermodynamics of the Exactly Solvable Spin-Electron Tetrahedral Chain

An exactly solvable spin-electron tetrahedral chain, where the Ising spins localized at nodal lattice sites regularly alternate with three equivalent lattice sites available for one mobile electron is considered. The system with ferromagnetic interaction between the Ising spins and electrons exhibits an enhanced magnetocaloric effect (MCE) in the limit $H/|J|\to 0$ when the entropy is very small, whereas the system with antiferromagnetic interaction between the Ising spins and electrons exhibits an enhanced MCE around the field $H/J=1$ when the entropy is sufficiently close to the value $S/2N = \ln[(1+\sqrt{5})/2]$. We study the thermodynamics of the system in these field regions.

Magnetic Grüneisen parameter and magnetocaloric properties of a coupled spin–electron double-tetrahedral chain

Magnetocaloric effect in a double-tetrahedral chain, in which nodal lattice sites occupied by the localized Ising spins regularly alternate with three equivalent lattice sites available for mobile electrons, is exactly investigated by considering the one-third electron filling and the ferromagnetic Ising exchange interaction between the mobile electrons and their nearest Ising neighbours. The entropy and the magnetic Grüneisen parameter, which closely relate to the magnetocaloric effect, are exactly calculated in order to investigate the relation between the ground-state degeneracy and the cooling efficiency of the hybrid spin–electron system during the adiabatic demagnetization.

Diamond-like phases obtained from nanotubes and three-dimensional graphites

The results of ab initio calculations of the structure and properties of thirteen carbon diamond-like phases with atoms located in equivalent crystallographic sites have been presented. The calculations have been performed by the B3LYP-GGA method. Nine of the studied phases have been obtained by linking or combining nanotubes, the other four phases have been formed from three-dimensional graphites. Two new spiral phases SA3 and SA4 whose precursors are 3D graphites have been studied for the first time. For all phases, structural characteristics, sublimation energies, electron densities of states, and bulk moduli have been determined. The X-ray powder diffraction patterns required for identifying new diamond-like phases in synthesized carbon materials have also been calculated.

Cation-π and CH-π Interactions in the Coordination and Solvation of Cu(+)(acetylene)n Complexes.

Copper-acetylene cation complexes of the form Cu(C2H2)n(+) (n = 1-8) are produced by laser ablation in a supersonic expansion of acetylene/argon. The ions are mass selected and studied via infrared laser photodissociation spectroscopy in the C-H stretching region (3000-3500 cm(-1)). The structure and bonding of these complexes are investigated through the number of infrared active bands, their relative intensities and their frequency positions. Density functional theory calculations are carried out in support of the experimental data. The combined data show that cation-π complexes are formed for the n = 1-3 species, resulting in red-shifted C-H stretches on the acetylene ligands. The coordination of the copper cation is completed with three acetylene ligands, forming a "propeller" structure with D3 symmetry. Surprisingly, complexes with even greater numbers of acetylenes than this (4-6) have distinctive infrared band patterns quite different from those of the smaller complexes. Experiment combined with theory establishes that there is a fascinating pattern of second-sphere solvation involving the binding of acetylenes in bifurcated CH-π binding sites at the apex of two core ligands. This binding motif leads to three equivalent sites for second-sphere ligands, which when filled form a highly symmetrical Cu(+)(C2H2)6 complex. Solvent binding in this complex induces a structural change to planarity in the core, producing an appealing "core-shell" structure with D(3h) symmetry.

Body Composition In Sport

Quantifying body composition (BC) has played an important role in monitoring athlete’s health and performance. Skinfolds (SK) is the most commonly used method, however, it is an indirect method, whereas ultrasound (US) measures subcutaneous adipose tissue (SAT) directly with high accuracy and precision. PURPOSE: Estimation of the inter- and intra-tester reliability of the US method for assessment of BC in athletes, compared with the widely used SF method. METHODS: 3 male and 3 female athletes (mean±SD: age: 24±1.7 yrs, weight: 61.5±6.7 kg, height: 1.73±0.8 m, BMI: 20.6±1.5 kg/m2) with competitive background in endurance sports were measured by three trained anthropometrists. SF were taken according to ISAK standardization at biceps, triceps, subscapular, suprailiac, supraspinale, abdomen, front thigh, and medial calf. For US measurements, some ISAK sites were replaced by sites which are better suited for the US technique: biceps, distal triceps, supraspinale, upper abdomen, lower abdomen, erector spinae, front thigh, and medial calf. For US image evaluation, the FAT software (Rotosport, Graz, Austria) was used. Inter- and intra-tester variations were calculated using pooled estimates. For intra-individual variation, a pooled standard diviation (SD) was computed for the six subjects per observer per site. For inter-individual variation, a SD was calculated for the six subjects by site combining all three observers’ data. RESULTS: At equivalent sites, US had lower SD at four sites compared with SF method. For US analysis, intra-tester reliability ranged from 0.03-0.79mm SD. For inter-tester values, US showed values ranging from 0.42-0.62mm SD (with exception of 0.70mm for the upper abdomen and 1.51mm for lower abdomen), while SF resulted in values ranging from 0.38-1.09mm SD. The larger values resulting in the abdominal area using US may be due to embedded structures within the region. CONCLUSION: The US method showed good reliability when compared with SF (one exception was abdomen which showed less reliability). US measures uncompressed SAT, whereas SF measures two layers of skin and SAT, both tissues with undefined thickness reduction due to compression.