bluuebunny/crossref_metadata_2025_split huggingface dataset:
[2
Fe
–2
S
] Oxidative‐Stress Sensor
Sox
R
Bound to
DNA
Authors: Watanabe Satoshi , Miki Kunio 
Published: December 2011

Abstract
SoxR, a member of the MerR (mercury resistance regulator) family, is a transcriptional activator that contains a [2Fe‐2S] cluster. In entric bacteria, SoxR functions as an oxidative‐stress sensor. However, in other nonentric bacteria, its physiological role appears to be different. SoxR is activated by reversible one‐electron oxidation of the [2Fe‐2S] cluster. In the active state, SoxR and other MerR family proteins activate transcription from unique promoters, which have a long 19 or 20 bp spacer between the −35 and −10 operator elements, by untwisting the promoter DNA. The crystal structures of SoxR and its complex with the target promoter in the oxidized (active) state have been reported. The structure of SoxR monomer consists of a winged helix‐turn helix DNA‐binding domain, a dimerization helix, and a Fe‐S cluster‐binding domain. The SoxR dimer is formed by an antiparallel long coiled coil. The [2Fe‐2S] cluster of SoxR is completely solvent‐exposed and surrounded by an asymmetric environment stabilized by interaction with the other subunit. The asymmetrically charged environment of the [2Fe‐2S] cluster probably causes redox‐dependent conformational changes of SoxR. The structure of the SoxR‐DNA complex provides a structural framework of the transcriptional activation by DNA distortion in the MerR family.
Metal Trafficking Via Siderophores in Gram‐Negative Bacteria
Authors: Cobessi David , Schalk Isabelle J 
Published: December 2011

AbstractIron is essential for life for practically all living organisms and plays a number of key roles in biology. However, under physiological conditions, iron forms highly insoluble ferric hydroxide complexes, which severely limits its bioavailability. To overcome the problem of iron inaccessibility, bacteria excrete high‐affinity iron‐chelators termedsiderophoresthat are able to solubilize iron and deliver it into the cells. In gram‐negative bacteria, the uptake of ferrisiderophores always involves, at the level of the outer membrane, specific transporters of the family of the TonB‐dependent receptors. The energy required for this uptake is provided by the proton‐motive force of the inner membrane by means of an inner membrane complex comprising three proteins, TonB, ExbB, and ExbD. Structures of TonB‐dependent receptors have been solved in different conformations. They are all composed of a β‐barrel occluded by a globular domain. The binding site is highly specific for a single siderophore and is located in the lumen on the extracellular side of the barrel. Some TonB‐dependent receptors have an additional N‐terminal domain located in the periplasm. These receptors, in parallel to transport ferrisiderophores across the outer membrane, are involved in a signaling cascade regulating expression of genes involved in iron acquisition.
Superoxide Reductase
Authors: Nivière Vincent , Bonnot Florence , Bourgeois Dominique 
Published: December 2011

Abstract

Superoxide reductase (SOR) is a small bacterial metalloprotein, which is present in the cytoplasm of some anaerobic or microaerophilic microorganisms. SOR is involved in the detoxification of the superoxide radical and catalyzes its one‐electron reduction into hydrogen peroxide. Three different classes of SOR have been identified and structurally characterized. They all contain a similar active site, which consists of an unusual nonheme iron center, coordinated in a square‐pyramidal geometry to four nitrogens from four histidine side chains in the equatorial plane and the sulfur of one cysteine residue along the fifth axial position. In the reduced state, the sixth axial coordinating site of the iron is vacant, suggesting the most obvious site for initial binding of the superoxide substrate. The reaction mechanism of SOR has been studied by pulse radiolysis. SOR reacts specifically at a nearly diffusion‐controlled rate with O
2
•−
, generating H
2
O
2
and the oxidized Fe
3+
active site. Reaction intermediates have been observed and proposed to be Fe
3+
‐(hydro)peroxo species, resulting from the fast electron transfer from the ferrous iron to the superoxide anion and from protonation step. Formation of Fe
3+
‐(hydro)peroxo intermediate species in the active site of SOR has been supported by resonance Raman spectroscopy and X‐ray structures of iron(III) peroxide species in the SOR from
Desulfoarculus baarsii
.
The Organomercurial LyaseMerB
Authors: Lello Paola Di , Lafrance‐Vanasse Julien , Omichinski James G 
Published: December 2011

AbstractMercury is introduced into the environment either from natural occurrences or from human activities, and consumption of mercury‐contaminated fish poses a serious human health issue. The three inorganic forms of mercury are elemental mercury, mercurous compounds, and mercuric compounds, while the most abundant organic form is methylmercury. Owing to its ability to permeate membranes and accumulate in organisms, methylmercury is more toxic than ionic mercury. Mercury‐resistant bacteria have developed a two enzyme system to convert both Hg (II) and methylmercury to the less toxic elemental mercury. The first enzyme is an organomercurial lyase (MerB) and the second enzyme is a mercuric ion reductase (MerA). MerB catalyzes the protonolysis of the carbon–mercury bond on a wide range of organomercurials, including methylmercury, resulting in a reduced carbon compound and ionic mercury. The cleavage of the carbon–mercury bond and the formation of the electrophile‐carbon bond are concerted (SE2). Structural studies demonstrated that MerB contains a unique fold and that significant conformational changes occur on binding of organomercurial substrates. On the basis of mutagenesis, structural, and computational studies, two cysteines and an aspartic acid residue in the active site are known to play key roles in the cleavage of the carbon–mercury bond.
Two‐Domain Multicopper Oxidase
Authors: Lawton Thomas J , Rosenzweig Amy C 
Published: December 2011

AbstractTwo‐domain multicopper oxidases (2dMCOs) couple the four‐electron reduction of dioxygen to the oxidation of a number of different substrates, including organic compounds and reduced ferricytochromes. The geometry of 2dMCO active sites is similar to that in other multicopper oxidases, but is formed by a significantly different protein architecture. This fold resembles the overall architecture of NO forming copper nitrite reductase (CuNIR). 2dMCOs are classified based on the location of their type‐1 copper centers.
3‐Ketosteroid‐9α‐Hydroxylase
Authors: Capyk Jenna K , Strynadka Natalie C , Eltis Lindsay D 
Published: December 2011

AbstractKshAB is a Rieske oxygenase (RO) in the aerobic steroid degradation pathways of bacteria. It is a monooxygenase responsible for the 9α‐hydroxylation of the nucleus of 3‐keto‐4‐ene steroids bearing short side chains at C17. It is composed of two domains arranged in a head‐to‐tail fashion to form the functional trimer. The N‐terminal Rieske domain harbors a Fe2S2cluster in which the two irons are coordinated by two cysteine and two histidine residues, respectively. The larger, C‐terminal catalytic domain contains a mononuclear nonheme iron coordinated by a His‐His‐Asp facial triad. Purified KshAB fromMycobacterium tuberculosisexhibits substrate specificities for 1,4‐androstadien‐3,17‐one and dioxygen 2‐3 orders of magnitude lower than those measured for other ROs and their best substrates. In agreement with the large fused‐ring substrate, the structure of KshA incorporates an active site channel and substrate binding pocket that are longer than those observed in other ROs, and positioned in a different relative orientation within the catalytic domain. KshA also possesses a C‐terminal helix which occupies a position not observed in other RO structures and which likely stabilizes trimeric quaternary structure. Finally, KshA exhibits a minimal core catalytic domain with respect to secondary structural elements that may prove archetypical for ROs.
Toluene 4‐Monooxygenase and its Complex with Effector ProteinT4moD
Authors: Bailey Lucas J , Fox Brian G 
Published: December 2011

AbstractToluene 4‐monooxygenase (T4MO) is a multiprotein diiron enzyme complex that catalyzes the regiospecific oxidation of toluene top‐cresol. Catalytic function requires the presence of a small protein, called theeffector protein. Effector protein exerts substantial control on the diiron hydroxylase catalytic cycle through protein–protein interactions. High‐resolution crystal structures of the stoichometric hydroxylase and effector protein complex described here reveal how protein–protein interactions and reduction of the diiron center produce an active site configuration poised for reaction with O2. Further information from crystal structures of mutated isoforms of the hydroxylase and a peroxo adduct is combined with catalytic results to give a fuller picture of the geometry of the enzyme–substrate complex used for the high fidelity oxidation of hydrocarbon substrates.
SR
‐Like Protein
ZRANB
2
Authors: Mansfield Robyn E , Mackay Joel P 
Published: December 2011

Abstract
ZRANB2 is an SR‐like pre‐mRNA splicing factor that is conserved across vertebrates. It contains two RNA‐binding zinc finger domains at the N‐terminus, each of which includes a tetrahedrally coordinated zinc ion which is essential for the 3D fold of the domain, and an arginine/serine‐rich (RS) domain near the C‐terminus. The 3D structures of each zinc finger domain have been solved by NMR spectroscopy, and a crystal structure of the second zinc finger in complex with RNA is also available. Similar zinc finger domains, known collectively as RanBP2‐type zinc fingers, have been observed in other proteins and display a range of substrate‐binding abilities.
Zinc TransporterYiiPfromEscherichia coli
Authors: Fu Dax 
Published: December 2011

AbstractYiiP fromEscherichia colibelongs to the protein family of cation diffusion facilitator (CDF). CDFs play critical roles in metal homeostatic controls in microbes, plants, and mammals. They utilize the proton motive force to drive effluxes of transition metal ions out of the cytoplasm. Bacterial CDFs primarily contribute to metal resistance while mammalian CDFs are more involved in metal metabolism and cellular signaling. The crystal structure of YiiP reveals a Y‐shaped dimeric architecture, consisting of a transmembrane domain and a cytoplasmic domain that adopts a metallochaperone‐like fold. The molecular details of three distinct zinc coordination sites in YiiP delineate how metallochemistry is tailored to three central functions of CDFs: selective metal binding, rapid transport kinetics, and allosteric regulation of the transport activity. An integration of the structural information and existing biochemical data allows us to propose a two‐modular model for the operation of YiiP. In this model, the transmembrane domain is responsible for a stoichiometric zinc‐for‐proton exchange across the membrane barrier. The cytoplasmic domain detects the fluctuation of zinc concentrations and responds with a conformational change that is transmitted to regulate the activity of the transmembrane domain. In addition, the cytoplasmic domain may also serve as a zinc receiving module for uploading of the zinc cargo from a putative zinc‐metallochaperone.
The Cytochromeb6fComplex of Oxygenic Photosynthesis
Authors: Cramer William A. , Yamashita Eiki , Baniulis Danas , Saif Hasan S. 
Published: December 2011

AbstractThe cytochromeb6fcomplex is the central complex in the electron transport chain of oxygenic photosynthesis. It provides the electronic connection between the two photosynthetic reaction centers and generates most of the transmembrane electrochemical proton gradient that is used for ATP synthesis. It is a hetero‐oligomeric 220‐kDa homo‐dimeric complex consisting of 8 polypeptide subunits, 13 transmembrane helical segments, and 7 tightly bound prosthetic groups per monomer. It is one of relatively few hetero‐oligomeric membrane proteins whose crystal structure has been solved to a resolution ≤3.0 Å. Among the seven prosthetic groups per monomer, five have a redox function: twob‐type hemes,bpandbn, on the electrochemically positive and negative sides of the complex, the p‐side heme of cytochromef, a uniquec‐type cytochrome, and a p‐side [2Fe–2S] center, and a unique hemecncovalently bound to the cytochromebsubunit, which interacts electronically with hembn. These groups are arranged to accomplish the oxidation and reduction of plastoquinol/plastoquinone (PQH2/PQ) on the p‐ and n‐sides of the membrane, and thereby accomplish a net transfer of as many as two protons across the membrane per electron transferred through the complex, thus providing the major input to the transmembrane proton electrochemical gradient. The redox reactions of PQ/PQH2occur within the two quinone‐exchange cavities formed by the two monomers of the complex. The p‐side redox reactions are similar to those of the cytochromebc1complex. However, redox reactions on the n‐side are different, partly because of the presence of hemecn.
Readaptation to the wild of rehabilitated loggerhead sea turtles (Caretta caretta) assessed by satellite telemetry
Authors: Cardona Luis , Fernández Gloria , Revelles Mónica , Aguilar Alejandro 
Published: December 2011

ABSTRACT

Satellite telemetry was used to assess the readaptation to the wild of six loggerhead sea turtles after a long and complicated rehabilitation process. Their behaviour in the wild after release was compared with that of 12 healthy control turtles captured in the same region and fitted with similar satellite tags.
The behaviour of the rehabilitated turtles was more variable than that of the control turtles and an outlier analysis revealed that only two of the six rehabilitated turtles did not differ in their behaviour from that of the control turtles. For the other turtles, the following anomalies were detected: a higher speed of travel, a negative cosine of the turning angle (the turtle turns back very often), a higher percentage of shelf use, a longer time at the surface at night, a higher averaged latitude during tracking, a shorter total tracking time and lower percentage of good quality fixes. Nevertheless, none of the turtles exhibited simultaneously these anomalies and only one turtle exhibited more than two anomalies.
These results suggest that most rehabilitated loggerhead sea turtles survive in the wild at least for several months after release, even after a long and complicated process of veterinarian treatment, but many may exhibit behavioural anomalies, which casts doubts on the success of readaptation in the long run. Copyright © 2011 John Wiley & Sons, Ltd.
Behavioural responses of harbour seals to human‐induced disturbances
Authors: Andersen S.M. , Teilmann J. , Dietz R. , Schmidt N.M. , Miller L.A. 
Published: December 2011

ABSTRACT

In Denmark, harbour seals, Phoca vitulina, were first protected in 1977, and since then a number of seal reserves have been established in Danish waters. The effectiveness of these reserves to prevent human‐induced disturbances to the seal population have, however, not been evaluated.
To evaluate this, experimental disturbances were conducted in one of the most important seal reserves in Denmark (Anholt seal reserve). Specifically, the behavioural responses (alert distance, flight initiation distance, flee distances and flight duration) of harbour seals to approaching pedestrians and boats were studied.
The project was conducted during three periods related to the breeding cycle of harbour seals. In all periods, harbour seals were alerted by boats at significantly greater distances compared with pedestrians (560–850 m and 200–425 m, respectively). Similar differences in the flight initiation distances were observed, 510–830 m for boats and 165–260 m for pedestrians. In most cases seals were alerted and began to flee when the approaching boat was outside the reserve, whereas seals did not respond to approaching pedestrians until after they had entered the reserve.
Harbour seals exhibited weaker and shorter‐lasting responses during the breeding season. They were more reluctant to flee and returned to the haul‐out site immediately after being disturbed, in some cases even during the disturbance. This seasonal tolerance is most likely attributed to a trade‐off between fleeing and nursing during the breeding season, and hence not an indication of habituation.
Based on the results of this study it is suggested that the reserve boundaries on land be placed at least 425 m from the haul‐out area and the boundary at sea should extend to at least 850 m from the haul‐out area in order to secure adequate year‐round protection from disturbances. Copyright © 2011 John Wiley & Sons, Ltd.
Comparing the rheology of mulberry and “wild” silkworm spinning dopes
Authors: Holland C. , Porter D. , Vollrath F. 
Published: December 2011

AbstractLepidoperan silks provide a superb opportunity for comparative studies of spinning and fiber characteristics. Comparing the four species, Bombyx mori (China), Actias selene (India), Antheraea yamamai (Japan), Gonometa postica (Africa), allows us to examine differences on the family, species, and race levels. Measured rheological properties were consistent with phylogenetic relationships and in the context of resource allocation and gland morphology. We propose that the thorough domestication of the mulberry silkworm B. mori for high silk yield has resulted in a compensatory optimization for spinning efficiency. This is in stark contrast to the wild silkworms, where Saturnids appear to minimize their energetic input toward silk output and G. postica seems to balance both. We conclude that comparative studies provide valuable baseline information for future biomimetic applications and modeling, as well as illuminating biologically important details of silk processing. © 2011 Wiley Periodicals, Inc. Biopolymers 97: 362–367, 2012.
Like‐charged residues at the ends of oligoalanine sequences might induce a chain reversal
Authors: Makowska Joanna , Liwo Adam , Żmudzińska Wioletta , Lewandowska Agnieszka , Chmurzyński Lech , Scheraga Harold A. 
Published: December 2011

AbstractWe have examined the effect of like‐charged residues on the conformation of an oligoalanine sequence. This was facilitated by circular dichroism (CD) and NMR spectroscopic and differential scanning calorimetric (DSC) measurements, and molecular dynamics calculations of the following three alanine‐based peptides: Ac‐K‐(A)5‐K‐NH2 (KAK5), Ac‐K‐(A)4‐K‐NH2 (KAK4), Ac‐K‐(A)3‐K‐NH2 (KAK3), where A and K denote alanine and lysine residues, respectively. Our earlier studies suggested that the presence of like‐charged residues at the end of a short polypeptide chain composed of nonpolar residues can induce a chain reversal. For all three peptides, canonical molecular dynamics simulations with NMR‐derived restraints demonstrate the presence of ensembles of structures with a tendency to form a chain reversal. The KAK3 peptide exhibits a bent shape with its ends close to each other, while KAK4 and KAK5 are more extended. In the KAK5 peptide, the lysine residues do not have any influence on each other and are very mobile. Nevertheless, the tendency to form a more or less pronounced chain reversal is observed and it seems to be stable in all three peptides. This chain reversal seems to be caused by screening of the nonpolar core from the solvent by the hydrated charged residues. © 2011 Wiley Periodicals, Inc. Biopolymers 97: 240–249, 2012.
Synthesis and Evaluation of a Fluorescent Non‐Peptidic Cholecystokinin‐B/Gastrin Receptor Specific Antagonist for Cancer Cell Imaging
Authors: Kumari Saroj , Chowdhury Joyita , Mishra Anil K. , Chandna Sudhir , Saluja Daman , Chopra Madhu 
Published: December 2011

AbstractFluorescent labeling has enabled a better understanding of the relationships between receptor location, function, and life cycle. Each of these perspectives contributes new insights into drug action, particularly for G protein‐coupled receptors (GPCRs). The aim of this study was to develop a fluorescein derivative, FLUO‐QUIN—a novel antagonist of the cholecystokinin‐B/gastrin receptor. A radioligand‐binding experiment revealed an IC50 of 4.79 nm, and the antagonist inhibited gastric acid secretion in an isolated lumen‐perfused mouse stomach assay (up to 51 % at 100 nm). The fluorescence properties altered upon binding to the receptor, and the fluorophore was quenched to a greater extent when free than in the bound form. FLUO‐QUIN specifically bound to human pancreatic carcinoma cells, MiaPaca‐2, which are known to express the receptor, as evidenced by rapid clustering followed by time‐dependent receptor internalization. This proves the stability of FLUO‐QUIN and its ability to penetrate vesicular membranes and reach various cell targets. Hence it might be used as an agent for the detection of CCK‐B‐receptor‐positive tumors by fluorescence imaging.
The Mechanism of Cleavage and Isomerisation of RNA Promoted by an Efficient Dinuclear Zn2+ Complex
Authors: Korhonen Heidi , Mikkola Satu , Williams Nicholas H. 
Published: December 2011

AbstractThe cleavage and isomerisation of uridine 3′‐alkylphosphates was studied in the presence of a dinuclear Zn2+complex, 3. The rate acceleration of the cleavage by 1 mM 3 is approximately 106‐fold under neutral conditions. Most remarkably, the complex also promotes the isomerisation of phosphodiester bonds, although the rate‐enhancement is more modest: under neutral conditions complex 3 (1 mM) catalyses isomerisation by about 500‐fold. The observation of this reaction shows that the reactions of these substrates catalysed by 3 proceed through a stepwise mechanism involving an intermediate phosphorane. A βlg value of −0.92 was determined for the 3‐promoted cleavage reaction, and modest kinetic solvent deuterium isotope effects ranging from 1.5 to 2.8 were observed. Isomerisation was less sensitive to the nature of the esterifying group, with a β value of −0.5, and the kinetic solvent deuterium isotope effects were less than 1.5. Most of these characteristics of the 3‐promoted cleavage are very similar to those for the cleavage of nucleoside 3′‐phosphotriesters. These data are explained by a mechanism in which the complex primarily acts as an electrophilic catalyst neutralising the charge on the phosphate and stabilising an intermediate phosphorane, with general acid catalysis promoting the cleavage reaction. In contrast to the behaviour of triesters, isomerisation is significantly slower than cleavage; this suggests that the changes in geometry that occur during isomerisation lead to a much less stable complex between 3 and the phosphorane intermediate.