bluuebunny/crossref_metadata_2025 huggingface dataset:
TheCorAMg2+Channel
Authors: Maguire Michael E
Published: December 2011

The CorA Mg2+channel is present in about 50% of bacteria and many archaea. Its ubiquitous eukaryotic homolog is Mrs2, the mitochondrial Mg2+channel. Physiologically, CorA mediates the influx of Mg2+down its electrochemical gradient. It can also mediate the influx of Ni2+and Co2+but only at concentrations that are toxic to the cell. A subclass of the CorA superfamily in the bacteria mediates the efflux of Zn2+. The sequence analysis of the CorA superfamily shows a complete lack of homology to any other protein. The crystal structure of CorA confirms its unique nature. CorA is a homopentamer shaped like a funnel with the stem of the funnel within the membrane. Each monomer has two transmembrane segments at the C terminus. All prokaryotic CorA proteins have the same basic structure. A 250–290 amino acid cytosolic N‐terminal domain is followed by transmembrane segment 1, which is followed by a nine amino acid periplasmic loop. This loop is followed by the transmembrane segment 2. Neither transmembrane segment contains any charged amino acids. The C‐terminal cytosolic tail of CorA is almost always six amino acids in length and contains three or four arginine and/or lysine residues. In the structures currently available, the Mg2+‐conducting pore is formed completely by transmembrane segment 1. The cytosolic domain is formed of a seven‐stranded antiparallel β sheet flanked on both sides by three α helices (α1–3β1–7α4–6). This domain is followed by the 100‐Å‐long α7helix, which forms most of the inner face of the funnel and transmembrane segment 1. In the cytosolic domain, a Mg2+cation is bound between an aspartate residue in the α7helix of one monomer and the α3helix of the adjacent monomer, giving five bound Mg2+cations per channel. These bound ions seem poised to act as ‘sensors’ of intracellular Mg2+, and their dissociation from the channel is proposed to allow the monomers to rotate apart, thus opening the channel.
Hydrophilic Domain of Respiratory ComplexIfromThermus thermophilus
Authors: Sazanov Leonid
Published: December 2011

Complex I (NADH:ubiquinone oxidoreductase) plays a central role in cellular energy production, coupling electron transfer between NADH and quinone to proton translocation. It is the largest protein complex of bacterial and mitochondrial respiratory chains. Mitochondrial complex I is a major source of reactive oxygen species (ROS), which may be one of the causes of aging. Dysfunction of the enzyme is implicated in many human neurodegenerative diseases. Complex I is an L‐shaped multisubunit protein assembly consisting of a hydrophilic peripheral arm and a hydrophobic membrane arm. The crystal structure of the hydrophilic domain of complex I fromThermus thermophiluswas solved recently. This subcomplex consists of eight subunits and contains all the redox centers of the enzyme, including nine iron–sulfur clusters. The electron transfer pathway through the enzyme is about 95 Å long, proceeding from the primary electron acceptor flavin mononucleotide through seven conserved iron–sulfur clusters to the quinone‐binding site at the interface with the membrane domain. The structure of the complete enzyme and the coupling mechanism are not yet known.
Iron‐Binding Protein
Fut
A
1
Authors: Koropatkin Nicole , Pakrasi Himadri B , Smith Thomas J
Published: December 2011

FutA1 belongs to the bacterial extracellular solute‐binding protein family 1 and is part of an ATP‐binding cassette‐type (ABC‐type) transport system involved in the uptake of iron. In
Synechocystis
6803, the
futA1
(
slr1295)
and
futA2
(
slr0513
) genes encode periplasmic binding proteins that have been proposed to be part of a high‐affinity iron‐transport system, although these genes, along with those encoding the transmembrane pore and intracellular ATPase proteins, are widely distributed throughout the genome. While the solute‐binding domains in the cluster 9 ABC transport systems have a relatively rigid α‐helix running down the back of the protein, which restricts domain movement, FutA1 has two β‐strands connecting the two domains of the protein. It is likely that these β‐strands permit the large domain movement observed during iron binding and release. In FutA1, iron is chelated by four tyrosine and one histidine residues. These tyrosine residues do not move during the opening and closing of the binding‐site cleft. This is likely due to a strong secondary shell of interacting residues which also improve iron‐tyrosine interactions by increasing the electronegativity of the tyrosine hydroxyls. Unlike a number of other periplasmic iron‐binding proteins, there are no apparent anion interactions with the bound ferric iron.
[
Ni
Fe
] Hydrogenase Maturing Proteins
Hyp
C
,
Hyp
D
,
Hyp
E
Authors: Watanabe Satoshi , Miki Kunio
Published: December 2011

[NiFe] hydrogenases carry an NiFe(CO)(CN)
2
center at the active site, which catalyzes the reversible oxidation of molecular hydrogen. Hyp proteins (HypABCDEF) are required for the maturation of [NiFe] hydrogenase. HypA and HypB are involved in the insertion of the nickel atom. HypE and HypF catalyze the biosynthesis of the cyanide ligand in the form of HypE‐thiocyanate. HypC and HypD are assumed to deliver the iron atom with diatomic ligands to the active site of hydrogenase. The structures of HypC consist of an OB‐fold like β‐barrel domain and C‐terminal one or two α helices. The C‐terminal helices are shown to be quite flexible. The structure of HypE consists of two α/β domains and is similar to other PurM superfamily proteins. The C‐terminal tail of HypE adopts an outward extended conformation in the absence of adenosine 5′ triphosphate (ATP) or an inward closed conformation in the presence of ATP. The structure of HypD is composed of two α/β domains and an Fe–S cluster binding domain. Conserved regions of HypD show its probable iron binding and active sites for cyanation. The [4Fe–4 S] cluster environment of HypD is shown to be quite similar to that of ferredoxin : thioredoxin reductase (FTR). The cyanation reaction can be catalyzed through thiol redox signaling in the HypCDE complex.
para‐AminobenzoateN‐Oxygenase
Authors: Zhao Huimin , Nair Satish K.
Published: December 2011

The monooxygenase AurF catalyzes the oxidation of a primary amine during the biosynthesis of the antibiotic aureothin. Biochemical reconstitution ofin vitroactivity demonstrates that AurF is a nonheme iron‐dependent enzyme. Crystallographic elucidation of the 3D structure reveals homology to the ribonucleotide reductase family of monooxygenases, despite a lack of appreciable similarity in the primary sequence.
4‐Hydroxybenzoyl‐CoenzymeAReductase
Authors: Boll Matthias
Published: December 2011

The dehydroxylating 4‐hydroxybenzoyl‐CoA reductase (HBCR) plays an important role in the degradation ofpara‐hydroxylated aromatic compounds in anaerobic bacteria. The enzyme catalyzes the removal of the phenolic hydroxyl group from 4‐hydroxybenzoyl‐CoA, yielding benzoyl‐CoA and water; a reduced ferredoxin serves as an electron donor. The enzyme belongs to the xanthine oxidase (XO) family of molybdenum cofactor containing enzymes and contains a molybdopterin‐cytosine dinucleotide cofactor, two [2Fe–2S] clusters, FAD and a [4Fe–4S] cluster per functional unit. HBCR is unique among XO family members in catalyzing the irreversible reduction of the substrate. A mechanism that differs from all other XO membersviahighly reactive radical intermediates has been suggested. The structural, electrochemical, spectroscopic, and kinetic properties of HBCR fromThauera aromaticaare highlighted and compared with other members of the xanthine oxidase family.
Hydroxyquinol 1,2‐Dioxygenase
Authors: Briganti Fabrizio , Ferraroni Marta
Published: December 2011

Hydroxyquinol 1,2‐dioxygenase (1,2‐HQD) is an intradiol dioxygenase that uses a nonheme ferric iron to activate the substrate for an electrophilic attack by molecular oxygen to cleave hydroxyquinol (1,2,4‐trihydroxybenzene) or chlorohydroxyquinols between the vicinal hydroxyls. This enzyme is involved in the aerobic metabolism of chloroaromatic compounds containing two or more chlorine substituents. The article focuses on the structure–function relationship of 1,2‐HQD and the comparison, at the molecular level, of the structural factors responsible for the differential substrate selectivity in known ring‐cleaving intradiol dioxygenases.
Structure, Spectroscopy, and Function of Tyrosinase; Comparison with Hemocyanin and Catechol Oxidase
Authors: Tepper Armand W J W , Lonardi Emanuela , Bubacco Luigi , Canters Gerard W
Published: December 2011

This article deals with tyrosinase, an enzyme that converts monophenols into diphenols and subsequently into orthoquinones with concomitant use of molecular oxygen as the source of oxygen atoms and oxidizing equivalents. The enzyme occurs widespread in nature. Its active center consists of a dinuclear copper site. The occurrence of tyrosinases and their biological function is reviewed. Information about primary (aa sequence, genetic organization), secondary, and tertiary structures is reviewed and, where appropriate, compared with similar information about related proteins with a dinuclear Cu site (hemocyanins, catechol oxidase). Methods to produce and purify tyrosinase are reviewed. Spectroscopic studies (optical; EPR, NMR, EXAFS) are reviewed in relation to the enzyme mechanism, which is discussed at the end of the article.
Peptidylglycine α‐Hydroxylating Monooxygenase (PHM)
Authors: Rudzka Katarzyna , Chufán Eduardo E , Eipper Betty , Mains Richard , Amzel Mario L
Published: December 2011

Numerous peptides function as hormones, neurotransmitters, and growth factors. Enzymatic α‐amidation is a biologically important posttranslational modification of the C‐terminus of many of these peptides. This modification alters the biological properties and enhances the stability of the peptides toward digestion by carboxypeptidases. Peptidylglycine α‐hydroxylating monooxygenase (PHM) is an ascorbate and copper‐dependent catalytic domain of an α‐amidating enzyme (peptidylglycine α‐amidating monooxygenase, PAM) that catalyzes the stereospecific hydroxylation of an α‐carbon of a terminal glycine residue, the first step in the amidation reaction. This reaction is followed by cleavage of the glycine N Cα bond, which is carried out by the second PAM catalytic domain, peptidyl‐α‐hydroxyglycine α‐amidating lyase (PAL). Detailed structural studies of PHM revealed that its catalytic core binds two copper ions that support the oxygenation reaction by cycling through Cu(II)/Cu(I) oxidation states. These two Cu ions (CuHand CuM) are located 11 Å apart and are separated by a solvent‐accessible cleft. The monooxygenation reaction requires the two‐electron activation of molecular oxygen, which is achieved by the binding of O2to a single Cu(I) center (CuM). Formation of this complex is dependent upon the presence of a peptidylglycine substrate and a reducing agent (ascorbate). Since the resting state of the enzyme contains two Cu(II) ions, the catalytic reaction requires transfer of two electrons from the reducing agent to the metal centers, and from the reduced copper ions to dioxygen. The reduced oxygen species then carries out the stereospecific hydroxylation of glycine after abstraction of thepro‐Shydrogen from Cα. Although, the structure and function of PHM have been broadly studied, the pathway of its electron transfer, the nature of the metal‐oxygen species, and details of the mechanism are still being investigated.
[2
Fe
–2
S
] Oxidative‐Stress Sensor
Sox
R
Bound to
DNA
Authors: Watanabe Satoshi , Miki Kunio
Published: December 2011

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

Iron 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

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

Mercury 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

Two‐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

KshAB 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

Toluene 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

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

YiiP 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

The 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

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

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

Lepidoperan 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

We 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

Fluorescent 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.
Tracy–Widom statistic for the largest eigenvalue of autoscaled real matrices
Authors: Saccenti Edoardo , Smilde Age K. , Westerhuis Johan A. , Hendriks Margriet M. W. B.
Published: December 2011

Eigenanalysis is common practice in biostatistics, and the largest eigenvalue of a data set contains valuable information about the data. However, to make inferences about the size of the largest eigenvalue, its distribution must be known. Johnstone's theorem states that the largest eigenvalues l1 of real random covariance matrices are distributed according to the Tracy–Widom distribution of order 1 when properly normalized to , where ηnp and ξnp are functions of the data matrix dimensions n and p. Very often, data are expressed in terms of correlations (autoscaling) for which case Johnstone's theorem does not work because the normalizing parameters ηnp and ξnp are not theoretically known. In this paper we propose a semi‐empirical method based on test‐equating theory to numerically approximate the normalization parameters in the case of autoscaled matrices. This opens the way of making inferences regarding the largest eigenvalue of an autoscaled data set. The method is illustrated by means of application to two real‐life data sets. Copyright © 2011 John Wiley & Sons, Ltd.
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

The 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.
A Generic Platform for the Addressable Functionalisation of Electrode Surfaces through Self‐Induced “Electroclick”
Authors: Orain Christophe , Le Poul Nicolas , Gomila Antoine , Kerbaol Jean‐Michel , Cosquer Nathalie , Reinaud Olivia , Conan Françoise , Le Mest Yves
Published: December 2011

A novel and general strategy for the immobilisation of functional objects onto electrodes is described. The concept is based on the addition of two pendant ethynyl groups onto a bis(pyridyl)amine derivative, which acts as a molecular platform. This platform is pre‐functionalised with an N3‐tagged object of interest by Huisgen cycloaddition to one of the ethynyl groups in biphasic conditions. Hence, when complexed by CuII, this molecular‐object holder can be immobilised, by a “self‐induced electroclick”, through the second ethynyl group onto N3‐alkanethiol self‐assembled monolayers on a gold electrode. Two different functional groups, a redox innocent ((CH2)3Ph) and an electrochemical probe (ferrocene), were immobilised by following this strategy. The in situ electrochemical grafting showed, for both systems, that the kinetics of immobilisation is fast. The voltammetric characterisation of the surface‐tagged functionalised copper complexes indicated that a good surface coverage was achieved and that a moderately fast electron‐transfer reaction occurs. Remarkably, in the case of the redox‐active ferrocenyl‐immobilised system, the electrochemical response highlighted the involvement of the copper ion of the platform in the kinetics of the electron transfer to the ferrocene moiety. This platform is a promising candidate for applications in surface addressing in areas as diverse as biology and materials.
Current Chemical Biology Tools for Studying Protein Phosphorylation and Dephosphorylation
Authors: H. S. Lu Candy , Liu Kai , Tan Lay Pheng , Yao Shao Q.
Published: December 2011

Amongst different posttranslational events involved in cellular‐signaling pathways, phosphorylation and dephosphorylation of proteins are the most prevalent. Aberrant regulations in the cellular phosphoproteome network are implicated in most major human diseases. Consequently, kinases and phosphatases are two of the most important groups of drug targets in medicinal research today. A major challenge in the understanding of protein phosphorylation and dephosphorylation is the sheer complexity of the phosphoproteome network and the lack of tools capable of studying protein phosphorylation and dephosphorylation as they occur in cells. We highlight herein various chemical biology tools that have emerged in the last decade for such studies. First, we discuss the use of small‐molecule mimics of phosphoamino acids and their use in elucidating the function of protein phosphorylation and dephosphorylation. We also introduce recent advances in the field of activity‐based protein profiling (ABPP) for proteome‐wide detection of protein phosphorylation and dephosphorylation. We next discuss the key concepts in the design of peptide‐ and protein‐based biosensors capable of real‐time reporting of phosphorylation/dephosphorylation events. Finally, we highlight the application of peptide and small‐molecule microarrays (SMMs), and their applications in high‐throughput screening and discovery of new compounds related to phosphorylation/dephosphorylation.
ChemInform Abstract: Anomalous Thermal Expansion in the Square‐Net Compounds RE4TGe8 (RE: Yb, Gd; T: Cr—Ni, Ag).
Authors: Peter Sebastian C. , Chondroudi Maria , Malliakas Christos D. , Balasubramanian Mahalingam , Kanatzidis Mercouri G.
Published: December 2011

Yb4Ag0.56Ge8 (I), Yb4Co1.17Ge8 (II), Yb4Cr1.07Ge8 (III), Yb4Cr1.04Ge8 (IV), Yb4Fe1.10Ge8 (V), Yb4Mn1.00Ge8 (VI), Yb4Ni1.12Ge8 (VII), and Gd4Cr1.33Ge8 (VIII) are synthesized from the elements (850 °C, 144 h) and characterized by XRD, XANES, and DFT band structure calculations.
ChemInform Abstract: Cs4UGe8O20: A Tetravalent Uranium Germanate Containing Four‐ and Five‐Coordinate Germanium.
Authors: Nguyen Quang Bac , Lii Kwang‐Hwa
Published: December 2011

The title compound is synthesized from a mixture of CsF, CsI, UO3, Al, and GeO2 in (gold ampule, autoclave, 160 MPa, 585 °C, 2 d).
ChemInform Abstract: Ba4KFe3O9: A Novel Ferrite Containing Discrete 6‐Membered Rings of Corner‐Sharing FeO4 Tetrahedra.
Authors: zur Loye Hans‐Conrad , et al. et al.
Published: December 2011

Single crystals of the new title compound are prepared from a mixture of Ba(OH)2, KOH, and Fe2O3 (alumina crucible, 750 °C, 5 h).
ChemInform Abstract: Introducing a Magnetic Guest to a Tetrel‐Free Clathrate: Synthesis, Structure, and Properties of EuxBa8‐xCu16P30 (0 ≤ x ≤ 1.5).
Authors: Kovnir Kirill , Stockert Ulrike , Budnyk Sergij , Prots Yurii , Baitinger Michael , Paschen Silke , Shevelkov Andrei V. , Grin Yuri
Published: December 2011

The title compounds are prepared by solid state reactions of the elements (1125 K, 360 h) and characterized by powder and single crystal XRD, XAS, electrical resistivity, specific heat, and magnetic susceptibility measurements.
ChemInform Abstract: Undulating Layers in a New Rhodate Network: Structure of Bi1.4CuORh5O10.
Authors: Mizoguchi Hiroshi , Michiue Yuichi , Sleight Arthur W. , Subramanian M. A.
Published: December 2011

The new title compound is prepared from a mixture of CuO and Rh2O3 in a Bi2O3/V2O5 (3:1) flux (Pt crucible, 1373 K, 10 h).
ChemInform Abstract: Synthesis of Novel 1,4‐Bissulfonamide Ligands for Enantioselective Addition of Diethylzinc to Aldehydes.
Authors: Yang Minghua , Sun Jiangtao , Zhu Chengjian
Published: December 2011

Several chiral sulfonamides ligands are synthesized and screened for their catalytic activity in the enantioselective addition of diethylzinc to aldehydes.
ChemInform Abstract: Design of Silver(I)‐Heteropolyacids: Toward the Molecular Control of Reactivity in Organic Chemistry.
Authors: Borghese Sophie , Louis Benoit , Blanc Aurelien , Pale Patrick
Published: December 2011

By tuning the amount of silver and the acidity, a bifunctional polyoxymetalate is designed exhibiting both metallic properties and Broensted acidity.
ChemInform Abstract: Efficient Oxidation of Benzylic Alcohols with Trichloroisocyanuric Acid and Ionic Liquid in Water.
Authors: Lee Jong Chan , Kim Jimi , Lee Seung Bae , Chang Soon‐Uk , Jeong Yeon Jin
Published: December 2011

The reaction is conducted under environmentally benign conditions.
ChemInform Abstract: AlBr3·6H2O Catalyzed Oxidation of Benzylic Alcohols.
Authors: Zhong Yun‐Mei , Ma Heng‐Chang , Wang Jin‐Xia , Jia Xiao‐Jie , Li Wen‐Feng , Lei Zi‐Qiang
Published: December 2011

Primary and secondary benzylic alcohols are transformed into the corresponding aldehydes and ketones with almost complete conversion and high selectivity.
ChemInform Abstract: Simple and Efficient One‐Step Conversion of Benzonitrile into Methylarene under Mild Conditions.
Authors: Ouellet Etienne , Poirier Donald
Published: December 2011

In most cases, clear transformation of the nitrile to a methyl group is observed.
ChemInform Abstract: Synthesis of N‐Acyl‐N,O‐acetals from N‐Aryl Amides and Acetals in the Presence of TMSOTf.
Authors: Downey C. Wade , Fleisher Alan S. , Rague James T. , Safran Chelsea L. , Venable Megan E. , Pike Robert D.
Published: December 2011

It is demonstrated, that TmsOTf mediates the one‐pot reactions shown.
ChemInform Abstract: Improved Ruthenium‐Catalyzed Amination of Alcohols with Ammonia: Synthesis of Diamines and Amino Esters.
Authors: Imm Sebastian , Baehn Sebastian , Zhang Min , Neubert Lorenz , Neumann Helfried , Klasovsky Florian , Pfeffer Jan , Haas Thomas , Beller Matthias
Published: December 2011

The homogeneous selective catalytic diamination of primary and secondary diols with ammonia gives the corresponding diamines in high yields.
ChemInform Abstract: Recyclable Catalysts for Palladium‐Catalyzed Aminations of Aryl Halides.
Authors: Dumrath Andreas , Luebbe Christa , Neumann Helfried , Jackstell Ralf , Beller Matthias
Published: December 2011

At low catalyst loadings of Pd(OAc)2 (0.25‐2.0 mol%) with PMI as ligand, aryl/heteroaryl chlorides or bromides are efficiently aminated by ammonia or primary and secondary amines.
ChemInform Abstract: Titanocene(III) Chloride Mediated Radical Induced Allylation of Aldimines: Formal Synthesis of C‐Linked 4′‐Deoxy Aza‐disaccharide.
Authors: Saha Sumit , Roy Subhas Chandra
Published: December 2011

The reaction allows a mild and convenient access to homoallyl amines as useful synthons.
ChemInform Abstract: anti‐Markovnikov Hydroalkylation of Allylic Amine Derivatives via a Palladium‐Catalyzed Reductive Cross‐Coupling Reaction.
Authors: DeLuca Ryan J. , Sigman Matthew S.
Published: December 2011

Palladium‐catalyzed hydroalkylation of allylic amines with alkylzinc reagents proceeds with high to excellent chemoselectivity in favor of anti‐Markovnikov products in most cases (linear‐to‐branched ratio from 8:1 up to <20:1).
ChemInform Abstract: Nickel‐Catalyzed C—H Arylation of Azoles with Haloarenes: Scope, Mechanism, and Applications to the Synthesis of Bioactive Molecules.
Authors: Yamamoto Takuya , Muto Kei , Komiyama Masato , Canivet Jerome , Yamaguchi Junichiro , Itami Kenichiro
Published: December 2011

Novel nickel‐based catalytic systems are developed for the arylation of a variety of N‐heterocycles with aryl/heteroaryl chlorides, bromides, iodides, and a triflate.
ChemInform Abstract: Ruthenium‐Catalyzed Ring‐Closing Metathesis Accelerated by Long‐Range Steric Effect.
Authors: Fujihara Tetsuaki , Tomike Yoshikazu , Ohtake Toshiyuki , Terao Jun , Tsuji Yasushi
Published: December 2011

Two highly active ruthenium‐based metathesis catalysts with N‐heterocyclic carbene ligands bearing 2,3,4,5‐tetraarylphenyl moieties are developed.
ChemInform Abstract: A Three‐Component Reaction Between Azaarenes (Phenanthridine, Quinoline or Isoquinoline), Acetylenic Esters and Phenol Derivatives.
Authors: Nassiri Mahmoud
Published: December 2011

The title reactions proceed smoothly at room temperature without any catalyst.
ChemInform Abstract: Cyclopropyl Iminium Activation: Reactivity Umpolung in Enantioselective Organocatalytic Reaction Design.
Authors: Sparr Christof , Gilmour Ryan
Published: December 2011

An unprecedented strategy for the enantioselective synthesis of 1,3‐dichlorides of type (II) and (IV) uses the ring opening of cyclopropylaldehydes under conditions A).
ChemInform Abstract: γ‐Selective Cross‐Coupling of Allylic Silanolate Salts with Aromatic Bromides Using Trialkylphosphonium Tetrafluoroborate Salts Prepared Directly from Phosphine·Borane Adducts.
Authors: Denmark Scott E. , Werner Nathan S.
Published: December 2011

The (Z) geometry of the silanolate (I) increases the γ‐selectivity to 99:1 except in the case of quinoline derivative (IV).
ChemInform Abstract: Simple, Stable, and Easily Accessible Well‐Defined CuCF3 Aromatic Trifluoromethylating Agents.
Authors: Tomashenko Olesya A. , Escudero‐Adan Eduardo C. , Martinez Belmonte Marta , Grushin Vladimir V.
Published: December 2011

Trifluoromethylation of various aryl iodides is achieved using two new Cu(I) trifluoromethylating agents (I) and (IV).
ChemInform Abstract: A Highly Versatile Catalytic System for N‐Arylation of Amines with Aryl Chlorides in Water.
Authors: Huang Manna , Lin Xiaoqin , Zhu Xinhai , Peng Weili , Xie Jianwei , Wan Yiqian
Published: December 2011

A novel efficient catalyst system is presented for the C—N coupling of various aryl chlorides (II) with a diversity of amines, including aniline (I), benzylamine (IV), N‐heterocycles like imidazole (VI) as well as ammonia, in aqueous solution.
ChemInform Abstract: Catalytic Diastereoselective Petasis Reactions.
Authors: Muncipinto Giovanni , Moquist Philip N. , Schreiber Stuart L. , Schaus Scott E.
Published: December 2011

Petasis reaction of boronates, protected α‐hydroxy aldehydes and amines is described.
ChemInform Abstract: N‐Heterocyclic Carbene Catalyzed Umpolung of Michael Acceptors for Intermolecular Reactions.
Authors: Biju Akkattu T. , Padmanaban Mohan , Wurz Nathalie E. , Glorius Frank
Published: December 2011

The transition‐metal free transformation of Baylis—Hillman products results in stereoselective formation of homocoupling products (II)/(III).
ChemInform Abstract: The Ugi Reaction in a Polyethylene Glycol Medium: A Mild, Protocol for the Production of Compound Libraries.
Authors: Niu Teng‐fei , Lu Guo‐ping , Cai Chun
Published: December 2011

An efficient, mild und eco‐friendly method for the Ugi reaction in PEG‐water is described.
ChemInform Abstract: Use of Magnesium (Turnings) as a Powerful Catalyst for the O‐Acylative Cleavage of Tetrahydrofuran.
Authors: Pasha M. A. , Manjula Krishnappa
Published: December 2011

A novel access to 4‐chlorobutyl esters (III) is described.
ChemInform Abstract: Applications of a Monomeric Orthopalladate Complex Containing Mixed Phosphorus—Nitrogen Donors in the Heck Reaction.
Authors: Hajipour Abdol Reza , Rafiee Fatemeh , Rouho Arnold E.
Published: December 2011

It is demonstrated that the thermally stable and oxygen‐insensitive PNB is highly efficient in a broad spectrum concerning reactions of olefins with aryl halides and sulfonyl chlorides.