bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nature of the Catecholate—
Fe
(
III
) Bond: High Affinity Binding and Substrate Activation in Bioinorganic Chemistry
Authors: Solomon Edward I. , Pau Monita Y. M. , Hocking Rosalie K. 
Published: December 2011

Abstract

Catecholate‐Fe(III) (high‐spin) bonds are important in many areas of bioinorganic chemistry. These exhibit low‐energy, intense ligand‐to‐metal charge transfer (LMCT) transitions reflecting highly covalent bonds. This high covalency can make a major contribution to function. In this review, we develop the method of metal L‐edge X‐ray absorption spectroscopy (XAS) as a probe of differential orbital covalency (DOC), the amount of ligand character in the different d orbitals of a metal site in a highly covalent environment. We then apply this method to experimentally determine the covalency of the ligand‐metal bonds related to the siderophores and computationally evaluate this contribution to their high stability constants. We then use variable‐temperature, variable‐field, magnetic circular dichroism (VTVH MCD) spectroscopy to assign the LMCT transitions of the catecholate‐, substrate‐bound Fe
III
site of the intradiol dioxygenases. A reaction coordinate is presented where this charge transfer can overcome the spin‐forbidden nature of the reaction of the bound catecholate (singlet) with dioxygen (triplet).
Selenium: Radionuclides
Authors: Shaw George , Ashworth Daniel 
Published: December 2011

AbstractSelenium in the environment has been studied intensively for several decades, since it is both a trace nutrient and a toxin. It is a ubiquitous element in soils, waters, and the atmosphere, with chemical similarities to the other group 16 elements sulfur, polonium, and tellurium. Important selenium species in environmental media include inorganic oxyanions as well as organic species produced by biological methylation mechanisms. The only probable long‐term source of radioactive selenium to the environment is the leakage from radioactive waste repositories. Only79Se is of concern in this respect, since it is the only long‐lived radioactive isotope of selenium (physical half‐life = 377 000 years). Under alkaline geochemical conditions, there is the potential for79Se to migrate from geological radioactive waste repositories in very small quantities over very long periods. It is expected that any79Se released into the environment will behave in the same way as nonradioactive selenium, though the kinetics of isotopic exchange between79Se and stable selenium in soils, sediments, and other environmental media have never been studied over timescales relevant to radioactive waste disposal. It is unlikely that environmental concentrations of79Se will ever lead to exposures approaching the intake levels associated with stable selenium. Any exposure that does occur is likely to be primarily through the dietary intake pathway, since the principal environmental reservoirs, and therefore potential sources, of selenium in the environment are waters and soils.
Thorium: Radionuclides
Authors: Wan Mahmood Zal Uyun , Rahim Mohamed Che Abd 
Published: December 2011

Abstract

Thorium is composed of 25 different isotopes with the common ones being
224
Th,
226
Th,
227
Th,
228
Th,
229
Th,
230
Th,
231
Th,
232
Th,
233
Th, and
234
Th. These decay with considerably different half‐lives and nuclear properties. Although thorium is considered one of the more highly radiotoxic elements, its toxicity is low because of its stability at ambient temperature. The intake of thorium isotopes by human being occurs mainly through animal products, cereals, vegetables, and waters. Thorium is widely distributed in small amounts, with an average lithospheric concentration of 8–12 mg g
−1
in the earth's crust (at an average concentration of 6 mg g
−1
in soil). Furthermore, thorium is quite useful, especially in industries, and it is also recognized as a potential fuel for fast breeder reactors, where it is converted to fissile
233
U. This article presents details on the occurrence, chemistry, speciation, separation, and analytical characterization techniques of the more common isotopes of thorium.
B
altic
S
ea: Radionuclides
Authors: Nielsen Sven P. , Lüning Maria , Ilus Erkki , Outola Iisa , Ikäheimonen Tarja , Mattila Jukka , Herrmann Jürgen , Kanisch Günter , Osvath Iolanda 
Published: December 2011

Abstract

The most significant source of anthropogenic radioactivity in the Baltic Sea is fallout from the accident at the Chernobyl nuclear power plant in 1986. The second most important source is global fallout from atmospheric nuclear weapons tests carried out during the late 1950s and early 1960s. Radioactivity inputs into the Baltic Sea from nuclear reprocessing plants in Western Europe have become of minor importance due to significant reduction of discharges in recent years. In terms of input of
137
Cs into the Baltic Sea, Chernobyl fallout has contributed about 82% and nuclear weapons test fallout about 14%. For
90
Sr in the Baltic Sea, input from atmospheric fallout from nuclear weapons tests has contributed about 81%, while the contribution from Chernobyl fallout was about 13%. Cesium‐137 is the main indicator of Baltic seawater with respect to anthropogenic radioactivity. The highest concentrations in seawater during 1999–2006 were found in the Baltic Proper and the Bothnian Sea. The general trend is steadily decreasing. Concentrations of anthropogenic radioactivity in fish generally show decreasing trends in agreement with concentrations in seawater. Among freshwater fish, pike showed large
137
Cs values due to their higher concentration factors (CFs). The larger
137
Cs values of pike were observed at the coast of the Bothnian Sea. The Baltic Sea is the regional sea in the world with the highest concentrations of
137
Cs. The Baltic Sea ranks third in the world with respect to
90
Sr in seawater; only the Irish Sea and the Black Sea show higher levels. In 1990, average concentrations of
137
Cs in fish from the Baltic Sea were similar to those in the Irish Sea, about 4 times higher than in the Black Sea and about 30 times higher than in the Mediterranean Sea.
Lithium–Ion Batteries:
L
i–6
MAS NMR
Studies on Materials
Authors: Cabana Jordi , Grey Clare P. 
Published: December 2011

Abstract
Lithium ion batteries have been pivotal in the development of mobile electronic devices such as laptops and mobile phones, and are now poised to make a significant impact in transportation applications, for example, in hybrid and plug‐in hybrid electric vehicles, and in applications on the electric grid. The push to develop new batteries for these diverse applications has lead to a wealth of new electrode chemistries. Yet, issues such as safety, cycle life, capacity, and power remain the specific concerns, depending very strongly on the chemistries and materials used as electrode materials in the different batteries. Thus, in order for these materials to be used in practical devices and to develop insight into how these materials function, we need to understand not only the structures of the as‐synthesized materials but also how they change during the cycling of the lithium ion battery. To this end, nuclear magnetic resonance (NMR) spectroscopy has played an important role in characterizing the local structures and dynamics of these materials. This review article provides a summary of some of the more recent applications of this methodology in this field. We focus on the use of NMR to study both positive and negative electrode materials, and show how this technique has helped understand the origins of the performance of a given material. The analysis of electrode materials, reacting via more traditional intercalation reactions, is covered in the first half of the article, whereas the second part is devoted to newer chemistries and reaction mechanisms, which offer the prospect of much needed improvements in energy density of Lithium ion batteries.
Supercapacitors: Electrode Materials Aspects
Authors: Zhang Li Li , Lei Zhibin , Zhang Jintao , Tian Xiaoning , Zhao Xiu Song 
Published: December 2011

AbstractGlobal warming and the finite nature of fossil fuels have driven the world to adopt sustainable and renewable energies. Electrochemical energy conversion and storage systems are considered as such energy sources. As a bridge between high‐power‐output conventional capacitors and high‐energy‐density batteries, supercapacitors (also known as ultracapacitors or electrical double layer capacitors) are an ideal electrochemical energy‐storage system, suitable for rapid storage and release of energy. In comparison with that of batteries, the energy density of supercapacitors is much lower. Therefore, improving the energy density without sacrificing the high power density of supercapacitors has been a key research direction in developing high‐performance supercapacitor devices. The properties of the active electrode materials, including surface area, pore size, pore connectivity, electric conductivity, and surface chemistry, play a crucial role in determining the ultimate performance of the supercapacitor. This article presents an overview of literature data on supercapacitor electrode materials. With a brief description of the structure and energy‐storage mechanism of supercapacitors, recent advancements in electrode materials including carbon‐based materials (e.g., activated carbon, templated carbon, carbon nanotubes, graphene), transition‐metal oxides, and conducting polymers are summarized and discussed.
Lithium–Ion Batteries
Authors: Lucht Brett L. , Markmaitree Tippawan , Yang Li 
Published: December 2011

AbstractCurrently used electrolytes for lithium ion batteries have poor thermal stability, which results in a decrease in their calendar life. The thermal decomposition reactions of LiPF6‐based electrolytes in solution and with the surfaces of the electrode materials are reviewed. Methods to inhibit thermal decomposition reactions and improve calendar life are also discussed.
Protein Prenyltransferases
Authors: Zhang Hong 
Published: December 2011

AbstractProtein prenyltransferases (PPT) are Zn metalloenzymes that catalyze the covalent attachment of farnesyl or geranylgeranyl isoprenoids to the C‐terminal cysteine residue(s) of many cellular proteins involved in signal transduction and intracellular vesicle transport. There are three subfamilies of protein prenyltransferases: protein farnesyltransferase (PFT), protein geranylgeranyltransferase type I (PGGT‐I), and protein geranylgeranyltransferase type II (PGGT‐II) or Rab geranylgeranyltransferase (RabGGT). All members of PPT are heterodimers composed of an α‐ and a β‐subunit. The crystal structures of PFT, RabGGT, and, in particular, the complex structures of PFT with its substrates or product elucidated the active site configuration and substrate‐binding mode of these enzymes. An intrinsically bound Zn ion was found to be coordinated to an aspartate, a cysteine, and a histidine residue from the β‐subunit. This Zn ion has been shown to be directly involved in the catalysis by activating the protein substrate cysteine thiol for the nucleophilic attack on the C1 atom of the farnesyl or geranylgeranyl diphosphate. PFT has been a primary anticancer drug target, and extensive biochemical and structural studies have been conducted on the kinetics and mechanistic aspects of the enzyme. Progress has also been made in the structural and enzymological studies of RabGGT and PGGT‐I.
Carbonic Anhydrases (γ‐Class)
Authors: Kisker Caroline , Iverson Tina M 
Published: December 2011

AbstractThe γ‐class carbonic anhydrase from the thermophilic archaeonMethanosarcina thermophilais involved in the aceticlastic pathway in which energy for growth is derived from the conversion of the methyl group of actetate to methane. This γ‐class carbonic anhydrase is arranged as a tightly packed trimer with each monomer folded into a left‐handed β‐helix. The catalytic active site zinc is located at the interface between subunits and is coordinated by three histidines, two from one monomer and the other from a second monomer. Interestingly, the arrangement of the histidine side chains ligating the metal show clear structural similarity to their counterparts in the well‐characterized α‐class carbonic anhydrases, despite the difference in overall fold. The conversion of CO2to bicarbonate has a maximal turnover number of 6 × 104s−1, and this reaction is believed to proceed by utilizing the zinc‐hydroxide mechanism previously proposed for α‐class carbonic anhydrases.
Metallo β‐Lactamases
Authors: Herzberg Osnat , Fitzgerald Paula MD 
Published: December 2011

AbstractThe metallo‐β‐lactamases (class B β‐lactamases) confer bacterial resistance to β‐lactam antibiotics and are therefore targets for the development of clinical agents against resistant strains of bacteria. They are found in a wide variety of bacteria and act on a broad spectrum of substrates including penicillins, cephalosporins, and carbapenems, as well as on some inhibitors of serine‐β‐lactamases. These ∼25 000 Da zinc‐dependent enzymes have been studied extensively in recent years, and crystal structures have been determined for the enzymes from five different bacteria representing two different sequence subclasses (B1 and B3). The active site is located at the interface between two α/β domains where two zinc atoms bind. This review surveys the current understanding of these enzymes, with emphasis on structural studies, spectroscopy, kinetics, and proposals for the catalytic mechanism.
Protein Interface Zinc Sites: The Role of Zinc in the Supramolecular Assembly of Proteins and in Transient Protein–Protein Interactions
Authors: Maret Wolfgang 
Published: December 2011

AbstractNew roles are emerging for zinc in protein quaternary structure and supramolecular assemblies. When zinc bridges the interfaces of proteins via ligands provided by different polypeptide chains, it is either essential for the interaction or it serves mainly as a stabilizing factor. Zinc can cross‐link four, three, or more commonly, two protein monomers. Functions of protein interface zinc sites include catalysis, inhibition of enzymatic or other activity, packaging of proteins for storage, dimerization of proteins, formation of protein/receptor complexes, and construction of molecular scaffolds. Tight control of the availability of zinc and ligand‐centered redox reactions in zinc/thiolate coordination environments of protein interface zinc sites suggest mechanisms for modulating transient protein–protein interactions.
Structural Calcium (Trypsin, Subtilisin)
Authors: Gilliland Gary L , Teplyakov Alexey 
Published: December 2011

AbstractThe presence of structural calcium in trypsin and subtilisin does not play a role in catalysis, but instead, stabilizes the structures. Trypsin and subtilisin are two large families of serine proteases with different folds that take advantage of the stabilizing effects of binding calcium ions. Representative structures of the different calcium binding sites found in each protein family are described along with the implications for the presence of the ions. This article reviews the details, the energetics, and the roles that calcium plays in the structures of both these families of enzymes.
C
2‐Domain Proteins Involved in Membrane Traffic
Authors: Rizo Josep 
Published: December 2011

Abstract

C
2
‐domains are the second‐most abundant Ca
2+
‐binding modules in nature. Their most common activity is Ca
2+
‐dependent phospholipid binding, but other types of interactions have been observed for these versatile protein modules. A variety of proteins involved in membrane traffic contain multiple C
2
‐domains, which often appear as two tandem C
2
‐domains as in the case of synaptotagmins and rabphilin. The structures of the C
2
‐domains of these proteins consist of a conserved β‐sandwich, formed by two four‐stranded β‐sheets, with variable loops at the top and the bottom that sometimes contain α‐helices. Multiple Ca
2+
‐ions bind in a tight cluster at the top loops, usually without inducing substantial conformational changes. Instead, electrostatic changes caused by Ca
2+
binding induce the Ca
2+
‐dependent interactions of C
2
‐domains, which can also be aided by hydrophobic interactions and partial coordination of Ca
2+
by the target molecules. Extensive analysis of the structure and Ca
2+
‐binding properties of the two synaptotagmin 1 C
2
‐domains has helped design genetic experiments that have strongly supported the notion that this protein acts as the major Ca
2+
sensor in neurotransmitter release. These studies have also suggested that Ca
2+
‐dependent phospholipid binding underlies the function of synaptotagmin 1 in triggering release.
Hemoglobin
Authors: Paoli Massimo , Nagai Kiyoshi 
Published: December 2011

AbstractFunctional ClassOccurrenceBiological FunctionAmino Acid Sequence InformationProtein Purification and Molecular CharacterizationMetal Content and CofactorsSpectroscopyX‐Ray Structure of NativeHbFunctional AspectsFunctional DerivativesRelated Articles
Cytochromec′
Authors: Romão Maria João , Archer Margarida 
Published: December 2011

AbstractCytochromes c′ are heme proteins presumably involved in electron transport and the name cytochrome c′ is used to distinguish these high‐spin heme proteins from the low‐spin mitochondrial cytochromesc. The heme group is covalently bound by thioether bonds between the two vinyl groups of the heme and the two cysteinyl side chains in a sequence, ‐Cys‐X‐Y‐Cys‐His‐, typical of cytochromesc. The histine occupies the fifth axial coordination position. Most cytochromes c′ are isolated as homodimers of ca 2 × 14 kDa and each monomer consists of an anti‐parallel four‐α‐helical bundle, which defines the heme‐binding pocket.
Succinate:Quinone Oxidoreductases
Authors: Lancaster C Roy D 
Published: December 2011

AbstractSuccinate:quinone oxidoreductases encompass the succinate:quinone reductase (SQR) enzymes of aerobic respiration (respiratory complex II) and the quinol:fumarate reductase (QFR) enzymes of anaerobic respiration. These enzymes couple the two‐electron oxidation of succinate to fumarate to the two‐electron reduction of quinone to hydroquinone (quinol), and also catalyse the reverse reaction, the reduction of fumarate by quinol. Members of the superfamily are composed of two hydrophilic subunits, a large flavoprotein subunit A and a smaller subunit B containing three iron–sulfur centers, and one large subunit C or two small subunits C and D hydrophobic polypeptides that are integral membrane proteins and bind two, one, or no hemebgroups. On the basis of the available crystal structures of members of the superfamily, structural and functional aspects of succinate:quinone oxidoreductases are comprehensively discussed.
The [2Fe–2S] Ferredoxins
Authors: Zanetti Giuliana , Binda Claudia , Aliverti Alessandro 
Published: December 2011

AbstractThe 2Fe ferredoxins (Fds) are simple iron–sulfur proteins, containing one 2Fe–2S cluster, that are involved mainly as electron carriers of low oxidation–reduction potential in fundamental metabolic processes. They can be subdivided into three families: class I, plant‐type; class II, adrenodoxin‐type; and class III,Clostridium‐type; according to the spacing in the sequence of the cysteinyl residues that bind the iron atoms of the cluster. All the Fds are monomers of 11–14 kDa, except for class III Fds that are dimer, with one cluster per subunit.The cluster of 2Fe Fds contains two atoms of iron, bridged by two acid‐labile inorganic sulfide atoms, and coordinated to four cysteinyl sulfurs of the polypeptide chain. Fds absorb light in the 300–500 nm visible region, mainly due to sulfur‐Fe3+charge‐transfer transitions. The cluster in the oxidized protein contains two antiferromagnetically coupled, high‐spin (S = 5/2) ferric irons and is, therefore, electron paramagnetic resonance (EPR) silent. Upon one‐electron reduction, Fds become paramagnetic.The three‐dimensional (3D) structure of several 2Fe Fds have been obtained either by X‐ray crystallography or by nuclear magneticresonance (NMR) spectroscopy. The solution structures are very similar to the 3D crystal structures. The protein structure motif characteristic of Fds has been named β‐grasp – a five‐stranded antiparallel β‐sheet with an α‐helix lying on top of the sheet. This central core (β1–β5 and α1) is surrounded by two short β‐strands, an α‐helix (α2), and a short C‐terminal helical turn (α3). Class II Fds have an additional interaction domain. Comparison of the structures of the different proteins reveals conformational differences especially between class I and II ferredoxins. The binuclear iron cluster lies in a solvent‐exposed pocket generated by the loop connecting helix α1 and strand β3 and comprising three of the cysteinyl ligands. This loop is anchored through several hydrogen bonds to different parts of the protein molecule. An extensive survey of the literature on the interactions of several 2Fe Fds with their respective partners is presented.
Purple Acid Phosphatase
Authors: Vogel Andreas , Spener Friedrich , Krebs Bernt 
Published: December 2011

AbstractPurple acid phosphatases (PAPs) hydrolyzing activated phosphoric acid esters and anhydrides have in common a two‐metal center with a tyrosine‐Fe(III) charge transfer transition responsible for the color. In the mammalian enzymes from the spleen, macrophages, osteoclasts, and uterine fluids, the second metal in the active site is Fe(II); whereas, the plant enzyme kidney bean PAP (kbPAP) has an Fe(III)–Zn(II) active center. The structure of the homodimeric 111‐kDa kbPAP shows the active site at the carboxy end of two sandwiched β–α–β–α–β motifs. The two metal ions are bridged monodentately by Asp164. The iron is further coordinated by Tyr167, His325, and Asp135, and the zinc by His286, His323, and Asn201. The active‐site structure is consistent with proposals on the mechanism of phosphate ester hydrolysis by nucleophilic attack on the phosphate by an Fe(III)‐coordinated hydroxide ion. Protein isolation, biological functions, sequences, activity, comparison of mammalian and plant PAPs, and the functional aspects of both types are discussed extensively.
Nitrogenase
Authors: Schmid Benedikt , Chiu Hsiu‐Ju , Ramakrishnan Vijay , Howard James B , Rees Douglas C 
Published: December 2011

AbstractNitrogenase catalyzes the enzymatic reduction of atmospheric dinitrogen to ammonia during the process of biological nitrogen fixation. Nitrogenase consists of two component metalloproteins, the iron (Fe‐) protein and the molybdenum‐iron (MoFe‐) protein, that together mediate the ATP‐hydrolysis–dependent reduction of substrates to products. Crystallographic studies have established the structures of the component proteins and the associated complex metallocenters of nitrogenase, including the iron‐molybdenum cofactor that provides the active site for substrate reduction and the P‐cluster that participates in electron transfer between the Fe‐protein and MoFe‐protein. Striking parallels are evident in the interaction of the nucleotides with the Fe‐protein and with a broad class of nucleotide‐binding proteins involved in signal and energy transduction processes. Together with kinetic, spectroscopic, and synthetic model compound studies, these structures provide a framework for addressing the mechanism of substrate reduction by nitrogenase.
Formaldehyde Ferredoxin Oxidoreductase
Authors: Roy Roopali , Dhawan Ish K , Johnson Michael K , Rees Douglas C , Adams Michael WW 
Published: December 2011

Abstract

Formaldehyde ferredoxin oxidoreductase (FOR) is a homotetramer where each subunit contains a [4Fe–4S] cluster and a mononuclear tungsten atom coordinated by the dithioline groups of two pterin molecules. It is a member of a family of five closely related tungstoenzymes found in organisms that grow at high temperatures in marine volcanic vents. FOR catalyzes the two‐electron oxidation of its aldehyde substrate to the corresponding acid with the concomitant reduction of ferredoxin, its physiological electron acceptor. FOR oxidizes short chain C
1
‐C
4
aldehydes as substrates but has the highest affinity for C
4
‐C
6
di‐ and semialdehydes. The enzyme is proposed to have a role in peptide metabolism.