bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fuel Cells: Direct Ethanol
Authors: Chia Zhi Wen , Lee Jim Yang 
Published: December 2011

AbstractAlcohols, and methanol in particular, have been investigated as potential fuels for use in direct fuel cells for mobile applications. However, the fuel cell community is now turning its attention to ethanol as the fuel of choice because of benefits such as renewability and low fuel toxicity. Nonetheless, the direct ethanol fuel cell (DEFC) has several technological problems that are more tenacious than the direct methanol fuel cell (DMFC). Among them, the slow anode kinetics presents the greatest challenge since it results in poor fuel cell performance in applications. Current anode catalysts, which are primarily an extension of the DMFC anode catalysts, do not prove to be very effective in delivering high current densities or sufficiently high conversions. Thus, there is a need to modify existing catalysts or to develop new catalysts that are able to oxidize ethanol molecules more effectively and more completely. This article provides a succinct account of the various catalysts currently in use at the anode and cathode of a DEFC, with emphasis on the anode catalysts used in an acidic environment, which require the most improvement. The use of cocatalysts, promoters, and catalyst support as well as catalysts used for ethanol oxidation in alkaline media are also briefly discussed.
Fuel Cells: Molecular Catalysis
Authors: Oyaizu Kenichi 
Published: December 2011

Abstract

Popularization of fuel cells has been impeded by the low activity of electrocatalysts for the O
2
reduction reaction that involves the four‐electron transfer step. Platinum nanoparticles have been considered the best cathode catalyst toward the reduction of O
2
by four electrons into H
2
O. However, platinum is an expensive and limited resource, and it is important to find platinum‐free catalysts. This article provides a review on the recent studies on various types of platinum‐free catalysts such as nonprecious metal nanoparticles and alloys, carbon‐based catalysts, and metal complexes, focusing on the role of structure of the catalytically active site of metal complex catalysts in the OO bond scission to produce H
2
O. Emphasis is placed on the studies on cobaltporphyrins, which have been demonstrated to serve as the catalysts for the four‐electron reduction of O
2
, especially in the forms of dicobalt cofacial porphyrins and multinuclear cobaltporphyrins. Simple metalloporphyrins with spontaneous face‐to‐face aggregation properties have also been examined as a catalyst. For practical application as fuel cell cathode catalysts, it is necessary to use metalloporphyrins dispersed on carbon particles with high surface area. We summarize the recent developments on porphyrin‐based catalysts and the attempts to prepare face‐to‐face aggregates of metalloporphyrins adsorbed dispersively on carbon black. A design principle for the active site to allow the O
2
reduction at positive potentials is proposed.
Photo–Initiated Electron–Transfer at the Interface between AnataseTiO2Nanocrystallites and Transition–Metal Polypyridyl Compounds: Recent Advances
Authors: Ardo Shane , Meyer Gerald J. 
Published: December 2011

AbstractMolecular control of solar light harvesting and interfacial charge transfer at mesoporous, nanocrystalline semiconductor thin films are described. Light absorption by transition‐metal coordination compounds anchored to wide band‐gap semiconductors can initiate electron‐transfer processes that ultimately reduce the semiconductor and oxidize the coordination compound. Such photo‐induced charge separation is a key step for solar energy conversion. Three different interfacial charge‐separation mechanisms are discussed in addition to regeneration processes wherein a mobile donor donates an electron to the oxidized coordination compound. Inorganic chemistry plays a central role in this approach to solar energy conversion, which may ultimately be optimized for practical applications.
Zn‐Dependent Medium‐Chain Dehydrogenases/Reductases
Authors: Meijers Rob , Cedergren‐Zeppezauer Eila S 
Published: December 2011

AbstractMedium‐chain dehydrogenases/reductases (MDRs) have about 350 to 390 amino acids and belong to a large superfamily of proteins including the Zn‐dependent alcohol dehydrogenases (ADHs) and several other Zn‐dependent activities. They are dimers or tetramers and utilize either NADH or NADPH as electron carriers referred to as cofactors. The oxidation/reduction process is a 2‐electron/1‐proton (hydride ion, H−) transfer between substrate and cofactor. The compounds oxidized or reduced by these enzymes vary considerably in structure ranging from small primary and secondary alcohols/aldehydes/ketones (aliphatic and aromatic), sugars (sorbitol/fructose, glucose) to large substances like fatty acids, steroids, and retinoids. ADHs are widely distributed in nature and some MDR members are found in all species. An essential Zn ion at the active site is common to all MDRs but some members have two zinc ions per subunit.The 3D Structures of Zn‐dependent MDRs are highly similar and they essentially have the same polypeptide fold. The low sequence identity found sometimes could not immediately reveal this close structural relationship. Now numerous structures have been examined indicating that the evolutionary strategy for MDRs has been to vary amino acids preferably at the reaction center and further away in the substrate binding area. Thus, the size and shape of the substrate channel is adapted for small or large substrates, hydrophilic or hydrophobic substances, modifications attained via few mutations, or significant deletions/additions of amino acids. A further opportunity to create multiplicity has been to vary the control mechanism for the protein conformation change and the oligomeric state. Some enzymes undergo significant structural changes upon cofactor binding, while others do not.A transition state intermediate of NADH in complex with horse liver alcohol dehydrogenase, resolved to atomic resolution (≈1 Å), has revealed structural modifications of the cofactor associated with the activation process for hydride transfer. This involves an OH−pyridine ring adduct, connected to the zinc center. The distortion of the nicotinamide at the enzyme site, affected by the presence of the negatively charged oxygen ligand, influences three parameters: (i) the puckering of the ring, (ii) a deviation from a standard carbon–carbon double bond length, and (iii) accumulation of negative charge at the C4 atom promoting hydride transfer. The active site Zn‐center of this large enzyme group shows great flexibility with respect to metal–ligand geometry and dynamics. Structural and spectroscopic evidence suggest that Zn‐dependent MDRs should be included in the general family of Zn‐enzymes, which require water and hydroxide ion as reactants during catalysis.
Carbonic Anhydrases (α‐Class)
Authors: Duda David M , McKenna Robert 
Published: December 2011

AbstractCarbonic anhydrases (CAs) are zinc metalloenzymes that catalyze the hydration of carbon dioxide and the dehydration of bicarbonate:\catcode`@=11\newdimen\budimen\newbox\budbox\def\rrlh@#1{\vcenter{\parindent=0pt\hbox{\ooalign{\raise0.21em\hbox to 2pc{$#1\lhupfill$}\crcr$#1\rhdownfill$}}}}\def\lhupfill{\m@th\mathrel\leftharpoonup\mkern-6mu \cleaders\hbox{$\mkern-2mu\mathord-\mkern-2mu$}\hfill \mkern-6mu\mathrel-}\def\rhdownfill{\m@th\mathrel-\mkern-6mu \cleaders\hbox{$\mkern-2mu\mathord-\mkern-2mu$}\hfill \mkern-6mu\mathrel\rightharpoondown}\def\lrharpoonsfill{\vcenter{\parindent=0pt\ooalign{\raise0.21em\hbox to \budimen{$\lhupfill$}\crcr\hbox to \budimen{$\rhdownfill$}}}}\def\leftrighthfill#1{\mathrel{\lower0.1em\hbox{\ooalign{\raise0.21em\hbox to #1{$\lhupfill$}\crcr\hbox to #1{$\rhdownfill$}}}}}\catcode`@=12$\hbox{CO}_{2} +\hbox{H}_{2}\hbox{O}{\leftrighthfill{2pc}}\hbox{HCO}{_{3}}^{-} + \hbox{H}^{+}$, a process that has physiological importance in respiration, acid–base homeostasis, photosynthesis, and biosynthetic pathways. The α‐class of CA (and the CA domains in more complex isoforms) is monomeric with a molecular weight of approximately 30 kDa. At present, 14 isoforms of the α‐class are known with varying tissue distributions and catalytic activity. The catalytic turnover number of CAs varies from the maximal rate of 106s−1for isozyme II to 103s−1for isozyme III. The central structural motif of the α‐CAs can be described as a 10‐stranded twisted β‐sheet, which is flanked by seven α‐helices. The active‐site cavity consists of a single zinc ion tetrahedrally coordinated by three histidine residues (His94, 96, and 119) and a bound water molecule. In most of the α‐CAs, the resultant proton formed by the dehydration reaction of bicarbonate is transferred to bulk solution through the formation of a proton wire, mediated by residue His64, that lies at the mouth of the active site. Known inhibitors of CAs have been shown to bind to the metal ion and displace the zinc‐bound water, whereas activators have been shown to bind at the entrance of the active site and mimic the characteristics of the proton‐shuttling residue His64.
Carbonic Anhydrases (β‐Class)
Authors: Yamashita Eiki , Mitsuhashi Satoshi , Tsukihara Tomitake 
Published: December 2011

Abstract

Carbonic anhydrase (CA) catalyzes the reversible hydration of CO
2
to HCO
3
−
in aqueous solution. CAs are divided into three distinct classes (α‐CAs, β‐CAs, and γ‐CAs) that have little sequence homology to one another. β‐CA plays an essential role in photosynthesis, by concentrating CO
2
in the proximity of ribulose bisphosphate carboxylase/oxygenase for CO
2
fixation. Little is known about the physiological roles performed by β‐CA in nonphotosynthetic organisms.

Two homologous motifs are repeated in the

Porphyridium purpureum

β‐CA polypeptide (55 kDa). Each motif is composed of two components: an α/β domain and an N‐terminal arm. The two motifs in a monomer are related by a pseudo twofold axis. The two monomers form a dimer with pseudo 222 symmetry.

Escherichia coli

β‐CA and

Pisum sativum

β‐CA are composed of a tetramer and an octamer respectively. The dimer of

P. purpureum

β‐CA resembles a tetramer of

E. coli

β‐CA. A dimer of

P. sativum

β‐CA, which resembles the monomer of

P. purpureum

β‐CA, is the basic building block of the octamer.

Both β‐CAs from

Methanobacterium thermoautotrophicum

and

E. coli

have one zinc atom per monomer, while β‐CA from

P. purpureum

contains two zinc atoms per monomer. The catalytic zinc atom at each catalytic site is coordinated by four ligands in a tetrahedral manner. A possible catalytic mechanism of β‐CA based on the structure of

P. purpureum

CA is proposed.
GTPCyclohydrolaseI
Authors: Nar Herbert 
Published: December 2011

AbstractGTP Cyclohydrolase I (GTP‐CH‐I) is a homodecameric protein complex of approximately 250 kDa molecular weight and it catalyzes the conversion of guanosine triphosphate (GTP) to dihydroneopterin triphosphate (H2NTP), the committing step in the biosynthesis of pteridines.The GTP‐CH‐I monomer forms a compact single‐domain α + β structure containing a predominantly α‐helical N‐terminal subdomain and a sequential, four‐stranded, antiparallel β‐sheet in the C‐terminal subdomain. Association to dimers occurs along an antiparallel α‐helix pair. Decamers are formed by five dimers through the association of the respective four‐stranded, antiparallel β‐sheets to two 20‐stranded β‐barrel structures in each pentameric substructure of the active enzyme complex.The active site is located at the interface of three monomers and is composed of a 12‐Å deep cavity that contains a guanine recognition motif at its bottom and a zinc binding site. The metal ion is coordinated by two cysteines and a histidine residue. A water molecule completes the coordination environment of the zinc in the resting state of the enzyme.The role of the Zn(II) ion in catalysis is probably similar to its role in Zn(II)‐dependent proteinases and involves water activation in the guanine hydrolysis steps of the reaction sequence.The product is formed by a subsequent Amadori rearrangement and ring closure. These steps involve acid–base catalysis and are probably performed by strictly conserved amino acid side chains in the vicinity of the zinc binding site.
Cocatalytic Zinc Sites
Authors: Auld David S 
Published: December 2011

AbstractCocatalytic zinc sites occur in enzymes where two or three metals are closely grouped to bring about catalysis. There are over four dozen representatives of this type of zinc site with the great majority belonging to the Class III hydrolases. A novel feature of these sites is the bridging of two of the metal sites by a side chain moiety of a single amino acid residue, such as the ring nitrogens of the imidazole group of histidine or the carboxylate oxygens of aspartic acid, glutamic acid, or of a carboxylated lysine, LysCO2−. Such an interaction requires the metals to be in close proximity to each other. The ligands to cocatalytic zinc sites often come from nearly the entire length of the protein, indicating that the metal sites may be important to the overall fold of the protein as well as to catalytic function. The secondary structure of the protein plays a major role in providing the ligands to these sites. In most cases, ligands are provided by amino acids residing within one or two residues before or after a β‐sheet or an α‐helix. The zinc ions are often penta‐coordinate and arranged in a trigonal bipyramidal geometry. The bridging amino acids and H2O probably have critical roles in catalysis. Their dissociation from either metal atom during catalysis will change the charge on the metal promoting its action as a Lewis acid or allowing interaction with an electronegative atom of the substrate. Thus, it can be envisioned for hydrolytic enzymes that substrate binding involves one zinc site acting as a template for substrate binding, while the other zinc site provides hydroxide for nucleophilic attack on the sp2center of the ester or amide bond of the substrate. In the next step, the roles of the metals can be reversed. In this manner, the metal atoms and their associated ligands play specific roles in each step of the reaction that works to bring about catalysis. The ligands in these sites, in particular the histidines, are often involved in further hydrogen‐bonding interactions with other amino acids. These interactions should effect the charge on the metal and the stability of the metal complex, thus fine‐tuning catalysis and the stability of the metal sites.
Metallothioneins
Authors: Zangger Klaus , Armitage Ian M 
Published: December 2011

AbstractMetallothioneins (MTs) are small cysteine‐rich polypeptides that bind a series of metal ions and have been found in a variety of animals and even some plants. In animals, the different isoforms of MTs occur in tissues ranging from liver and kidney (isoforms 1 and 2) to the brain (isoform 3) and stratified epithelia (isoform 4). Today, the term metallothionein (MT) is used to denote ‘polypeptides resembling equine renal metallothionein in several of their features.’ On the basis of differing amino acid sequences and structural characteristics, MTs have been subdivided into three classes (I, II, and III), the first of which describes proteins with locations of cysteines closely related to those in equine renal metallothionein. Proteins with cysteine locations only distantly related to equine renal metallothionein are described in class II and atypical, nontranslationally synthesized metal‐thiolate polypeptides are contained in class III. Here we will focus on the structurally well‐characterized class I MTs, which bind zinc or its isomorphous metal‐ion substitute, cadmium. Specifically, these are MT2 from rabbit, rat, and human; MT1 from mouse, blue crab, and lobster; mouse MT3 and sea urchin MTA. In addition, the only structurally characterized class II zinc/cadmium‐containing MT, the cyanobacterial Smta will be discussed.With the exception of the prokaryotic Smta, all these proteins show a dumbbell‐shaped two‐domain structure with six (blue crab and lobster MT1) or seven (all others) divalent metals bound in two separate metal–cysteine clusters. Although the exact physiological function of MTs is still not clear, a number of presumed functions have been put forward. In addition to the originally proposed dual role of MTs in zinc and copper homeostasis and heavy metal detoxification, they are also thought to be involved in the stress response to reactive oxygen species and possibly play a role at inflammatory sites as scavengers of nitric oxide.
RINGDomain Proteins
Authors: Dominguez Cyril , Folkers Gert E , Boelens Rolf 
Published: December 2011

AbstractThe RING domain is a cysteine‐rich sequence motif that can bind two zinc atoms. In the canonical RING motif, also called the C3HC4 motif, one zinc ion is bound to four cysteines, and the other ion to three cysteines and a histidine. The tetrahedral coordination is atypical and referred to as a ‘cross‐brace’ motif. There are now more than 380 RING motifs identified in the human genome. The RING domain has been shown to mediate a crucial step in the ubiquitination pathway that targets protein substrates for degradation by the 26 S proteasome. This pathway involves three enzymes, and the RING finger proteins have been classified in this scheme as ubiquitin ligases. There are actually nine structures of RING domains solved by X‐ray and NMR. The βαβ fold of the RING domain is conserved among all structures. The structures of RING domains in complex with other proteins involved in the ubiquitination pathway provide considerable insight into the molecular basis of ubiquitination. Recently, ubiquitination has been shown to be not only a simple protein removal system but also an indispensable regulatory process. This is underscored by the observation that many diseases, such as cancer and Parkinson's disease, are due to mutations in RING domains that prevent an efficient ubiquitination and degradation process. In this review, we compare the different structures of RING domains, analyze their functional aspects through structural information of RING domains in complex with other proteins, and describe medical aspects of RING finger proteins involved in cancer and Parkinson's disease.
FYVE
Domain
Authors: Kutateladze Tatiana G , Overduin Michael 
Published: December 2011

Abstract
The FYVE domain is a 65‐residue module that contains two tetrahedral zinc coordination centers. The zinc ions are bound by eight cysteine residues in a cross‐braced topology, providing structural stability. The FYVE domain is usually present as a single module or, more rarely, as a tandem repeat in eukaryotic proteins involved in a variety of biological processes including membrane trafficking and phosphoinositide metabolism. The biochemical function of the FYVE domain is the specific recognition of phosphatidylinositol 3‐phosphate [PtdIns(3)P], a phospholipid that is most concentrated in endocytic membranes. Structures, zinc coordination, and PtdIns(3)P binding modes of three FYVE domains have recently been characterized, providing mechanistic insights into their contributions to endocytosis, signal transduction, and cytoskeletal organization.
Astacin
Authors: Stöcker Walter , Yiallouros Irene 
Published: December 2011

AbstractThe mono‐zinc endopeptidase astacin (EC 3.4.24.21) is a prototype for the astacin family and for the metzincin superfamily of metalloproteinases. Some astacins are digestive enzymes of invertebrates, but the majority serve functions during embryonic development, pattern formation, and epithelial differentiation throughout the animal kingdom. The catalytic protease domain of the astacins is topologically similar to the corresponding domains of the matrix metalloproteinases (MMPs), the adamalysins/reprolysins/ADAMs (a disintegrin and metalloprotease), the bacterial serralysins, and several other groups of zinc peptidases. They have in common a conserved zinc binding sequence, HEXXHXXGXXH, containing three histidines and a catalytically important glutamic acid residue, which acts as a general base during catalysis. Furthermore, there is a strictly conserved methionine‐containing turn structure beneath the active site, the Met‐turn, which gave rise to the designationmetzincinsfor this superfamily of metalloproteins. In astacin, in addition to the three histidine residues of the zinc binding motif, the metal is ligated by the Glu93‐bound ‘activated’ water and by Tyr149, positioned in the Met‐turn, resulting in a trigonal bipyramidal coordination sphere. This overview treats the structural basis for the function of astacin‐like proteases, including proenzyme activation, cleavage specificity, substrate and inhibitor kinetics, catalysis, and metal binding. It also pinpoints shared commonalities and subtle differences between astacin and other metzincins.
Matrix Metalloproteinases
Authors: Bode Wolfram , Maskos Klaus 
Published: December 2011

AbstractThe matrix metalloproteinases (MMPs) constitute a family of (in man) 23 different extracellular soluble/cell surface–anchored multidomain zinc endopeptidases, all of which exhibit a common catalytic domain of a metzincin‐like topology, that is, possess a Met‐containing tight turn and carry an extended His‐Glu‐Xaa‐Xaa‐His‐Xaa‐Xaa‐Gly‐Xaa‐Xaa‐His zinc‐binding consensus segment enwrapping the catalytic zinc, with the three histidine imidazole side chains and a nucleophilic water ligating the catalytic zinc, and the glutamine side chain presumably acting as a proton shuttle. The MMPs are involved not only in extracellular matrix degradation but also in a number of other biological processes such as shedding of membrane‐bound growth factor and cytokine precursors, pro‐proteinase activation, or inhibitor inactivation. Normally, their proteolytic activity is precisely regulated by endogenous protein inhibitors, in particular, by the tissue inhibitors of metalloproteinases (TIMPs). Disruption of this balance results in serious diseases such as arthritis, tumor growth, and metastasis, thus rendering the MMPs attractive targets for inhibition therapy. Individual vertebrate MMPs have been named according to their presumed substrates or classified by sequential (chronological) numbers, which run from MMPs 1 to 28. These MMPs are synthesized with an N‐terminal signal sequence, a pro‐domain, and a catalytic domain containing the catalytic zinc, a structural zinc, and up to three calcium ions. Additionally, most MMPs possess a C‐terminal ion containing hemopexin‐like domain, which, in the membrane‐bound MMPs, is followed by a transmembrane helix and a cytoplasmic domain, or a glycosil phosphatidyl inositol (GPI) anchor. This overview presents common and special structural features of the MMPs, in particular of their catalytic domain.
Bacillus SubtilisD‐AminopeptidaseDppA
Authors: Remaut Han , Goffin Colette , Frère Jean‐Marie , Beeumen Jozef Van 
Published: December 2011

AbstractTheD‐aminopeptidase DppA, identified inBacillusspecies, represents the prototype of a separate family of dinuclear zinc proteases. The catalytic domain of the enzyme comprises a Rossmann‐like α/β/α‐fold that coordinates two zinc ions near the C‐terminal edge of a six‐stranded parallel β‐sheet. Despite the lack in sequence and structural homology, the zinc coordination is highly similar to that found in established dinuclear zinc proteases. Furthermore, DppA forms a decameric molecule that encloses a central cavity that sequesters the 10 active sites. The architecture of the complex strongly resembles that found in a group of enzymes known as self‐compartmentalizing proteases, with bacterial and eukaryotic proteasomes as most characteristic examples.