bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hybrid Cluster Protein
Authors: Bailey Susan , Cooper Serena J , Hagen WF , Arendsen AF , Lindley Peter F 
Published: April 2006

Abstract

Genes encoding hybrid cluster proteins (HCPs) are widespread among bacterial and archaeal species and are found within the nitrate assimilation gene region. The crystal structure of HCP from

Desulfovibrio vulgaris

(Hildenborough) reveals two 4Fe clusters with an edge‐to‐edge distance of 10.9 Å. The first cluster is a conventional [4Fe4S] cubane cluster. The second cluster has an unusual asymmetric structure and has been named the hybrid cluster to reflect the variety of protein ligands. Both the hybrid cluster and the cubane cluster give rise to unusual EPR signals and the hybrid cluster has four stable oxidation states. The physiological role of HCP is currently uncertain, although HCP from

Rhodobacter capsulatus

catalyzes hydroxylamine reduction, suggesting a role in the assimilation of hydroxylamine.
Naphthalene 1,2‐Dioxygenase
Authors: Ramaswamy S 
Published: April 2006

AbstractNaphthalene 1,2 dioxygenase (NDO) belongs to the Rieske non‐heme iron oxygenase (RO) family of enzymes. ROs catalyze the first step in the break down of several toxic aromatic compounds and play a key role in global carbon recycling. NDO is an α3β3type enzyme, with one Rieske iron–sulfur cluster and a catalytic mono‐nuclear iron center in every α subunit. They carry outcis‐dihydroxylation, mono‐hydroxylation, sulfoxidation, and demethylation reactions, amongst other reactions on a wide variety of substrates. Yet, the reactions catalyzed by these enzymes are very regio‐ and stereospecific. The article focuses on the structure–function relationship of ROs with NDO as the model.
Protocatechuate 3,4‐Dioxygenase
Authors: Ohlendorf Douglas H , Vetting Matthew W 
Published: April 2006

Abstract

A key step in the degradation of aromatic compounds in the biosphere is the ring‐opening step. Intradiol dioxygenases typically use a nonheme ferric iron to activate the substrate for an electrophilic attack by molecular oxygen to cleave catechol derivatives between the vicinal hydroxyls. Protocatechuate 3,4‐dioxygenase (PCD) has been the most thoroughly studied of the intradiol dioxygenases because of the presence of optical and electron paramagnetic resonance (EPR) spectroscopic signals. The structures of PCD from
Pseudomonas putida
and
Acinetobacter calcoaceticus
alone and in complexes with more than a dozen substrates and inhibitors have been used to visualize steps in substrate binding and ligand dissociation.
DeacetoxycephalosporinCSynthase
Authors: Andersson Inger , Terwisscha van Scheltinga Anke C , Ranghino Graziella , Valegård Karin 
Published: April 2006

AbstractDeacetoxycephalosporin C synthase (DAOCS) is a mononuclear ferrous enzyme, which catalyzes the expansion of the five‐membered thiazolidine ring of the penicillin nucleus into the six‐membered dihydrothiazine ring of the cephalosporin nucleus. The reaction requires dioxygen and 2‐oxoglutarate as co‐substrates to create a reactive iron–oxygen intermediate (a ferryl or peroxo compound) from a ferrous iron in the active site of DAOCS. The extended family of 2‐oxoacid‐dependent ferrous enzymes, to which DAOCS belongs, possesses a common jelly roll β‐barrel fold with the ferrous iron ligated by two histidines and a carboxylate. Here we describe the high‐resolution structures of apo‐DAOCS, and of the enzyme in complex with Fe(II) and co‐substrate 2‐oxoglutarate. On the basis of the structures and the quantum‐chemical calculations, a mechanism is proposed whereby the reactive oxidizing species may be stored in a safe form within the enzyme to await the reaction with the penicillin substrate when it is available.
FeSuperoxide Dismutase
Authors: Miller Anne‐Frances 
Published: April 2006

AbstractIron‐containing superoxide dismutases (FeSOD) are generally dimers of identical 21‐kDa monomers, each of which contains a single active site. Each active site binds one Fe ion with roughly trigonal bipyramidal geometry, employing two His and an Asp−residue as equatorial ligands, and one more His and a coordinated solvent as axial ligands. In the course of the catalytic cycle, the Fe alternates between the +3 and +2 states, and the coordinated solvent is believed to alternate between OH−and H2O, in concert. Activity is inhibited by coordination of F−, N3−, or OH−to the oxidized state. Decreased activity at high pH reflects the latter in addition to ionization of the conserved Tyr34 in the reduced state of the enzyme at pH 8.5. Despite strong structural homologies with the manganese containing superoxide dismutases (MnSODs), many FeSODs are inactive when reconstituted with Mn, and in the case ofEscherichia coliSODs this appears to reflect, at least in part, very large differences in the reduction potentials produced by the two different SOD proteins, either Fe or Mn. Subtle changes in strengths of key active site H‐bonds could differently tune the pKs of the coordinated solvent molecule, whose participation in proton‐coupled electron transfer would in turn cause these differences to contribute to different reduction potentials, in the two proteins. Thus, SOD suggests that H‐bond mediated tuning of the protonation state and pKs of redox‐coupled coordinated solvents may serve as a means of tuning the Emin other cases as well.
Ferritin
Authors: Theil Elizabeth C 
Published: April 2006

Abstract
The ferritin superfamily of protein nanocages oxidizes ferrous ions to form hydrated ferric oxide nanominerals consisting of thousands of iron and oxygen atoms, in a central, internal cavity; varying amounts of phosphate are incorporated. Maxi‐ferritins, found in all eukaryotes and many bacteria and Archea, have diameters of 10–12 nm, constructed from 24 self‐assembling polypeptide subunits (four‐α‐helix bundles) with cavities of ∼8 nm, while mini‐ferritins in bacteria assemble from 12 subunits, are ∼8 nm in diameter, and have cavities of ∼5 nm. Ferritins function in concentrating iron for protein co‐factor synthesis (heme, FeS, etc.), recovering iron during senescence, and trapping excess iron and oxygen; mini‐ferritins, also called Dps proteins, protect bacterial DNA from chemical/physical damage during stress, in some cases binding the DNA in bacterial “chromatin” structures. There are three types of Fe–protein interaction sites in the nanocages, although when mineralized, most of the iron atoms are in the inorganic phase: 1 – catalytic sites, related by simple DNA coding changes to di‐iron oxygenase co‐factors, that couple two ferrous with oxygen atoms into diferric peroxo and ferric oxy/hydroxo mineral precursors; 2 – nucleation sites on the cavity surface that initiate mineral formation; 3 – gated pores at triple subunit junctions, that control access of reductants and chelators to recover the mineral.
Genetic regulation of ferritin synthesis is unusually complex, depending both on DNA, and, in animals, on mRNA structures that link ferritin to both antioxidant response proteins (DNA regulation) and iron trafficking proteins (mRNA regulation). The lethality of ferritin gene deletion in animals and the recent demonstration that humans absorb ferritin iron from seeds such as soybeans, illustrate the key role played by ferritins in the normal physiology of iron and oxygen. Exploring ferritin interactions with external cellular components that deliver/remove substrates/products, intra‐cage translocation of oxidation products/mineral precursors and reductants, and the potential use of the protein nanocage in materials or pharmacology are directions for the future.
Transferrins
Authors: Lindley Peter F 
Published: April 2006

AbstractThere are three major classes of transferrins; serum transferrins, ovotransferrins, and lactoferrins. The serum transferrins are responsible for the transportation of iron in serum and its delivery to cells by receptor‐mediated endocytosis. Ovotransferrins are found in the avian egg whites and are identical to their serum counterpart except for the attached carbohydrates, but cannot normally bind to mammalian receptors. Lactoferrins are found in numerous extracellular fluids and in the specific granules of polymorphonuclear lymphocytes and are known to be multifunctional. The transferrins are monomeric glycoproteins with an approximate molecular mass of 80 kDa, which adopt a bilobal structure. Each of the structurally homologous lobes contains two dissimilar domains with a single ferric iron‐binding site buried within the inter‐domain cleft. The uptake of iron is preceded by the uptake of the synergistic (bi‐)carbonate anion.
Urease
Authors: Hausinger Robert P , Karplus P Andrew 
Published: April 2006

AbstractUrease catalyzes the hydrolysis of urea by all plants and many algae, fungi, and bacteria. The homohexameric enzyme from jack bean was crystallized in 1926 and shown to contain nickel in 1975, but the structure of the dinuclear metal site was first revealed in 1995 by using the heterotrimeric [(UreABC)3] bacterial enzyme fromKlebsiella aerogenes. A carbamylated lysine side chain and a water molecule bridge the nickel ions at each active site, with Ni‐1 also coordinated to two histidine side chains plus a terminal water and Ni‐2 bound to two histidines, one aspartate, and a terminal water. The kinetic properties and structures of various inhibited or mutant forms of the protein provide insights into the mechanism of urease catalysis.
Nitrogenase
Authors: Schmid Benedikt , Chiu Hsiu‐Ju , Ramakrishnan Vijay , Howard James B , Rees Douglas C 
Published: April 2006

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.
Dissimilatory Nitrate Reductase
Authors: João Romão Maria , Miguel Dias João , Moura Isabel 
Published: April 2006

AbstractThe dissimilatory nitrate reductase (NAP) fromDesulfovibrio desulfuricansATCC 27774 catalyses the reduction of nitrate to nitrite for respiration. It belongs to the DMSO reductase family of molybdoenzymes and contains one single subunit of 755 amino acids with one molybdenum cofactor and one [4Fe–4S] cluster. The Mo atom is coordinated by twocis‐dithiolene groups of two molybdopterin guanine dinucleotides (MGD), by the sulfur atom of Cys140 and by one OH/OH2ligand. One of the MGD cofactors is directly involved in the electron transfer between the molybdenum center and the [4Fe–4S] cluster.
Formaldehyde Ferredoxin Oxidoreductase
Authors: Roy Roopali , Dhawan Ish K , Johnson Michael K , Rees Douglas C , Adams Michael WW 
Published: April 2006

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.
Aldehyde Ferredoxin Oxidoreductase
Authors: Roy Roopali , Dhawan Ish K , Johnson Michael K , Rees Douglas C , Adams Michael WW 
Published: April 2006

Abstract
Aldehyde ferredoxin oxidoreductase (AOR) is a homodimer where each subunit contains a [4Fe–4S] cluster and a mononuclear tungsten atom coordinated by the dithioline groups of two pterin molecules. The two subunits of the dimer are bridged by a monomeric iron site. AOR is a member of a family of five closely related tungstoenzymes found in organisms that grow at high temperatures in marine volcanic vents. The enzyme catalyzes the two‐electron oxidation of its aldehyde substrate to the corresponding acid with the concomitant reduction of ferredoxin, its physiological electron acceptor. The enzyme can oxidize a wide range of aliphatic and aromatic aldehydes. The most efficient substrates for AOR are acetaldehyde, isovaleraldehyde, phenylacetaldehyde, and indoleacetaldehyde, the aldehyde derivatives of some of the most common amino acids.
Plastocyanin
Authors: Freeman Hans C , Guss J Mitchell 
Published: April 2006

AbstractPlastocyanin was the first ‘blue’ or ‘type 1’ copper protein to be structurally characterized. Its biological role is to transfer electrons between photosystems II and I in oxygenic photosynthesis. Structures of plastocyanin from several plants, green algae, and cyanobacteria have been solved either by X‐ray diffraction or nuclear magnetic resonance (NMR) spectroscopy. Several of the structures have been determined with the copper atom in both the +1 and +2 oxidation states, and at several pH values. The polypeptide has a highly conserved β‐sandwich fold with a Greek‐key topology. The copper atom is coordinated by the side chains of two histidines, a cysteine, and a methionine.
Azurin and Azurin Mutants
Authors: Kolczak U. , Dennison C. , Messerschmidt A. , Canters G.W. 
Published: April 2006

AbstractAn overview is presented of the structural, spectroscopic, and mechanistic properties of the azurins, a sub‐class of the small blue copper proteins. Sequence information, methods to produce and purify the proteins, and structures as determined by X‐ray diffraction and nuclear magnetic resonance (NMR) are reviewed. The NMR and electron paramagnetic resonance (EPR) properties of the paramagnetic native and metal‐substituted azurins are discussed for wild type and variant (as obtained by site‐directed mutagenesis) forms. Electron transfer properties are discussed in the light of recent electron transfer theories.
Pseudoazurin
Authors: Adman Elinor T 
Published: April 2006

AbstractPseudoazurin is a small blue copper protein isolated from denitrifying bacteria. Its amino acid sequence and molecular structure are distinct from plastocyanin, azurin, and other members of the cupredoxin family. The Type I Cu center responsible for the intense blue color has copper with 2 His, Cys, and Met ligands in a distorted tetrahedral array. Structures of oxidized and reduced forms of the protein show small, but significant differences. Pseudoazurin transfers electrons to and from nitrite reductase. Site‐directed mutagenesis and other techniques have shown that the likely interaction surface is the hydrophobic surface to which the copper atom is closest, surrounded by positively charged residues that interact with negatively charged counterparts on its electron transfer partners.
Cucumber Basic Protein
Authors: Guss J Mitchell , Freeman Hans C 
Published: April 2006

Abstract
The ‘blue’ or ‘type 1’ copper protein family has several sub‐families. One of these sub‐families, the phytocyanins, has several sub‐sub‐families: plantacyanins, stellacyanins, and uclacyanins. The cucumber basic protein, now known as cucumber plantacyanin, was the first structurally characterized as phytocyanin. As in the archetypal ‘blue’ copper protein plastocyanin, the copper atom in cucumber plantacyanin is coordinated by the side chains of two histidines, one cysteine, and one methionine. The polypeptide has a β‐sandwich fold resembling that of plastocyanin, with the exception that one hairpin is bent at a right angle to the rest of the β‐sandwich. As a result, the copper site is more exposed to solvent than in other ‘blue’ copper proteins. The biological functions of phytocyanins are still uncertain.
Copper Nitrite Reductase
Authors: Adman Elinor T , Murphy Michael EP 
Published: April 2006

AbstractCopper nitrite reductase catalyzes the one electron reduction of nitrite to nitric oxide as part of the dissimilatory denitrification pathway. Copper nitrite reductases are found in some fungi and archaea and in many divisions of bacteria. The crystal structure of the enzyme reveals a homotrimer, each of which has a type 1 Cu site that mediates electron transfer to a type 2 Cu site. The three type 2 Cu sites are found at the subunit interfaces and catalyze nitrite reduction. Extensive mutagenic, spectroscopic, kinetic, and crystallographic studies have explored the catalytic mechanism that is proposed to include a copper–nitrosyl intermediate.
Statistical Upscaling and Downscaling in Hydrology
Authors: Blöschl Günter 
Published: April 2006

AbstractUpscaling and downscaling methods are needed to transfer information from small‐scale data to large‐scale predictions and vice versa. There are two types of methods; methods focusing on how the equations and parameters of dynamic models change with scale, which are treated in other articles of this Encyclopedia, and methods focusing on how to best represent variability statistically, which is the subject of this article. This article gives a brief overview of scale concepts and illustrates first‐order effects of upscaling and downscaling. The most important statistical upscaling/downscaling methods are then reviewed for various hydrological processes – rainfall, floods, soil moisture, and subsurface flow and transport.
Concepts of Hydrologic Modeling
Authors: Rosbjerg Dan , Madsen Henrik 
Published: April 2006

Abstract
Hydrological modeling is introduced as an indispensable tool for testing new hypotheses and obtaining a better understanding of hydrological processes and their interaction. The difficulties in developing generic model tools because of natural heterogeneity and multiscaling are emphasized, and the concept of appropriate modeling is introduced for the application of a parameter parsimonious model that ensures a realistic simulation or prediction including assessment of the uncertainty. In model development, the basic conceptualization of a model is governing the crucial choices of scale, dimension, discretization, and process delimitation. Hydrological models are classified according to their primary application area. In model calibration and validation, the use of split sampling techniques and automatic calibration procedures is underlined. The sources of model uncertainty are presented and different assessment techniques including first‐order analysis, Monte Carlo‐based methods, the GLUE framework, and Bayesian procedures are briefly introduced along with data assimilation techniques to enhance the predictive capabilities.
Upscaling and Downscaling – Dynamic Models
Authors: Wigmosta Mark , Prasad Rajiv 
Published: April 2006

AbstractTransferring information from one spatial or temporal scale to another (scaling) presents one of the most daunting scientific challenges in hydrology. This is particularly true in hydrological modeling where disparities in scale exist in nearly every phase of model development and application. This article discusses scales, hydrological processes, heterogeneity, upscaling, and downscaling as applied to dynamic hydrological modeling. It is not meant to be an exhaustive discussion covering the entire range of scale issues in hydrology, or of hydrological modeling, rather it attempts to summarize the relevant issues and illustrate some approaches using specific examples to address upscaling and downscaling in hydrological model development and application.
Hydroinformatics and its Contributions to Hydrology: From Computation to Communication
Authors: Abbott Michael B , Mynett Arthur E , O'Kane J Philip 
Published: April 2006

AbstractHydroinformatics is concerned with the application of information and communication technologies for the planning, management, and conservation of the aquatic environment. With the rapidly increasing capabilities of computer‐based systems, considerable advances were made during the past decade or more. Some historic developments are outlined in this article and the development of hydroinformatics as a sociotechnology is explained. The transition from computation to communication is illustrated by examples from present day flood simulation and flood early warning systems; emerging applications of data‐mining and evolutionary computing are demonstrated for the fields of ecohydraulics and ecohydrology. The impact of hydroinformatics on the future role of hydrology in a multiuser environment is discussed. The contours of a next (fifth) generation software systems making use of agent‐based communication over a network of computers and developers are outlined. The scope and content of all subsequent articles within this chapter are presented; these can be broadly grouped into areas of (i) physics‐based numerical modeling; (ii) data‐driven modeling and evolutionary computing; and (iii) design and decision support systems.
Shallow Water Models with Porosity for Urban Flood Modeling
Authors: Guinot Vincent 
Published: April 2006

Abstract
The modeling of urban floods has to cope with highly variable geometries and flow parameters. Among the various types of models available, distributed, physically based models offer the best insight into the processes. However, the application of such models to refined urban flood modeling is not foreseeable in the near future. An alternative approach could be to use two‐dimensional macroscopic models based on a modified version of the classical shallow–water equations, in which the fraction of the land surface occupied by the buildings is accounted for via a porosity. In such models, a cell covers part or totality of a house block. Such models provide a viable alternative to classical semidistributed models, as illustrated by a computational example on a small‐sized urban area.
Rainfall‐Runoff Modeling Based on Genetic Programming
Authors: Babovic Vladan , Keijzer Maarten 
Published: April 2006

Abstract
The runoff formation process is believed to be highly nonlinear, time varying, spatially distributed, and not easily described by simple models. Considerable time and effort has been directed to model this process, and many hydrologic models have been built specifically for this purpose. All of them, however, require significant amounts of data for their respective calibration and validation. Using physical models raises issues of collecting the appropriate data with sufficient accuracy. In most cases, it is difficult to collect all the data necessary for such a model.
By using data‐driven models such as genetic programming (GP), one can attempt to model runoff on the basis of available hydrometeorological data. This work addresses the use of GP for creating rainfall‐runoff (R‐R) models both on the basis of data alone, as well as in combination with conceptual models (i.e taking advantage of knowledge about the problem domain).