bluuebunny/crossref_metadata_2025 huggingface dataset:
Thermolysin
Authors: Matthews Brian W
Published: April 2006

Thermolysin is a thermostable, zinc‐dependent endopeptidase. It is the prototypical member of the very large family of proteases characterized by the HEXXH sequence motif in which the two histidines coordinate the zinc ion and the glutamic acid is critical for catalysis.
Leishmanolysin
Authors: Metcalf Peter , Etges Robert
Published: April 2006

Leishmanolysin is a major surface antigen of the promastigote insect form of the parasitic protozoanLeishmania, and is thought to play a role preventing complement‐mediated lysis after infection of the mammalian host by the sand fly vector. Leishmanolysin is a ∼52 kDa membrane‐bound neutral zinc proteinase of the metzincin class, with some resemblance to collagenase in the active site region. Leishmanolysin can be inhibited by collagenase inhibitors but it does not cleave native collagen. Thein vivosubstrates have not been determined. The crystal structure, determined using protein purified fromLeishmania majorpromastigotes, revealed three domains where the N‐terminal domain has a similar fold to the catalytic domains of zinc proteinases and the central and cysteine‐rich C‐terminal domains have novel folds. The active site is located in a cleft between the N‐terminal and central domains. The molecule is attached to the outer membrane of the promastigote via a C‐terminal‐linked GPI anchor.
3
D
Structures of the Calcium and Zinc Binding
S
100 Proteins
Authors: Fritz Günter , Heizmann Claus W
Published: April 2006

S100 proteins are involved in many cellular processes such as cell growth and motility, cell cycle regulation, transcription, and differentiation. Twenty members have been discovered so far, and altogether, S100 proteins represent the largest subgroup within the EF‐hand Ca
2+
‐protein family. In resting cells, S100 proteins are localized in specific cellular compartments from which they relocate upon activation, hereby transducing the Ca
2+
/Zn
2+
signals by interacting with various target proteins. Some members are even secreted from cells exerting extracellular, cytokine‐like activities by interacting with the surface receptor RAGE.
Dockerin Domains
Authors: Volkman Brian F , Lytle Betsy L , David Wu J H
Published: April 2006

Bacterial protein domains known as dockerins serve as anchoring or tethering modules for the assembly of large extracellular cellulase complexes called cellulosomes. Dockerins function through interactions with another class of protein‐interaction module, the cohesins, and both domain families are currently divided into two subclasses (type I and type II) originally based on binding specificity. Dockerin sequences contain a pair of 22‐residue motifs with homology to calcium‐binding loops of the EF‐hand family. When exposed to calcium, the dockerin adopts a novel fold distinct from EF‐hand proteins that binds its cognate cohesin with high affinity. Conversely, in the absence of calcium, the dockerin domain is unfolded and does not bind cohesin. Thus, dockerin domains serve as calcium‐regulated mediators of protein complex formation. Analysis of conserved sequence features in the context of the three‐dimensional dockerin structure may identify elements that confer class and species specificity of dockerin–cohesin binding reactions.
Calsequestrin
Authors: Kang ChulHee
Published: April 2006

The contraction/relaxation of the muscle cell is controlled by the transient increase/decrease of Ca
2+
concentration. A large fraction of this Ca
2+
is stored in and released from the sarcoplasmic reticulum (SR) by the presence of high concentrations of an acidic protein, calsequestrin, in the lumen of the junctional terminal cisternae of SR. Calsequestrin binds and releases large quantities of Ca
2+
ion rapidly: about 40 to 50 ions per molecule with a binding constant of approximately 1 mM under physiological conditions. The cation binding by calsequestrin is nonspecific and the Ca
2+
binding sites incorporate the numerous acidic residues that comprise over one‐third of the total residues. The crystal structure of calsequestrin shows that it is made up of three domains, each with a thioredoxin fold. Ca
2+
ions are bound on the protein surface and between domains. Two distinct dimerization contacts in calsequestrin crystals suggested a mechanism for Ca
2+
regulation resulting from the occurrence of coupled Ca
2+
binding and protein polymerization. Ca
2+
‐induced formation of one contact was proposed to lead to dimerization followed by Ca
2+
‐induced formation of the second contact to bring about polymerization. Strong cooperative calcium binding accompanies the polymerization of calsequestrin into insoluble, extended, and often needle‐like structures. The polymerization of calsequestrin also provides a highly charged surface onto which calcium is adsorbed. A sparingly soluble ion such as Ca
2+
would tend to spread over the surface of the polymer, forming a readily exchangeable film. The propensity of Ca
2+
‐bound calsequestrin to form linear structures would make Ca
2+
dissociation and diffusion a more rapid event.
The Superfamily of Cadherins: Calcium‐Dependent Cell Adhesion Receptors
Authors: Ahrens Thomas , Stetefeld Jörg , Häussinger Daniel , Engel Jürgen
Published: April 2006

Specific cell–cell contacts are important in tissue morphogenesis, development, and during signal transduction of vertebrates as well as invertebrates. Cadherins are cell‐surface transmembrane receptors that mediate such specific, homotypic cell–cell adhesion. The adhesive activity of cadherins requires calcium binding by the ectodomain of the protein. The extracellular part of cadherins is composed of different numbers of individually folding cadherin repeats (CAD). Calcium binding pockets are located in the interdomain sections and conserved peptide sequences in consecutive domains are involved in coordination of three calcium ions per binding pocket. Low‐ and high‐affinity calcium binding sites have been detected and binding constants in the micromolar (Kd = 30–330 µM) to millimolar (Kd = 2 mM) range were determined. When calcium is added to purified cadherin ectodomains, rigidification and conformational changes are observed, exposing interaction surfaces that are involved in homoassociation of cadherins. This review summarizes electron micrographic, crystallographic, and recent NMR data analyzing the molecular details and functional consequences of calcium binding by cadherins.
Mitochondrial Cytochrome

c

Oxidase
Authors: Yoshikawa Shinya , Shinzawa‐Itoh Kyoko , Yamashita Eiki , Tsukihara Tomitake
Published: April 2006

Cytochrome
c
oxidase reduces molecular oxygen (O
2
) to water (coupled with proton pumping) at its O
2
reduction site composed of an iron ion (heme
a
3
) and a copper ion (Cu
B
) by electrons transferred from cytochrome
c
in the intermembrane space by Cu
A
and heme
a
in the enzyme protein and by protons from the matrix space. Mitochondrial cytochrome
c
oxidase, isolated from bovine heart muscle as early as in 1941, was crystallized to determine the X‐ray structure at 2.3/2.35 Å resolutions in the fully oxidized/reduced states in 1998, showing 13 different subunits and Cu
B
, liganded with three histidine imidazole groups in a trigonal‐planer coordination in the fully reduced state. A tyrosine phenol group is fixed close to the O
2
reduction site with a covalent link with one of the three imidazole groups. This O
2
reduction site structure suggests that Fe

a
3

O
2
and Fe

a
3

OOH are stable and unstable, respectively, to form FeO as the second intermediate in the O
2
reduction process, consistent with the resonance Raman results for the process. A fairly big redox‐coupled X‐ray structural change in an aspartate (Asp51) located near the intermembrane surface of the enzyme molecule suggesting a large redox‐coupled pKa change in Asp51 and a hydrogen bond network connecting Asp51 with the matrix surface indicate that Asp51 is the site for proton pumping. A peptide bond in the hydrogen bond network facilitates the unidirectional proton transfer through the hydrogen bond network up to Asp51.
ba3‐CytochromecOxidase FromThermus Thermophilus
Authors: Than Manuel E , Soulimane Tewfik
Published: April 2006

ba3‐Cytochromecoxidase fromThermus thermophilusis a terminal enzyme of respiration that catalyzes the reduction of dioxygen to water. It is produced at low oxygen tension and is one of the most divergent members of the heme–copper oxidase superfamily.ba3‐Oxidase has been isolated fromT. thermophilusmembranes, purified and characterized using several biochemical and biophysical techniques. Its crystal structure has been solved at high resolution. The current review summarizes the results on structure and function relationship ofba3‐oxidase that have been elucidated during the last decade.
Hybrid Cluster Protein
Authors: Bailey Susan , Cooper Serena J , Hagen WF , Arendsen AF , Lindley Peter F
Published: April 2006

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

Naphthalene 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

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

Deacetoxycephalosporin 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

Iron‐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

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

There 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

Urease 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

Nitrogenase 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

The 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

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

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

Plastocyanin 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

An 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

Pseudoazurin 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

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

Copper 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

Upscaling 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

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

Transferring 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

Hydroinformatics 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

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

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).
Numerical Flood Simulation
Authors: Stelling Guus S , Verwey Adri
Published: April 2006

This contribution describes the state of the art of numerical flood simulation, in particular, the models based upon hydraulic laws. Both theory and practical aspects are discussed. In the introduction, various types of applications of these models are listed with their requirements in terms of robustness, accuracy, speed of operation, and engineering staff time. After introducing the 1D Saint Venant unsteady flow equations and describing the meaning of their terms, the concepts of kinematic and diffusive wave approximations are discussed. These provide better ways of understanding the physical behavior of flood waves and demonstrate the link between hydraulic and hydrologic flood propagation models. Numerical discretization of the unsteady flow equations is introduced with special attention given to the correct and robust modeling of rapidly varying flow, as occurring around hydraulic structures, discontinuities in channel beds, and flood‐generating breaches of river embankments and reservoir dams. Proceeding with the 2D flow description and its numerical discretization principles, the emergence of hybrid 1D/2D models is discussed with their different options of linking model components of flood‐prone areas. The quality of models also relies very much on the availability of detailed and correct data. This contribution briefly introduces the impact of new data collection techniques on numerical flood model schematization.
Global Energy and Water Balances
Authors: Ohmura Atsumu
Published: April 2006

The earth's energy and water balances are summarised with the most recent observational and computational results. A special reference is given to the earth's surface. After a brief discussion of the limits of the observational accuracy, the author explains the mean state of the energy balance starting with the sun, through the atmosphere and to the earth's surface. The main contents are the Total Solar Irradiance (earlier called solar constant) and its variability, the climatic effect of the earth's orbital change, extinction processes of solar radiation in the atmosphere, the distributions of solar radiation on the earth's surface, reflection and albedo, terrestrial radiation from the atmosphere and the earth's surface, net radiation, sensible and latent heat fluxes, subsurface heat flux, and latent heat of melt. The distributions of the individual components are presented in maps. The important points of geographical distributions and energy fluxes are explained in the text. The energy balance climatology in the present article differs from earlier works mainly on three topics: 1) larger atmospheric absorption of solar radiation; 2) smaller solar radiation on the earth's surface; and 3) larger terrestrial counter radiation. These new situations are the results of the recent advances in spectrometry, observational technology both on the earth's surface and in the space, and also in computational skill. Therefore, the historical development of the understanding of the earth's energy balance is added. The article ends with a brief description of the mean hydrological cycle, allowing unsteady conditions due to the melt of glaciers during the twentieth century.
Models of Global and Regional Climate
Authors: von Storch Hans
Published: April 2006

The concept of climate simulations with quasi‐realistic climate models is discussed and illustrated with examples. The relevant problem of deriving regional and local specifications is considered as well.
Precipitation Measurement: Gauge Deployment
Authors: Robinson Mark
Published: April 2006

The deployment of a network of rain gauges involves two stages: first, the broad distribution of gauges across a region or catchment and, second, the specific location of each gauge. The spatial distribution of gauges across a region will be determined by a combination of: (a) physical characteristics of the region, including the topography and the natural variability of precipitation, and (b) institutional factors, such as the purpose of the network (setting the accuracy and level of detail of data required as well as the resources available). The specific location of gauges will be determined by purely local factors, which would affect the accuracy of the measurements. These are primarily concerned with site exposure and wind effects that could lead to errors in catch and make the data unrepresentative of a larger area.
Evaporation Measurement
Authors: Verhoef Anne , Campbell Claire L
Published: April 2006

This chapter summarises the practical methods available to estimate evaporation,
E
. It describes the background of methods based on soil physical, micrometeorological and plant physiological concepts. The most appropriate method will mainly depend on required spatial and temporal scales of
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, accuracy needed, and the available resources (financial and manpower). These issues are taken into account during the discussion.
Actual Evaporation
Authors: Dolman Albertus Johannes
Published: April 2006

Actual evaporation concerns the evaporation from natural surfaces. Globally actual evaporation from the land amounts to around 71 103 km3year−1. Measurement of evaporation occurs by water balance techniques or directly through micrometeorological techniques. Actual evaporation depends on land cover and meteorological conditions. Evaporation can be predicted by various equations, amongst the Penman‐Monteith equation which takes into account both the vegetation properties as well as the meteorological conditions. In the case of sparsely vegetated areas soil evaporation and plant evaporation need to be treated separately. Estimating the correct value of surface conductance is a critical issue in applying the Penman‐Monteith equation, but models exists. Evaporation from bare soil can be treated as a two stage process, with rapid evaporation at potential rates after rain, and subsequent drying. At larger than catchment scales, feedbacks with the atmospheric boundary layer make it possible to apply evaporation equations based on equilibrium concepts, such as the Priestley‐Taylor equation. There has been substantial progress in evaporation modeling and measurements over the last 25 years. This knowledge can be used much more in assessing changes in evaporation of catchments that may result from perturbations in land use and climate.
Satellite‐Based Estimation of Precipitation Using Microwave Sensors
Authors: Huffman George J
Published: April 2006

Satellite‐borne sensors provide critical input to estimating precipitation over the vast majority of the Earth's surface that lacks adequate in situ observing systems. This article reviews the legacy of sensors, satellites, and data archives that have accrued throughout the Space Age, and that largely governs the precipitation estimates that are available to the hydrological community, both currently and over the long term. Tables of publicly available, quasi‐global, satellite‐based precipitation data sets are introduced, examples are provided, data quality is considered, and future prospects are outlined. One major theme throughout the article is to raise the key issues that users should consider in determining whether a particular set of precipitation estimates is appropriate for their particular application.
Land‐Cover Classification and Change Detection
Authors: Hansen Matthew C , Goetz Scott J
Published: April 2006

Various multispectral data sets and tools are available for mapping land cover and land‐cover change for inputs to hydrologic applications. The best choice is often a function of the specific application. New sensors offer increased capability in mapping spatial detail and temporal variation of land‐cover categories. Algorithms have advanced in robustness and include distribution‐free methods that are superior to traditional approaches in terms of modeling the multispectral distributions of reference data. Advanced subpixel methods of mapping land cover offer greater thematic coherency and the possibility of using consecutive land‐cover characterizations to map change. The success of deriving a meaningful result, such as deriving a relationship between aquatic biotic indices and land‐cover change, relies on a high‐quality land‐cover reference map. By choosing the most appropriate data sources, constructing a defensible land‐cover definition set, and employing robust algorithms, analysts allow for the meaningful incorporation of land‐cover map information into hydrological studies.
Estimation of Glaciers and Sea‐Ice Extent and their Properties
Authors: Stroeve Julienne , Long David , Comiso Josefino C , Scambos Ted A , Shuman Chris A
Published: April 2006

Past satellite missions have demonstrated the utility of spaceborne remote sensing in studies of polar ice. Because of their ability to “see” into polar ice without regard to cloud cover or solar lighting, microwave remote sensing instruments have played and will continue to play an increasing role in such studies and in long‐term monitoring the polar regions. Microwave sensors can be either active radars which transmit and receive, or receive‐only radiometers. Spaceborne microwave sensors such as radiometers and scatterometers offer wide‐area, frequent coverage but at lower resolution and a longer historical database. The historic data sets are particularly important since they provide a baseline for studies of global change. Synthetic aperture radar systems possess high resolution capability but have restricted spatial and temporal coverage. Microwave sensors are sensitive to snow and ice structure and are particularly sensitive to freeze/thaw conditions. Optical sensors can also be active (Lidars) or passive. Laser altimeters are an example of an active optical sensor. They provide accurate ice sheet topography information. Passive optical sensing is useful in change detection and infrared ice temperature sensing. In this chapter, essential background in microwave and optical remote sensing of sea‐ice, glaciers and ice sheets is provided, along with application examples.
Hydrology of Swelling Clay Soils
Authors: Smiles David , Raats Peter A C
Published: April 2006

Theory of water flow in nonswelling soils has been used for more than 50 years but liquid flow in porous media that change volume with liquid content is not well established in soil science, although it is considered increasingly in chemical and mining engineering and in soil mechanics. Theory of water flow in swelling systems must satisfy material continuity; it must also account for changes in the gravitational potential energy of the system during swelling and for anisotropic stresses that constrain the soil laterally but permit vertical movement. A macroscopic, phenomenological analysis based on Darcy's law provides a useful first approach to the hydrology of such soils and, if we presume that volume change, in the large, is essentially one‐dimensional, material coordinates based on the vertical distribution of the solid phase result in a water flow equation analogous to the Richards equation for nonswelling soils. This framework fully accounts for the vertical strain of the solid phase, and solutions to the flow equation are available for a wide range of practically important initial and boundary conditions. The approach has been well tested in clay suspensions and in saturated systems such as mine tailings and sediments. It is also applied in soil mechanics and, here, we apply it to swelling soils. As with the use of the Richards equation in rigid soils, we recognize that complications arise, but the approach remains the most coherent and profitable to support current needs and serve as a point of departure for future research. The use of material coordinates is simple. We discuss some experimental difficulties in using the approach and also consider extension of the approach to more than one dimension.
Water Movement in Hydrophobic Soils
Authors: Doerr Stefan H , Ritsema Coen J
Published: April 2006

Hydrophobicity (water repellency) can reduce the affinity for soils to water such that infiltration or wetting may be delayed for periods ranging from as little as a few seconds to in excess of weeks. Soil hydrophobicity is thought to be caused primarily by a coating of long‐chained hydrophobic organic molecules on individual soil particles. These substances may be released from a range of plants, decaying organic matter, soil fauna, and microorganisms either naturally or during burning. Hydrophobicity tends to be spatially and temporally highly variable, which makes its effects difficult to observe and predict. It is often most prominent after prolonged dry spells and usually disappears after prolonged contact with water. Owing to the cultivation of certain frequently introduced plant species and the increase in wildfires in some regions, hydrophobicity has developed in previously unaffected areas. Amongst its effects are inhibited plant growth, increased overland flow and soil erosion, uneven spatial and vertical wetting patterns, reduced evaporation, and enhanced risk of groundwater contamination associated with enhanced preferential flow. Recent modeling approaches have been successful in predicting the effects of hydrophobicity on soil water movement at plot or small‐field scales, however, approaches to predict in detail its hydrological effects at larger scales are yet to be developed.
Transpiration and Root Water Uptake
Authors: de Willigen Peter , Heinen Marius , Kirkham Mary Beth
Published: April 2006

Root water uptake is one of the major components of the water balance of a soil. In this article, both the physical as well as the physiological aspects of root water uptake and transpiration are dealt with. The regulation of transpiration by different mechanisms on different levels (e.g. through hormones, adaptation of vessel diameter, root radius, and vertical extension of the root system) is discussed. Attention is paid to the modeling of water uptake by single roots and root systems. The last section deals with the different techniques used to measure root water uptake, for example, lysimeter, sap flow, inverse modeling, and discusses the advantages and disadvantages of the different methods.
Measuring Soil Water Content
Authors: Topp G Clarke , Ferré Ty PA
Published: April 2006

Major advances in the measurement of soil water content have arisen from electromagnetic (EM) methods that have developed rapidly in the last 20 years. Estimates of water content from EM measurements make use of the large relative permittivity of water compared to other soil components. Time domain reflectometry (TDR) and capacitance approaches use “probes” that convey signal into the soil and thus can measure principally the upper one‐meter depth. Ground penetrating radar (GPR) using noninvasive, transmitting, and receiving antennae possesses the capability to measure to even greater depths without causing soil disturbance. Remote radar and passive microwave methods, operating generally above 1 GHz, derive their information from within a few centimeters of the ground surface. Thermogravimetric and neutron moderation continue as viable long‐standing methods but are being used less as these methods are not amenable to data‐logging. The variety of instruments has increased the surface and near‐surface soil water measurement capabilities. Now it is possible for hydrologists to make informed choices among methods, and it is important to do so to optimize their study results.