bluuebunny/crossref_metadata_2025 huggingface dataset:
Kinetics of Liquid - Phase Hydrogenation of Straight Chain C10 to C13 Di-Olefins Over Ni/Al2O3 Catalyst
Authors: Rajeshwer D. , Sreenivasa Rao G. , Krishnamurthy K.R. , Padmavathi G. , Subrahmanyam N. , Rachh Jagdish D
Published: April 2006

Straight chain C10 to C13 di-olefins were selectively hydrogenated to increase the mono-olefins content in the feed to alkylation reactor in the process of production of Linear Alkyl Benzene (LAB). The reaction was carried out in a liquid phase up-flow fixed bed reactor at temperature of 448-503 °K and pressure of 1.08-1.96 MPa, which keeps hydrogen dissolved in the hydrocarbon feed. Under the above process conditions the reactor will be virtually two phase (solid-liquid) instead of three phase (solid-liquid-vapour). Kinetics of hydrogenation of straight chain C10 to C13 di-olefins on nickel  alumina (Ni/Al2O3) catalyst was studied in the temperature range of 458-488 °K. The reaction scheme considered includes two consecutive hydrogenation reactions. Various rate models based on the modified Power Law, Horiuti-Polanyi mechanism & proposed by Somers. A.; were derived for the two consecutive hydrogenation reactions and subjected to model discrimination. Parameter estimation was done utilizing the Levenberg-Marquardt Algorithm for global convergence using MATLAB software. Out of the various models tested, rate model based on power law with modification fitted the data well. The estimated rate constants of the best model are thermodynamically sound and statistically consistent.
Biosorption of Combined Industrial Effluents using Phanerochaete Chrysosporium
Authors: Pogaku Ravindra , Kulkarni Sripathi
Published: April 2006

The biosorption of eight different metals from aqueous solutions of combined industrial effluent by live or dead cells of Phanerochaete chrysosporium was investigated. Growth rate studies of P. chrysosporium were carried out in a selected medium as well as in the effluent. The specific growth rate of the fungus was in the range of 0.0890.102 h1 in the medium. The biosorption of metal ions increased as the initial concentration of metal ions increased in the medium. Biosorption equilibrium was established in about 1 h and the concentration of adsorbed metal ions did not change further with time. The equilibrium was well described by Langmuir, Freundlich and Reidlich  Peterson isotherms. The dead fungal biomass was more effective than living fungus for biosorption of metals. The optimum pH for the fungal growth was at 4.5 but enhanced Biosorption was at pH 6 for maximum reduction of hexavalent chromium to trivalent.
A VSC Transmission System Using Flying Capacitor Multilevel Converters and Selective Harmonic Elimination PWM Control
Authors: Xu Lie , Agelidis Vassilios G.
Published: April 2006

A transmission system based on voltage-source three-level flying capacitor (FC) multilevel converters with selective harmonic elimination pulse-width modulation (SHE-PWM) control is presented in this paper. The generation of the switching patterns for each power device is described taking into account the natural balancing of the FC voltages. A new and simple control method for balancing the FC voltages of the FC converter when using SHE-PWM is proposed which is based on the small change of the firing angle according to the load current polarity. Implementation of the SHE-PWM with capacitor voltage balancing is provided. Simulation studies for a 300MW/+-150kV transmission system are presented to confirm the satisfactory performance of the proposed system.
Controlling Inrush Currents in Inductively Coupled Power Systems
Authors: Boys John T , Chen Chan-I , Covic Grant A
Published: April 2006

In an Inductively Coupled Power Transfer (ICPT) system, a multiplicity of (moving) loads take power from an elongated conductive loop (track) excited by a current in the range of 15-125A by magnetic induction at a VLF frequency of between 5-50kHz. In this application, the track performs the same function as a distribution line in a power system. However, frequency deviations cannot be tolerated in ICPT systems and therefore there are difficulties with inrush power surges as loads switch on. In severe cases, the inrush surge may compromise the security of the whole system.This paper proposes a solution to this problem using an ICPT pickup controller with input shaping where the poles that can cause an inrush are not excited. The paper is supported by theoretical analysis and experimental measurements and is applicable across a wide range of ICPT sizes and applications. The solution reduces the inrush effects to 10% of an uncontrolled system.
Wage and Benefit Changes in Response to Rising Health Insurance
Authors: Goldman Dana P , Sood Neeraj , Leibowitz Arleen
Published: April 2006

Many companies have defined-contribution benefit plans requiring employees to pay the full cost (before taxes) of more generous health insurance choices. Research has shown that employee decisions are quite responsive to these arrangements. What is less clear is how the total compensation package changes when health insurance premiums rise. This paper examines employee compensation decisions during a three-year period when health insurance premiums were rising rapidly. The data come from a single large firm with a flexible benefits plan wherein employees explicitly choose how to allocate compensation between cash wages and other benefits. Under such an arrangement, higher health insurance premiums must induce changes in the composition of total compensationeither in lower after-tax wages or in decreased contributions to other benefits. The results suggest that about two-thirds of the premium increase is financed out of cash wages and the remaining one-thirds is financed by a reduction in benefits.
Why Do Some Firms Spend So Much on Medical Care? Accounting for Variation
Authors: Eichner Matthew , McClellan Mark , Wise David A.
Published: April 2006

We are engaged in a long-term project to analyze the determinants of health care cost differences across firms. An important first step is to summarize the nature of expenditure differences across plans. The goal of this article is to develop methods for identifying and quantifying those factors that account for the wide differences in health care expenditures observed across plans.We consider eight plans that vary in average expenditure for individuals filing claims, from a low of $1,645 to a high of $2,484. We present a statistically consistent method for decomposing the cost differences across plans into component parts based on demographic characteristics of plan participants, the mix of diagnoses for which participants are treated, and the cost of treatment for particular diagnoses. The goal is to quantify the contribution of each of these components to the difference between average cost and the cost in a given firm. The demographic mix of plan enrollees accounts for wide differnces in cost ($649). Perhaps the most noticeable feature of the results is that, after adjusting for demographic mix, the difference in expenditures accounted for by the treatment costs given diagnosis ($807) is almost as wide as the unadjusted range in expenditures ($838). Differences in cost due to the different illnesses that are treated, after adjusting for demographic mix, also accounts for large differences in cost ($626). These components of cost do not move together; for example, demographic mix may decrease expenditure under a particular plan while the diagnosis mix may increase costs.Our hope is that understanding the reasons for cost differences across plans will direct more focused attention to controlling costs. Indeed, this work is intended as an important first step toward that goal.
Public Financing and the Market for Long-Term Care
Authors: Lakdawalla Darius , Philipson Thomas
Published: April 2006

Concern about the effect of aging on long-term care has intensi
Carbonic Anhydrases (β‐Class)
Authors: Yamashita Eiki , Mitsuhashi Satoshi , Tsukihara Tomitake
Published: April 2006

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.
Carbonic Anhydrases (γ‐Class)
Authors: Kisker Caroline , Iverson Tina M
Published: April 2006

The γ‐class carbonic anhydrase from the thermophilic archaeonMethanosarcina thermophilais involved in the aceticlastic pathway in which energy for growth is derived from the conversion of the methyl group of actetate to methane. This γ‐class carbonic anhydrase is arranged as a tightly packed trimer with each monomer folded into a left‐handed β‐helix. The catalytic active site zinc is located at the interface between subunits and is coordinated by three histidines, two from one monomer and the other from a second monomer. Interestingly, the arrangement of the histidine side chains ligating the metal show clear structural similarity to their counterparts in the well‐characterized α‐class carbonic anhydrases, despite the difference in overall fold. The conversion of CO2to bicarbonate has a maximal turnover number of 6 × 104s−1, and this reaction is believed to proceed by utilizing the zinc‐hydroxide mechanism previously proposed for α‐class carbonic anhydrases.
GTP
Cyclohydrolase
I
Authors: Nar Herbert
Published: April 2006

GTP 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 (H
2
NTP), 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.
Metallo β‐Lactamases
Authors: Herzberg Osnat , Fitzgerald Paula MD
Published: April 2006

The metallo‐β‐lactamases (class B β‐lactamases) confer bacterial resistance to β‐lactam antibiotics and are therefore targets for the development of clinical agents against resistant strains of bacteria. They are found in a wide variety of bacteria and act on a broad spectrum of substrates including penicillins, cephalosporins, and carbapenems, as well as on some inhibitors of serine‐β‐lactamases. These ∼25 000 Da zinc‐dependent enzymes have been studied extensively in recent years, and crystal structures have been determined for the enzymes from five different bacteria representing two different sequence subclasses (B1 and B3). The active site is located at the interface between two α/β domains where two zinc atoms bind. This review surveys the current understanding of these enzymes, with emphasis on structural studies, spectroscopy, kinetics, and proposals for the catalytic mechanism.
NucleaseP1
Authors: Volbeda Anne , Romier Christophe , Suck Dietrich
Published: April 2006

Nuclease P1 of the moldPenicillium citrinumis a zinc‐dependent enzyme that cleaves all PO3′ bonds in single‐stranded DNA and RNA substrates, independent of base sequence. Crystallographic studies of the native enzyme have shown that the trinuclear zinc active site is inaccessible for phosphate groups in regular A‐ and B‐DNA structures, whereas crystal structures of complexes with thio‐ and dithiophosphorylated oligonucleotides as substrate analogs show the importance of stacking and hydrogen‐bonding interactions with unpaired bases. These studies provide, in addition, a structural basis for the understanding of the low pH optimum of the enzyme and of its catalytic mechanism. This is most likely to be very similar to the three–metal ion mechanisms proposed forBacillus cereusphospholipase C andEscherichia coliendonuclease IV, although the latter enzyme has a completely different structure. In each case, the phosphate‐attacking nucleophile is a water or hydroxide molecule that is activated by two closely spaced zinc ions, assisted by hydrogen bonding to a nearby carboxylate group, and with stabilization of the leaving PO3′ anion by a third, more exposed zinc ion. Sequence comparisons with P1‐related nucleases confirm the importance of an invariant asparagine in the proper orientation of the substrate by hydrogen bonding to the O4′ atom of the ribose moiety that is situated next to the cleaved PO3′ bond.
Structural Zinc Sites
Authors: Auld David S
Published: April 2006

Structural zinc binding sites in proteins have a combination of four nitrogen, oxygen, and sulfur ligands provided by the side chains of amino acids of the protein. In marked contrast to catalytic zinc sites, no metal‐coordinated water molecule is present. There are over seven dozen representatives of structural zinc sites. While the sulfur of a cysteine is by far the preferred ligand for such sites, it is also found in combination with an imidazole nitrogen of a histidine, and/or a carboxylate oxygen from aspartate or glutamate. Of the 22 possible permutations of these 4 ligands, 8 have been observed. The ligands to these metal sites are provided by protein sequences as small as 10 amino acids and as large as 210 amino acids but the majority fall within the range of 25 to 50 amino acids. The ligands are frequently supplied from within or just before or after a β‐sheet secondary structure. The role of a structural zinc site is probably twofold. It maintains the structure of the protein in the immediate vicinity of the metal site. In this manner, it may influence enzymatic activity by providing active site residues involved in catalysis and/or affecting the chemical environment of catalytic groups through interaction with amino acids originating from within its metal‐binding spacers. However, in many cases these metal sites also affect the overall stability of the protein as judged by temperature and pH criteria.
Cocatalytic Zinc Sites
Authors: Auld David S
Published: April 2006

Cocatalytic 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.
Protein Interface Zinc Sites: The Role of Zinc in the Supramolecular Assembly of Proteins and in Transient Protein–Protein Interactions
Authors: Maret Wolfgang
Published: April 2006

New roles are emerging for zinc in protein quaternary structure and supramolecular assemblies. When zinc bridges the interfaces of proteins via ligands provided by different polypeptide chains, it is either essential for the interaction or it serves mainly as a stabilizing factor. Zinc can cross‐link four, three, or more commonly, two protein monomers. Functions of protein interface zinc sites include catalysis, inhibition of enzymatic or other activity, packaging of proteins for storage, dimerization of proteins, formation of protein/receptor complexes, and construction of molecular scaffolds. Tight control of the availability of zinc and ligand‐centered redox reactions in zinc/thiolate coordination environments of protein interface zinc sites suggest mechanisms for modulating transient protein–protein interactions.
Zinc Modules in Nuclear Hormone Receptors
Authors: Devarakonda Srikripa , Rastinejad Fraydoon
Published: April 2006

Nuclear hormone receptors are a family of transcription factors that modulate the transcription of target genes in response to their respective hormones. By activating expression of gene networks, they coordinate complex events involving development, differentiation, and response to diverse stimuli. Most receptors function as homo‐ or heterodimers and activate the target genes by binding selectively to regulatory sequences called DNA response elements (DRE) in the promoter region of the gene. The majority of members in this family recognize slight variations of the same consensus hexameric sequence – AGGTCA, through their DNA binding domains (DBD). The DREs contain the core hexameric sequence in various extended and bipartite configurations. The DBD consists of two zinc binding modules that fold onto each other to form a scaffold that is responsible for DNA binding and recognition. A series of three‐dimensional structures obtained from NMR and X‐ray crystallography have allowed the visualization of the DBDs alone and in their functional assemblies on the corresponding DREs. This chapter describes in detail the molecular and structural characteristics of the DBDs including their C‐terminal extensions as well as the topology of the various DREs that these receptors bind to. These features illustrate how a superfamily of receptors with highly conserved DNA binding domains can distinguish between closely related response elements. The structures described also indicate how cooperation between receptors enhances their joint affinity and selectivity for correctly configured sites.
Insulin
Authors: David Smith G
Published: April 2006

The protein hormone insulin, produced in the pancreas and stored in granules, interacts, after secretion into the blood stream, with the extracellular domain of the insulin receptor. This interaction initializes a signal transduction cascade that ultimately results in glucose absorption and metabolism. In the presence of zinc ion, insulin crystallizes as a threefold symmetric T
6
hexamer complexed to two zinc ions. When phenol,
m
‐cresol, or resorcinol is present in the crystallizing media, the first eight residues of all B‐chains undergo a conformational change from extended to α‐helical producing an R
6
hexamer. In the presence of thiocyanate or chloride ion, only residues 4 through 8 in the B‐chains of one trimer undergo the conformational change to produce a T
3
R
3
f
hexamer. This allosteric behavior of the insulin hexamer has been observed in the solid state as well as in solution. Like the T
6
hexamer, each zinc ion that lies on the crystallographic threefold axis is octahedrally coordinated by NE2s of three symmetry related HisB10 residues and three water molecules. Because of the conformational transition from T to either R or R
f
, there is not sufficient space in an R‐ or R
f
‐state trimer to accommodate octahedral coordination, and, therefore, zinc adopts tetrahedral coordination through bonds to the three symmetry related HisB10 NE2 atoms and either to a water molecule or to a chloride ion. In the case of T
3
R
3
f
hexamers, three additional zinc binding sites exist between symmetry related R
f
‐state monomers in which each zinc ion is coordinated by NE2 of a second orientation of the side chain of HisB10, NE2 of HisB5 of an adjacent monomer, and two chloride ions. From a total of 34 crystal structures of hexameric insulin, mean ZnNE2 bond distances of 2.00 or 2.10 Å are observed in tetrahedral or octahedral geometry, respectively.
RINGDomain Proteins
Authors: Dominguez Cyril , Folkers Gert E , Boelens Rolf
Published: April 2006

The 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.
LIM domain proteins
Authors: Kontaxis Georg , Bister Klaus , Konrat Robert
Published: April 2006

LIM domain proteins are implicated in fundamental developmental processes, and the functional hallmark of all LIM domains is presumably the mediation of protein–protein interactions. Although originally identified in LIM‐homeodomain proteins, LIM domains have now been identified in a variety of proteins that lack homeodomains, either being entirely composed of LIM domains or containing additional functional domains of various types (e.g. kinase domains). The LIM domain contains a distinct cysteine‐rich motif that was first identified in the protein products of three genes –lin‐1,isl1, andmec‐3. The LIM motif is composed of two zinc finger structures separated by a two‐amino acid spacer and comprises the conserved sequence CX2CX16 − 23HX2CX2CX2CX16 − 21CX2(C/H/D).
FYVE
Domain
Authors: Kutateladze Tatiana G , Overduin Michael
Published: April 2006

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.
Methionine Aminopeptidase
Authors: Matthews Brian W
Published: April 2006

The methionine aminopeptidases represent a novel class of metalloprotease generally having two cobalt ions in the active site. The proteins consist of two topologically similar domains folded with a ‘pita‐bread’ motif. Structural analysis of various inhibitor complexes with theEscherichia colienzyme and other members of the family have suggested a putative mechanism of catalysis related to that originally proposed for thermolysin.
Neprilysin
Authors: Dale Glenn E , Oefner Christian
Published: April 2006

Neprilysin (NEP), a thermolysin‐like zinc metalloendopeptidase, is the major enzyme involved in the metabolic inactivation of a number of bioactive peptides including the enkephalins, substance P, endothelin, bradykinin, and the atrial natriuretic factor. NEP is an integral plasma membrane endopeptidase of the M13 family of zinc peptidases. Other related mammalian NEP‐like enzymes include the endothelin‐converting enzymes (ECE‐1 and ECE‐2), KELL and PEX. A number of novel mammalian homologues of NEP have also recently been described. Owing to the physiological importance of NEP in the modulation of nociceptive and pressor responses, there is considerable interest in inhibitors of this enzyme as novel analgesics and antihypertensive agents. Here we provide an overview of this pharmacologically important protein protease family.
Astacin
Authors: Stöcker Walter , Yiallouros Irene
Published: April 2006

The 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: April 2006

The 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.
Serralysin
Authors: Baumann Ulrich
Published: April 2006

Serralysins (EC 3.4.24.40) are a family of 50‐kDa metalloproteases from gram‐negative enterobacteria. They are members of the metzincin clan of endopeptidases and possess the conserved zinc binding HEXXHXXGXXHP sequence motif, followed by a conserved methionine. The three‐dimensional structure shows that serralysins possess two domains; besides the typical metzincin‐protease domain that resides within the N‐terminal 220 amino acids, there is an extended C‐terminal β‐sheet domain. This domain contains six glycine‐rich tandem repeats GGXGXDXLX characteristic for the RTX‐toxin family. These repeats bind calcium ions.

Recent studies include directed mutagenesis in order to clarify the function of the conserved methionine as well as the crystal‐structure determination of complexes between serralysins and their cognate inhibitors. The latter shows inhibition by a coordinative bond between the inhibitor's N‐terminus and the catalytic zinc ion.
Metallocarboxypeptidases
Authors: Vendrell Josep , Aviles Francesc X , Fricker Lloyd D
Published: April 2006

Metallocarboxypeptidases (CP) catalyze the removal of C‐terminal amino acids from proteins and/or peptides. The different members of the CP family differ in their specificity for C‐terminal residues and physiological function and can be divided into two subfamilies. Members of the A/B subfamily are generally produced as proenzymes, contain an approximately 300‐residue CP catalytic domain, have greatest amino acid sequence identity to the exocrine pancreatic enzymes CPA and CPB, and prefer hydrophobic or basic residues. They function in the breakdown of peptides in food or in other physiological processes ranging from inflammation to fibrinolysis. Members of the N/E group cleave C‐terminal basic residues and are not produced as inactive proenzymes but contain an approximately 80‐residue region following the 300‐residue CP domain with structural homology to transthyretin. They act either extra‐ or intracellularly in the processing of peptide hormones and neurotransmitters and other physiologically relevant peptides.

The tertiary folding of CPs corresponds to the α/β hydrolase fold and is formed by a central mixed parallel/antiparallel eight‐strand β‐sheet, with a 120° twist between the first and the last strand, over which eight α‐helices pack on both sides to form a globular molecule. All of the enzymatically active CPs bind one atom of Zn2+at the active site. Some members of the CP family that are inactive against standard CP substrates lack some of the cation‐binding ligands and may therefore not be able to bind the metal.
Pitrilysins/Inverzincins
Authors: Maskos Klaus
Published: April 2006

Inverzincins are characterized by an inverted zinc‐binding motif (HxxEH) rather than the classical zincin motif (HExxH). Pitrilysin fromEscherichia coliis the prototype of one subfamily, which also contains eukaryotic family members such as the insulin‐degrading enzyme (IDE) and theN‐arginine dibasic convertase (NRDc), both playing important roles in hormone metabolism and cellular regulation. The topology of active site residues shows some similarity to zincins, suggesting a convergent evolution for these types of metalloproteases. The closely related members of the mitochondrial processing peptidase (MPP) subfamily function as soluble heterodimers or as building blocks of the cytochrome c reductase complex and share the tendency with pitrilysin‐like enzymes to cleave peptides at hydrophobic or positively charged sites in a context‐dependent manner. For several family members, binding and cleavage of substrate is supposed to depend on secondary or tertiary structure and seems to proceed within a compartment formed by the respective enzyme.
Bacillus SubtilisD‐AminopeptidaseDppA
Authors: Remaut Han , Goffin Colette , Frère Jean‐Marie , Beeumen Jozef Van
Published: April 2006

TheD‐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.
Calmodulin
Authors: Yap Kyoko L , Ikura Mitsuhiko
Published: April 2006

CaM is a ubiquitous eukaryotic calcium binding protein that interacts with hundreds of proteins including kinases and phosphatases, transmembrane ion channels and pumps, and cytoskeletal regulatory proteins. In response to an increase in intracellular calcium, CaM undergoes a major conformational change enabling target binding and activation. In some cases, CaM is able to bind target proteins in the absence of, or independently of, Ca2+; in others, CaM binding may induce inactivation. The structural plasticity of calmodulin is demonstrated by the diversity observed in its interaction with various targets.
Troponin
C
Authors: Gagné Stéphane M
Published: April 2006

Regulation of contraction in skeletal and cardiac muscle occurs through calcium binding to the protein troponin C (TnC). The N‐terminal domain of TnC (NTnC) carries out the regulatory role through the binding of calcium ions – two calcium ions in skeletal muscle and one in cardiac muscle.

Thirty‐nine sequences of TnC have been sequenced so far. Of the 39 sequences of TnC, 5 have had their three‐dimensional structures determined in various forms by NMR and X‐ray. Available structures include 26 uncomplexed structures in various calcium states, and 13 structures in which cardiac and skeletal TnC is complexed with fragments of troponin I and/or troponin T.
Gating Domain of Calcium‐Activated Potassium Channel with Calcium and Calmodulin
Authors: Schumacher Maria A
Published: April 2006

Small conductance Ca2+‐activated K+channels (SK channels) are voltage‐independent and gated solely by increases in intracellular Ca2+such as that occurs during an action potential. SK channels are heteromeric complexes and consist of pore‐forming α‐subunits and calmodulin (CaM). CaM is constitutively associated with an intracellular region of the α‐subunit immediately C‐terminal to the pore, the CaM binding domain (CaMBD). In order to trigger channel opening, Ca2+must only bind the EF hands in the CaM N‐lobe. The 1.60‐Å crystal structure of the SK channel Ca2+/CaM/CaMBD complex reveals that the CaMBD forms an elongated dimer with a CaM bound at each end and each CaM wraps around three α‐helices, two from one CaMBD subunit and one from the other. The structure also provides a view of both Ca2+‐dependent and Ca2+‐independent protein interactions; only the CaM N‐lobe is calcified while the noncalcified C‐lobe is responsible for the CaM/CaMBD constitutive interaction. This structure combined with biochemical data suggests a possible gating mechanism in which Ca2+binding to each CaM N‐lobe exposes its hydrophobic patch, thus allowing it to interact with an adjacent CaMBD monomer. As each N‐lobe on adjacent monomers interacts with the other CaMBD C‐terminal region, a rotary force would be created between them and transmitted to the attached S6 pore helices in the gate region. In this chemo‐mechanical model, two CaMBD dimers would serve as mechanical levers to drive open the channel.
Basement Membrane Protein
BM
‐40
Authors: Hohenester Erhard , Timpl Rupert
Published: April 2006

BM‐40, also known as SPARC or osteonectin, is a secreted glycoprotein present in all metazoa. The protein is expressed in tissues undergoing morphogenesis, remodeling, and repair.
In vitro
, BM‐40 binds to several collagens and is both antiproliferative and counteradhesive. Human BM‐40 consists of an acidic N‐terminal domain, a follistatin‐like (FS) domain, and an α‐helical (EC) domain that contains two functional EF‐hand calcium‐binding motifs. The crystal structure of the FS–EC domain pair has been determined. Calcium and collagen binding to the EC domain has been studied using site‐directed mutagenesis, spectroscopy, and binding assays.
PEFLINS: A Family of PentaEF‐Hand Proteins
Authors: Cygler Miroslaw
Published: April 2006

Penta‐EF hand proteins, or PEFLINs, belong to the superfamily of regulatory Ca2+‐binding proteins with EF‐hand motifs. The calcium‐binding domain is ∼170 residues long and contains five EF‐hand motifs, of which only some retain the ability to bind calcium. Within individual molecules the (1st + 2nd) and (3rd + 4th) EF‐hands are associated in pairs while the 5th EF‐hand is unpaired. This domain is associated with an N‐terminal domain of varying length, usually 20 to 100 residues long and with a Gly/Pro‐rich region. Binding of Ca2+promotes association of these proteins with membranes, andin vitroleads to aggregation. On the basis of the 1st EF‐hand, these proteins are divided into two subfamilies. Calpain, grancalcin, and sorcin have a one‐residue deletion in the Ca2+‐binding loop between helices E and F and form a distinct variant of calcium binding. ALG‐2 and peflin have the canonical EF1 hand and bind calcium in a standard way. All penta‐EF hand proteins form homo‐ or heterodimers. The dimerization is promoted by pairing of the 5th EF‐hand of each molecule; thus in the dimer all EF‐hands are paired. Binding of Ca2+promotes only small, mostly local, conformational changes and it is plausible that binding of a concomitant partner molecule is required for larger rearrangements to occur.
Calcium‐Binding
EGF
‐Like Domains
Authors: Boswell Emma J , Kurniawan Nyoman D , Downing A Kristina
Published: April 2006

Epidermal growth factor‐like (EGF) domains are one of the more abundant modules found in functionally diverse extracellular proteins. The domain is characterized by six cysteine residues, which normally disulphide bond in a 1–3, 2–4, 5–6 pattern. A particular subset (cbEGF) contains the consensus sequence [DEQN]‐x‐[DEQN]
2
‐x

m

‐[DN]*‐x

n

‐[YF] (where
m
and
n
are variables and * indicates possible β‐hydroxylation) associated with the ability to bind calcium. At present, cbEGFs have three main functional roles, as a spacer unit, in protein–protein interactions, and in structural stabilization. High‐resolution structures of cbEGF domains have identified a common fold, comprising a major and a minor double‐stranded β‐hairpin, stabilized by the three consensus disulphide bonds. A single calcium ion binds to the amino terminus and is coordinated by a pentagonal bipyramidal arrangement of oxygen atoms. Each individual cbEGF domain contains a calcium‐binding site, whose affinity may be considerably enhanced by N‐terminal linkage to another domain. A number of inherited diseases caused by missense mutations within cbEGFs highlight the importance of the domain.
Annexins: Calcium Binding Proteins with Unusual Binding Sites
Authors: Rosengarth Anja , Luecke Hartmut
Published: April 2006

Annexins comprise a multigene family of calcium‐ and phospholipid‐binding proteins. They are structurally divided into a conserved core domain and a flexible N‐terminal domain. The core domain contains four (in the case of annexin A6, eight) repeats, which fold into five α‐helices (named A through E) each. The overall shape of the annexin core is a curved disk with the calcium binding sites located on the concave face and the N‐terminal domain on the convex face. Annexins contain three different calcium binding sites: type II, type III, and AB′ sites. Type II and AB′ sites are found in the loops between the A and the B helix of each repeat. The coordination sphere for the calcium ion in the type II site generally comprises three backbone carbonyl oxygens, the side chain of an acidic residue 39 residues downstream of the AB loop, and two water molecules. The AB′ site is formed by one backbone carbonyl oxygen, one nearby acidic residue, and four to five water molecules. The calcium ion in the type III binding site, which is usually located in the loop between the D and E helix, is coordinated by two backbone carbonyl oxygens, one acidic residue nearby, and three to four water molecules. In comparison to EF hand calcium‐binding proteins, the affinity for calcium ions of annexins is rather low, which might be due to the large number of water molecules involved in the coordination of the calcium ions. In this review, we will give an overview on the structure and function of several mammalian annexins. We will also discuss in detail the coordination of calcium ions in the different types of calcium binding sites found in annexins.
Calcium Pump (
ATPase
) of Sarcoplasmic Reticulum
Authors: Toyoshima Chikashi
Published: April 2006

Ca
2+
‐ATPase of sarcoplasmic reticulum is a membrane protein of 110 kDa and pumps Ca
2+
from the cytoplasm into the sarcoplasmic reticulum, an intracellular organelle, to relax muscle cells. Two Ca
2+
ions can be transported per ATP hydrolyzed and two or three protons are countertransported. The Ca
2+
‐binding sites are located side by side in the transmembrane region. The crystal structures of this ATPase obtained for Ca
2+
‐bound and unbound states show that large conformation changes take place during Ca
2+
binding and dissociation.
C
‐Type Animal Lectins
Authors: Weis William I
Published: April 2006

C‐type animal lectins are a large family of carbohydrate‐binding proteins, which display a strict dependence on Ca
2+
for their activity. Family members contain one or more carbohydrate‐recognition domains (CRDs) approximately 110 to 150 amino acids in length. Structural analysis of these proteins reveals that binding to sugars is mediated by direct coordination of a conserved Ca
2+
. The Ca
2+
dependence of sugar binding is exploited in a number of family members that serve as cell surface endocytic receptors, where the acidic environment of the endosome causes changes in Ca
2+
coordination and release of the bound ligand.
Hemopexin Domains
Authors: Xavier Gomis‐Rüth F
Published: April 2006

The mammalian serum glycoprotein hemopexin is engaged in the metabolism of heme and in the protection against oxidative stress. It is the lead structure of the hemopexin domains, which are made up of several hemopexin‐type repeats of about 40 residues. Such domains are also found as C‐terminal domains in matrix metalloproteinases, zinc‐dependent hydrolases belonging to the metzincin clan of metalloproteinases. In these proteases, they deal with protein–substrate and protein–inhibitor interactions and in activation events. Both protein classes have been characterized at three‐dimensional structural level. Moreover, hemopexin domains are present within vitronectins, extracellular matrix glycoproteins. In this case, similarity with the former has been just based on sequence information. The presence of hemopexin domains in hemopexins, vitronectins, and matrix metalloproteinases' C‐terminal domains suggests that these repeating peptide motifs have arisen by divergent evolution.
C
2‐Domain Proteins Involved in Membrane Traffic
Authors: Rizo Josep
Published: April 2006

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