bluuebunny/crossref_metadata_2025_split huggingface dataset:
Methane Monooxygenase Hydroxylase
Authors: Whittington Douglas A , Lippard Stephen J 
Published: December 2011

AbstractSoluble methane monooxygenase (sMMO) catalyzes the conversion of methane and dioxygen to methanol and water. It is a cytoplasmic system of three proteins produced in methanotrophic bacteria grown under conditions of low copper stress. The best characterized sMMO stems fromMethylococcus capsulatus(Bath). Under physiological conditions inM. capsulatus(Bath), three protein components are required for sMMO activity. These included a 251‐kDa hydroxylase (MMOH), which contains the carboxylate‐bridged, dinuclear iron active site; a 16‐kDa regulatory protein known as protein B (MMOB); and a 38.6‐kDa reductase (MMOR) that contains FAD and a Fe2S2center. MMOH has been characterized by several spectroscopic techniques (UV/vis, X‐ray absorption, Mössbauer, EPR, ENDOR, CD, MCD), which established the nature of the dinuclear iron active site.The crystal structure of the MMOH component of sMMO fromM. capsulatus(Bath) has been solved in two crystal forms, one of which was refined to a resolution of 1.7 Å. The enzyme is composed of two copies each of three subunits (α2ß2γ2), and all three subunits are almost completely α‐helical. The active site of each α‐subunit contains one dinuclear iron center, housed in a four‐helix bundle. The two iron atoms are octahedrally coordinated by 2 histidine and 4 glutamic acid residues, as well as by a bridging hydroxide ion, a terminal water molecule, and at 4°C, a bridging acetate ion, which is replaced at −160°C with a bridging water molecule. Comparison of the results of the two crystal forms shows one structural difference, namely, the altered side chain conformation of Leu110 at the active site cavity. It is suggested that this residue serves as one component of a hydrophobic gate controlling the access of substrates to and products from the active site. MMOB and MMOR bind to the α‐ and ß‐subunits of MMOH, respectively. The structure of MMOB has been known from NMR. X‐ray structures of reduced MMOH and of DMSO‐soaked MMOH have been determined. During the turnover, Hperoxoand Q intermediate states could be trapped and structures proposed from density functional theory studies.
Peptide Deformylase
Authors: Becker Andreas , Kabsch Wolfgang 
Published: December 2011

AbstractPeptide deformylase (EC 3.5.1.31) is a mononuclear iron enzyme that cleaves the formyl group of theN‐terminal formyl‐methionine residue of nascent polypeptide chains in eubacteria. It is strictly stereospecific for aL‐amino acid as the first residue of formyl‐peptide substrates and strongly prefers substrates with at least two or more residues. The native enzyme fromEscherichia coliis a monomeric protein of 168 amino acid residues that contains one tightly bound Fe2+ion. The metal ion is tetrahedrally coordinated by a water molecule and the side chains of residues Cys90, His132, and His136. Similar to thermolysin, the two histidines are part of the HEXXH motif and the glutamate residue is required for enzymatic activity. The native iron form of peptide deformylase is extremely sensitive to oxidative destruction. On substitution of the iron ion by Ni2+or Co2+the enzyme is insensitive to oxidation and maintains its activity, whereas the Zn2+form is nearly inactive.
ConcanavalinA
Authors: Kalb (Gilboa) A Joseph , Helliwell John R 
Published: December 2011

AbstractConcanavalin A is a metalloprotein containing manganese and calcium in a bimetallic metal‐binding site. As isolated from the Jack bean (Canavalia ensiformis), the protein binds saccharides such as α‐methyl mannoside and α‐methyl glucoside. Acid treatment produces a demetallized form that does not bind saccharides and that which can be remetallized to produce various metal‐substituted forms, such as (Ni, Ca), (Co, Ca), (Cd, Ca), (Zn, Ca), and (Cd, Cd). Structural studies of the crystal structures of the native, demetallized, and remetallized proteins, as well as its complexes with saccharides, have helped clarify the nature of the interaction between the metal‐binding site and the saccharide‐binding site. The protein has been well‐characterized structurally, namely, at an X‐ray crystallographic resolution of 0.94 Å (Mn, Ca form), by neutron protein crystallography to define the hydration details (at 2.4 Å resolution), by molecular dynamics to better define the protein saccharide recognition, by EPR using the manganese d5 high spin state, and by EXAFS (Zn, Ca form). These structural characterizations include studies at 12 K, 100 K, and room temperature.
MethylmalonylCoAMutase
Authors: Gruber Karl , Kratky Christoph 
Published: December 2011

AbstractThe 5′‐adenosylcobalamin dependent methylmalonyl‐CoA mutase (MCM) catalyzes the reversible and stereospecific equilibration of (2R)‐methylmalonyl CoA and succinyl CoA through a radical mechanism. Its occurrence ranges from bacteria to mammals, where it is required for the metabolism or biosynthesis of propionate. MCM fromPropionibacterium shermaniiis an αβ‐heterodimer of total molecular weight 150 kDa, containing an inactive β‐subunit along with an active α‐subunit, the latter binding one adenosylcobalamin molecule close to the active site. The protein was found to occur in two fundamentally different conformations: in the presence of substrates it crystallizes in a “closed” conformation, whereas in the absence of substrates an “open” conformation is observed. This dramatic conformational change suggests a mechanism for the first step of the MCM‐catalyzed reaction cycle, i.e. the substrate‐induced homolysis of the Co–C bond.
Cucumber Basic Protein
Authors: Guss J Mitchell , Freeman Hans C 
Published: December 2011

Abstract
The ‘blue’ or ‘type 1’ copper protein family has several sub‐families. One of these sub‐families, the phytocyanins, has several sub‐sub‐families: plantacyanins, stellacyanins, and uclacyanins. The cucumber basic protein, now known as cucumber plantacyanin, was the first structurally characterized as phytocyanin. As in the archetypal ‘blue’ copper protein plastocyanin, the copper atom in cucumber plantacyanin is coordinated by the side chains of two histidines, one cysteine, and one methionine. The polypeptide has a β‐sandwich fold resembling that of plastocyanin, with the exception that one hairpin is bent at a right angle to the rest of the β‐sandwich. As a result, the copper site is more exposed to solvent than in other ‘blue’ copper proteins. The biological functions of phytocyanins are still uncertain.
Tetraheme CytochromesC3
Authors: Bento Isabel , Louro Ricardo O , Soares Cláudio M , Carrondo M Arménia 
Published: December 2011

AbstractTetraheme cytochromesc3constitute the best‐studied group among the multiheme cytochromes belonging to the class III of Ambler's classification. Since 1954, when cytochromec3was isolated fromDesulfovibrio vulgarisfor the first time by Postgate, these proteins have been widely characterized, especially those from theDesulfovibrio(D.) genus. All these cytochromes have their heme group attached to the polypeptide chain by cysteine residues and show bis‐histidinyl coordination of the heme iron and a highly conserved heme‐binding motif (CXXCH or CXXXXCH). Cytochromesc3show a wide variety of redox potentials, ranging from 0 to −400 mV, are usually periplasmatic proteins, and are believed to play key roles in the electron transfer chains. Recently, the cytochromec3group was divided into two main types on the basis of structural, functional, and genetic differences: type I cytochromec3(TpI‐c3) and type II cytochromec3(TpII‐c3). This paper reviews their structural, spectroscopic, and functional properties, based on the wealth of information currently available. These include physicochemical properties, redox mechanisms, coupling between electron and proton transfer, and data concerning the interaction with their redox partners obtained by experimental and molecular modeling methods.
TheNrfHCytochromecQuinol Dehydrogenase
Authors: Rodrigues Maria Luisa , Pereira Inês AC , Archer Margarida 
Published: December 2011

AbstractNrfH is a membrane‐anchored tetraheme cytochromecthat oxidizes menaquinol and transfers electrons to the cytochromecnitrite reductase, NrfA. It belongs to a family of cytochromecquinol dehydogenases, known as theNapC/NirT family, which plays an important role in bacterial anaerobic respiration. Here, we describe the major structural and biochemical features of NrfH that has been isolated in the form of a native NrfHA complex from someProteobacteriaspecies. The notable heme coordination of NrfH, revealed uponDesulfovibrio vulgarisNrfHA structure determination, is discussed in light of primary structure analysis within the NrfH proteins and within the family of cytochromecquinol dehydogenases. Interestingly, NrfH shows a higher sequence variation than other members of the NapC/NirT family. The crystal structure of NrfHA bound to the HQNO inhibitor is also presented and analyzed together with inhibition studies.
BAK
Authors: Moldoveanu Tudor , Liu Qian , Green Douglas R , Gehring Kalle 
Published: December 2011

AbstractThe effector BCL‐2 (B cell lymphoma‐2) protein BAK (B cell lymphoma‐2 homologous antagonist/killer) directly mediates mitochondrial outer membrane permeabilization to drive the mitochondrial pathway of apoptosis. The structures of BAK are presented to reveal two different modes of homodimerization. Noncovalent dimerization is mediated by one Zn2+atom to inhibit the release of cytochromecfrom mitochondrial intermembrane space. Covalent oxidative homodimerization occurs through disulfide bond formation at Cys166 and is thought to prevent the Zn2+‐mediated inhibition by abolishing the Zn2+‐dependent homodimerization interface. Neither mode of dimerization affects the putative B cell lymphoma‐2 homology 3 (BH3)‐binding pocket, which remains occluded in BAK to preclude high affinity BH3 peptide binding.
The Sodium PotassiumATPase
Authors: Nyblom Maria , Morth Jens Preben , Nissen Poul 
Published: December 2011

AbstractAt the expense of adenosine triphosphate (ATP), the P‐type ATPase family of membrane proteins actively transports different cations or lipids, in a reaction cycle that includes the phosphorylation/dephosphorylation of a conserved aspartate residue. These proteins share a common structural and mechanistic core, but Na+, K+‐ATPase is the first multisubunit P‐type ATPase to be structurally determined. The Na+, K+‐ATPase exports three Na+‐ ions per ATP molecule from the cytoplasm, while at the same time transporting two K+‐ ions in the opposite direction. This electrogenic pump is critical for human and animal cells where the gradients of these ions are important for maintaining the resting potential and for electrical excitability of e.g. muscle and nerve cells, and for energization of secondary transporters and osmotic control. This article reviews the currently available structural knowledge of the Na+, K+‐ATPase. Hitherto, there are only structures of one of the catalytic forms reported representing the potassium‐occluded state ([K2]E2·Pi). The overall architecture of the αβγ‐complex is presented and the differences compared to the previously characterized structures of the sarco(endo)plasmic reticulum Ca2+‐ATPase (SERCA) are pinpointed. Furthermore, the properties of the K+‐ion binding sites are described and the functional relevance of the C‐terminus is addressed.
Potassium Channels
Authors: Lenaeus Michael J , Gross Adrian 
Published: December 2011

Abstract
Potassium channels are membrane proteins that allow for and regulate the passive flow of potassium ions in and out of cells. Potassium channels are often multidomain proteins consisting of a central ion‐conducting pore domain and peripheral gating domains sensitive to channel‐specific stimuli (e.g., voltage). This article deals with the structure of the pore domain, where important ion–protein interactions occur. Several structures of potassium channel pore domains have been published and these are discussed herein, along with the current hypotheses regarding channel function, gating, and ion movement.
Corrinoid Adenosyltransferases
Authors: Mera Paola E. , Rayment Ivan , Escalante‐Semerena Jorge C. 
Published: December 2011

Abstract

ATP corrinoid adenosyltransferase (ACA) enzymes catalyze the transfer of the adenosyl moiety from ATP to cob(I)alamin, resulting in the formation of the unique organometallic C–Co bond characteristic of coenzyme B
12
(adenosylcobalamin, AdoCbl). In the last decade, our knowledge of how these enzymes catalyze the adenosylation of cobalamin has grown rapidly. ACA enzymes also facilitate the thermodynamically unfavorable reduction of cob(II)alamin. Studies with ACA enzymes revealed an unprecedented four‐coordinate square‐planar corrinoid conformation. ACA enzymes bring the reduction potential of cob(II)alamin to within physiological range by generating the four‐coordinate Co(II) corrinoid species. Recently, visual evidence of the existence of a Co(II) corrinoid species was obtained when the 3D crystal structure of the human‐type ACA enzyme was solved with ATP and cob(II)alamin bound in the active site. To date, three types of ACA enzymes have been identified, CobA, PduO, and EutT. The PduO‐type is the most widely distributed ACA enzyme and is the form found in humans where ACA enzymes play an essential role in metabolism; malfunctioning of this enzyme cause severe health defects. Detailed analyses of the catalytic mechanism of ACA enzymes have provided an understanding of how some mutations in the human ACA enzyme render it inactive.
DNA
‐Binding Proteins From Starved Cells (
Dps
Proteins)
Authors: Stefanini Simonetta , Ceci Pierpaolo , Ardini Matteo , Ilari Andrea 
Published: December 2011

Abstract
In the recent past over 200 Dps (DNA‐binding proteins from starved cells) proteins have been identified in bacterial genomes. Dps proteins belong to the ferritin superfamily. They are expressed under conditions of oxidative and/or nutritional stress and are characterized by a highly conserved shell‐like structure of 12 identical subunits assembled with 23 symmetry. The internal cavity is designed to accommodate up to 500 iron/atoms per molecule in a soluble and bioavailable form. Dps proteins play an important role in the complex protection mechanism against oxidative damage. The presence of a highly conserved ferroxidase center, which uses hydrogen peroxide as physiological iron oxidant, confers to all Dps proteins the capacity to decrease the production of the hydroxyl‐radicals and, hence, to prevent the damage to DNA and other cellular components. Ferroxidase activity is of special importance in pathogenic bacteria since production of hydrogen peroxide in macrophages and neutrophiles represents one of the first host defense mechanisms. The capacity to bind DNA in a nonspecific manner and pack it into condensed structures, an attribute limited to some members of the family, represents the second distinctive mechanism used to advantage by Dps proteins for the survival of the organism.
Calmodulin Interactions withCav1 andCav2 Voltage‐Gated Calcium ChannelIQDomains
Authors: Kim Eun Young , Findeisen Felix , Minor Daniel L 
Published: December 2011

AbstractHigh‐voltage‐activated calcium channels (CaV1s and CaV2s) are transmembrane protein complexes that couple membrane depolarization to cellular calcium entry. Because calcium is an intracellular messenger and CaVs are important calcium sources, CaVs have a key role in the conversion of electrical signals into the chemical signaling cascades that drive a variety of vital physiological processes in nerve and muscle. These include excitation‐contraction coupling, hormone release, gene regulation, and synaptic transmission. CaVs are regulated by a diverse set of feedback mechanisms. Two important forms of activity‐dependent feedback modulation involve interactions between calcium‐calmodulin (Ca2+/CaM) and the CaVα1pore‐forming subunit of CaV1s and CaV2s: calcium‐dependent inactivation (CDI) in which calcium influx promotes channel closing following activation, and calcium‐dependent facilitation (CDF), a process that enhances channel opening in response to elevated cytoplasmic calcium. The main site of action for Ca2+/CaM is a motif, known as anIQ domain, located on the C‐terminal cytoplasmic tail of the CaVα1pore‐forming subunit. Strikingly, different Ca2+/CaM lobes are responsible for CDI and CDF in CaV1 and CaV2 channels. Crystallographic studies have indicated a structural basis for the apparent inversion of lobe‐specific roles in CDI and CDF in which Ca2+/CaM binds CaV1 and CaV2 IQ domains in opposite orientations.
Mo–Se‐Containing Nicotinate Dehydrogenase
Authors: Dobbek Holger , Pierik Antonio J 
Published: December 2011

AbstractSe Mo‐containing nicotinate dehydrogenase (NDH) of the anaerobic soil bacteriumEubacterium barkericatalyzes the hydroxylation of nicotinate with water and NADP+to 6‐hydroxynicotinate, one proton, and NADPH. This reaction is the first step in the degradation of nicotinate to pyruvate and propionate in a unique fermentation pathway. NDH is constituted by four different subunits and contains a Mo‐bound pyranopterin cofactor linked to cytosine dinucleotide, two different [2Fe2S] centers, and flavin adenine dinucleotide to facilitate the transfer of a hydride ion on NADP+. NDH is a member of the family of molybdenum hydroxylases and shares several distinctive features with other members of this enzyme family, such as xanthine oxidoreductase, aldehyde oxidase, and the Mo‐containing carbon monoxide dehydrogenase. The reactivity of NDH critically depends on the presence of selenium in the active site, where it is bound as a labile nonselenocysteinyl selenium ligand to molybdenum. The role of the selenium ligand is likely to accelerate the formal hydride transfer from the substrate into the Mo Se bond, displaying a novel reactivity of selenium in nature.
Symmetry and Steric Effects on Spin States in Transition Metal Complexes
Authors: Meier Ryan M. , Hanusa Timothy P. 
Published: December 2011

Abstract

Changes in the magnetic characteristics of transition metal complexes, particularly, their metal spin states, are most commonly achieved by varying the electron donor/acceptor properties of coordinated ligands. In some systems, it is possible to increase the steric bulk of ligands so that intramolecular crowding leads to changes in metal‐ligand bond distances; longer bonds produce weaker ligand fields and stabilize high‐spin or spin‐crossover complexes. Steric effects are also often associated, albeit indirectly, with a mechanism for influencing spin states that relies on modifying the symmetry‐based interactions of metal and ligand orbitals. Particular ligand orientations, as in bis(indenyl) compounds [M(R
9
C
7
)
2
], can be changed as the result of interligand steric pressure or crystal packing effects; such differences can alter metal d‐orbital energy levels and hence the stability of spin states. Both steric and symmetry effects add to the repertoire of techniques that can be used to control magnetic properties in transition metal complexes.
Biocompatible Nanoparticles with Aggregation‐Induced Emission Characteristics as Far‐Red/Near‐Infrared Fluorescent Bioprobes for In Vitro and In Vivo Imaging Applications
Authors: Qin Wei , Ding Dan , Liu Jianzhao , Yuan Wang Zhang , Hu Yong , Liu Bin , Tang Ben Zhong 
Published: December 2011

AbstractLight emission of 2‐(2,6‐bis((E)‐4‐(diphenylamino)styryl)‐4H‐pyran‐4‐ylidene)malononitrile (TPA‐DCM) is weakened by aggregate formation. Attaching tetraphenylethene (TPE) units as terminals to TPA‐DCM dramatically changes its emission behavior: the resulting fluorogen, 2‐(2,6‐bis((E)‐4‐(phenyl(4′‐(1,2,2‐triphenylvinyl)‐[1,1′‐biphenyl]‐4‐yl)amino)styryl)‐4H‐pyran‐4‐ylidene)malononitrile (TPE‐TPA‐DCM), is more emissive in the aggregate state, showing the novel phenomenon of aggregation‐induced emission (AIE). Formulation of TPE‐TPA‐DCM using bovine serum albumin (BSA) as the polymer matrix yields uniformly sized protein nanoparticles (NPs) with high brightness and low cytotoxicity. Applications of the fluorogen‐loaded BSA NPs for in vitro and in vivo far‐red/near‐infrared (FR/NIR) bioimaging are successfully demonstrated using MCF‐7 breast‐cancer cells and a murine hepatoma‐22 (H22)‐tumor‐bearing mouse model, respectively. The AIE‐active fluorogen‐loaded BSA NPs show an excellent cancer cell uptake and a prominent tumor‐targeting ability in vivo due to the enhanced permeability and retention effect.
Risk of intraparenchymal hemorrhage with magnetic resonance imaging‐defined leukoaraiosis and brain infarcts
Authors: Folsom Aaron R. , Yatsuya Hiroshi , Mosley Thomas H. , Psaty Bruce M. , Longstreth W. T. 
Published: December 2011

AbstractObjective:To determine whether the burden of leukoaraiosis and the number of brain infarcts, defined by magnetic resonance imaging (MRI), are prospectively and independently associated with intraparenchymal hemorrhage (IPH) incidence in a pooled population‐based study.Methods:Among 4,872 participants initially free of clinical stroke in the Atherosclerosis Risk in Communities Study and the Cardiovascular Health Study, we assessed white matter grade (range, 0–9), reflecting increasing leukoaraiosis, and brain infarcts using MRI. Over a median of 13 years of follow‐up, 71 incident, spontaneous IPH events occurred.Results:After adjustment for other IPH risk factors, the hazard ratios (95% confidence intervals) across white matter grades 0 to 1, 2, 3, and 4 to 9 were 1.00, 1.68 (0.86–3.30), 3.52 (1.80–6.89), and 3.96 (1.90–8.27), respectively (p for trend <0.0001). These hazard ratios were weakened only modestly (p for trend = 0.0003) with adjustment for MRI‐defined brain infarcts. The IPH hazard ratios for 0, 1, 2, or ≥3 MRI‐defined brain infarcts were 1.00, 1.97 (1.10–3.54), 2.00 (0.83–4.78), and 3.12 (1.31–7.43) (p for trend = 0.002), but these were substantially attenuated when adjusted for white matter grade (p for trend = 0.049).Interpretation:Greater MRI‐defined burden of leukoaraiosis is a risk factor for spontaneous IPH. Spontaneous IPH should be added to the growing list of potential poor outcomes in people with leukoaraiosis. ANN NEUROL 2012;
Demyelination affects temporal aspects of perception: An optic neuritis study
Authors: Raz Noa , Dotan Shlomo , Chokron Sylvie , Ben‐Hur Tamir , Levin Netta 
Published: December 2011

AbstractObjective:Visual Evoked Potentials (VEPs) following optic neuritis (ON) remain chronically prolonged, although standard visual tests indicate full recovery. We hypothesized that dynamic visual processes, such as motion perception, may be more vulnerable to slowed conduction in the optic nerve, and consequently be better associated with projection rates.Methods:Twenty‐one patients with acute unilateral, first‐ever ON were studied during 1 year. Static visual functions (visual acuity, color perception, visual field, and contrast sensitivity), dynamic visual functions (motion perception), and VEPs were assessed repeatedly.Results:Visual and electrophysiological measurements reached maximal performance 4 months following the acute phase, with no subsequent improvement. Whereas VEP amplitude and static visual functions recovered, VEP latency remained significantly prolonged, and motion perception remained impaired throughout the 12‐month period. A strong correlation was found between VEP latencies and motion perception. Visual performance at 1 month was strongly predictive of visual outcome. For static functions, patients who showed partial recovery at 1 month subsequently achieved full recovery. For dynamic functions, the rate of improvement was constant across patients, independent of the initial deficit level.Interpretation:Conduction velocity in the visual pathways correlated closely with dynamic visual functions, implicating the need for rapid transmission of visual input to perceive motion. Motion perception level may serve as a tool to assess the magnitude of myelination in the visual pathways. The constancy across patients may serve as a baseline to assess the efficacy of currently developing neuroprotective and regenerative therapeutic strategies, targeting myelination in the central nervous system. ANN NEUROL 2012