bluuebunny/crossref_metadata_2025_split huggingface dataset:
CEDAR‐GEM Challenge for Systematic Assessment of Ionosphere/Thermosphere Models in Predicting TEC During the 2006 December Storm Event
Authors: Shim J. S. , Rastätter L. , Kuznetsova M. , Bilitza D. , Codrescu M. , Coster A. J. , Emery B. A. , Fedrizzi M. , Förster M. , Fuller‐Rowell T. J. , Gardner L. C. , Goncharenko L. , Huba J. , McDonald S. E. , Mannucci A. J. , Namgaladze A. A. , Pi X. , Prokhorov B. E. , Ridley A. J. , Scherliess L. , Schunk R. W. , Sojka J. J. , Zhu L. 
Published: September 2017

AbstractIn order to assess current modeling capability of reproducing storm impacts on total electron content (TEC), we considered quantities such as TEC, TEC changes compared to quiet time values, and the maximum value of the TEC and TEC changes during a storm. We compared the quantities obtained from ionospheric models against ground‐based GPS TEC measurements during the 2006 AGU storm event (14–15 December 2006) in the selected eight longitude sectors. We used 15 simulations obtained from eight ionospheric models, including empirical, physics‐based, coupled ionosphere‐thermosphere, and data assimilation models. To quantitatively evaluate performance of the models in TEC prediction during the storm, we calculated skill scores such as RMS error, Normalized RMS error (NRMSE), ratio of the modeled to observed maximum increase (Yield), and the difference between the modeled peak time and observed peak time. Furthermore, to investigate latitudinal dependence of the performance of the models, the skill scores were calculated for five latitude regions. Our study shows that RMSE of TEC and TEC changes of the model simulations range from about 3 TECU (total electron content unit, 1 TECU = 1016el m−2) (in high latitudes) to about 13 TECU (in low latitudes), which is larger than latitudinal average GPS TEC error of about 2 TECU. Most model simulations predict TEC better than TEC changes in terms of NRMSE and the difference in peak time, while the opposite holds true in terms of Yield. Model performance strongly depends on the quantities considered, the type of metrics used, and the latitude considered.
FeS
Cluster Assembly:
NIF
System in Nitrogen‐Fixing Bacteria
Authors: Santos Patricia C. Dos , Dean Dennis R. 
Published: September 2017

Abstract

Biological nitrogen fixation is restricted to a specialized group of microorganisms, called diazotrophs, and is catalyzed by the complex metalloenzyme nitrogenase. All diazotrophs recognized so far produce a molybdenum‐containing nitrogenase. However, some diazotrophs also produce paralogous nitrogenases that utilize a transition metal other than Mo as a constituent of the active site cofactor called FeMo‐cofactor. Early genetic studies established that proteins required to produce, activate, and sustain nitrogenase are not limited to the catalytic components but also include other proteins involved in the assembly of nitrogenase‐associated metal‐containing cofactors, protein folding, electron transfer, and regulation. The number of genes associated with nitrogen fixation varies among different species, and the involvement of accessory proteins depends on the metabolic and environmental conditions encountered during growth. To date, nearly all nitrogen‐fixing species having sequenced genomes contain a minimum of six genes dedicated to nitrogen fixation. These include genes encoding the nitrogenase catalytic components,
nifH
,
nifD
,
nifK
, and three genes,
nifE
,
nifN
, and
nifB
, whose products are required for FeMo‐cofactor formation. In some instances, genes associated with nitrogen fixation encode proteins that mirror other related cellular process. For example, the products of
nifU
and
nifS
are specifically involved in the assembly of [Fe–S] clusters dedicated to nitrogenase activation, whereas the structurally and functionally related housekeeping genes
iscU
and
iscS
are involved in [Fe–S] cluster formation that supports other Fe–S proteins.

The best‐studied diazotrophic organism is the strict aerobic microbe
Azotobacter vinelandii
. This organism is capable of producing three genetically distinct, but mechanistically similar, nitrogenases: Mo‐, V‐, and Fe‐only‐dependent enzymes. Under conditions of diazotrophy,
A
.
vinelandii
specifically elevates the expression of more than 60 genes. Among those, NifU and NifS are known to affect the synthesis and accumulation of active nitrogenase catalytic components in all three systems. In this chapter, we describe the initial assembly of [Fe–S] clusters necessary for the formation of both simple and complex [Fe–S] clusters associated with nitrogen fixation. This minimal toolkit for [Fe–S] cluster assembly includes a cysteine desulfurase, encoded by
nifS
, and an [Fe–S] cluster assembly scaffold, encoded by
nifU
. Studies on the nitrogenase specific system have also indicated that electron transfer reactions are required for effective [Fe–S] cluster formation and that preformed [Fe–S] clusters are likely trafficked to client proteins by specific carrier proteins. All of these features have provided a framework for studies on the general process of [Fe–S] cluster assembly that appears to be conserved throughout nature.
FeSCluster Assembly:SUFSystem in Bacteria, Plastids and Archaea
Authors: Dong Guangchao , Witcher Savannah , Outten F. Wayne , Pilon Marinus 
Published: September 2017

AbstractIron–sulfur (Fe–S) clusters are essential cofactors in biology due to their use in critical pathways such as nitrogen fixation, photosynthesis, and respiration. Fe–S cluster biogenesis requires complex systems to mobilize iron and sulfide, assemble the nascent cluster, and target Fe–S clusters to downstream target proteins. All of these steps must be coordinated to protect Fe–S cluster biogenesis intermediates from reactive oxygen species and other stressors. Multiple Fe–S cluster biogenesis pathways exist in different organisms and organelles. The Suf (sulfurformation) pathway is phylogenetically the most ancient of the cluster biogenesis systems and is distributed across all domains of life. It can be found as the primary Fe–S cluster biogenesis pathway or as an auxiliary pathway adapted to maintain Fe–S cluster metabolism under stress conditions. Here we describe the biochemical, genetic, and physiological characterization of the Suf system, in all of its iterations.
Assembly of Nitrogenase
FeMoco
and
P
Cluster
Authors: Sickerman Nathaniel S. , Rettberg Lee A. , Hu Yilin , Ribbe Markus W. 
Published: September 2017

Abstract

The catalytic reduction of dinitrogen by nitrogenase metalloenzymes to form ammonia is a critically important process in the global nitrogen cycle. Accomplishing this difficult reduction reaction under ambient conditions requires the cooperation of a series of nitrogenase proteins. The three main nitrogenase variants known are the iron/molybdenum‐containing Mo‐nitrogenase, the iron/vanadium‐containing V‐nitrogenase, and the iron‐only nitrogenase. All three variants utilize a MgATP‐dependent reductase component and perform substrate reduction within a larger catalytic component. In the case of Mo‐nitrogenase (encoded by
nif
genes), the reductase component, NifH, contains a canonical [Fe
4
S
4
] cluster; the catalytic component, NifDK, contains two unique metal‐containing clusters that are necessary for N
2
reduction: the site of catalytic substrate reduction, the [MoFe
7
S
9
C(
R
‐homocitrate)] FeMo cofactor, also called M cluster, and a capacitor‐like [Fe
8
S
7
]‐core unit called the P cluster. Biosynthesis of these two sophisticated metalloclusters involves the concerted effort of several nitrogenase assembly proteins. For both clusters, simple 2Fe units are first converted to [Fe
4
S
4
] clusters on the scaffold protein NifU with assistance by the cysteine desulfurase enzyme NifS. For M‐cluster biosynthesis, the 4Fe building blocks are supplied to the scaffold protein NifB to equip this radical
S
‐adenosylmethionine (SAM) enzyme with a SAM‐responsive cluster and a pair of 4Fe units called the “K cluster”. One equivalent of SAM donates a methyl group to the K cluster on NifB, while a second equivalent of SAM abstracts a hydrogen atom from the transferred methyl group. The
S
–CH
2
⋅ species formed by the second SAM equivalent facilitates cluster fusion, and following concomitant addition of a “9th sulfur” atom and deprotonation of the methylene unit, the [Fe
8
S
9
C]‐core L cluster is generated. The L cluster is handed off from NifB to another scaffold protein NifEN for further processing. On NifEN, the precursor cluster is matured to the M cluster through the actions of NifH, inserting homocitrate and a reduced form of Mo to produce completed M cluster. Following a conformational rearrangement, NifEN directly transfers the M cluster to a high‐affinity site on NifDK, which embeds the cofactor within the catalytic active site. P cluster biosynthesis begins on NifDK with a pair of protein subunit‐bridging 4Fe clusters termed the P* cluster. Through the actions of NifH and assistance by the chaperone‐like protein NifZ, reductive coupling of the clusters occurs to form functional P cluster. Genetic deletion mutants of NifDK suggest that P‐cluster maturation occurs in a stepwise manner and that M‐cluster insertion is only possible after P‐cluster assembly. This chapter outlines the complex facets of Mo‐nitrogenase metallocluster biosynthesis.
FeFe
‐Hydrogenase Assembly
Authors: Caserta Giorgio , Pecqueur Ludovic , Papini Cecilia , Fontecave Marc 
Published: September 2017

Abstract

Hydrogenases are a class of enzymes involved in the conversion of dihydrogen into protons and electrons and the reverse reaction, reduction of protons into hydrogen. The reaction takes place at a unique 6Fe‐metallocenter, named the H cluster. It consists of a classical [4Fe–4S] cluster and a unique [2Fe] subcluster linked to each other via a cysteine bridge. Maturation of [FeFe]‐hydrogenases involves the synthesis of the ligands of the [2Fe] subcluster, namely CO, CN
−
, and azapropanedithiolate (adt
2−
), and the assembly of the [2Fe] subcluster, depending on the concerted action of three metalloproteins, HydE, HydF, and HydG. HydE and HydG are “radical SAM” enzymes involved in the synthesis of the ligands. HydF functions as a scaffold protein in which a precursor of the [2Fe] subcluster is assembled before being transferred to the hydrogenase. An original chemical approach for the maturation of [FeFe]‐hydrogenases has been recently developed: a small synthetic complex, [Fe
2
(adt)(CO)
4
(CN)
2
]
2−
, mimicking the hydrogenase active site, can transform an inactive hydrogenase, lacking the [2Fe] subcluster, into a fully active enzyme, with no need for the HydEFG maturation machinery. Here, we review the current knowledge regarding the structure and the function of the three maturases and the assembly of the [2Fe] subcluster of [FeFe]‐hydrogenases via natural and chemical maturation.
CODehydrogenase and Acetyl‐CoASynthase Assembly
Authors: Dobbek Holger 
Published: September 2017

AbstractNi,Fe‐containing carbon monoxide dehydrogenases (CODHs) and acetyl‐CoA synthases (ACSs) are ubiquitous among anaerobic bacteria and archaea. CODHs catalyze the reversible reduction of CO2with two electrons and two protons to CO and water. ACSs catalyze the reversible condensation of CO, coenzyme A, and a methyl cation to acetyl‐CoA, and both enzymes can occur in a monofunctional or as a stable bifunctional complex. Compared to what is known about the maturation of other Ni‐containing enzymes, how CODH and ACS mature is just beginning to emerge. Despite differences in active‐site metal content (CODH: 1xNi, 4xFe; ACS: 2xNi, 4xFe), architecture (CODH: Ni integrated in a NiFe3S4cubanoidal subcluster; ACS: two Ni next to a [4Fe4S] cluster), active‐site accessibility, and protein fold, both Ni,Fe‐clusters are matured by homologous ATPases of the MinD/Mrp‐family called CooC (CODH maturation) and AcsF (ACS maturation).CooC sustains the ATP‐dependent Ni insertion into the active‐site cluster of CODHs in the presence of physiological nickel concentrations. CooC can bind nickel at a GCXC motif in the dimer interface and ADP/ATP binding changes the coordination of nickel. AcsF forms a tight complex with Ni‐free ACS, together creating a binding platform for two nickel ions. The Ni‐loaded ACS–AcsF complex remains inactive until MgATP is added to it, resulting in fully active ACS. Details of the mechanisms and structures known to date are discussed in the chapter.
MoCu CO Dehydrogenase Assembly
Authors: Mickoleit Frank 
Published: September 2017

AbstractAerobic chemolithoautotrophic bacteria likeOligotropha carboxidovoransbiosynthesize CO (carbon monoxide) dehydrogenases to utilize CO as energy and carbon source. The enzyme comprises an (LMS)2heterohexameric structure with each heterotrimer building up an electron transport chain. CO oxidation proceeds at a unique bimetallic [CuSMoO2] cluster within the CoxL subunit. Released electrons are subsequently transferred to the [2Fe–2S] clusters of the iron–sulfur protein CoxS. Finally, the electrons are transmitted to the FAD (flavin‐adenine‐dinucleotide) cofactor in CoxM and released to the electron transport system of the cytoplasmic membrane, generating a proton‐motive force. Using substrate analogues and performing quantum chemical modeling, different schemes for the CO oxidation reaction cycle were developed. In the first case, a thiocarbonate transition state was proposed, whereas in the second case it was assumed that binding of CO via its carbon atom to the Cu1+ion is the first step in the catalytic cycle, followed by the transfer of the equatorial oxygen‐derived ligand on the molybdenum. The metal cluster matures post‐translationally with the molybdenum cofactor already being integrated into the completely folded and fully assembled apo‐CO dehydrogenase. Furthermore, the accessory proteins CoxD, CoxE, and CoxF are required. It was suggested that biosynthesis starts with the MgATP‐dependent, reductive sulfuration of [MoVIO3] to [MoVO2SH], which involves the function of the AAA+‐ATPase chaperone CoxD. After reoxidation of the molybdenum, Cu1+is inserted. The latter is supplied by soluble CoxF, which forms a complex with the membrane‐bound von Willebrand protein CoxE. Within this complex, Cu2+is reduced to Cu1+by electrons from respiration. Copper appears as Cu2+‐phytate, is mobilized through the phosphatase/phytase activity of CoxF, and is subsequently transferred to the CoxF copper‐binding site. Knowledge of the molybdenum and copper oxidation states during active‐site cluster assembly also enables the chemical reconstitution of the active site. CoxD, CoxE, and CoxF combine motifs of a DEAD‐box RNA helicase, which leads to a mutual translation of the polypeptides. The presence of a pleckstrin homology (PH) domain on CoxG suggests a role in recruiting CO dehydrogenase to the cytoplasmic membrane enabling electron transfer from the enzyme to the respiratory chain.
Photoassembly of the

CaMn
5
O
5

Catalytic Core and Its Inorganic Mutants in Photosystem
II
Authors: Gates Colin , Ananyev Gennady , Dismukes G. Charles 
Published: September 2017

Abstract
“What I cannot create (build), I do not understand”—Richard Feynman

The ability to take apart and reassemble atom by atom the elements of the water‐oxidizing complex (WOC) of photosynthetic enzymes and substitute each cofactor, while monitoring the consequences on photolytic charge separation and catalytic activity, has given deep insights into how photosynthetic water oxidation works, equal to any other method or technique. Here we summarize the literature covering the reconstitution of the inorganic core (Mn
4
CaO
5
) of photosystem II water‐oxidizing complexes (PSII‐WOCs), called photoassembly, and the consequences of substitution of the inorganic cofactors with nonnative cofactors. We give the evidence that explains the universal utilization of manganese as the sole redox‐active element for O
2
evolution by all native PSII‐WOCs. The selection of Mn
2+
over other more abundant transition metals during uptake and photooxidation by apo‐WOC‐PSII is shown to be achieved by a combination of thermodynamic advantage (bicarbonate stabilization of Mn
3+
photoproduct) and kinetic advantage favoring slow charge recombination from its intermediates. Manganese is shown to be favored over other transition metals because it can operate over a wider range of turnover rates produced by solar fluxes from morning to midday to dusk. The speciation of aqueous manganese in cells in equilibrium with air and bicarbonate is described from thermodynamic data and used to explain how (bi)carbonate stabilizes Mn
2+
→ Mn
3+
photooxidation and provides the core oxo bridges that build the Mn
4
CaO
5
cluster. The oxidation states of manganese obtained from photoassembly experiments are described and compared to spectroscopic results. The functional role of Ca
2+
in photoassembly and catalysis is revealed by substitution with Sr
2+
and Cd
2+
. These properties are advanced in order to understand how it is that evolution of only a single enzymatic blueprint for photosynthetic water oxidation has emerged, despite the access to every ecological niche on Earth and over 3 billion years of evolutionary history.
Urease Activation
Authors: Hausinger Robert P. 
Published: September 2017

Abstract

Synthesis of the urease dinuclear nickel active site requires the apoprotein (Apo), nickel ions, bicarbonate/CO
2
, Mg·GTP, and the participation of several accessory proteins beyond those that transport this metal ion into the cell. Bacteria and archaea typically require UreD (alternatively named UreH in some microorganisms), UreE, UreF, and UreG maturation proteins, whereas fungi and plants possess homologues of UreD, UreF, and UreG but lack proteins comparable to UreE. Unique to the bacterium
Helicobacter pylori
, the hydrogenase activation proteins HypA and HypB are also required for urease maturation. The various components have been shown to form specific protein–protein complexes: Apo·UreD, Apo·UreD·UreF, Apo·UreD·UreF·UreG, UreH·UreF, UreD/H·UreF·UreG, HypA·HypB, HypA·UreE, and UreE·UreG under defined conditions. In the current model for urease activation, (i) a lysine residue at the nascent active site of urease is carbamylated by CO
2
to form a metal‐bridging ligand, (ii) the metallochaperone UreE donates nickel to UreG, (iii) nickel‐bound UreG forms the Apo·UreD·UreF·UreG·Ni preactivation complex, (iv) nickel transfer from UreG to Apo is driven by the GTPase activity of UreG, (v) nickel ions pass through a molecular tunnel within the UreF and UreD/H scaffold proteins, (vi) metallocenter assembly is followed by dissociation of the accessory proteins from the urease holoenzyme. In
H. pylori
, HypA and HypB are thought to provide nickel to UreE. Here, evidence supporting the current model for urease maturation is summarized and the remaining open questions related to this process are discussed.
Topaquinone Biogenesis in Cu Amine Oxidases
Authors: Dooley David M. , Brown Doreen E. , Shepard Eric M. 
Published: September 2017

AbstractCopper‐containing amine and lysyl oxidase (LOX) enzymes are responsible for catalyzing the oxidative deamination of biogenic primary amines or lysine residues in connective tissue precursor proteins. These two enzyme classes each undergo remarkable posttranslational, self‐processing reactions that are dependent solely on copper and molecular oxygen. The formation of the mature enzymes involves oxidation of an absolutely conserved tyrosine residue within the polypeptide sequence of the protein and results in formation of a quinone species. The autocatalytic process generates trihydroxyphenylalanine quinone (TPQ) in copper‐containing amine oxidases (CuAO) and lysyl tyrosine quinone (LTQ) in LOXs. The discovery of TPQ was the first of its kind and helped establish a new paradigm in biology for the modification and synthesis of amino acid derivatives that in turn exhibit unique chemical functionality. For copper‐containing amine and LOX enzymes, the quinone cofactors themselves are responsible for the coordination of amine substrates in Schiff base complexes, which then can be hydrolyzed to yield aldehyde product and a reduced aminoquinol that must then be reoxidized to afford the resting state of the enzyme. In terms of the biogenesis mechanisms, the tyrosine residue that undergoes oxidation is bound in close proximity to a type II copper center. Initial steps in TPQ and LTQ biosynthesis are proposed to be identical, and one possibility invokes coordination of tyrosine to copper(II) to introduce some radical or charge‐transfer character into the ring that could increase susceptibility to attack by molecular oxygen to yield a copper(II)‐peroxoquinone species; this moiety is then converted into 3,4‐dihydroxyphenylalanine quinone or dopaquinone. At this stage, TPQ biogenesis proceeds through attack of solvent water or hydroxide to the O2 position of the ring, whereas LTQ biogenesis proceeds through attack of a conserved polypeptide‐derived lysine residue to the O2 position of the ring. This chapter summarizes the discoveries of TPQ and LTQ and the large repertoire of experimental work that has gone into understanding the biogenesis mechanisms for these two extraordinary biological cofactors.
A patient safety education program in a medical physics residency
Authors: Ford Eric C. , Nyflot Matthew , Spraker Matthew B. , Kane Gabrielle , Hendrickson Kristi R. G. 
Published: September 2017

AbstractEducation in patient safety and quality of care is a requirement for radiation oncology residency programs according to accrediting agencies. However, recent surveys indicate that most programs lack a formal program to support this learning. The aim of this report was to address this gap and share experiences with a structured educational program on quality and safety designed specifically for medical physics therapy residencies. Five key topic areas were identified, drawn from published recommendations on safety and quality. A didactic component was developed, which includes an extensive reading list supported by a series of lectures. This was coupled with practice‐based learning which includes one project, for example, failure modes and effect analysis exercise, and also continued participation in the departmental incident learning system including a root‐cause analysis exercise. Performance was evaluated through quizzes, presentations, and reports. Over the period of 2014–2016, five medical physics residents successfully completed the program. Evaluations indicated that the residents had a positive experience. In addition to educating physics residents this program may be adapted for medical physics graduate programs or certificate programs, radiation oncology residencies, or as a self‐directed educational project for practicing physicists. Future directions might include a system that coordinates between medical training centers such as a resident exchange program.