bluuebunny/crossref_metadata_2025_split huggingface dataset:
The crystal structure of NADPH: Ferredoxin reductase from azotobacter vinelandii
Authors: Prasad G. Sridhar , Kresge N. , Muhlberg A. B. , Shaw A. , Stout C. D. , Jung Y. S. , Burgess B. K. 
Published: February 2009

AbstractNADPH: ferredoxin reductase (AvFPR) is involved in the response to oxidative stress in Azotobacter vinelandii. The crystal structure of AvFPR has been determined at 2.0 Å resolution. The polypeptide fold is homologous with six other oxidoreductases whose structures have been solved including Escherichia coli flavodoxin reductase (EcFldR) and spinach, and Anabaena ferredoxin:NADP+ reductases (FNR). AvFPR is overall most homologous to EcFldR. The structure is comprised of a N‐terminal six‐stranded antiparallel β‐barrel domain, which binds FAD, and a C‐terminal five‐stranded parallel β‐sheet domain, which binds NADPH/NADP+ and has a classical nucleotide binding fold. The two domains associate to form a deep cleft where the NADPH and FAD binding sites are juxtaposed. The structure displays sequence conserved motifs in the region surrounding the two dinucleotide binding sites, which are characteristic of the homologous enzymes. The folded over conformation of FAD in AvFPR is similar to that in EcFldR due to stacking of Phe255 on the adenine ring of FAD, but it differs from that in the FNR enzymes, which lack a homologous aromatic residue. The structure of AvFPR displays three unique features in the environment of the bound FAD. Two features may affect the rate of reduction of FAD: the absence of an aromatic residue stacked on the isoalloxazine ring in the NADPH binding site; and the interaction of a carbonyl group with N10 of the flavin. Both of these features are due to the substitution of a conserved C‐terminal tyrosine residue with alanine (Ala254) in AvFPR. An additional unique feature may affect the interaction of AvFPR with its redox partner ferredoxin I (FdI). This is the extension of the C‐terminus by three residues relative to EcFldR and by four residues relative to FNR. The C‐terminal residue, Lys258, interacts with the AMP phosphate of FAD. Consequently, both phosphate groups are paired with a basic group due to the simultaneous interaction of the FMN phosphate with Arg51 in a conserved FAD binding motif. The fourth feature, common to homologous oxidoreductases, is a concentration of 10 basic residues on the face of the protein surrounding the active site, in addition to Arg51 and Lys258.
Crystal structure of two quaternary complexes of dethiobiotin synthetase, enzyme‐MgADP‐AlF3‐diaminopelargonic acid and enzyme‐MgADP‐dethiobiotin‐phosphate; implications for catalysis
Authors: Käck Helena , Sandmark Jenny , Schneider Gunter , Lindqvist Ylva , Gibson Katharine J. 
Published: February 2009

AbstractThe crystal structures of two complexes of dethiobiotin synthetase, enzyme‐diaminopelargonic acid‐MgADP‐AlF3 and enzyme‐dethiobiotin‐MgADP‐Pi, respectively, have been determined to 1.8 Å resolution. In dethiobiotin synthetase, AlF3 together with carbamylated diaminopelargonic acid mimics the phosphorylated reaction intermediate rather than the transition state complex for phosphoryl transfer. Observed differences in the binding of substrate, diaminopelargonic acid, and the product, dethiobiotin, suggest considerable displacements of substrate atoms during the ring closure step of the catalytic reaction. In both complexes, two metal ions are observed at the active site, providing evidence for a two‐metal mechanism for this enzyme.
Unfolding and refolding of dimeric creatine kinase equilibrium and kinetic studies
Authors: Fan Ying‐Xin , Zhou Jun‐Mei , Tsou Chen‐Lu , Kihara Hiroshi 
Published: February 2009

AbstractEquilibrium and kinetic studies of the guanidine hydrochloride induced unfolding‐refolding of dimeric cytoplasmic creatine kinase have been monitored by intrinsic fluorescence, far ultraviolet circular dichroism, and 1‐anilinonaphthalene‐8‐sulfonate binding. The GuHCl induced equilibrium‐unfolding curve shows two transitions, indicating the presence of at least one stable equilibrium intermediate in GuHCl solutions of moderate concentrations. This intermediate is an inactive monomer with all of the thiol groups exposed. The thermodynamic parameters obtained by analysis using a three‐state model indicate that this intermediate is similar in energy to the fully unfolded state. There is a burst phase in the refolding kinetics due to formation of an intermediate within the dead time of mixing (15 ms) in the stopped‐flow apparatus. Further refolding to the native state after the burst phase follows biphasic kinetics. The properties of the burst phase and equilibrium intermediates were studied and compared. The results indicate that these intermediates are similar in some respects, but different in others. Both are characterized by pronounced secondary structure, compact globularity, exposed hydrophobic surface area, and the absence of rigid side‐chain packing, resembling the “molten globule” state. However, the burst phase intermediate shows more secondary structure, more exposed hydrophobic surface area, and more flexible side‐chain packing than the equilibrium intermediate. Following the burst phase, there is a fast phase corresponding to folding of the monomer to a compact conformation. This is followed by rapid assembly to form the dimer. Neither of the equilibrium unfolding transitions are protein concentration dependent. The refolding kinetics are also not concentration dependent. This suggests that association of the subunits is not rate limiting for refolding, and that under equilibrium conditions, dissociation occurs in the region between the two unfolding transitions. Based upon the above results, schemes of unfolding and refolding of creatine kinase are proposed.
Quantum chemical calculations of the reorganization energy of blue‐copper proteins
Authors: Olsson Mats H.M. , Ryde Ulf , Roos Björn O. 
Published: February 2009

AbstractThe inner‐sphere reorganization energy for several copper complexes related to the active site in blue‐copper protein has been calculated with the density functional B3LYP method. The best model of the blue‐copper proteins, Cu(Im)2(SCH3)(S(CH3)2)0/+, has a self‐exchange inner‐sphere reorganization energy of 62 kJ/mol, which is at least 120 kJ/mol lower than for Cu(H2O)4+/2+. This lowering of the reorganization energy is caused by the soft ligands in the blue‐copper site, especially the cysteine thiolate and the methionine thioether groups. Soft ligands both make the potential surfaces of the complexes flatter and give rise to oxidized structures that are quite close to a tetrahedron (rather than tetragonal). Approximately half of the reorganization energy originates from changes in the copper‐ligand bond lengths and half of this contribution comes from the Cu‐SCys bond. A tetragonal site, which is present in the rhombic type 1 blue‐copper proteins, has a slightly higher (16 kJ/mol) inner‐sphere reorganization energy than a trigonal site, present in the axial type 1 copper proteins. A site with the methionine ligand replaced by an amide group, as in stellacyanin, has an even higher reorganization energy, about 90 kJ/mol.
Atomic resolution structure of the cytoplasmic domain of Yersinia pestis YscU, a regulatory switch involved in type III secretion
Authors: Lountos George T. , Austin Brian P. , Nallamsetty Sreedevi , Waugh David S. 
Published: February 2009

AbstractCrystal structures of cleaved and uncleaved forms of the YscU cytoplasmic domain, an essential component of the type III secretion system (T3SS) in Yersinia pestis, have been solved by single‐wavelength anomolous dispersion and refined with X‐ray diffraction data extending up to atomic resolution (1.13 Å). These crystallographic studies provide structural insights into the conformational changes induced upon auto‐cleavage of the cytoplasmic domain of YscU. The structures indicate that the cleaved fragments remain bound to each other. The conserved NPTH sequence that contains the site of the N263‐P264 peptide bond cleavage is found on a β‐turn which, upon cleavage, undergoes a major reorientation of the loop away from the catalytic N263, resulting in altered electrostatic surface features at the site of cleavage. Additionally, a significant conformational change was observed in the N‐terminal linker regions of the cleaved and noncleaved forms of YscU which may correspond to the molecular switch that influences substrate specificity. The YscU structures determined here also are in good agreement with the auto‐cleavage mechanism described for the flagellar homolog FlhB and E. coli EscU.
Dematin exhibits a natively unfolded core domain and an independently folded headpiece domain
Authors: Chen Lin , Jiang Zhenghui G. , Khan Anwar A. , Chishti Athar H. , McKnight C. James 
Published: February 2009

AbstractDematin is an actin‐binding protein originally identified in the junctional complex of the erythrocyte plasma membrane, and is present in many nonerythroid cells. Dematin headpiece knockout mice display a spherical red cell phenotype and develop a compensated anemia. Dematin has two domains: a 315‐residue, proline‐rich “core” domain and a 68‐residue carboxyl‐terminal villin‐type “headpiece” domain. Expression of full‐length dematin in E. coli as a GST recombinant protein results in truncation within a proline, glutamic acid, serine, threonine rich region (PEST). Therefore, we designed a mutant construct that replaces the PEST sequence. The modified dematin has high actin binding activity as determined by actin sedimentation assays. Negative stain electron microscopy demonstrates that the modified dematin also exhibits actin bundling activity like that of native dematin. Circular dichroism (CD) and NMR spectral analysis, however, show little secondary structure in the modified dematin. The lack of secondary structure is also observed in native dematin purified from human red blood cells. 15N‐HSQC NMR spectra of modified dematin indicate that the headpiece domain is fully folded whereas the core region is primarily unfolded. Our finding suggests that the core is natively unfolded and may serve as a scaffold to organize the components of the junctional complex.
Structure and function of Pseudomonas aeruginosa protein PA1324 (21–170)
Authors: Mercier Kelly A. , Cort John R. , Kennedy Michael A. , Lockert Erin E. , Ni Shuisong , Shortridge Matthew D. , Powers Robert 
Published: February 2009

AbstractPseudomonas aeruginosa is the prototypical biofilm‐forming gram‐negative opportunistic human pathogen. P. aeruginosa is causatively associated with nosocomial infections and with cystic fibrosis. Antibiotic resistance in some strains adds to the inherent difficulties that result from biofilm formation when treating P. aeruginosa infections. Transcriptional profiling studies suggest widespread changes in the proteome during quorum sensing and biofilm development. Many of the proteins found to be upregulated during these processes are poorly characterized from a functional standpoint. Here, we report the solution NMR structure of PA1324, a protein of unknown function identified in these studies, and provide a putative biological functional assignment based on the observed prealbumin‐like fold and FAST‐NMR ligand screening studies. PA1324 is postulated to be involved in the binding and transport of sugars or polysaccharides associated with the peptidoglycan matrix during biofilm formation.
Conformation of a plasmid replication initiator protein affects its proteolysis by ClpXP system
Authors: Pierechod Marcin , Nowak Agnieszka , Saari Anna , Purta Elzbieta , Bujnicki Janusz M. , Konieczny Igor 
Published: February 2009

AbstractProteins from the Rep family of DNA replication initiators exist mainly as dimers, but only monomers can initiate DNA replication by interaction with the replication origin (ori). In this study, we investigated both the activation (monomerization) and the degradation of the broad‐host‐range plasmid RK2 replication initiation protein TrfA, which we found to be a member of a class of DNA replication initiators containing winged helix (WH) domains. Our in vivo and in vitro experiments demonstrated that the ClpX‐dependent activation of TrfA leading to replicationally active protein monomers and mutations affecting TrfA dimer formation, result in the inhibition of TrfA protein degradation by the ClpXP proteolytic system. These data revealed that the TrfA monomers and dimers are degraded at substantially different rates. Our data also show that the plasmid replication initiator activity and stability in E. coli cells are affected by ClpXP system only when the protein sustains dimeric form.
Computational studies of H5N1 influenza virus resistance to oseltamivir
Authors: Wang Nick X. , Zheng Jie J. 
Published: February 2009

AbstractInfluenza A (H5N1) virus is one of the world's greatest pandemic threats. Neuraminidase (NA) inhibitors, oseltamivir and zanamivir, prevent the spread of influenza, but drug‐resistant viruses have reduced their effectiveness. Resistance depends on the binding properties of NA‐drug complexes. Key residue mutations within the active site of NA glycoproteins diminish binding, thereby resulting in drug resistance. We performed molecular simulations and calculations to characterize the mechanisms of H5N1 influenza virus resistance to oseltamivir and predict potential drug‐resistant mutations. We examined two resistant NA mutations, H274Y and N294S, and one non‐drug‐resistant mutation, E119G. Six‐nanosecond unrestrained molecular dynamic simulations with explicit solvent were performed using NA‐oseltamivir complexes containing either NA wild‐type H5N1 virus or a variant. MM_PBSA techniques were then used to rank the binding free energies of these complexes. Detailed analyses indicated that conformational change of E276 in the Pocket 1 region of NA is a key source of drug resistance in the H274Y mutant but not in the N294S mutant.
Opposite allosteric mechanisms in TetR and CAP
Authors: Seedorff Jennifer E. , Rodgers Michael E. , Schleif Robert 
Published: February 2009

AbstractRegulation of the DNA binding affinity of an oligomeric protein can be considered to consist of an intrinsic component, in which the affinity of an individual DNA‐binding domain is modulated in response to effector binding, and an extrinsic component, in which the relative position of the protein's two DNA‐binding domains are altered so that they can or cannot contact both half‐site operators simultaneously. We demonstrated directly that the TetR repressor utilizes an extrinsic mechanism and CAP, the catabolite activator protein, utilizes an intrinsic mechanism.
Effect of seven new orchard pesticides on Galendromus occidentalis in laboratory studies
Authors: Bostanian Noubar J , Thistlewood Howard A , Hardman John M , Laurin Marie‐Claude , Racette Gaétan 
Published: February 2009

AbstractBACKGROUND: Biological control of phytophagous mites in orchards requires that pesticides used to manage other arthropod pests or diseases are harmless to predacious mites, as these are essential to keep phytophagous mites at non‐injurious population levels. This study evaluates the possible toxic attributes of acetamiprid, imidacloprid, thiacloprid, thiamethoxam, spirodiclofen, spinosad and methoxyfenoxide currently used in western Canadian orchards.RESULTS: None of these pesticides has any ovicidal properties against Galendromus occidentalis (Nesbitt). Imidacloprid and acetamiprid were highly toxic to the adults and reduced fecundity significantly. Thiamethoxam and spirodiclofen were non‐toxic to adults, but they slightly reduced fecundity. Thiacloprid, spinosad and methoxyfenoxide were harmless to adults and had no effect on fecundity. All compounds showed some repellence at 24 h intervals for 72 h.CONCLUSIONS: Imidacloprid and acetamiprid are incompatible with IPM programs because they are toxic to adults and negatively affect fecundity. Thiamethoxam and spirodiclofen need further field evaluation to determine if they are compatible with IPM programs because they slightly reduced fecundity. Thiacloprid, spinosad and methoxyfenoxide are harmless to adults, but they are slightly repellent. Therefore, with the exception of imidacloprid and acetamiprid, all these compounds should be field tested for compatibility in an IPM program. © Her Majesty the Queen in Right of Canada, as represented by the Minister of Agriculture and Agri‐Food Canada. Published by John Wiley & Sons, Ltd
The oxidation metabolites of endomorphin 1 and its fragments induced by free radicals
Authors: Gong Pin , Chen Fu Xin , Zhao Qianyu , Ma Guo Fen , Wang Rui 
Published: February 2009

AbstractEndomorphin 1 (EM1), an endogenous µ‐opioid receptor agonist, acts as a free radical scavenger in vitro and an antioxidant in vivo. The modification of EM1 by ROS and the properties of the OM attracted our attention. In vitro assays were performed via RP‐HPLC, spectrophotometric measurements, EPR and amino acid analysis, Schmorl's reaction to define the formation of melanin‐like compounds transformed from EM1, collectively named EM1–melanin and by solubility assay, radioligand‐binding assay, NADH oxidation, superoxide anion scavenging assay to study some physical and chemical properties of EM1–melanin. Possible pathways of the formation of EM1–melanin were proposed. Copyright © 2009 European Peptide Society and John Wiley & Sons, Ltd.
Assimilation of IASI at the Met Office and assessment of its impact through observing system experiments
Authors: Hilton F. , Atkinson N. C. , English S. J. , Eyre J. R. 
Published: February 2009

AbstractObservations from the Infrared Atmospheric Sounding Interferometer (IASI), onboard EUMETSAT's MetOp satellite, have been assimilated at the Met Office in global and regional numerical weather‐prediction systems since 27 November 2007. Pre‐operational trials of IASI assimilation in the global model during the summer of 2007 delivered a positive impact on forecasts approximately twice as large as that shown by the Atmospheric InfraRed Sounder (AIRS) on the EOS‐Aqua satellite. A series of observing system experiments confirmed the relative performance of IASI and AIRS, and showed that impact from IASI is equivalent to a single Advanced Microwave Sounding Unit‐A (AMSU‐A) combined with a single Microwave Humidity Sounder (MHS). The results of an IASI assimilation trial for the winter of 2007 were consistent with those of the summer trial, although the impact was slightly lower overall. The assessment of impact is strongly dependent on the variables and methods chosen for verification: assimilation trials with the regional model showed similar improvements to the large‐scale fields (e.g. mean‐sea‐level pressure and geopotential height) as seen in the global model, but no forecast impact was seen for variables such as visibility and rain‐rate. © Crown Copyright 2009. Reproduced with the permission of the Controller of HMSO. Published by John Wiley & Sons, Ltd.
Ground verification of the feasibility of telepresent on‐orbit servicing
Authors: Stoll Enrico , Walter Ulrich , Artigas Jordi , Preusche Carsten , Kremer Philipp , Hirzinger Gerd , Letschnik Jürgen , Pongrac Helena 
Published: February 2009

AbstractIn an ideal casetelepresenceachieves a state in which a human operator can no longer differentiate between an interaction with a real environment and a technical mediated one. This state is called transparent telepresence. The applicability of telepresence to on‐orbit servicing (OOS), i.e., an unmanned servicing operation in space, teleoperated from ground in real time, is verified in this paper. For this purpose, a communication test environment was set up on the ground, which involved the Institute of Astronautics (LRT) ground station in Garching, Germany, and the European Space Agency (ESA) ground station in Redu, Belgium. Both were connected via the geostationary ESA data relay satellite ARTEMIS. Utilizing the data relay satellite, a teleoperation was accomplished in which the human operator as well as the (space) teleoperator was located on the ground. The feasibility of telepresent OOS was evaluated, using an OOS test bed at the Institute of Mechatronics and Robotics at the German Aerospace Center (DLR). The manipulation task was representative for OOS and supported real‐time feedback from the haptic‐visual workspace. The tests showed that complex manipulation tasks can be fulfilled by utilizing geostationary data relay satellites. For verifying the feasibility of telepresent OOS, different evaluation methods were used. The properties of the space link were measured and related to subjective perceptions of participants, who had to fulfill manipulation tasks. An evaluation of the transparency of the system, including the data relay satellite, was accomplished as well. © 2009 Wiley Periodicals, Inc.
The onset of dominance in balls‐in‐bins processes with feedback
Authors: Oliveira Roberto Imbuzeiro 
Published: February 2009

AbstractConsider a balls‐in‐bins process in which each new ball goes into a given bin with probability proportional to f(n), where n is the number of balls currently in the bin and f is a fixed positive function. It is known that these so‐called balls‐in‐bins processes with feedback have a monopolistic regime: if f(x) = xp for p > 1, then there is a finite time after which one of the bins will receive all incoming balls.Our goal in this article is to quantify the onset of monopoly. We show that the initial number of balls is large and bin 1 starts with a fraction α > 1/2 of the balls, then with very high probability its share of the total number of balls never decreases significantly below α. Thus a bin that obtains more than half of the balls at a “large time” will most likely preserve its position of leadership. However, the probability that the winning bin has a non‐negligible advantage after n balls are in the system is ∼const. × n1‐p, and the number of balls in the losing bin has a power‐law tail. Similar results also hold for more general functions f. © 2009 Wiley Periodicals, Inc. Random Struct. Alg., 2009
Greedy colorings of uniform hypergraphs
Authors: Pluhár András 
Published: February 2009

AbstractWe give a very short proof of an Erdős conjecture that the number of edges in a non‐2‐colorable n‐uniform hypergraph is at least f(n)2n, where f(n) goes to infinity. Originally it was solved by József Beck in 1977, showing that f(n) at least clog n. With an ingenious recoloring idea he later proved that f(n) ≥ cn1/3+o(1). Here we prove a weaker bound on f(n), namely f(n) ≥ cn1/4. Instead of recoloring a random coloring, we take the ground set in random order and use a greedy algorithm to color. The same technique works for getting bounds on k‐colorability. It is also possible to combine this idea with the Lovász Local Lemma, reproving some known results for sparse hypergraphs (e.g., the n‐uniform, n‐regular hypergraphs are 2‐colorable if n ≥ 8). © 2009 Wiley Periodicals, Inc. Random Struct. Alg., 2009
Regression analysis of mean quality‐adjusted survival time based on pseudo‐observations
Authors: Tunes‐da‐Silva G. , Klein J. P. 
Published: February 2009

AbstractRegression models for the mean quality‐adjusted survival time are specified from hazard functions of transitions between two states and the mean quality‐adjusted survival time may be a complex function of covariates. We discuss a regression model for the mean quality‐adjusted survival (QAS) time based on pseudo‐observations, which has the advantage of directly modeling the effect of covariates in the QAS time. Both Monte Carlo simulations and a real data set are studied. Copyright © 2009 John Wiley & Sons, Ltd.