bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Nucleobase‐Cation‐Symport‐1 Family of Membrane Transport Proteins
Authors: Weyand Simone , Ma Pikyee , Saidijam Massoud , Baldwin Jocelyn , Beckstein Oliver , Jackson Scott , Suzuki Shun'ichi , Patching Simon G , Shimamura Tatsuro , Sansom Mark SP , Iwata So , Cameron Alexander D , Baldwin Stephen A , Henderson Peter JF 
Published: December 2011

AbstractThe evolutionary relationships of membrane transport proteins of the nucleobase‐cation‐symport (NCS‐1) family from bacteria, fungi, and plants are described. The reported substrates of the NCS‐1 family include nucleobases, hydantoins, and vitamins. Secondary active transport of substrate accompanied by a sodium ion, or possibly a proton, is the usual mechanism of energization. A strategy for the amplified expression, purification, and activity assays of bacterial members of the NCS‐1 family is described. Conditions are given for the production of diffracting crystals of one member, the Na+‐coupled transporter for aromatic hydantoins, ‘Mhp1’, fromMicrobacterium liquefaciens. The 3D structures of three forms of the Mhp1 protein are discussed in terms of one open‐outward, one substrate‐occluded, and one open‐inward conformation contributing to a molecular dynamics simulation of the alternating‐access model of membrane transport. The unexpected similarity of the protein fold of Mhp1 to those of transport proteins, hitherto thought to be from different evolutionary families, is discussed.
Phosphotriesterase
Authors: Bigley Andrew N , Raushel Frank M 
Published: December 2011

AbstractPhosphotriesterase (PTE) is a member of the amidohydrolase superfamily with the ability to hydrolyze numerous organophosphate substrates including many insecticides and nerve agents. The native active site metal is zinc, but the enzyme is fully active with a variety of metals. The overall fold of PTE is a (β/α)8TIM‐barrel with the active site located at the C‐terminal end of the barrel. The active site contains the binuclear metal center with the metal ligands being four histidines, an aspartate, and a carboxylated lysine from the C‐terminal ends of the β‐strands. In addition, the metal center contains a bridging hydroxyl that serves as the nucleophile in the SN2‐like reaction. The substrate‐binding site is external to the metal center and is made of residues from the loops connecting the C‐terminal end of each β‐strand to the subsequent α‐helix. The best known substrate for PTE is the insecticide paraoxon, which has a kinetic efficiency that approaches the limits of diffusion. PTE has significant potential as an enzyme tool for the detection and decontamination of pesticides and nerve agents. Numerous variants of PTE have been developed by directed evolution with improved kinetic efficiency toward various organophosphates.
Cadmium‐Carbonic Anhydrase
Authors: Xu Yan , Supuran Claudiu T , Morel François M M 
Published: December 2011

Abstract

Cadmium‐carbonic anhydrase (CDCA1) is a ζ‐carbonic anhydrase (CA) isolated from the marine diatom
Thalassiosira weissflogii
, which naturally uses Cd as its metal cofactor. Its homolog gene has been found in a number of diatom species as well as natural assemblages. The expression of
cdca1
gene at both transcript and protein levels is regulated by pH/
p
CO
2
and Cd and Zn availabilities in seawater. The amino acid sequence contains a triple repeat with high identity among repeats, and each single repeat is a functional CA and a structural mimic of a functional β‐CA dimer. CDCA1 incorporates either Zn or Cd at its active site and readily exchanges one with the other. The metal cofactor is tetrahedrally coordinated by two Cys, a His, and a water molecule and an open conformation is adapted at the active site when the metal is absent. The catalytic efficiencies of both the Cd‐ and Zn‐bound CDCA1 are pH dependent and the Zn‐bound CDCA1 is more active than the Cd‐bound CDCA1.
Octaheme CytochromecNitrite Reductase
Authors: Tikhonova Tamara V , Polyakov Konstantin M , Boyko Konstantin M , Safonova Tatiana N , Popov Vladimir O 
Published: December 2011

AbstractOctaheme cytochromecnitrite reductase (TvNiR) from bacteriumThioalkalivibrio nitratireducenscatalyzes the six‐electron reduction of nitrite and two‐electron reduction of hydroxylamine to ammonium without release of any intermediates. TvNiR also catalyzes the six‐electron reduction of sulfite to sulfide. High‐resolution structures of the TvNiR apo‐form and its complexes with the substrates (nitrite and sulfite) and inhibitors (azide and phosphate) were obtained. The subunit of TvNiR consists of two domains. The N‐terminal domain has a unique fold and contains three hemes. The remaining five hemes are located in the catalytic C‐terminal domain, with the heme arrangement, including the catalytic heme, being identical to that found in pentaheme cytochromecnitrite reductases (ccNiRs). The catalytic machinery of TvNiR resembles that of ccNiRs. It comprises the lysine residue in the proximal position of the catalytic heme, the catalytic triad of tyrosine, histidine, and arginine on the distal side, channels for the substrate and product transport, and two conserved Ca2+‐binding sites. The complete set of eight hemes forms a spatial pattern characteristic of other structurally characterized octaheme cytochromes. In the crystalline state and in solution, TvNiR exists as a stable hexamer containing 48 hemes, which are clustered into three isolated groups, each group comprising 16 interacting hemes.
Human Cytosolic
X
‐Prolyl Aminopeptidase
Authors: Li Xin , Bartlam Mark , Rao Zihe 
Published: December 2011

Abstract
X‐prolyl aminopeptidases catalyze the removal of a penultimate prolyl residue from the N‐termini of peptides. Mammalian X‐prolyl aminopeptidases are responsible for the degradation of bradykinin, a blood pressure regulator peptide, and have been linked to myocardial infarction. The X‐ray crystal structure of human cytosolic X‐prolyl aminopeptidase (XPNPEP1) reveals a dimer with a unique three‐domain organization in each subunit, rather than the two domains common to all other known structures of X‐prolyl aminopeptidases and prolidases. The C‐terminal catalytic domain of XPNPEP1 coordinates two metal ions and shares a similar fold with other prolyl aminopeptidases. Metal content analysis and activity assays confirm that the enzyme is double Mn(II) dependent for its activity, which contrasts with the previous notion that each XPNPEP1 subunit contains only one Mn(II) ion.
Peptidyl‐α‐Hydroxyglycine α‐Amidating Lyase (PAL)
Authors: Chufán Eduardo E , Eipper Betty , Mains Richard , Amzel Mario L 
Published: December 2011

AbstractMany peptide hormones and neuropeptides require an amidated carboxy terminal for full biological activity. This reaction is carried out in two steps: hydroxylation of a C‐terminal glycine and cleavage of the C N bond with the release of glyoxylate. The enzyme peptidyl‐α‐hydroxyglycine α‐amidating lyase (PAL; EC 4.3.2.5) catalyzes the second step of this reaction,N‐dealkylation of the peptidyl‐α‐hydroxyglycine to generate the α‐amidated peptide and glyoxylate. The X‐ray crystal structure of the PAL catalytic core (PALcc), alone and in complex with the nonpeptidic substrate α‐hydroxyhippuric acid, shows that PAL folds as a six‐bladed β‐propeller. The active site is formed by a Zn2+ion coordinated by three histidine residues; the substrate binds to this site with its α‐hydroxyl group coordinated to the Zn2+ion. A tyrosine residue (Tyr654) at the active site acts as the catalytic base for hydroxyl deprotonation, an unusual role for tyrosine residue. In the reaction mechanism, proposed on the basis of the structure and validated by biochemical analysis of site‐directed PALcc mutants, the substrate α‐hydroxyl that coordinates the catalytic Zn2+directly is deprotonated by Tyr654. The generation of the required tyrosinate is aided by an arginine residue that, together with the Zn2+, lowers the pKaof the catalytic tyrosine.
Etherification of Functionalized Phenols with Chloroheteroarenes at Low Palladium Loading: Theoretical Assessment of the Role of Triphosphane Ligands in CO Reductive Elimination
Authors: Platon Mélanie , Cui Luchao , Mom Sophal , Richard Philippe , Saeys Mark , Hierso Jean‐Cyrille 
Published: December 2011

AbstractThe present study highlights the potential of robust tridentate ferrocenylphosphanes with controlled conformation as catalytic auxiliaries in CO bond formation reactions. Air‐stable palladium triphosphane systems are efficient for selective heteroaryl ether synthesis by using as little as 0.2 mol% of catalyst. These findings represent an economically attractive and clean etherification of functionalized phenols, electron‐rich, electron‐poor and para‐, meta‐ or ortho‐substituted substrates, with heteroaryl chlorides, including pyridines, hydroxylated pyridine, pyrimidines and thiazole. The etherification tolerates very important functions in various positions, such as cyano, methoxy, amino, and fluoro groups, which is useful to synthesize bioactive molecules. DFT studies furthermore demonstrate that triphosphane ligands open up various new pathways for the CO reductive elimination involving the third phosphane group. In particular, the rate for one of these new pathways is calculated to be about 1000 times faster than for reductive elimination from a complex with a similar ferrocenyl ligand, but without a phosphane group on the bottom Cp‐ring. Coordination of the third phosphane group to the palladium(II) center is calculated to stabilize the transition state in this new pathway, thereby enhancing the reductive elimination rate.
Semi‐parametric area under the curve regression method for diagnostic studies with ordinal data
Authors: Rajan Kumar B. , Zhou Xiao‐Hua 
Published: December 2011

AbstractThe classification accuracy of new diagnostic tests is based on receiver operating characteristic (ROC) curves. The area under the ROC curve (AUC) is one of the well‐accepted summary measures for describing the accuracy of diagnostic tests. The AUC summary measure can vary by patient and testing characteristics. Thus, the performance of the test may be different in certain subpopulation of patients and readers. For this purpose, we propose a direct semi‐parametric regression model for the non‐parametric AUC measure for ordinal data while accounting for discrete and continuous covariates. The proposed method can be used to estimate the AUC value under degenerate data where certain rating categories are not observed. We will discuss the non‐standard asymptotic theory, since the estimating functions were based on cross‐correlated random variables. Simulation studies based on different classification models showed that the proposed model worked reasonably well with small percent bias and percent mean‐squared error. The proposed method was applied to the prostate cancer study to estimate the AUC for four readers, and the carotid vessel study with age, gender, history of previous stroke, and total number of risk factors as covariates, to estimate the accuracy of the diagnostic test in the presence of subject‐level covariates.
Targeting Zinc Finger Domains with Small Molecules: Solution Structure and Binding Studies of the RanBP2‐Type Zinc Finger of RBM5
Authors: Farina Biancamaria , Fattorusso Roberto , Pellecchia Maurizio 
Published: December 2011

AbstractThe RNA binding motif protein 5 (RBM5), also known as Luca15 or H37, is a component of prespliceosomal complexes that regulates the alternative splicing of several mRNAs, such as Fas and caspase‐2. The RBM5 gene is located at the 2p21.3 chromosomal region, which is strongly associated with lung cancer and many other cancers. Both increased and decreased levels of RBM5 can play a role in tumor progression. In particular, downregulation of rbm5 is involved in lung cancer and other cancers upon Ras activation, and, also, represents a molecular signature associated with metastasis in various solid tumors. On the other hand, upregulation of RBM5 occurs in breast and ovarian cancer. Moreover, RBM5 was also found to be involved in the early stage of the HIV‐1 viral cycle, representing a potential target for the treatment of the HIV‐1 infection. While the molecular basis for RNA recognition and ubiquitin interaction has been structurally characterized, small molecules binding this zinc finger (ZF) domain that might contribute to characterizing their activity and to the development of potential therapeutic agents have not yet been reported. Using an NMR screening of a fragment library we identified several binders and the complex of the most promising one, compound 1, with the RBM5 ZF1 was structurally characterized in solution. Interestingly, the binding mechanism reveals that 1 occupies the RNA binding pocket and is therefore able to compete with the RNA to bind RBM5 RanBP2‐type ZF domain, as indicated by NMR studies.
Gold Nanoparticles Incarcerated in Nanoporous Syndiotactic Polystyrene Matrices as New and Efficient Catalysts for Alcohol Oxidations
Authors: Buonerba Antonio , Cuomo Cinzia , Ortega Sánchez Sheila , Canton Patrizia , Grassi Alfonso 
Published: December 2011

AbstractThe controlled synthesis of gold nanoparticles (AuNPs), incarcerated in a semicrystalline nanoporous polymer matrix that consisted of a syndiotactic polystyrene‐co‐cis‐1,4‐polybutadiene multi‐block copolymer is described. This catalyst was successfully tested in the oxidation of primary and secondary alcohols, in which we used dioxygen as the oxidant under mild conditions. Accordingly, (±)‐1‐phenylethanol was oxidised to acetophenone in high yields (96 %) in 1 h, at 35 °C, whereas benzyl alcohol was quantitatively oxidised to benzaldehyde with a selectivity of 96 % in 6 h. The specific rate constants calculated from the corresponding kinetic plots were among the highest found for polymer‐incarcerated AuNPs. Similar values in terms of reactivity and selectivity were found in the oxidation of primary alcohols, such as cinnamyl alcohol and 2‐thiophenemethanol, and secondary alcohols, such as indanol and α‐tetralol. The remarkable catalytic properties of this system were attributed to the formation, under these reaction conditions, of the nanoporous ε crystalline form of syndiotactic polystyrene, which ensures facile and selective accessibility for the substrates to the gold catalyst incarcerated in the polymer matrix. Moreover, the polymeric crystalline domains produced reversible physical cross‐links that resulted in reduced gold leaching and also allowed the recovery and reuse of the catalyst. A comparison of catalytic performance between AuNPs and annealed AuNPs suggested that multiple twinned defective nanoparticles of about 9 nm in diameter constituted the active catalyst in these oxidation reactions.
Molecular Recognition at the Active Site of Factor Xa: Cation–π Interactions, Stacking on Planar Peptide Surfaces, and Replacement of Structural Water
Authors: Salonen Laura M. , Holland Mareike C. , Kaib Philip S. J. , Haap Wolfgang , Benz Jörg , Mary Jean‐Luc , Kuster Olivier , Schweizer W. Bernd , Banner David W. , Diederich François 
Published: December 2011

AbstractFactor Xa, a serine protease from the blood coagulation cascade, is an ideal enzyme for molecular recognition studies, as its active site is highly shape‐persistent and features distinct, concave sub‐pockets. We developed a family of non‐peptidic, small‐molecule inhibitors with a central tricyclic core orienting a neutral heterocyclic substituent into the S1 pocket and a quaternary ammonium ion into the aromatic box in the S4 pocket. The substituents were systematically varied to investigate cation–π interactions in the S4 pocket, optimal heterocyclic stacking on the flat peptide walls lining the S1 pocket, and potential water replacements in both the S1 and the S4 pockets. Structure–activity relationships were established to reveal and quantify contributions to the binding free enthalpy, resulting from single‐atom replacements or positional changes in the ligands. A series of high‐affinity ligands with inhibitory constants down to Ki=2 nM were obtained and their proposed binding geometries confirmed by X‐ray co‐crystal structures of protein–ligand complexes.
ChemInform Abstract: Pressure‐Induced Formation of Molecular B2X4(μ‐X)2 (X: Cl, Br, I) Species.
Authors: Patchkovskii Serguei , Klug Dennis D. , Yao Yansun 
Published: December 2011

AbstractGas‐phase formation and decomposition of the boron(III) halides of title is explored by CCSD(T) and MP2 ab initio calculations.
ChemInform Abstract: MIIGe(PO4)2 (M: Ca, Sr, Ba): Crystal Structure, Phase Transitions and Thermal Expansion.
Authors: Popa Karin , Wallez Gilles , Bregiroux Damien , Loiseau Pascal 
Published: December 2011

AbstractThe title compounds are prepared by solid state reaction of stoichiometric amounts of MCO3 (M: Ca, Sr, Ba), GeO2, and NH4H2PO4 (1000—1150 °C, 18—100 h).
ChemInform Abstract: Synthesis, Structure, and Thermally Stable Luminescence of Eu2+‐Doped Ba2Ln(BO3)2Cl (Ln: Y, Gd and Lu) Host Compounds.
Authors: Xia Zhiguo , Wang Xiaoming , Wang Yingxia , Liao Libing , Jing Xiping 
Published: December 2011

AbstractPowders of Ba2Ln(BO3)2Cl:0.03Eu2+ (Ln: Y, La—Nd, Sm—Lu) are prepared by solid state reaction of BaCO3, Ln2O3 (except for CeO2 and Tb4O7), H3BO3, BaCl2, and Eu2O3 (CO atmosphere,1000 °C, 3 h).
ChemInform Abstract: Site‐Preferential Design of Itinerant Ferromagnetic Borides: Experimental and Theoretical Investigation of MRh6B3 (M: Fe, Co).
Authors: Misse Patrick R. N. , Gillessen Michael , Fokwa Boniface P. T. 
Published: December 2011

AbstractPolycrystalline samples of the title compounds and single crystals of CoRh6B3 are prepared by arc‐melting of the elements.
ChemInform Abstract: Two New Cluster Ions, Ga[GaH3]5‐4 with a Neopentane Structure in Rb8Ga5H15 and [GaH2]n‐n with a Polyethylene Structure in Rbn(GaH2)n, Represent a New Class of Compounds with Direct Ga—Ga Bonds Mimicking Common Hydrocarbons.
Authors: Fahlquist Henrik , Noreus Dag , Callear Samantha , David William I. F. , Hauback Bjoern C. 
Published: December 2011

AbstractThe title compounds are prepared from mixtures of Ga and Rb under 5 MPa H2 at 573 K and characterized by powder XRD and neutron powder diffraction.
ChemInform Abstract: Antiferromagnetic Ground State of Quantum Spins in the Synthetic Imanite, Ca3Ti2Si3O12: The Lost Child of the Garnet Family.
Authors: Valldor Martin , Urthe Andre , Rueckamp Reinhard 
Published: December 2011

AbstractLarge single crystals of the title compound are grown from mixtures of CaSiO3, Ti2O3, and Ti by the floating zone technique.
ChemInform Abstract: Two Open‐Framework Germanates with Nickel Complexes Incorporated into the Framework.
Authors: Huang Shiliang , Christensen Kirsten , Peskov Maxim V. , Yang Sihai , Li Kuo , Zou Xiaodong , Sun Junliang 
Published: December 2011

AbstractThe crystal structures of (III) and (IV) are determined by single crystal XRD.
ChemInform Abstract: [Pd3Sn8Bi6]4‐: A 14‐Vertex Sn/Bi Cluster Embedding a Pd3 Triangle.
Authors: Lips Felicitas , Clerac Rodolphe , Dehnen Stefanie 
Published: December 2011

AbstractBlack rhombus‐like crystals of [K([2.2.2]crypt)]4 [Pd3Sn8Bi6]·0.6en are synthesized from a mixture of [K([2.2.2]crypt)]2[Sn2Bi2]·en dissolved in en and Pd(dppe)2 (dppe: bis[1,2‐bis(diphenylphosphino)ethane]) suspended in toluene (3 h, 15% yield).
ChemInform Abstract: Readily Accessible Chiral Diene Ligands for Rh‐Catalyzed Enantioselective Conjugate Additions of Boronic Acids.
Authors: Trost Barry M. , Burns Aaron C. , Tautz Thomas 
Published: December 2011

AbstractThe chiral diene ligand is prepared from commercial materials in simply 2 steps remarkably compared to formerly described 6 or 7 steps.
ChemInform Abstract: In situ Generation and Intramolecular Schmidt Reaction of Keto Azides in a Microwave‐Assisted Flow Format.
Authors: Painter Thomas O. , Thornton Paul D. , Orestano Mario , Santini Conrad , Organ Michael G. , Aube Jeffrey 
Published: December 2011

AbstractThe scope and limitations of the title two‐step method are studied for cyclic and acyclic chloro‐ or bromoalkyl ketones.
ChemInform Abstract: Palladium‐Catalyzed Regioselective Aerobic Oxidative C—H/N—H Carbonylation of Heteroarenes under Base‐Free Conditions.
Authors: Zhang Hua , Liu Dong , Chen Caiyou , Liu Chao , Lei Aiwen 
Published: December 2011

AbstractUsing air as oxidant and a balloon pressure of CO, indoles, thiophenes and benzothiophenes are converted in the presence of different alcohols into carboxylic acid esters.
ChemInform Abstract: (Bromodimethyl)sulfonium Bromide Mediated Rapid and Facile Protection of Amines.
Authors: Shailaja M. , Manjula A. , Rao B. Vittal 
Published: December 2011

AbstractBromodimethylsulfonium bromide catalyzes both Cbz‐ and Boc‐protection of a wide variety of primary and secondary amines.
ChemInform Abstract: La/Ag Heterobimetallic Cooperative Catalysis: A Catalytic Asymmetric Conia‐Ene Reaction.
Authors: Matsuzawa Akinobu , Mashiko Tomoyuki , Kumagai Naoya , Shibasaki Masakatsu 
Published: December 2011

AbstractA new catalyst system consisting of La(O‐iPr)3 and AgO‐Ac as hard and soft Lewis acids and an amide‐based ligand ((S)‐(I)) is used for the simultaneous activation of intramolecular 1,3‐dicarbonyl and alkyne moieties to afford enantioenriched cyclopentane derivatives.
ChemInform Abstract: Interception of a Rautenstrauch Intermediate by Alkynes for [5 + 2] Cycloaddition: Rhodium‐Catalyzed Cycloisomerization of 3‐Acyloxy‐4‐ene‐1,9‐diynes to Bicyclo[5.3.0]decatrienes.
Authors: Shu Xing‐zhong , Huang Suyu , Shu Dongxu , Guzei Ilia A. , Tang Weiping 
Published: December 2011

AbstractThe intramolecular [5 + 2] cycloaddition is accompanied by a 1,2‐acyloxy migration to produce various ring systems annellated with a cycloheptatriene moiety.
ChemInform Abstract: An Additional Coordination Group Leads to Extremely Efficient Chiral Iridium Catalysts for Asymmetric Hydrogenation of Ketones.
Authors: Xie Jian‐Hua , Liu Xiao‐Yan , Xie Jian‐Bo , Wang Li‐Xin , Zhou Qi‐Lin 
Published: December 2011

AbstractAn efficient chiral iridium catalyst that bears a tridentate spiro P—N—N ligand catalyzes the asymmetric hydrogenation of ketones with excellent enantioselectivities and extremely high turnover numbers.
ChemInform Abstract: Carboxylation of Alkylboranes by N‐Heterocyclic Carbene Copper Catalysts: Synthesis of Carboxylic Acids from Terminal Alkenes and Carbon Dioxide.
Authors: Ohishi Takeshi , Zhang Liang , Nishiura Masayoshi , Hou Zhaomin 
Published: December 2011

AbstractA broad spectrum of substrates bearing a free allyl moiety can be transformed to carboxylic acids in good to excellent yields and various functionalities are tolerated.
ChemInform Abstract: Rapid Access to α‐Alkoxy and α‐Amino Acid Derivatives Through Safe Continuous‐Flow Generation of Diazoesters.
Authors: Bartrum Hannah E. , Blakemore David C. , Moody Christopher J. , Hayes Christopher J. 
Published: December 2011

AbstractUnder Bamford—Stevens conditions starting from arylsulfonylhydrazones, a range of diazoesters is prepared in a flow reactor.
ChemInform Abstract: Beckmann Rearrangement of Oximes Using Pivaloyl Chloride/DMF Complex.
Authors: Narahari Srinivasa Reddy , Reguri Buchi Reddy , Mukkanti K. 
Published: December 2011

AbstractThe complex acts as mild and nontoxic reagent for the conversion of ketoximes into the corresponding amides within a relatively short reaction time.
ChemInform Abstract: Synthesis and Reactivity of Sulfamoyl Azides and 1‐Sulfamoyl‐1,2,3‐triazoles.
Authors: Culhane Jeffrey C. , Fokin Valery V. 
Published: December 2011

AbstractThe transfer reagent (IV) is formed as a stable solid which can be stored at 0—4 °C for at least 3 months without a detectable decomposition.
ChemInform Abstract: Homocoupling of Arylboronic Acids Catalyzed by Simple Gold Salts.
Authors: Matsuda Takanori , Asai Taro , Shiose Shigeru , Kato Kotaro 
Published: December 2011

AbstractA convenient method including 2 different Au salts is presented for the oxidative homo‐coupling of arylboronic acids to give symmetrical biaryls in low to good yields.