0000000000608432

AUTHOR

Roberto Tejero

showing 44 related works from this author

Quality assessment of protein NMR structures.

2013

Biomolecular NMR structures are now routinely used in biology, chemistry, and bioinformatics. Methods and metrics for assessing the accuracy and precision of protein NMR structures are beginning to be standardized across the biological NMR community. These include both knowledge-based assessment metrics, parameterized from the database of protein structures, and model versus data assessment metrics. On line servers are available that provide comprehensive protein structure quality assessment reports, and efforts are in progress by the world-wide Protein Data Bank (wwPDB) to develop a biomolecular NMR structure quality assessment pipeline as part of the structure deposition process. These qu…

Models MolecularProtein structure; NMR spectroscopyMagnetic Resonance SpectroscopyProtein ConformationAnalytical chemistryBiology010402 general chemistrycomputer.software_genre01 natural sciencesArticle03 medical and health sciencesStructural BiologyServerDatabases ProteinMolecular BiologyNuclear Magnetic Resonance Biomolecular030304 developmental biology0303 health sciencesExtramuralQuality assessmentData assessmentResearchProteinsReproducibility of ResultsNuclear magnetic resonance spectroscopycomputer.file_formatProtein Data Bank0104 chemical sciencesData miningcomputerDeposition processCurrent opinion in structural biology
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High-resolution solution NMR structure of the Z domain of staphylococcal protein A

1997

Staphylococcal protein A (SpA) is a cell-wall-bound pathogenicity factor from the bacterium Staphylococcus aureus. Because of their small size and immunoglobulin (IgG)-binding activities, domains of protein A are targets for protein engineering efforts and for the development of computational approaches for de novo protein folding. The NMR solution structure of an engineered IgG-binding domain of SpA, the Z domain (an analog of the B domain of SpA), has been determined by simulated annealing with restrained molecular dynamics on the basis of 671 conformational constraints. The Z domain contains three well-defined alpha-helices corresponding to polypeptide segments Lys7 to Leu17 (helix 1), G…

Models MolecularMagnetic Resonance SpectroscopyProtein ConformationChemistryMolecular Sequence DataProtein engineeringHydrogen-Ion ConcentrationCrystallography X-RayAntiparallel (biochemistry)CrystallographyModels ChemicalStructural BiologyHelixHumansHydrogen–deuterium exchangeAmino Acid SequenceB3 domainStaphylococcal Protein AMolecular BiologyTwo-dimensional nuclear magnetic resonance spectroscopyConformational isomerismHeteronuclear single quantum coherence spectroscopyJournal of Molecular Biology
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Simulated annealing with restrained molecular dynamics using a flexible restraint potential: Theory and evaluation with simulated NMR constraints

1996

A new functional representation of NMR-derived distance constraints, the flexible restraint potential, has been implemented in the program CONGEN (Bruccoleri RE, Karplus M, 1987, Biopolymers 26:137-168) for molecular structure generation. In addition, flat-bottomed restraint potentials for representing dihedral angle and vicinal scalar coupling constraints have been introduced into CONGEN. An effective simulated annealing (SA) protocol that combines both weight annealing and temperature annealing is described. Calculations have been performed using ideal simulated NMR constraints, in order to evaluate the use of restrained molecular dynamics (MD) with these target functions as implemented i…

Coupling constantQuantitative Biology::BiomoleculesChemistryCrambinNuclear magnetic resonance spectroscopyDihedral angleEnergy minimizationBiochemistryMolecular physicsMaxima and minimaMolecular dynamicsCrystallographySimulated annealingMolecular BiologyProtein Science
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A procedure for predicting sorption equilibrium in ternary polymer systems from Flory–Huggins binary interaction parameters and the inversion point o…

1989

A procedure has been developed, based on the Flory–Huggins theory as generalized by Pouchlý, which permits the calculation of preferential (λ) and total (Y) sorption coefficients from previous information on the binary interaction parameters, χ, χ, and g12(ϕ10) and on the mixture composition at which the sign of λ inverts. The expressions obtained were applied to 10 cosolvent polymer systems for which experimental values of λ and Y are known. Practically in all the studied systems, the theoretical predictions are in fair accordance with the experimental data.

chemistry.chemical_classificationPolymers and PlasticsChemistrySolvationBinary numberThermodynamicsSorptionPolymerFlory–Huggins solution theoryCondensed Matter PhysicsThermodynamic modelPolymer chemistryMaterials ChemistryChemical solutionPhysical and Theoretical ChemistryTernary operationJournal of Polymer Science Part B: Polymer Physics
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Synthetic single and double aza-scorpiand macrocycles acting as inhibitors of the antioxidant enzymes iron superoxide dismutase and trypanothione red…

2014

The anti-chagasic activity of a series of eleven derivatives of aza-scorpiand-like macrocycles, some of them newly synthesised, was assayed. The four compounds with the best selectivity indices in vitro were subjected to in vivo assays. Tests in a murine model of the acute phase of Chagas disease showed a two-fold reduction in parasitaemia compared to that with benznidazole. Furthermore, compounds 7 and 11, with 4-pyridine and phenanthroline substituents in the lateral chain, caused a remarkable decrease in parasitaemia reactivation during the chronic phase after inducing immunosuppression in mice. These activity studies were complemented by measuring their inhibitory effect towards the ant…

chemistry.chemical_classificationChagas diseaseAntioxidantbiologyChemistryStereochemistryGeneral Chemical EngineeringPhenanthrolinemedicine.medical_treatmentGeneral Chemistrybiology.organism_classificationmedicine.diseaseIn vitrochemistry.chemical_compoundEnzymeBiochemistryBenznidazoleIn vivomedicineTrypanosoma cruzimedicine.drugRSC Adv.
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A Flory–Huggins thermodynamic approach for predicting sorption equilibrium in ternary polymer systems

1989

The Flory–Huggins theory as modified by Pouchlý has been applied to calculate preferential (λ) and total (Y) sorption coefficients for a ternary polymer system. The ternary interaction function (ϕ1ϕ2ϕ3GT(u1, ϕ3)) is described as the product of three independent binary functions. This expression allows prediction of λ and Y from binary interaction parameters χ, χ, g, g, and g12(ϕ10). Three ternary polymer systems are used to check the validity of the expression. Moreover for polymer systems in which the parameters g and/or g are unknown, a procedure to evaluate them has been developed and verified on systems for which sufficient experimental information is available.

chemistry.chemical_classificationPolymers and PlasticsChemistryThermodynamicsBinary numberSorptionPolymerFlory–Huggins solution theoryExpression (computer science)Condensed Matter PhysicsInteraction functionPolymer chemistryMaterials ChemistryChemical solutionPhysical and Theoretical ChemistryTernary operationJournal of Polymer Science Part B: Polymer Physics
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Homology modeling using simulated annealing of restrained molecular dynamics and conformational search calculations with CONGEN: application in predi…

1997

We have developed an automatic approach for homology modeling using restrained molecular dynamics and simulated annealing procedures, together with conformational search algorithms available in the molecular mechanics program CONGEN (Bruccoleri RE, Karplus M, 1987, Biopolymers 26:137-168). The accuracy of the method is validated by "predicting" structures of two homeodomain proteins with known three-dimensional structures, and then applied to predict the three-dimensional structure of the homeodomain of the murine Msx-1 transcription factor. Regions of the unknown protein structure that are highly homologous to the known template structure are constrained by "homology distance constraints,"…

Models MolecularSaccharomyces cerevisiae ProteinsProtein ConformationMSX1 Transcription FactorMolecular Sequence DataSaccharomyces cerevisiaeBiologyProtein EngineeringBiochemistryProtein Structure SecondaryMolecular dynamicsMiceProtein structureAnimalsComputer SimulationHomology modelingAmino Acid SequenceMolecular BiologyHomeodomain ProteinsMSX1 Transcription FactorSequence Homology Amino AcidNuclear ProteinsProtein engineeringProtein superfamilyengrailedRepressor ProteinsCrystallographyAntennapedia Homeodomain ProteinThreading (protein sequence)AlgorithmsInformation SystemsTranscription FactorsResearch ArticleProtein science : a publication of the Protein Society
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Assessing model accuracy using the homology modeling automatically software

2007

Homology modeling is a powerful technique that greatly increases the value of experimental structure determination by using the structural information of one protein to predict the structures of homologous proteins. We have previously described a method of homology modeling by satisfaction of spatial restraints (Li et al., Protein Sci 1997;6:956-970). The Homology Modeling Automatically (HOMA) web site,http://www-nmr.cabm.rutgers.edu/HOMA, is a new tool, using this method to predict 3D structure of a target protein based on the sequence alignment of the target protein to a template protein and the structure coordinates of the template. The user is presented with the resulting models, togeth…

Models MolecularProtein Conformationbusiness.industryProteinsSequence alignmentStructure validationComputational biologyProtein superfamilyMachine learningcomputer.software_genreBiochemistryHomology (biology)Structural genomicsProtein structureStructural BiologyArtificial intelligenceTarget proteinHomology modelingbusinessMolecular BiologycomputerSoftwareMathematicsProteins: Structure, Function, and Bioinformatics
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The mechanism of binding staphylococcal protein A to immunoglobin G does not involve helix unwinding.

1996

Structural changes in staphylococcal protein A (SpA) upon its binding to the constant region (Fc) of immunoglobulin G (IgG) have been studied by nuclear magnetic resonance and circular dichroism (CD) spectroscopy. The NMR solution structure of the engineered IgG-binding domain of SpA, the Z domain (an analogue of the B domain of SpA), has been determined by simulated annealing with molecular dynamics, using 599 distance and dihedral angle constraints. Domain Z contains three alpha-helices in the polypeptide segments Lys7 to His18 (helix 1), Glu25 to Asp36 (helix 2), and Ser41 to Ala54 (helix 3). The overall chain fold is an antiparallel three-helical bundle. This is in contrast to the previ…

Models MolecularCircular dichroismProtein FoldingMagnetic Resonance SpectroscopyStereochemistryMolecular Sequence DataPlasma protein bindingDihedral angleBiochemistryProtein Structure SecondaryProtein structureComputer GraphicsAmino Acid SequenceBinding siteStaphylococcal Protein ABinding SitesChemistryCircular DichroismNuclear magnetic resonance spectroscopyRecombinant ProteinsImmunoglobulin Fc FragmentsModels StructuralCrystallographyIgG bindingImmunoglobulin GMutagenesis Site-DirectedProtein foldingProtein BindingBiochemistry
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Acid–base behaviour and binding to double stranded DNA/RNA of benzo[g]phthalazine-based ligands

2019

The affinity and the binding mode of two benzo[g]phthalazine compounds, functionalized with one or two 2-(imidazole-4-yl)-ethylamine groups, to DNA and RNA models have been evaluated by means of UV-Vis, fluorescence and circular dichroism (CD) spectroscopies in combination with viscometry and molecular dynamics. Both organic molecules bind strongly to all nucleic acid models via the intercalation mode in the duplex structure, especially compound 1. Intriguingly, 1 exhibits different emission responses depending on the base composition of duplex DNA/RNAs, which points out the possibility of using it as a base selective nucleic acid probe. Moreover, the acid-base behaviour of both compounds h…

Circular dichroismChemistryStereochemistryIntercalation (chemistry)Protonation02 engineering and technologyGeneral Chemistry010402 general chemistry021001 nanoscience & nanotechnologyDiprotic acid01 natural sciencesCatalysis0104 chemical scienceschemistry.chemical_compoundMaterials ChemistryNucleic acidMoiety0210 nano-technologyPhthalazineDNANew Journal of Chemistry
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Development of Polyamine‐Substituted Triphenylamine Ligands with High Affinity and Selectivity for G‐Quadruplex DNA

2019

Currently, significant efforts are devoted to designing small molecules able to bind selectively to guanine quadruplexes (G4s). These noncanonical DNA structures are implicated in various important biological processes and have been identified as potential targets for drug development. Previously, a series of triphenylamine (TPA)-based compounds, including macrocyclic polyamines, that displayed high affinity towards G4 DNA were reported. Following this initial work, herein a series of second-generation compounds, in which the central TPA has been functionalised with flexible and adaptive linear polyamines, are presented with the aim of maximising the selectivity towards G4 DNA. The acid-bas…

Biochemistry & Molecular BiologyCircular dichroismChemistry Medicinal0601 Biochemistry and Cell BiologyLigands010402 general chemistryTriphenylamineG-quadruplex01 natural sciencesBiochemistryFluorescence spectroscopyStructure-Activity Relationshipchemistry.chemical_compoundFluorescence Resonance Energy TransferPolyaminesPharmacology & PharmacyCOORDINATION CHEMISTRYPROBEMolecular BiologyScience & Technology0304 Medicinal and Biomolecular Chemistry010405 organic chemistryOrganic ChemistryDNACombinatorial chemistrySmall molecule0104 chemical sciences* G-quadruplex DNA * G4 selectivity * polyamine-based ligand *fluorescenceG-QuadruplexesFörster resonance energy transferchemistryDrug DesignFRETEQUILIBRIUM-CONSTANTSMolecular MedicineCOMPLEXESfluorescenceEMISSIONSelectivityLife Sciences & BiomedicineDNAChemBioChem
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A topology-constrained distance network algorithm for protein structure determination from NOESY data.

2005

This article formulates the multidi- mensional nuclear Overhauser effect spectroscopy (NOESY) interpretation problem using graph theory and presents a novel, bottom-up, topology-con- strained distance network analysis algorithm for NOESY cross peak interpretation using assigned resonances. AutoStructure is a software suite that implements this topology-constrained distance net- work analysis algorithm and iteratively generates structures using the three-dimensional (3D) protein structure calculation programs XPLOR/CNS or DY- ANA. The minimum input for AutoStructure in- cludes the amino acid sequence, a list of resonance assignments, and lists of 2D, 3D, and/or 4D-NOESY cross peaks. AutoStru…

Software suiteMagnetic Resonance SpectroscopybiologyProtein ConformationProteinsReproducibility of ResultsGraph theoryNuclear Overhauser effectCyanaModels TheoreticalNet (mathematics)biology.organism_classificationCrystallography X-RayBiochemistryProtein Structure SecondaryInterpretation (model theory)CrystallographyProtein structureStructural BiologyImage Processing Computer-AssistedMolecular BiologyTwo-dimensional nuclear magnetic resonance spectroscopyAlgorithmAlgorithmsMathematicsProteins
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Simulated annealing with restrained molecular dynamics using CONGEN: Energy refinement of the NMR solution structures of epidermal and type-αtransfor…

1996

The new functionality of the program CONGEN (Bruccoleri RE, Karplus M, 1987, Biopolymers 26:137-168; Bassolino-Klimas D et al., 1996, Protein Sci 5:593-603) has been applied for energy refinement of two previously determined solution NMR structures, murine epidermal growth factor (mEGF) and human type-alpha transforming growth factor (hTGF alpha). A summary of considerations used in converting experimental NMR data into distance constraints for CONGEN is presented. A general protocol for simulated annealing with restrained molecular dynamics is applied to generate NMR solution structures using CONGEN together with real experimental NMR data. A total of 730 NMR-derived constraints for mEGF a…

Maxima and minimaMolecular dynamicsCrystallographyProtein structureChemistrySimulated annealingMoleculeNuclear magnetic resonance spectroscopyProtein superfamilyType (model theory)Molecular BiologyBiochemistryProtein Science
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A water molecule in the interior of a 1H-pyrazole Cu2+ metallocage

2016

Water has a great tendency to associate through hydrogen bonding with water molecules or other hydrogen bond donor or acceptor groups. Here the case of a water molecule encapsulated in the interior of a metallocage receptor is presented. The association of four copper(II) ions and two aza-macrocyclic receptors in which two 1H-pyrazole units are connected by cadaverine diamines leads to the inclusion of a water molecule into the cage, as proved by X-ray analysis and infrared spectroscopy. The included water molecule shows no hydrogen bonding with any component of the cage presenting only a weak hydrogen bond with an oxygen atom of a perchlorate counter-anion. The IR stretching vibrations pre…

010405 organic chemistryHydrogen bondInorganic chemistryInfrared spectroscopychemistry.chemical_elementGeneral ChemistryPyrazole010402 general chemistry01 natural sciencesAcceptorCopperCatalysis0104 chemical sciencesIonchemistry.chemical_compoundCrystallographyPerchloratechemistryMaterials ChemistryMoleculeNew Journal of Chemistry
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Homology modeling of an RNP domain from a human RNA-binding protein: Homology-constrained energy optimization provides a criterion for distinguishing…

1998

We have recently described an automated approach for homology modeling using restrained molecular dynamics and simulated annealing procedures (Li et al, Protein Sci., 6:956-970,1997). We have employed this approach for constructing a homology model of the putative RNA-binding domain of the human RNA-binding protein with multiple splice sites (RBP-MS). The regions of RBP-MS which are homologous to the template protein snRNP U1A were constrained by "homology distance constraints," while the conformation of the non-homologous regions were defined only by a potential energy function. A full energy function without explicit solvent was employed to ensure that the calculated structures have good …

Quantitative Biology::BiomoleculesBiologyEnergy minimizationBiochemistryHomology (biology)CrystallographyMolecular dynamicsProtein structureStructural BiologySimulated annealingHomology modelingLoop modelingThreading (protein sequence)Biological systemMolecular BiologyProteins: Structure, Function, and Genetics
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Synthesis, Characterization, and Cu(2+) Coordination Studies of a 3-Hydroxy-4-pyridinone Aza Scorpiand Derivative.

2016

The synthesis, acid-base behavior, and Cu(2+) coordination chemistry of a new ligand (L1) consisting of an azamacrocyclic core appended with a lateral chain containing a 3-hydroxy-2-methyl-4(1H)-pyridinone group have been studied by potentiometry, cyclic voltammetry, and NMR and UV-vis spectroscopy. UV-vis and NMR studies showed that phenolate group was protonated at the highest pH values [log K = 9.72(1)]. Potentiometric studies point out the formation of Cu(2+) complexes of 1:2, 2:2, 4:3, 1:1, and 2:1 Cu(2+)/L1 stoichiometries. UV-vis analysis and electrochemical studies evidence the implication of the pyridinone moieties in the metal coordination of the 1:2 Cu(2+)/L1 complexes. L1 shows …

inorganic chemicalsMagnetic Resonance SpectroscopyStereochemistryPyridinesPyridonesPotentiometric titrationProtonationChemistry Techniques Synthetic010402 general chemistry010403 inorganic & nuclear chemistryElectrochemistryCrystallography X-Ray01 natural sciencesMedicinal chemistryAntioxidantsCoordination complexInorganic Chemistrychemistry.chemical_compoundStructure-Activity RelationshipCoordination ComplexesHumansChelationPhysical and Theoretical ChemistryCell ProliferationChelating Agentschemistry.chemical_classificationLigandHydrogen-Ion Concentration0104 chemical scienceschemistryPotentiometrySpectrophotometry UltravioletCyclic voltammetryDerivative (chemistry)CopperHeLa CellsInorganic chemistry
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1988

Deviations in the determination of the unperturbed dimensions of polymers arising in ternary polymer systems (solvent (1)/solvent (2)/polymer) can be explained by the inaccurate use of an interaction parameter independent of polymer molecular weight. On this basis, a new formalism for the calculation of the second virial coefficient from intrinsic viscosity is proposed. This formalism was tested (and compared with well established formalisms) for all ternary polymer systems with simultaneous intrinsic viscosity and second virial coefficient data in the literature.

Alkanechemistry.chemical_classificationQuantitative Biology::BiomoleculesTernary numeral systemChemistryIntrinsic viscosityPolymerFlory–Huggins solution theoryCondensed Matter::Soft Condensed Matterchemistry.chemical_compoundVirial coefficientPolymer chemistryTernary operationAcetonitrileDie Makromolekulare Chemie
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1988

The unperturbed dimensions parameter KΘ is one of the most important characteristics of a polymer chain. For binary systems (polymer/solvent) and mostly for ternary systems (polymer/solvent(1)/solvent(2)) the KΘ values show large discrepancies with respect to those under thetaconditions in a single solvent. These discrepancies can be explained by considering that the interaction parameter χ (and consequently the coil dimensions or the number of intramolecular contacts between polymer segments) changes with molecular weight M. Assuming this dependency, a modified Stockmayer-Fixman equation is proposed from which a unique value of KΘ for a given polymer, independent of M, is obtained. The use…

chemistry.chemical_classificationPhysics::Biological PhysicsQuantitative Biology::BiomoleculesTernary numeral systemChemistryPolymerFlory–Huggins solution theoryGibbs free energyCondensed Matter::Soft Condensed MatterSolventsymbols.namesakePolymer chemistrysymbolsBinary systemPhysics::Chemical PhysicsSolvent effectsTernary operationDie Makromolekulare Chemie
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Protein NMR Structures Refined with Rosetta Have Higher Accuracy Relative to Corresponding X-ray Crystal Structures

2014

We have found that refinement of protein NMR structures using Rosetta with experimental NMR restraints yields more accurate protein NMR structures than those that have been deposited in the PDB using standard refinement protocols. Using 40 pairs of NMR and X-ray crystal structures determined by the Northeast Structural Genomics Consortium, for proteins ranging in size from 5-22 kDa, restrained Rosetta refined structures fit better to the raw experimental data, are in better agreement with their X-ray counterparts, and have better phasing power compared to conventionally determined NMR structures. For 37 proteins for which NMR ensembles were available and which had similar structures in solu…

Models MolecularChemistryProtein ConformationProtein Data Bank (RCSB PDB)X-rayProteinsGeneral ChemistryNuclear magnetic resonance crystallographyCrystal structureCrystallography X-RayBiochemistryCatalysisArticleStructural genomicsCrystalCrystallographyColloid and Surface ChemistryMolecular replacementComputer SimulationNuclear Magnetic Resonance BiomolecularSoftwareJournal of the American Chemical Society
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A novel RNA-binding motif in influenza A virus non-structural protein 1.

1997

The solution NMR structure of the RNA-binding domain from influenza virus non-structural protein 1 exhibits a novel dimeric six-helical protein fold. Distributions of basic residues and conserved salt bridges of dimeric NS1(1-73) suggest that the face containing antiparallel helices 2 and 2′ forms a novel arginine-rich nucleic acid binding motif.

Helix bundleModels MolecularBinding SitesMagnetic Resonance SpectroscopyChemistryStructural proteinViral Nonstructural ProteinsAntiparallel (biochemistry)medicine.disease_causeVirusProtein Structure SecondaryBiochemistryStructural BiologyInfluenza A virusInfluenza A virusmedicineNucleic acidRNAStructural motifMolecular BiologySterile alpha motifDimerizationNature structural biology
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Equilibrium, Kinetic, and Computational Studies on the Formation of Cu2+ and Zn2+ Complexes with an Indazole-Containing Azamacrocyclic Scorpiand: Evi…

2015

Cu(2+) and Zn(2+) coordination chemistry of a new member of the family of scorpiand-like macrocyclic ligands derived from tris(2-aminoethyl)amine (tren) is reported. The new ligand (L1) contains in its pendant arm not only the amine group derived from tren but also a 6-indazole ring. Potentiometric studies allow the determination of four protonation constants. UV-vis and fluorescence data support that the last protonation step occurs on the indazole group. Equilibrium measurements in the presence of Cu(2+) and Zn(2+) reveal the formation of stable [ML1](2+), [MHL1](3+), and [ML1(OH)](+) complexes. Kinetic studies on the acid-promoted decomposition of the metal complexes were carried out usi…

Models Molecularchemistry.chemical_classificationAza CompoundsIndazoleIndazolesMacrocyclic CompoundsMolecular StructureLigandPotentiometric titrationProtonationPhotochemistryMedicinal chemistryTautomerCoordination complexInorganic ChemistryKineticsZincchemistry.chemical_compoundchemistryOrganometallic CompoundsQuantum TheoryMoleculeAmine gas treatingPhysical and Theoretical ChemistryCopper
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Tritopic phenanthroline and pyridine tail-tied aza-scorpiands

2010

The synthesis of two new tritopic double-scorpiand receptors in which two equivalent 5-(2-aminoethyl)-2,5,8-triaza[9]-(2,6)-pyridinophane moieties have been linked with 2,6-dimethylpyridine (L1) or 2,9-dimethylphenanthroline (L2) units is reported for the first time. Their acid-base behaviour and Zn(2+) coordination chemistry have been studied by pH-metric titrations, molecular dynamic calculations, NMR, UV-Vis and steady-state fluorescence techniques. L1 and L2 behave, respectively, as hexaprotic and heptaprotic bases in the experimental conditions used (298.1 +/- 0.1 K, 0.15 mol dm(-3) NaCl, pH range under study 2.0-11.0). These ligands are able to form mono-, bi- and trinuclear Zn(2+) co…

chemistry.chemical_classificationStereochemistryPhenanthrolineOrganic ChemistryPotentiometric titrationBiochemistryFluorescenceMedicinal chemistryPyrophosphateCoordination complexchemistry.chemical_compoundMolecular dynamicschemistryPyridineTitrationPhysical and Theoretical ChemistryOrganic & Biomolecular Chemistry
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Structural characterization in solution of multifunctional nucleotide coordination systems

2000

The interaction in aqueous solution of the cyclophane receptors 2,6,10,13,17,21-hexaaza[22]orthocyclophane (L11) and 2,6,10,13,17,21-hexaaza[22]paracyclophane (L22) with the nucleotides ATP, ADP and AMP has been studied by pH titration and NMR. The obtained results are compared with those previously reported for the analogous meta-substituted receptor 2,6,10,13,17,21-hexaaza[22]metacyclophane (L). All the experimental data support the actuation of these cyclophane molecules as multi-point binders of nucleotides through electrostatic, hydrogen bonding and π-stacking interactions. The combined use of NMR and molecular dynamics permits us to get a rather reliable picture of the way in which th…

chemistry.chemical_classificationchemistry.chemical_compoundCrystallographyMolecular dynamicsAqueous solutionchemistryHydrogen bondStereochemistryIntermolecular forceMoleculeTitrationNucleotideCyclophaneJournal of the Chemical Society, Perkin Transactions 2
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Oxidative stress protection by manganese complexes of tail-tied aza-scorpiand ligands.

2015

The Mn2+ coordination chemistry of double scorpiand ligands in which two polyazacyclophane macrocycles have been connected by pyridine, phenanthroline and bipyridine spacers has been studied by potentiometry, paramagnetic NMR and electrochemistry. All ligands show high stability with Mn2+ and the complexes were formed in a wide pH range. DFT calculations support the structures and coordination geometries derived from the study. A remarkable antioxidant activity was evidenced for these systems by the McCord-Fridovich assay and in Escherichiacoli sodAsodB deficient bacterial cells. The three systems were tested as anti-inflammatory drugs in human macrophages measuring the accumulation of cyto…

AntioxidantStereochemistrymedicine.medical_treatmentPhenanthrolineInorganic chemistrychemistry.chemical_elementManganese010402 general chemistryElectrochemistry01 natural sciencesBiochemistryAntioxidantsCoordination complexInorganic ChemistrySuperoxide dismutasechemistry.chemical_compoundBipyridineBacterial ProteinsCoordination ComplexesCell Line TumorPyridinemedicineEscherichia coliHumanschemistry.chemical_classificationManganesebiology010405 organic chemistryChemistrySuperoxide DismutaseMacrophagesAnti-Inflammatory Agents Non-Steroidal0104 chemical sciencesOxidative Stressbiology.proteinJournal of inorganic biochemistry
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Quantitative Prediction of Concentration Effects in Steric Exclusion Chromatography

1986

Abstract A semiempirical model, based on a previous one quantitatively describing the dependence of the elution volume, V(cA), on the concentration of injected polymer, cA, in exclusion chromatography (SEC) at dilute solutions, has been developed. In the derived equation, concentration effects are mainly governed by the Huggins' coefficient, kA, and by the quadratic coefficient in the polynomial expansion of the reduced specific viscosity, kA. Because of the incertitudes on reliable kA and kA' values, these are respectively removed from the model through she Imai's equation and the empirical correlation kA' + 0.122=kA, here obtained. Thus, A predicted elution volumes besides polymer concent…

Steric effectsGel permeation chromatographychemistry.chemical_classificationRange (particle radiation)ChromatographyChemistryElutionIntrinsic viscosityMolecular MedicinePolymerConstant (mathematics)Polynomial expansionJournal of Liquid Chromatography
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Combined use of 13C chemical shift and 1H alpha-13C alpha heteronuclear NOE data in monitoring a protein NMR structure refinement.

1995

A large portion of the 13C resonance assignments for murine epidermal growth factor (mEGF) at pH 3.1 and 28 degrees C has been determined at natural isotope abundance. Sequence-specific 13C assignments are reported for 100% of the assignable C alpha, 96% of the C beta, 86% of the aromatic and 70% of the remaining peripheral aliphatic resonances of mEGF. A good correlation was observed between experimental and back-calculated C alpha chemical shifts for regions of regular beta-sheet structure. These assignments also provide the basis for interpreting 1H alpha-13C alpha heteronuclear NOE (HNOE) values in mEGF at natural isotope abundance. Some of the backbone polypeptide segments with high in…

Models MolecularProtein FoldingMagnetic Resonance SpectroscopyProtein ConformationMolecular Sequence DataAlpha (ethology)Natural abundanceBiochemistryProtein Structure SecondaryMolecular dynamicsMiceProtein structureAnimalsAmino Acid SequenceBinding siteSpectroscopyCarbon IsotopesEpidermal Growth FactorMolecular StructureChemistryChemical shiftResonanceProteinsCrystallographyHeteronuclear moleculeThermodynamicsHydrogenJournal of biomolecular NMR
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Enhancement of SOD activity in boehmite supported nanoreceptors

2018

The binuclear Cu2+ complex of a pyridinophane polyamine ligand ranking amongst the fastest SOD mimetics so far reported displays a remarkable SOD activity enhancement when grafted to the surface of boehmite (γ-AlO(OH)) nanoparticles (BNPs).

Boehmite010405 organic chemistryLigandChemistryMetals and AlloysNanoparticleGeneral ChemistryQuímica010402 general chemistry01 natural sciencesCatalysis0104 chemical sciencesSurfaces Coatings and FilmsElectronic Optical and Magnetic Materialschemistry.chemical_compoundPolymer chemistryMaterials ChemistryCeramics and CompositesPolyamine
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Evaluating protein structures determined by structural genomics consortia.

2006

Structural genomics projects are providing large quantities of new 3D structural data for proteins. To monitor the quality of these data, we have developed the protein structure validation software suite (PSVS), for assessment of protein structures generated by NMR or X-ray crystallographic methods. PSVS is broadly applicable for structure quality assessment in structural biology projects. The software integrates under a single interface analyses from several widely-used structure quality evaluation tools, including PROCHECK (Laskowski et al., J Appl Crystallog 1993;26:283-291), MolProbity (Lovell et al., Proteins 2003;50:437-450), Verify3D (Luthy et al., Nature 1992;356:83-85), ProsaII (Si…

Models MolecularComputer scienceProtein Data Bank (RCSB PDB)GenomicsComputational biologycomputer.software_genreCrystallography X-RayBiochemistryStructural genomicsProtein structureStructural BiologySoftware DesignHumansDatabases ProteinMolecular BiologyNuclear Magnetic Resonance BiomolecularSoftware suiteComputational BiologyProteinsGenomicsProtein Structure TertiaryCrystallographyStructural biologyQuality ScorecomputerData integrationProteins
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Mapping molecular binding by means of conformational dynamics measurements

2017

[EN] Protein-protein interactions are key in virtually all biological processes. The study of these interactions and the interfaces that mediate them play a key role in the understanding of biological function. In particular, the observation of protein¿protein interactions in their dynamic environment is technically difficult. Here two surface analysis techniques, dual polarization interferometry and quartz crystal microbalance with dissipation monitoring, were paired for real-time mapping of the conformational dynamics of protein¿ protein interactions. Our approach monitors this dynamics in real time and in situ, which is a great advancement within technological platforms for drug discover…

0301 basic medicinePhysicsDrug discoveryMechanism (biology)General Chemical EngineeringDynamics (mechanics)Molecular bindingGeneral ChemistryQuartz crystal microbalance03 medical and health sciences030104 developmental biologyDual-polarization interferometryQUIMICA ANALITICABiological systemRSC Advances
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High Resolution Solution NMR Structure of the Z Domain of Staphylococcal Protein A. Analysis of Secondary Structure for Free Z Domain and Bounded to …

1997

Staphylococcal protein A (SpA) is a cell-wall-bound pathogenicity factor from the bacterium Staphylcoccus aureus. It exhibits tight binding to many IgG, IgA and IgM molecules at site(s) different from antigen-combining site. Because of their small size and immunoglobulin (IgG)-binding activities, domains of protein A are important targets for protein engineering efforts and for the development of computational approaches for de novo protein folding.

biology'de novo' protein foldingChemistryStaphylococcal proteinProtein engineeringbiology.organism_classificationCrystallographyBiochemistryDomain (ring theory)biology.proteinAntibodyProtein AProtein secondary structureBacteria
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Specific interaction of citrate with bis(fluorophoric) bibrachial lariat aza-crown in comparison with the other components of the Krebs cycle

2006

Clares Garcia, M. Paz, M.Paz.Clares@uv.es ; Garcia-España Monsonis, Enrique, Enrique.Garcia-Es@uv.es ; Soriano Soto, Concepcion, Concepcion.Soriano@uv.es ; Tejero Toquero, Roberto, Roberto.Tejero@uv.es

Citrate ; Krebs cycle ; Fluorescence ; NaphthaleneUNESCO::QUÍMICACrown (botany)UNESCO::QUÍMICA::Química analíticaMetals and AlloysGeneral ChemistryFluorescenceMedicinal chemistry:QUÍMICA [UNESCO]CatalysisFluorescenceSurfaces Coatings and FilmsElectronic Optical and Magnetic MaterialsCitric acid cyclechemistry.chemical_compoundchemistryBiochemistryMaterials ChemistryCeramics and Composites:QUÍMICA::Química analítica [UNESCO]CitrateKrebs cycleThe Krebs CycleNaphthaleneNaphthalene
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A community resource of experimental data for NMR / X-ray crystal structure pairs

2015

We have developed an online NMR / X-ray Structure Pair Data Repository. The NIGMS Protein Structure Initiative (PSI) has provided many valuable reagents, 3D structures, and technologies for structural biology. The Northeast Structural Genomics Consortium was one of several PSI centers. NESG used both X-ray crystallography and NMR spectroscopy for protein structure determination. A key goal of the PSI was to provide experimental structures for at least one representative of each of hundreds of targeted protein domain families. In some cases, structures for identical (or nearly identical) constructs were determined by both NMR and X-ray crystallography. NMR spectroscopy and X-ray diffraction …

0301 basic medicineChemistryNuclear magnetic resonance crystallographyNuclear magnetic resonance spectroscopyBiochemistryStructural genomics03 medical and health sciencesCrystallographyStructural bioinformatics030104 developmental biologyProtein structureStructural biologyTriple-resonance nuclear magnetic resonance spectroscopyMolecular BiologyProtein Structure InitiativeProtein Science
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A bibracchial lariat aza-crown ether as an abiotic catalyst of malonic acid enolization

2007

A bibracchial lariat aza-crown ether (L) consisting of 2-aminoethylnaphthyl moieties appended to a 2 : 2 azapyridinophane structure displays significant activation of H–D exchange in malonic acid. The compound forms very stable adducts with malonate anions (MA) in the 2–10 pH range. Molecular dynamics studies performed for the species resulting from the interaction of the hexaprotonated macrocycle and the dianion show that malonate is encapsulated by L with distances between the CH2 group of malonate and the pyridine nitrogens of ca. 3.5 A. The pendant arms of L cap above and below the anion, defining a pseudo-cage structure. Quantum chemical calculations for α-proton abstraction from malon…

chemistry.chemical_classificationLigandStereochemistryEtherGeneral ChemistryMalonic acidMedicinal chemistryCatalysischemistry.chemical_compoundMalonatechemistryPyridineMaterials ChemistryMoietyCarboxylateCrown etherNew Journal of Chemistry
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Protein structure prediction assisted with sparse NMR data in CASP13

2019

CASP13 has investigated the impact of sparse NMR data on the accuracy of protein structure prediction. NOESY and 15 N-1 H residual dipolar coupling data, typical of that obtained for 15 N,13 C-enriched, perdeuterated proteins up to about 40 kDa, were simulated for 11 CASP13 targets ranging in size from 80 to 326 residues. For several targets, two prediction groups generated models that are more accurate than those produced using baseline methods. Real NMR data collected for a de novo designed protein were also provided to predictors, including one data set in which only backbone resonance assignments were available. Some NMR-assisted prediction groups also did very well with these data. CAS…

Models MolecularProtein FoldingMagnetic Resonance SpectroscopyProtein ConformationComputer scienceCrystallography X-RayBiochemistryArticle03 medical and health sciencesProtein structureStructural BiologyComputer SimulationCASPMolecular Biology030304 developmental biology0303 health sciences030302 biochemistry & molecular biologyProteinsReproducibility of ResultsRangingProtein structure predictionNmr dataData setResidual dipolar couplingTwo-dimensional nuclear magnetic resonance spectroscopyAlgorithmAlgorithmsProteins: Structure, Function, and Bioinformatics
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1987

The intrinsic viscosities, [η], for the ternary systems alkane (1)/2-butanone (2)/poly(dimethylsiloxane) (PDMS)(3), with the alkanes decane, dodecane and hexadecane, are determined at 20,0°C. The constants a of the Mark-Houwink equation and the constant of the unperturbed dimensions, KΘ, of the polymer are evaluated over the whole composition range of the binary solvent mixture. [η] shows a pronounced maximum at intermediate compositions as found in cosolvent mixtures. In these cosolvent mixtures, the numerical values of KΘ are higher than in the single-component solvents, because the cosolvent mixtures correspond to a mixed solvent with an excess free energy, GE ≥ 0, the increase in KΘ bei…

Alkanechemistry.chemical_classificationchemistry.chemical_compoundViscositychemistryVirial coefficientDodecaneIntrinsic viscosityPolymer chemistryDecaneHexadecaneTernary operationDie Makromolekulare Chemie
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NMR Exchange Format: a unified and open standard for representation of NMR restraint data

2015

SCOPUS: le.j

0303 health sciencesElectronic Data ProcessingMagnetic Resonance SpectroscopyComputer sciencebusiness.industryeducationRepresentation (systemics)virus diseasesGénéralitésNuclear magnetic resonance spectroscopy010402 general chemistry01 natural sciencesArticle0104 chemical sciencesComputational science03 medical and health sciencesSoftwareNuclear magnetic resonanceStructural BiologyOpen standard[CHIM.ANAL]Chemical Sciences/Analytical chemistrybusinessMolecular BiologySoftware030304 developmental biologyNature structural & molecular biology
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Analysis of the structural quality of the CASD-NMR 2013 entries

2015

We performed a comprehensive structure validation of both automated and manually generated structures of the 10 targets of the CASD-NMR-2013 effort. We established that automated structure determination protocols are capable of reliably producing structures of comparable accuracy and quality to those generated by a skilled researcher, at least for small, single domain proteins such as the ten targets tested. The most robust results appear to be obtained when NOESY peak lists are used either as the primary input data or to augment chemical shift data without the need to manually filter such lists. A detailed analysis of the long-range NOE restraints generated by the different programs from t…

BiochimieProteinNMR NOE Protein Structure determination Validation Spectroscopy Biochemistry Structural BiologyBiochemistryQualityArticleNMRBlind testingSpectroscopie [électromagnétisme optique acoustique]CASD-NMRValidationSpectroscopie [état condense]Structure determinationSpectroscopyNOE
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The second round of Critical Assessment of Automated Structure Determination of Proteins by NMR: CASD-NMR-2013

2015

The second round of the community-wide initiative Critical Assessment of automated Structure Determination of Proteins by NMR (CASD-NMR-2013) comprised ten blind target datasets, consisting of unprocessed spectral data, assigned chemical shift lists and unassigned NOESY peak and RDC lists, that were made available in both curated (i.e. manually refined) or un-curated (i.e. automatically generated) form. Ten structure calculation programs, using fully automated protocols only, generated a total of 164 three-dimensional structures (entries) for the ten targets, sometimes using both curated and un-curated lists to generate multiple entries for a single target. The accuracy of the entries could…

Models MolecularProtein ConformationBiochimieProton Magnetic Resonance SpectroscopyDatasets as TopicBiochemistryArticleBlind testingAutomationCASD-NMRValidationSpectroscopie [état condense]Carbon-13 Magnetic Resonance SpectroscopyNuclear Magnetic Resonance BiomolecularStructure determinationSpectroscopyAccuracyautomationNOEaccuracyProteinChemical shiftProteinsReproducibility of ResultsPrecisionQualityNMRPRECISIONSpectroscopie [électromagnétisme optique acoustique]qualityprotein
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CCDC 1468808: Experimental Crystal Structure Determination

2016

Related Article: Javier Pitarch-Jarque, Raquel Belda, Salvador Blasco, Pilar Navarro, Roberto Tejero, José Miguel Junquera-Hernández, Vicente Pérez-Mondéjar, Enrique García-España|2016|New J.Chem.|40|5670|doi:10.1039/C5NJ03234B

bis(mu4-39121316222526-Octa-azatricyclo[22.2.1.11114]octacosa-1(27)11(28)1324-tetraene)-diaqua-bis(perchlorato)-tetra-copper diperchlorate dihydrateSpace GroupCrystallographyCrystal SystemCrystal StructureCell ParametersExperimental 3D Coordinates
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CCDC 892312: Experimental Crystal Structure Determination

2016

Related Article: Javier Pitarch-Jarque, Raquel Belda, Salvador Blasco, Pilar Navarro, Roberto Tejero, José Miguel Junquera-Hernández, Vicente Pérez-Mondéjar, Enrique García-España|2016|New J.Chem.|40|5670|doi:10.1039/C5NJ03234B

Space GroupCrystallography(mu2-39121316222526-Octa-azatricyclo[22.2.1.11114]octacosa-1(27)11(28)1324-tetraenato)-di-copper bis(mu4-39121316222526-octa-azatricyclo[22.2.1.11114]octacosa-1(27)11(28)1324-tetraene)-diaqua-tetra-copper octaperchlorate trihydrateCrystal SystemCrystal StructureCell ParametersExperimental 3D Coordinates
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CCDC 1468807: Experimental Crystal Structure Determination

2016

Related Article: Javier Pitarch-Jarque, Raquel Belda, Salvador Blasco, Pilar Navarro, Roberto Tejero, José Miguel Junquera-Hernández, Vicente Pérez-Mondéjar, Enrique García-España|2016|New J.Chem.|40|5670|doi:10.1039/C5NJ03234B

Space GroupCrystallographyCrystal SystemCrystal StructureCell Parametersbis(mu-39121316222526-octaazatricyclo[22.2.1.11114]octacosa-1(27)1114(28)24-tetraen-1225-diyl)-diperchlorato-diaqua-tetra-copper (mu-39121316222526-octaazatricyclo[22.2.1.11114]octacosa-1(27)1114(28)24-tetraen-1225-diyl)-diperchlorato-di-copper diperchlorate hydrateExperimental 3D Coordinates
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CCDC 1472832: Experimental Crystal Structure Determination

2016

Related Article: Luis M. López-Martínez, Javier Pitarch-Jarque, Àlvar Martínez-Camarena, Enrique García-España, Roberto Tejero, Hisila Santacruz-Ortega, Rosa-Elena Navarro, Rogerio R. Sotelo-Mundo, Mario Alberto Leyva-Peralta, Antonio Doménech-Carbó, and Begoña Verdejo|2016|Inorg.Chem.|55|7564|doi:10.1021/acs.inorgchem.6b01006

Space GroupCrystallographyCrystal System6-(2-(3-hydroxy-2-methyl-4-oxopyridin-1(4H)-yl)ethyl)-615-diaza-39-diazoniabicyclo[9.3.1]pentadeca-1(15)1113-triene diperchlorate hemihydrateCrystal StructureCell ParametersExperimental 3D Coordinates
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CCDC 892315: Experimental Crystal Structure Determination

2016

Related Article: Javier Pitarch-Jarque, Raquel Belda, Salvador Blasco, Pilar Navarro, Roberto Tejero, José Miguel Junquera-Hernández, Vicente Pérez-Mondéjar, Enrique García-España|2016|New J.Chem.|40|5670|doi:10.1039/C5NJ03234B

Space GroupCrystallographyCrystal SystemCrystal StructureCell Parameters91213222526-hexaaza-316-diazoniatricyclo[22.2.1.11114]octacosa-1(26)11(28)1324(27)-tetraene diperchlorateExperimental 3D Coordinates
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CCDC 892316: Experimental Crystal Structure Determination

2016

Related Article: Javier Pitarch-Jarque, Raquel Belda, Salvador Blasco, Pilar Navarro, Roberto Tejero, José Miguel Junquera-Hernández, Vicente Pérez-Mondéjar, Enrique García-España|2016|New J.Chem.|40|5670|doi:10.1039/C5NJ03234B

Space GroupCrystallographyCrystal SystemCrystal Structure(mu-39121316222526-octaazatricyclo[22.2.1.11114]octacosa-1(26)11(28)1324(27)-tetraene-1225-diyl)-di-copper diperchlorate hemihydrateCell ParametersExperimental 3D Coordinates
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