Roberto Tejero

Roberto Tejero
University of Valencia | UV · Physical Chemistry

Ph. D.

About

69
Publications
5,433
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2,388
Citations
Additional affiliations
January 2007 - December 2008
January 1999 - December 2006
Universitat de València
January 1994 - December 2009
Rutgers, The State University of New Jersey
Education
September 1972 - June 1977

Publications

Publications (69)
Article
Full-text available
Recent advances in molecular modeling using deep learning have the potential to revolutionize the field of structural biology. In particular, AlphaFold has been observed to provide models of protein structures with accuracies rivaling medium-resolution X-ray crystal structures, and with excellent atomic coordinate matches to experimental protein NM...
Preprint
Recent advances in molecular modeling using deep learning have the potential to revolutionize the field of structural biology. In particular, AlphaFold has been observed to provide models of protein structures with accuracy rivaling medium-resolution X-ray crystal structures, and with excellent atomic coordinate matches to experimental protein NMR...
Article
Currently significant efforts are devoted to designing small molecules able to bind selectively to guanine‐quadruplexes (G4s). These non‐canonical DNA structures are implicated in various important biological processes and have been identified as potential targets for drug development. Previously, we reported a series of triphenylamine(TPA)‐based c...
Article
Full-text available
CASP13 has investigated the impact of sparse NMR data on the accuracy of protein structure prediction. NOESY and 15N‐1H residual dipolar coupling data, typical of that obtained for 15N,13C‐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 predi...
Article
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, emission fluorescence and circular dichroism (CD) spectroscopies in combination with viscometry and dynamic modelling studies. Both organic molecul...
Article
The binuclear Cu ²⁺ 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...
Article
Full-text available
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...
Article
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 grou...
Article
Full-text available
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 con...
Article
Full-text available
We have developed an on-line 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 pr...
Article
Full-text available
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 ref...
Article
Full-text available
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...
Article
Full-text available
We present a unified, easily adaptable, open-source NMR exchange format (NEF) for NMR restraints and associated data. Developers of the major software packages for NMR structure determination and refinement have agreed to make their software able to read and write NEF-compliant files. Detailed specifications can be found at https://github.com/NMREx...
Article
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 protonatio...
Article
Full-text available
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...
Article
Full-text available
Maximizing the scientific impact of NMR-based structure determination requires robust and statistically sound methods for assessing the precision of NMR-derived structures. In particular, a method to define a core atom set for calculating superimpositions and validating structure predictions is critical to the use of NMR-derived structures as targe...
Article
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 prot...
Article
Full-text available
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 s...
Article
Full-text available
The heterogeneous array of software tools used in the process of protein NMR structure determination presents organizational challenges in the structure determination and validation processes, and creates a learning curve that limits the broader use of protein NMR in biology. These challenges, including accurate use of data in different data format...
Article
Full-text available
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 p...
Article
Disordered or unstructured regions of proteins, while often very important biologically, can pose significant challenges for resonance assignment and three-dimensional structure determination of the ordered regions of proteins by NMR methods. In this article, we demonstrate the application of (1)H/(2)H exchange mass spectrometry (DXMS) for the rapi...
Article
The influence of Mg(II) and organic solvents on the structure-activity relationship of spleen phosphodiesterase II was analyzed using UV and fluorescence spectroscopies. An increase in the RNase activity found in the presence of Mg(II) was related to the enzyme-Mg(II) interaction detected by UV spectroscopy. In the fluorescence spectra of phosphodi...
Article
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 con...
Article
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)....
Article
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 f...
Article
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;6:956-97...
Article
Full-text available
Among the Krebs cycle components, just citrate enhances the fluorescence of a new bi(brachial) lariat aza-crown containing appended naphthalene fluorophores.
Article
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...
Article
This article formulates the multidimensional nuclear Overhauser effect spectroscopy (NOESY) interpretation problem using graph theory and presents a novel, bottom-up, topology-constrained distance network analysis algorithm for NOESY cross peak interpretation using assigned resonances. AutoStructure is a software suite that implements this topology...
Article
Recent developments provide automated analysis of NMR assignments and three-dimensional (3D) structures of proteins. These approaches are generally applicable to proteins ranging from about 50 to 150 amino acids. In this chapter, we summarize progress by the Northeast Structural Genomics Consortium in standardizing the NMR data collection process f...
Article
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...
Article
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 c...
Article
Full-text available
Genome sequencing projects have already determined nearly complete genome sequences of several organisms, including human. The products of these genes are widely recognized as the next generation of therapeutics and targets for the development of pharmaceuticals. While identification of these genes is proceeding quickly, elucidation of their three-...
Article
beta-Helix structures are of particular interest due to their capacity to form transmembrane channels with different transport properties. However, the relatively large number of beta-helices configurations does not allow a direct conformational analysis of beta-helical oligopeptides. A synthetic alternating D,L-oligopeptide with twelve norleucines...
Article
The interaction in aqueous solution of the cyclophane receptors 2,6,10,13,17,21-hexaaza[22]orthocyclophane (L-1) and 2,6,10,13,17,21-hexaaza[22]paracyclophane (L-2) 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 recep...
Article
Calmodulin is known to bind to various amphipathic helical peptide sequences, and the calmodulin-peptide binding surface has been shown to be remarkably tolerant sterically. D-Amino acid peptides, therefore, represent potential nonhydrolysable intracellular antagonists of calmodulin. In the present study, synthetic combinatorial libraries have been...
Article
Full-text available
A new computer program, HYPER, has been developed for automated analysis of protein dihedral angle values and CH2 stereospecific assignments from NMR data. HYPER uses a hierarchical grid-search algorithm to determine allowed values of , , and 1 dihedral angles and CH2 stereospecific assignments based on a set of NMR-derived distance and/or scalar-c...
Article
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-M...
Article
Interaction of the macrocyclic polyamine 1,4,7,10,13,16,19-heptaazacyclohenicosane ([21]aneN(7)) in its protonated forms with the dinucleotides NAD(+) and NADP(+) has been followed by pH-metric titration, NMR and cyclic voltammetry. Both dinucleotides interact strongly with [21]aneN(7) forming adduct species with protonation degrees varying from 3...
Article
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 (REP-M...
Article
The major cold-shock protein (CspA) from Escherichia coli is a single-stranded nucleic acid-binding protein that is produced in response to cold stress. We have previously reported its overall chain fold as determined by NMR spectroscopy [Newkirk, K., Feng, W., Jiang, W., Tejero, R., Emerson, S. D., Inouye, M., and Montelione, G. T. (1994) Proc. Na...
Article
Sequence specific 1H NMR resonance assignments are reported here for 95 amino acids of reduced plastocyanin from the cyanobacterium Synechocystis sp. PCC 6803 at pH 5.4. Spin systems of different amino acids were classified and identified using DQF-COSY and TOCSY spectra in D2O and H2O solvents. A variety of temperature conditions and two magnetic...
Article
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.
Article
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...
Article
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” str...
Chapter
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 prote...
Article
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 dete...
Article
A large portion of the 13C resonance assignments for murine epidermal growth factor (mEGF) at pH 3.1 and 28°C has been determined at natural isotope abundance. Sequence-specific 13C assignments are reported for 100% of the assignable Ca, 96% of the Cß, 86% of the aromatic and 70% of the remaining peripheral aliphatic resonances of mEGF. A good corr...
Article
Full-text available
Sequence-specific 1H and 15N resonance assignments have been determined for the major cold shock protein (CspA) from Escherichia coli with recently developed three-dimensional triple-resonance NMR experiments. By use of these assignments, five antiparallel beta-strands were identified from analysis of NMR data. Strands 1-4 have a classical 3-2-1-4...
Article
Diverse theoretical expressions have been used to describe the deviations in solute retention in size exclusion chromatography (s.e.c.) with mixed eluents. Most of them are based on the Flory-Huggins (FH) thermodynamic model of polymer solutions. Recently, and using a modified FH theory, we have calculated distribution coefficients Kp, in s.e.c. wi...
Article
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 p...
Article
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...
Article
There are two formalisms to describe the sorption equilibrium in a polymer-mixed solvent system (TPS). In the Flory-Huggins (FH) thermodynamic model, empirical ternary interaction parameters, gT and XT, are necessary to evaluate the preferential adsorption coefficient (λ) and total sorption potential (Y). These ternary parameters have already been...
Article
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...
Article
From a thermodynamic point of view, theoretical expressions for the distribution coefficient of solute-gel interactions in g.p.c., kp, and the preferential sorption coefficient, λ, have been developed. In the light of these expressions, a criterion to define an ideal reference system in which solutes are separated solely by steric exclusion, kp = 1...
Article
Dynamic viscosities eta , of n-alkane plus 2-butanone mixtures (n-alkane equals n-heptane, n-nonane, n-decane, n-undecane, n-dodecane, and n-hexadecane) have been measured at 20 degree C. Deviations from ideality, as defined by eta minus eta //i//d ( eta //i//d varies directly as ideal viscosity), are negative in n-heptane plus 2-butanone, null in...
Article
Second virial (A2) and preferential solvation (λ) coefficients, as well as binary interaction potential (g12), as measured by light scattering, for the system n-decane (1)-butanone (MEK) (2)-poly(dimethylsiloxane) (PDMS) (3) have been determined at 20°. The system displays cosolvency, as the inversion in λ and the maximum in A2 at seem to indicate....
Article
A model quantitatively describing the experimental shifts in elution volumes of polymeric solute A in the presence of another polymer B is developed. The concentration-dependent shrinkage of A coils has been evaluated from the intrinsic viscosity displayed by polymer A in the ternary solution formed by itself at cA concentration + polymer B at cB c...
Article
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...
Article
The concentration effects on the elution volume in theta binary and ternary polymeric systems have been studied by size-exclusion chromatography (s.e.c.). The experimental results have been compared with the predicted ones from a simple theoretical model mainly governed by the Huggins' coefficient, k. Different problems in the evaluation of k for t...
Article
Reactivity ratios for the radical copolymerisation of the methylmethacrylate (MMA) (1)/methyl isopropenyl ketone (MIK) (2) system have been evaluated at 60°C as r1=0·97; r2=1·09. Copolymers with MIK contents from 0 to 15% have been prepared. Films were exposed to sunlight under environmental conditions at ground level and buried under-ground at a d...
Article
Second virial coefficients, A2, intrinsic viscosities, [η], and solvation preferential coefficients, γ, for the ternary systems n-hexane, HEX, (1)/butanone, MEK, (2)/poly(dimethylsiloxane), PDMS, (3) and n-heptane, HEP, (1)/MEK (2)/PDMS (3) have been determined at 20.0°. Binary interaction parameters, g2, have also been measured by light scattering...
Article
A model has been developed that gives a quantitative description for the dependence of the elution volume, Ve, on the concentration of injected solute, c, in exclusion chromatography (SEC). The concentration-dependent shrinkage of coils has been evaluated from the intrinsic viscosity displayed by a polymer in a binary dilute solution formed by itse...

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