Biomedical subjects

Beatriz Jiménez

Publications and source records attributed to Beatriz Jiménez.

12 recordsLinked to original sources

PubMed2006

13C direct detected COCO-TOCSY: a tool for sequence specific assignment and structure determination in protonless NMR experiments.

A novel experiment is proposed to provide inter-residue sequential correlations among carbonyl spins in (13)C detected, protonless NMR experiments. The COCO-TOCSY experiment connects, in proteins, two carbonyls separated from each other by three, four or even five bonds. The quantitative analysis provides structural information on backbone dihedral angles phi as well as on the side chain dihedral angles of Asx and Glx residues. This is the first dihedral angle constraint that can be obtained via a protonless approach. About 75% of backbone carbonyls in Calbindin D(9K), a 75 amino acid dicalcium protein, could be sequentially connected via a COCO-TOCSY spectrum. 49(3)J(C')(C') values were measured and related to backbone phi angles. Structural information can be extended to the side chain orientation of aminoacids containing carbonyl groups. Additionally, long range homonuclear coupling constants, (4)J(CC) and (5)J(CC), could be measured. This constitutes an unprecedented case for proteins of medium and small size.

Calbindins↗

PubMed2006

Assignment strategy for fast relaxing signals: complete aminoacid identification in thulium substituted calbindin D 9K.

Paramagnetic proteins generally contain regions with diverse relaxation properties. Nuclei in regions far from the metal center may behave like those in diamagnetic proteins, but those closer to the metal experience rapid relaxation with accompanying line broadening. We have used a set of NMR experiments optimized to capture data from these various concentric regions in assigning the signals from a paramagnetic Calbindin D 9K derivative in which one of the two calcium ions has been replaced by thulium(III). Normal double- and triple-resonance experiments with 1H detection were used in collecting data from nuclei in the diamagnetic-like region; these approaches identified signals from fewer than 50% of the amino acid residues (those with d > 17.5 A from thulium(III)). Paramagnetism-optimized two-dimensional NMR experiments with 1H detection were used in collecting data from nuclei in the next nearer region (d > 15 A). Standard (d > 14 A) and optimized (d > 9 A) 13C direct-detection experiments were used to capture data from nuclei in the next layer. Finally nuclei closest to the metal were detected by one-dimensional 13C (d > 5 A) and one-dimensional 15N data collection (d > 4.2 A). NMR signals were assigned on the basis of through-bond correlations and, for signals closest to the metal, pseudocontact shifts. The latter were determined from chemical shift differences between assigned signals in thulium(III) and lanthanum(III) derivatives of Calbindin D 9K and they were interpreted on the basis of a structural model for the lanthanide-substituted protein. This approach yielded assignments of at least one resonance per amino acid residue, including those in the thulium(III) coordination sphere.

Amino Acids↗

PubMed2005

Asymmetry in 13C-13C COSY spectra provides information on ligand geometry in paramagnetic proteins.

The relative intensity of Calpha-C' cross-peaks in homonuclear 13C COSY spectra depends on the relaxation properties of Calpha and C' spins, which, in the proximity of a paramagnetic center, are related to the metal-to-carbon distance. Their quantitative analysis has lead, for the cerium-substituted dicalcium protein, calbindin D9k, to the straightforward identification of peaks arising from metal-coordinating groups. The monodentate or bidentate metal binding mode of carboxylates was identified directly via NMR.

Algorithms↗

PubMed2005

13C direct detected experiments: optimization for paramagnetic signals.

To optimize 13C direct detected experiments for the observation of signals close to a paramagnetic center, we have assessed the sensitivity of different sequences based on CO-Cali coherence transfer. Features of CACO experiments were tested for Calbindin D9k, in which one of the two native Ca2+ ions is replaced by the paramagnetic Ce3+ ion. We have studied the comparison of single vs multiple quantum coherence transfer evolution as well as the influence of in-phase vs anti-phase detection of 13CO signals and finally the comparison of a coherence transfer step based on a CyO in plane with respect to a Cy ali in plane. The acquisition of the anti-phase component of the signal, accomplished by the removal of the last refocusing steps, allowed the identification of some signals unobserved with other pathways. The structural dependency of paramagnetism-induced nuclear relaxation is such that the identification of the most suitable coherence transfer pathway is not known "a priori" but it is driven by the relative proximity of Cali and CO to the paramagnetic center.

Animals↗

PubMed2005

An NMR view of the unfolding process of rusticyanin: Structural elements that maintain the architecture of a beta-barrel metalloprotein.

The unfolding process of the blue copper protein rusticyanin (Rc) as well as its dynamic and D(2)O/H(2)O exchange properties in an incipient unfolded state have been studied by heteronuclear NMR spectroscopy. Titrations of apo, Cu(I), and Cu(II)Rc with guanidinium chloride (GdmCl) show that the copper ion stabilizes the folded species and remains bound in the completely unfolded state. The oxidized state of the copper ion is more efficient than the reduced form in this respect. The long loop of Rc (where the first ligand of the copper ion is located) is one of the most mobile domains of the protein. This region has no defined secondary structure elements and is prone to exchange its amide protons. In contrast, the last loop (including a short alpha-helix) and the last beta-strand (where the other three ligands of the metal ion are located) form the most rigid domain of the protein. The results taken as a whole suggest that the first ligand detaches from the metal ion when the protein unfolds, while the other three ligands remain bound to it. The implications of these findings for the biological folding process of Rc are also discussed.

Azurin↗

PubMed2004

Biochemical modulation of NMDA receptors: role in conditioned taste aversion.

Glutamate neurotransmission plays a crucial role in a variety of functions in the central nervous system, including learning and memory. However, little is known about the mechanisms underlying this process in mammals because of the scarceness of experimental models that permit correlation of behavioral and biochemical changes occurring during the different stages of learning and the retrieval of the acquired information. One model that has been useful to study these mechanisms is conditioned taste aversion (CTA), a paradigm in which animals learn to avoid new tastes when they are associated with gastrointestinal malaise. Glutamate receptors of the N-methyl-D-aspartate (NMDA) type appear to be necessary in this process, because blockade of this receptor prevents CTA. Phosphorylation of the main subunits of the NMDA receptor is a well-established biochemical mechanism for the modulation of the receptor response. Such modulation seems to be involved in CTA, because inhibitors of protein kinase C (PKC) block CTA acquisition and because the exposure to an unfamiliar taste results in an increased phosphorylation of tyrosine and serine residues of the NR2B subunit of the receptor in the insular cortex, the cerebral region where gustatory and visceral information converge. In this work we review these mechanisms of NMDA receptor modulation in CTA.

Animals↗

PubMed2003

Monitoring the early steps of unfolding of dicalcium and mono-Ce3+-substituted forms of P43M calbindin D9k.

Early steps of unfolding of P43M Calbindin D(9k) have been evaluated by NMR spectroscopy on the native dicalcium and on the paramagnetic monocerium-substituted derivative. Although at 2 M GdmHCl the protein core maintains its overall folding and structure, amide (15)N R(2) measurements and cross correlation rates between N-H dipole-dipole relaxation and (15)N CSA relaxation reveal a closer and stronger packing of the hydrophobic interactions in the protein as a response to the presence of denaturing agents in solution. A complete reorientation of the Met43 side chain toward the hydrophobic core is accomplished by the disappearance of the millisecond dynamics observed on the native form of Calbindin D(9k), while cross correlation rates provide evidence that the two-way hydrogen bond between Leu23 and Val61 is broken or substantially weakened. The substitution of the calcium ion in site II with the paramagnetic Ce(3+) ion allowed us to obtain a number of long-range nonconventional constraints, namely, pseudocontact shifts, which were used, together with the NOEs collected on the native state, to monitor subtle structural variations occurring in the non-native state of the protein. Although the average rmsd between the structures of native and non-native states is small (0.48 A), structural rearrangements could be reliably identified. Our results provide unprecedented information about the behavior of Calbindin D(9k) during the early steps of unfolding. Furthermore, they constitute strong evidence of the efficiency of paramagnetism-based constraints in monitoring subtle structural changes that are beyond the sensitivity of an approach based only on NOE.

Amides↗

PubMed2003

Backbone dynamics of rusticyanin: the high hydrophobicity and rigidity of this blue copper protein is responsible for its thermodynamic properties.

Local dynamics and solute-solvent exchange properties of rusticyanin (Rc) from Thiobacillus ferrooxidans have been studied by applying heteronuclear ((1)H, (15)N) NMR spectroscopy. (15)N relaxation parameters have been determined for the reduced protein, and a model-free analysis has been applied. The high average value of the generalized order parameter, S(2) (0.93), indicates that Rc is very rigid. The analysis of cross correlation rates recorded in both the reduced and the oxidized forms conclusively proves that Rc possesses the same dynamic features in both oxidation states. The accessibility of backbone amide protons to the solvent at different time scales has also been studied by applying specific heteronuclear pulse sequences and by H(2)O/D(2)O exchange experiments. These experiments reveal that rusticyanin is extremely hydrophobic. The first N-35 amino acids, not present in the other BCPs, protect the beta-barrel core from its interaction with the solvent, and thus, this is one of the main factors contributing to the hydrophobicity. Both characteristics (high rigidity and hydrophobicity) are maintained in the metal ion surroundings.

Azurin↗

PubMed2003

Cloning, sequencing, and expression of the chitinase gene chiA74 from Bacillus thuringiensis.

The endochitinase gene chiA74 from Bacillus thuringiensis serovar kenyae strain LBIT-82 was cloned in Escherichia coli DH5 alpha F'. A sequence of 676 amino acids was deduced when the gene was completely sequenced. A molecular mass of 74 kDa was estimated for the preprotein, which includes a putative 4-kDa signal sequence located at the N terminus. The deduced amino acid sequence showed high degree of identity with other chitinases such as ChiB from Bacillus cereus (98%) and ChiA71 from Bacillus thuringiensis serovar pakistani (70%). Additionally, ChiA74 showed a modular structure comprised of three domains: a catalytic domain, a fibronectin-like domain, and a chitin-binding domain. All three domains showed conserved sequences when compared to other bacterial chitinase sequences. A ca. 70-kDa mature protein expressed by the cloned gene was detected in zymograms, comigrating with a chitinase produced by the LBIT-82 wild-type strain. ChiA74 is active within a wide pH range (4 to 9), although a bimodal activity was shown at pH 4.79 and 6.34. The optimal temperature was estimated at 57.2 degrees C when tested at pH 6. The potential use of ChiA74 as a synergistic agent, along with the B. thuringiensis insecticidal Cry proteins, is discussed.

Amino Acid Sequence↗

PubMed2002

Metal-ligand interplay in blue copper proteins studied by 1H NMR spectroscopy: Cu(II)-pseudoazurin and Cu(II)-rusticyanin.

The blue copper proteins (BCPs), pseudoazurin from Achromobacter cycloclastes and rusticyanin from Thiobacillus ferrooxidans, have been investigated by (1)H NMR at a magnetic field of 18.8 T. Hyperfine shifts of the protons belonging to the coordinated ligands have been identified by exchange spectroscopy, including the indirect detection for those resonances that cannot be directly observed (the beta-CH(2) of the Cys ligand, and the NH amide hydrogen bonded to the S(gamma)(Cys) atom). These data reveal that the Cu(II)-Cys interaction in pseudoazurin and rusticyanin is weakened compared to that in classic blue sites (plastocyanin and azurin). This weakening is not induced by a stronger interaction with the axial ligand, as found in stellacyanin, but might be determined by the protein folding around the metal site. The average chemical shift of the beta-CH(2) Cys ligand in all BCPs can be correlated to geometric factors of the metal site (the Cu-S(gamma)(Cys) distance and the angle between the CuN(His)N(His) plane and the Cu-S(gamma)(Cys) vector). It is concluded that the degree of tetragonal distortion is not necessarily related to the strength of the Cu(II)-S(gamma)(Cys) bond. The copper-His interaction is similar in all BCPs, even for the solvent-exposed His ligand. It is proposed that the copper xy magnetic axes in blue sites are determined by subtle geometrical differences, particularly the orientation of the His ligands. Finally, the observed chemical shifts for beta-CH(2) Cys and Ser NH protons in rusticyanin suggest that a less negative charge at the sulfur atom could contribute to the high redox potential (680 mV) of this protein.

Alcaligenes↗

PubMed2002

Neuronal organization and cell interactions of the cat stellate ganglion.

The functional structure of the cat stellate ganglion (SG) and, in particular, its extra- and intraganglionic connections and neuronal organization, were investigated using histochemical, immunohistochemical, morphological and histological methods. Retrograde axonal transport of horseradish peroxidase was used to determine most of the extraganglionic interactions. Of the targets tested, the most extensive efferent connections of the SG were with the stemocleidomastoid muscle, trachea, esophagus and heart. Neurons of the SG also send a small number of postganglionic efferents to the thyroid and stomach. Furthermore, ganglion cells send axons to the spinal ganglia. Several afferent connections of the SG were determined. Sympathetic preganglionic neurons of segments C8-T10 of the spinal cord, sensory neurons of C8-T9 spinal ganglia, intramural ganglia of the thoracic viscera and the reticular formation of the medulla oblongata send their axons to the SG. Intraganglionic interactions of intemeurons with principal ganglionic cells were assumed to occur, based on the presence of interneurons immunoreactive to GABA and substance P. GABA- and substance P-immunoreactive fibers located around a small number of postganglionic neurons were also identified. Morphological study revealed asymmetry between the left and right ganglia: the right ganglion is larger than the left and contains more cells. This asymmetry was also reflected in basic structural parameters of neurons, such as average neuronal area and average diameter of cell somata. The present data has been used to develop a scheme for the basic inter- and intraneuronal connections of the cat SG. This ganglion is a true nervous center, with postganglionic neurons, some of which might be performing sensory functions, and interneurons. The ganglion is connected not only with the spinal cord and spinal ganglia, but also with neurons of the intramural ganglia and, by direct links, with efferent neurons of the medulla oblongata. Thus, the SG may play an essential role in viscera-visceral reflexes.

Afferent Pathways↗

PubMedDate not supplied

Circuits and projections of cat stellate ganglion.

BACKGROUND: Although connections of stellate ganglion (SG) have been widely explored, some features of pathways and projections remain unknown, such as the source and fate of preganglionic axons present in output branches, including both synaptically interrupted and traversing pathways as well as axon composition (efferent and afferent) of these output nerves. METHODS: Circuits and central projections of cat SG were investigated using horseradish peroxidase (HRP) tracer and electrophysiologic techniques including stimulation of ganglionic branches during recording of genesis of compound action potentials in other nerves or centrally evoked responses. RESULTS: All branches of SG including vertebral nerve are mixed, i.e., they contain axons that synapse in the periphery or traverse ganglia. A novel synaptically interrupted pathway bi-directionally coursing along subclavian branches and inferior cardiac nerve was identified. Preganglionic axons traversing stellate ganglion course in communicating branch to vagus nerve and to inferior cardiac nerve, a small number of these preganglionic axons traversing stellate ganglion reach cervical sympathetic trunk via subclavian branches. For the first time, a small number of preganglionic traversing pathways were also detected in vertebral nerve. Afferent axons with somata located in C8-T7 dorsal root ganglia, identified in all branches of SG, projected centrally to neurons in thalamus and somatosensory zones of cerebral cortex and coincided with afferent projections of brachial plexus. CONCLUSIONS: Present data contribute to the morphologic description of autonomic regulation of thoracic organs, including centrally independent peripheral autonomic axon reflexes.

Animals↗