Biomedical subjects

Javier Navarro

Publications and source records attributed to Javier Navarro.

8 recordsLinked to original sources

PubMed2002

Bacteriorhodopsin: a high-resolution structural view of vectorial proton transport.

Recent 3-D structures of several intermediates in the photocycle of bacteriorhodopsin (bR) provide a detailed structural picture of this molecular proton pump in action. In this review, we describe the sequence of conformational changes of bR following the photoisomerization of its all-trans retinal chromophore, which is covalently bound via a protonated Schiff base to Lys216 in helix G, to a 13-cis configuration. The initial changes are localized near the protein's active site and a key water molecule is disordered. This water molecule serves as a keystone for the ground state of bR since, within the framework of the complex counter ion, it is important both for stabilizing the structure of the extracellular half of the protein, and for maintaining the high pK(a) of the Schiff base (the primary proton donor) and the low pK(a) of Asp85 (the primary proton acceptor). Subsequent structural rearrangements propagate out from the active site towards the extracellular half of the protein, with a local flex of helix C exaggerating an early movement of Asp85 towards the Schiff base, thereby facilitating proton transfer between these two groups. Other coupled rearrangements indicate the mechanism of proton release to the extracellular medium. On the cytoplasmic half of the protein, a local unwinding of helix G near the backbone of Lys216 provides sites for water molecules to order and define a pathway for the reprotonation of the Schiff base from Asp96 later in the photocycle. A steric clash of the photoisomerized retinal with Trp182 in helix F drives an outward tilt of the cytoplasmic half of this helix, opening the proton transport channel and enabling a proton to be taken up from the cytoplasm. Although bR is the first integral membrane protein to have its catalytic mechanism structurally characterized in detail, several key results were anticipated in advance of the structural model and the general framework for vectorial proton transport has, by and large, been preserved.

Bacteriorhodopsins↗

PubMed2002

Structural basis for sensory rhodopsin function.

The crystal structure of sensory rhodopsin II from Natronobacterium pharaonis was recently solved at 2.1 A resolution from lipidic cubic phase-grown crystals. A critical analysis of previous structure-function studies is possible within the framework of the high-resolution structure of this photoreceptor. Based on the structure, a molecular understanding emerges of the efficiency and selectivity of the photoisomerization reaction, of the interaction of the sensory receptor and its cognate transducer protein HtrII, and of the mechanism of spectral tuning in photoreceptors. The architecture of the retinal binding pocket is compact, representing a major determinant for the selective binding of the chromophore, all-trans retinal to the apoprotein, opsin. Several chromophore-protein interactions revealed by the structure were not predicted by previous mutagenesis and spectroscopic analyses. The structure suggests likely mechanisms by which photoisomerization triggers the activation of sensory rhodopsin II, and highlights the possibility of a unified mechanism of signaling mediated by sensory receptors, including visual rhodopsins. Future investigations using time-resolved crystallography, structural dynamics, and computational studies will provide the basis to unveil the molecular mechanisms of sensory receptors-mediated transmembrane signaling.

Amino Acid Sequence↗

PubMed2002

Identification of a signal transduction switch in the chemokine receptor CXCR1.

Chemokine receptors belong to the superfamily of G protein-coupled receptors, which regulate the trafficking and activation of leukocytes, and operate as coreceptors in the entry of HIV-1. To investigate the early steps in the signal transmission from the chemokine-binding site to the G protein-coupling region we engineered metal ion-binding sites at putative extracellular sites in the chemokine receptor CXCR1. We introduced histidines into sites located in the second and third putative extracellular loops of CXCR1, creating single, double, and triple mutant receptors: R199H, R203H, D265H, R199H/R203H, R199H/D265H, R203H/D265H, R203H/H207Q, and R199H/R203H/D265H. Cells expressing the double mutants R199H/D265H and R203H/D265H and the triple mutant R199H/R203H/D265H failed to trigger interleukin 8-dependent calcium responses. Interestingly, calcium responses mediated by the single mutant R203H and the double mutants R199H/R203H and R203H/H207Q were blocked by Zn(II), indicating the creation of a functional metal ion-binding site. On the other hand, cells expressing all single, double, or triple histidine-substituted CXCR1 demonstrated high affinity binding to interleukin 8 in the presence and absence of metal ions. These findings indicate that occupation of the engineered metal-binding site uncouples the chemokine-binding site from the activation mechanism in CXCR1. Most importantly, we identify for the first time elements of an early signal transduction switch of chemokine receptors before the activation of cytoplasmic G proteins.

Amino Acid Sequence↗

PubMed2002

Functional role of internal water molecules in rhodopsin revealed by X-ray crystallography.

Activation of G protein-coupled receptors (GPCRs) is triggered and regulated by structural rearrangement of the transmembrane heptahelical bundle containing a number of highly conserved residues. In rhodopsin, a prototypical GPCR, the helical bundle accommodates an intrinsic inverse-agonist 11-cis-retinal, which undergoes photo-isomerization to the all-trans form upon light absorption. Such a trigger by the chromophore corresponds to binding of a diffusible ligand to other GPCRs. Here we have explored the functional role of water molecules in the transmembrane region of bovine rhodopsin by using x-ray diffraction to 2.6 A. The structural model suggests that water molecules, which were observed in the vicinity of highly conserved residues and in the retinal pocket, regulate the activity of rhodopsin-like GPCRs and spectral tuning in visual pigments, respectively. To confirm the physiological relevance of the structural findings, we conducted single-crystal microspectrophotometry on rhodopsin packed in our three-dimensional crystals and show that its spectroscopic properties are similar to those previously found by using bovine rhodopsin in suspension or membrane environment.

Animals↗

PubMed2002

Receptor-dependent G-protein activation in lipidic cubic phase.

The primary step in cellular signaling by G-protein-coupled receptors (GPCRs) is the interaction of the agonist-activated transmembrane receptor with an intracellular G-protein. Understanding the underlying molecular mechanisms requires the structural determination of receptor G-protein complexes that are not yet achieved. The crystal structure of the bovine photoreceptor rhodopsin, a prototypical GPCR, was solved recently and the structures of different states of engineered G-proteins were reported. Posttranslational hydrophobic modifications of G-proteins are in most cases removed for crystallization but play functional roles for interactions among G-protein subunits with receptors, as well as membranes. Bovine rhodopsin is reconstituted into lipidic cubic phases to assess their potential for crystallization of receptor G-protein complexes under conditions that may preserve the structural and functional roles of hydrophobic protein modifications. Three-dimensional bilayers of a bicontinuous lipidic cubic phase are successfully employed for crystallization of membrane and soluble proteins. UV-visible absorption and attenuated total reflection Fourier transform IR difference spectroscopy reveal that light activation of cubic phase reconstituted rhodopsin results in the generation of a metarhodopsin II-like state. Via diffusion along aqueous channels, transducin couples efficiently to this photoproduct as evidenced by the nucleotide-dependent increase of transducin fluorescence. Thus, rhodopsin transducin interactions do not crucially depend on the presence of sn1 and sn2 acyl chains, phospholipid head groups, or membrane planarity. Because lipidic cubic phases preserve the essential functional and structural properties of native rhodopsin and transducin, they appear suitable for the detergent-free crystallization of receptor G-protein complexes carrying a normal pattern of hydrophobic modifications.

Animals↗

PubMed2002

Crystallization of membrane proteins in cubo.

Our understanding of lipidic cubic phases for the crystallization of membrane proteins has advanced greatly since the inception of the concept in 1996, and the method is becoming well accepted. Several protocols that allow the efficient screening of crystallization conditions and handling of crystals are presented. State-of-the art micro techniques allow a large number of crystallization conditions to be tested using very small amounts of protein, and diffraction quality crystals can be grown in larger volumes in glass vials. In cubo crystallization conditions differ from those employed for detergent-solubilized proteins. Variations comprise the type of lipid matrix, detergent, protein, salt, temperature, hydration, pH, and pressure. Commercially available screening kits may be applied in order to define lead conditions. Once obtained, crystals may be removed from the surrounding cubic phase mechanically, by enzymatic hydrolysis, or by detergent solubilization. We anticipate this set of protocols to be applied successfully to larger, less stable, and noncolored membrane proteins in order to obtain well-diffracting crystals of membrane proteins that have so far evaded crystallization in the detergent-solubilized state.

Crystallization↗

PubMed2002

Early structural rearrangements in the photocycle of an integral membrane sensory receptor.

Sensory rhodopsins are the primary receptors of vision in animals and phototaxis in microorganisms. Light triggers the rapid isomerization of a buried retinal chromophore, which the protein both accommodates and amplifies into the larger structural rearrangements required for signaling. We trapped an early intermediate of the photocycle of sensory rhodopsin II from Natronobacterium pharaonis (pSRII) in 3D crystals and determined its X-ray structure to 2.3 A resolution. The observed structural rearrangements were localized near the retinal chromophore, with a key water molecule becoming disordered and the retinal's beta-ionone ring undergoing a prominent movement. Comparison with the early structural rearrangements of bacteriorhodopsin illustrates how modifications in the retinal binding pocket of pSRII allow subtle differences in the early relaxation of photoisomerized retinal.

Archaeal Proteins↗

PubMedDate not supplied

S-100 protein serum levels in patients with benign and malignant diseases: false-positive results related to liver and renal function.

S-100 serum concentrations were analyzed in 39 healthy people, 130 patients with benign diseases and 304 patients with malignancies, including 49 patients with locoregional diseases and 255 with advanced diseases. S-100 was determined by a commercial immunoluminometric assay, and 0.20 ng/ml was considered to be the upper limit of normality. In none of the healthy people was S-100 higher than 0.2 ng/ml. Slightly high S-100 concentrations were found in 33 out of 130 patients (25%) with benign diseases (mean 0.21 +/- 0.45 ng/ml). Significantly higher S-100 serum levels were found in patients with liver cirrhosis (63%, 10/16) (p = 0.024) or renal failure (45%, 8/18) (p = 0.03) than in patients with other benign diseases or in healthy people. Abnormal S-100 serum levels were found in 68 of the patients (22.5%) with malignancy (mean 1.01 +/- 5.9 ng/ml). The highest S-100 concentrations were found in patients with malignant melanomas (p = 0.001). Excluding melanoma patients, the S-100 serum levels in patients with malignancies were not related to tumor origin or stage but were clearly related to the site of metastasis, with patients with liver metastases showing higher values than patients with metastases without liver involvement (p = 0.02). No statistical differences were found among patients with liver cirrhosis, primary liver cancer or liver metastases. In conclusion, S-100 is a useful marker for melanoma, but abnormal levels of this tumor marker may be found in benign and malignant diseases associated with liver or renal injury.

Adult↗