Biomedical subjects

G Rivas

Publications and source records attributed to G Rivas.

At least 37 records · Page 2Linked to original sources

PubMed1996

The spectrin repeat folds into a three-helix bundle in solution.

Spectrin, a major component of the membrane skeleton, is mainly composed of tandemly repeated segments of approx. 106 amino acids. We have undertaken the determination of the three-dimensional structure of a chicken brain alpha-spectrin repeat by heteronuclear multidimensional NMR. Sedimentation equilibrium demonstrates that this repeat is monomeric at the concentration used for NMR (1 mM). Its secondary structure was identified using a collection of sequential and medium range NOEs, chemical shifts, HN-Halpha coupling constants, and relaxation measurements. These data unequivocally demonstrate the presence of three long helices connected by two loops. A set of interhelical NOEs indicates that the helices assemble into a triple helical structure. Our results provide experimental evidence supporting the triple-helical bundle proposed by modelling.

Amino Acid Sequence↗

PubMed1996

Structural organization of the major autolysin from Streptococcus pneumoniae.

LytA amidase is the best known bacterial autolysin. It breaks down the N-acetylmuramoyl-L-alanine bonds in the peptidoglycan backbone of Streptococcus pneumoniae and requires the presence of choline residues in the cell-wall teichoic acids for activity. Genetic experiments have supported the hypothesis that its 36-kDa chain has evolved by the fusion of two independent modules: the NH2-terminal module, responsible for the catalytic activity, and the COOH-terminal module, involved in the attachment to the cell wall. The structural organization of LytA amidase and of its isolated COOH-terminal module (C-LytA) and the variations induced by choline binding have been examined by differential scanning calorimetry and analytical ultracentrifugation. Deconvolution of calorimetric curves have revealed a folding of the polypeptide chain in several independent or quasi-independent cooperative domains. Elementary transitions in C-LytA are close but not identical to those assigned to the COOH-terminal module in the complete amidase, particularly in the absence of choline. These results indicate that the NH2-terminal region of the protein is important for attaining the native tertiary fold of the COOH terminus. Analytical ultracentrifugation studies have shown that LytA exhibits a monomer <--> dimer association equilibrium, through the COOH-terminal part of the molecule. Dimerization is regulated by choline interaction and involves the preferential binding of two molecules of choline per dimer. Sedimentation velocity experiments give frictional ratios of 1.1 for C-LytA monomer and 1.4 for C-LytA and LytA dimers; values that deviated from that of globular rigid particles. When considered together, present results give evidence that LytA amidase might be described as an elongated molecule consisting of at least four domains per subunit (two per module) designated here in as N1, N2, C1, and C2. Intersubunit cooperative interactions through the C2 domain in LytA dimer occur under all experimental conditions, while C-LytA requires the saturation of low affinity choline binding sites. The relevance of the structural features deduced here for LytA amidase is examined in connection with its biological function.

Calorimetry, Differential Scanning↗

PubMed1996

A leucine zipper motif determines different functions in a DNA replication protein.

RepA is the replication initiator protein of the Pseudomonas plasmid pPS10 and is also able to autoregulate its own synthesis. Here we report a genetic and functional analysis of a leucine zipper-like (LZ) motif located at the N-terminus of RepA. It is shown that the LZ motif modulates the equilibrium between monomeric and dimeric forms of the protein and that monomers of RepA interact with sequences at the origin of replication, oriV, while dimers are required for interactions of RepA at the repA promoter. Further, different residues of the LZ motif are seen to have different functional roles. Leucines at the d positions of the putative alpha-helix are relevant in the formation of RepA dimers required for transcriptional autoregulation. They also modulate other RepA-RepA interactions that result in cooperative binding of protein monomers to the origin of replication. The residues at the b/f positions of the putative helix play no relevant role in RepA-RepA interactions. These residues do not affect RepA autoregulation but do influence replication, as demonstrated by mutants that, without affecting binding to oriV, either increase the host range of the plasmid or are inactive in replication. It is proposed that residues in b/f positions play a relevant role in interactions between RepA and host replication factors.

Amino Acid Sequence↗

PubMed1996

Conformational studies of a short linear peptide corresponding to a major conserved neutralizing epitope of human respiratory syncytial virus fusion glycoprotein.

The conformational properties of a 21-residue peptide, corresponding to amino acids 255 to 275 (F255-275) of the human respiratory syncytial virus fusion (F) glycoprotein have been studied by CD and nmr spectroscopy. This peptide includes residues 262, 268, and 272 of the F polypeptide that are essential for integrity of most epitopes that mapped into a major antigenic site of the F molecule. CD data indicate that F255-275 adopts a random coil conformation in aqueous solution at low peptide concentrations. However, as the concentration of peptide is increased, a higher percentage of peptide molecules adopts an organized structure. This effect can be more easily observed when trifluoroethanol (30%) is added to peptide solutions, giving rise to CD spectra that resemble those of alpha-helix structures. These conformational changes were confirmed by nmr spectroscopy. The nuclear Overhauser effects observed in 30% trifluoroethanol/ water together with the conformational H alpha chemical shift data allowed us to propose a structural model of helix-loop-helix for the peptide in solution. In addition, these helical regions contain the amino acid residues essential for epitope integrity in the native F molecule. These results give new insights into the antigenic structure of the respiratory syncytical virus F glycoprotein.

Amino Acid Sequence↗

PubMed1996

Dimerization of A82846B, vancomycin and ristocetin: influence on antibiotic complexation with cell wall model peptides.

The thermodynamics of glycopeptide antibiotic dimerization have been studied by means of sedimentation equilibrium, using A82846B, vancomycin, ristocetin and complexes formed with several cell wall model peptides. These results indicate that vancomycin dimerization can be strongly promoted in two ways: i) stabilization of the antibiotic conformation in which the carbonyl group of residue three is on the back face of the molecule and ii) preferential interaction of the dimer with the lysine residue of N,N'-diacetyl-lysyl-D-alanyl-D-alanine. This effect was not found in ristocetin. A82846B forms stable dimers at very low antibiotic concentration. Two conformational forms have been found for complexed A82846B by 1H NMR. However, calorimetric binding experiments have shown that all its binding sites are thermodynamically equivalent. The affinity of the A82846B dimer for the tripeptide has been estimated to be about 3kJ x mol-1 higher than that of the vancomycin monomer and about -2.6kJ x mol-1 lower than that of dimeric vancomycin. The possible role of dimerization in the biological activity of glycopeptide antibiotics is discussed further on the basis of present thermodynamic data.

Amino Acid Sequence↗

PubMed1995

The thermodynamics of association and unfolding of the 205-316 C-terminal fragment of thermolysin.

The 205-316 C-terminal fragment of thermolysin has been studied by differential scanning calorimetry at pH values 2.5, 3.0, 3.5, 4.0 and 5.0 and at a constant ionic strength of 130 mM. The thermal unfolding of the fragment occurs at thermodynamic equilibrium under our experimental conditions. The effect of sample concentration at the different pH values on the calorimetric traces is consistent with a monomer-dimer equilibrium of the folded fragment, which undergoes thermal unfolding into individual fragments. Equilibrium sedimentation experiments at 10 degrees C and different pH values confirm the presence of the association equilibrium and provide the value of the dimerization constants. The global analysis of the calorimetric, heat capacity curves has been carried out by a multidimensional fitting to the model N2<-->2N<-->2U. The analysis leads to a complete thermodynamic characterization of both the association and unfolding processes of the fragment. The resulting thermodynamic functions suggest a partially unfolded structure for both the monomeric and dimeric fragment, as well as a conformational change linked to the association process. Our results are discussed in terms of the structural information currently available and compared with the energetics of unfolding of the shorter 255-316 dimeric C-terminal fragment of thermolysin (Conejero-Lara, F., De Filippis, V., Fontana, A. and Mateo, P.L. (1994) FEBS Lett. 344, 154-156). The presence of the additional 50 residues increases the relative population of the 205-316 monomeric fragment versus that of the 255-316 fragment.

Calorimetry, Differential Scanning↗

PubMed1994

Ca(2+)-linked association of human complement C1s and C1r.

The weight-average molecular weight of Clr, an activated serine protease subcomponent of complement Cl, was measured in the presence of widely varying concentrations of Ca2+ and the other serine protease subcomponent, Cls, by utilizing the technique of tracer sedimentation equilibrium. A quantitative model for heteroassociation between the two subcomponents, which takes into account the previously observed Ca(2+)-dependent self-association of Cls, was fit to the combined data at each Ca2+ concentration. The results indicate that Clr, which exists as a dimer under all of the conditions explored in this work, can bind up to two molecules of Cls at both low and high Ca2+ concentrations, but the association constant for binding a single molecule of Cls to dimeric Clr is estimated to increase on the order of a 1000-fold as [Ca2+] increases from 1 nM to 1.0 mM. Heteroassociation of Clr and Cls is favored over self-association of Cls at all conditions. The results clearly indicate the necessity of taking into account a multiplicity of states of association when attempting to understand the equilibrium average properties of a mixture of the two subcomponents and their binding to Clq in solution.

Binding Sites↗

PubMed1994

A short linear peptide that folds into a native stable beta-hairpin in aqueous solution.

The conformational properties of a 16 residue peptide, corresponding to the second beta-hairpin of the B1 domain of protein G, have been studied by nuclear magnetic resonance spectroscopy (NMR). This fragment is monomeric under our experimental conditions and in pure water adopts a population containing up to 40% native-like beta-hairpin structure. The detection by NMR of a native-like beta-hairpin in aqueous solution, reported here for the first time, indicates that these structural elements may have an important role in the early steps of protein folding. It also provides a good model to study in detail the sequence determinants of beta-hairpin structure stability, as has been done with alpha-helices.

Amino Acid Sequence↗

PubMed1993

Glycoprotein IIb peptide 656-667 mimics the fibrinogen gamma chain 402-411 binding site on platelet integrin GPIIb/IIIa.

The human integrin glycoprotein IIb/IIIa complex plays a central role in haemostasis as an inducible receptor for fibrinogen and other adhesive proteins at the platelet plasma membrane. Current evidence indicates that the ligand-binding domain of GPIIb/IIIa is discontinuous and placed at the subunit interface. Here we show that a synthetic peptide containing the polypeptide stretch GPIIb 656-667, which is hidden within the resting platelet GPIIb/IIIa heterodimer but becomes exposed following platelet activation with thrombin, binds to soluble fibrinogen (n = 2.3 +/- 1.3; Kd = 2 +/- 0.8 x 10(-5) M). This interaction is Ca(2+)-independent and can be partially inhibited with synthetic fibrinogen gamma-chain peptide 400-411 but not with GRGDS. In addition, peptide GPIIb 656-667 inhibits in a dose-dependent manner the aggregation of activated platelets (IC50 = 170 microM). Altogether, our results indicate that the GPIIb 656-667 region may form part of the inducible fibrinogen binding site and may not overlap with the integrin RGD-recognition domain.

Amino Acid Sequence↗

PubMed1993

Rapid and accurate microfractionation of the contents of small centrifuge tubes: application in the measurement of molecular weight of proteins via sedimentation equilibrium.

The contents of small centrifuge tubes containing solutions of radiolabeled proteins that had been centrifuged to sedimentation equilibrium were fractionated using a new device based upon the mechanical design of Attri and Minton (Anal. Biochem. 152, 319-328, 1986). Individual fractions, corresponding to laminae of 0.15 mm column height within the tube, were collected using one of two methods: (a) automatic mixing with scintillation fluid and delivery to vials mounted in a fraction collector, or (b) collection of undiluted fractions on scintillation vial caps impregnated with solid scintillator. Gradients of protein concentration were obtained via scintillation counting of sequential fractions. Molecular weights of proteins ranging from 4 x 10(4) to 3.5 x 10(5) were calculated by fitting the theoretical expression for sedimentation equilibrium of an ideal homogeneous solute to the experimental gradients. The values so obtained agree well with values obtained by optical scanning of the unfractionated centrifuge tube, and with values obtained from the literature.

Animals↗

PubMed1993

A structural model for the GroEL chaperonin.

Individual particle analysis of end views from negatively stained specimens of purified GroEL from Escherichia coli showed the presence of two different particle populations, those with a six-fold symmetry and those with a seven-fold symmetry, when studied at pH 7.7 and 5.0. Image processing of particles from frozen-hydrated specimens revealed at both pH values a homogeneous population of particles with a strong seven-fold symmetry component and an average image with seven asymmetric units. Biochemical analysis of purified GroEL showed unequivocally the presence of a single polypeptide with the N-terminal sequence identical to that of GroEL. These results are compatible with a structural model of GroEL as an asymmetric aggregate built up by two rings of seven-fold and six-fold symmetries, respectively.

Amino Acid Sequence↗

PubMed1993

Sedimentation equilibrium-quantitative polyacrylamide gel electrophoresis (SE-QPAGE): a new technique for the detection of associations in multicomponent solutions.

A new technique for the characterization of self- and hetero-associations in multicomponent solutions without chemical modification of the solutes is described. Solutions containing between one and four distinct protein components were first centrifuged to sedimentation equilibrium in swinging bucket rotors. Following centrifugation, the contents of each centrifuge tube were fractionated into 3-microliter aliquots deriving from sequential laminae of solution, and each aliquot was diluted into sodium dodecyl sulfate-containing buffer. Following incubation, 20 microliters of each aliquot was applied to individual lanes of a polyacrylamide gel. Following electrophoresis, proteins on the gel were stained with Coomassie blue R-250. The pattern of stained bands on the gel was digitized and the resulting image file analyzed to yield relative intensities of individual bands. A quantitative relationship between band intensity and amount of protein in a band was established by means of calibration gels. This relationship was found to be essentially constant for a variety of different proteins except for a protein-dependent scaling factor. Analysis of the dependence of band intensity of a single protein component upon the radial position of the original lamina from which the fraction was derived yielded reliable estimates of the molecular weight of that component in the original solution and in some cases showed that two components were cosedimenting as a complex.

Animals↗

PubMed1993

New developments in the study of biomolecular associations via sedimentation equilibrium.

The measurement and analysis of sedimentation equilibrium provide one of the most powerful techniques for quantitative characterization of reversible and irreversible macromolecular associations in solution. The use of this technique by nonspecialists has been greatly helped in recent years by the development of new instrumentation, new types of experiments and new PC-based software for computer-aided analysis of experimental results.

Chemical Phenomena↗

PubMed1992

Calcium-linked self-association of human complement C1s.

The weight-average molecular weight of C1s, an activated serine protease subcomponent of human complement C1, has been measured by means of sedimentation equilibrium over a wide range of both protein and calcium ion concentrations. The combined data may be accounted for quantitatively by a simple model for Ca(2+)-dependent self-association of C1s to a dimer. According to this model, the monomer contains a single Ca2+ binding site with K approximately equal to 3 x 10(5) M-1, and the dimer contains three independent Ca binding sites, two having a Ca2+ affinity lower than that of the monomer (K approximately equal to 3 x 10(4) M-1). The third binding site in the dimer, which presumably lies at the interface between the two amino-terminal alpha domains, has a higher Ca2+ affinity (K approximately equal to 1 x 10(8) M-1) and provides the driving force for C1s dimerization in the presence of calcium.

Binding Sites↗

PubMed1989

Interchain and intrachain disulphide bonds in human platelet glycoprotein IIb. Localization of the epitopes for several monoclonal antibodies.

The single interchain disulphide bond in platelet glycoprotein IIb (GPIIb) is accessible to extracellular reductants, and selective cleavage does not liberate GPIIb alpha from platelet plasma membrane, confirming that non-covalent interactions contribute to maintaining attachment of this subunit to the membrane. Eosin-maleimide labelling of isolated GPIIb after selective cleavage of this interchain disulphide bond, followed by full reduction and alkylation, CNBr cleavage, and analysis of the cleavage products allowed us to establish that this interchain disulphide bridge is formed between GPIIb beta (GPIIb beta-subunit) Cys-9 and GPIIb alpha Cys-826, and this conclusion was confirmed by independent routes. The other two cysteines of GPIIb beta (Cys-14 and Cys-19) form the single intrachain disulphide bond in this subunit. Last, the intrachain disulphides in GPIIb alpha (GPIIb alpha-subunit) are distributed in four main peptide domains which are not disulphide-bonded among themselves. The linear epitope for monoclonal antibody M1 is localized between Pro-4 and Met-24 (or Met-31) of GPIIb beta. The linear epitope for M3 is situated between Cys-826 and the C-terminus of GPIIb alpha. The M4 epitope is also linear and localized somewhere between residues 115 and 285 of GPIIb alpha. Finally, the epitopes for M5 and M6 are somewhere between Cys-608 and Met-704, within a 35 kDa membrane-bound chymotryptic product of digestion of GPIIb in whole platelets. The N-terminal amino acid sequences determined for eight different cleavage products of GPIIb alpha and GPIIb beta agree with the corresponding amino acid sequences predicted by cDNA sequence for human-erythroleukaemic-cell GPIIb [Poncz, Eisman, Heindenreich, Silver, Vilaire, Surrey, Schwartz & Bennett (1987) J. Biol. Chem. 262, 8476-8482].

Amino Acid Sequence↗

PubMed1988

Tryptic digestion of human GPIIIa. Isolation and biochemical characterization of the 23 kDa N-terminal glycopeptide carrying the antigenic determinant for a monoclonal antibody (P37) which inhibits platelet aggregation.

Early digestion of pure human platelet glycoprotein IIIa (GPIIIa) leads to a single cleavage of the molecule at 23 kDa far from one of the terminal amino acids. Automated Edman degradation demonstrates that GPIIIa and the smaller (23 kDa) tryptic fragment share the same N-terminal amino acid sequence. A further cleavage occurs in the larger fragment (80 kDa), reducing its apparent molecular mass by 10 kDa. The 23 kDa fragment remains attached to the larger ones in unreduced samples. Stepwise reduction of early digested GPIIIa with dithioerythritol selectively reduces the single disulphide bond joining the smaller (23 kDa) to the larger (80/70 kDa) fragments. Two fractions were obtained by size-exclusion chromatography of early digested GPIIIa after partial or full reduction and alkylation. The larger-size fraction contains the 80/70 kDa fragments, while the 23 kDa fragment is isolated in the smaller. The amino acid compositions of these fractions do not differ very significantly from the composition of GPIIIa; however the 23 kDa fragment contains only 10.2% by weight of sugars and is richer in neuraminic acid. Disulphide bonds are distributed four in the 23 kDa glycopeptide and 20-21 in the 80/70 kDa glycopeptide. The epitope for P37, a monoclonal antibody which inhibits platelet aggregation [Melero & González-Rodríguez (1984) Eur. J. Biochem. 141, 421-427] is situated within the first 17 kDa of the N-terminal region of GPIIIa, which gives a special functional interest to this extracellular region of GPIIIa. On the other hand, the epitopes for GPIIIa-specific monoclonal antibodies, P6, P35, P40 and P97, which do not interfere with platelet aggregation, are located within the larger tryptic fragment (80/70 kDa). Thus, the antigenic areas available in the extracellular surface of GPIIIa for these five monoclonal antibodies are now more precisely delineated.

Amino Acids↗

PubMed1987

Identification of a glycoprotein III a dimer in polyacrylamide gel separations of human platelet membranes.

Membrane glycoproteins IIb and IIIa play a major role in human blood platelet aggregation. The absence or the severe reduction of these two membrane glycoproteins, as observed in platelets of Glanzmann's thrombasthenic patients, is related to a lack of platelet aggregation. Separation of Glanzmann's thrombasthenic platelet samples by two-dimensional polyacrylamide O'Farrell gels show the absence of a high and several low molecular mass glycoproteins, in addition to the loss of glycoproteins IIb and IIIa (McGregor J. L. et al. Eur. J. Biochem. 1981; 116: 379-388). The aim of this study was to identify the nature of the high molecular mass component, absent in thrombasthenic platelets. A high molecular mass glycoprotein (200 kDa), present in two-dimensional SDS-polyacrylamide O-Farrell gel separations, was recognized by a monoclonal antibody (MP37) directed against glycoprotein IIIa. Moreover, the tryptic peptide map of this high molecular mass glycoprotein was nearly identical to that of glycoprotein IIIa. These results indicate that this high molecular mass glycoprotein present in SDS-polyacrylamide gels is a dimer of glycoprotein IIIa. This work raises the possibility that the high molecular mass glycoprotein, absent in two-dimensional O'Farrell gel separations of thrombasthenic platelets, is a dimer of glycoprotein IIIa.

Blood Platelets↗

PubMedDate not supplied

Binding of fibrinogen to platelet integrin alpha IIb beta 3 in solution as monitored by tracer sedimentation equilibrium.

Fibrinogen showed essentially no binding (KD > 1 mM) to platelet alpha IIb beta 3 integrin in solution in the presence of Triton or octylglucoside above critical micellar concentrations. Under these conditions the integrin was an alpha beta monomer. After removal of the detergent from the Triton containing buffer (25 mM Tris/HCl;, 150 mM NaCl, 1 mM CaCl2, 1 mM MgCl2, pH 7.4) the integrin formed aggregates with hexamers as the most prominent species, as demonstrated by analytical ultracentrifugation and electron microscopy. Tracer sedimentation equilibrium experiments indicate that fibrinogen binds to the integrin aggregates, but with a surprisingly large KD (at least 3 microM). This value is 10- to 100-fold higher than values determined by solid phase assays or with integrins reconstituted onto lipid bilayers.

Blood Platelets↗