Biomedical subjects

Aitziber L Cortajarena

Publications and source records attributed to Aitziber L Cortajarena.

9 recordsLinked to original sources

PubMed2006

Repeat motions and backbone flexibility in designed proteins with different numbers of identical consensus tetratricopeptide repeats.

The tetratricopeptide repeat (TPR) is a 34-residue helix-turn-helix motif that occurs as three or more tandem repeats in a wide variety of proteins. We have determined the repeat motions and backbone fluctuations of proteins containing two or three consensus TPR repeats (CTPR2 and CPTR3, respectively) using 15N NMR relaxation measurements. Rotational diffusion tensors calculated from these data for each repeat within each TPR protein indicate that there is a high degree of motional correlation between different repeats in the same protein. This is consistent with the prevailing view that repeat proteins, such as CTPR2 and CTPR3, behave as single cooperatively folded domains. The internal motions of backbone NH groups were determined using the Lipari-Szabo model-free formalism. For most residues, there was a clear separation between the influence of internal motion and the influence of global rotational tumbling on the observed magnetic relaxation. The local internal motions are highly restricted in most of the helical elements, with slightly greater flexibility in the linker elements. Comparisons between CTPR2 and CTPR3 indicate that an addition of a TPR repeat to the C-terminus (before the solvation helix) of CTPR2 slightly reduces the flexibility of the preceding helix.

Helix-Loop-Helix Motifs↗

PubMed2006

Ligand binding by TPR domains.

Tetratricopeptide repeat (TPR) domains bind specific peptide ligands and are thought to mediate protein-protein interactions in a variety of biological systems. Here we compare peptide ligand-binding by several different TPR domains. We present specific examples that demonstrate that TPR domains typically undergo little or no structural rearrangement upon ligand binding. Our data suggest that, contrary to a recent proposal, coupled folding and binding is not the common mechanism of ligand recognition by TPR domains.

Binding Sites↗

PubMed2006

Consensus design as a tool for engineering repeat proteins.

Repeat proteins were first identified because of their unusual primary structure, in which short amino acid sequences, typically between 20 and 40 residues, are repeated in tandem, often many times. After identification at the sequence level, the three-dimensional structures of representatives from several classes (e.g., ankyrin, tetratricopeptide, leucine rich repeat) have been solved. The structures indeed reveal unusual, nonglobular structures, a linear "string" of the tandem motifs. Perhaps because of the large surface area that is presented as a consequence of such elongated structures, repeat domains are often involved in mediating protein-protein interactions. Here we udescribe methods of consensus-based design and engineering of repeat proteins. We pay particular attention to the attributes of repeat proteins that make them well-suited to such approaches. In addition, we discuss practical issues related to producing and characterizing such designed proteins. We use the tetratricopeptide repeat, which is well-studied in our group, to illustrate many ideas, but also draw comparisons to other work on repeat proteins, where relevant.

Ankyrin Repeat↗

PubMed2005

Membrane insertion of Escherichia coli alpha-hemolysin is independent from membrane lysis.

Escherichia coli alpha-hemolysin (HlyA) is a protein exotoxin that binds and lyses eukaryotic cell and model membranes in the presence of calcium. Previous studies have been able to distinguish between reversible toxin binding to the membrane and irreversible insertion into the lipid matrix. Membrane lysis occurs as the combined effect of protein insertion plus a transient perturbation of the membrane bilayer structure. In the past, insertion and bilayer perturbation have not been experimentally dissected. This has now been achieved by studying HlyA penetration into lipid monolayers at the air-water interface, in which three-dimensional effects (of the kind required to break down the bilayer permeability barrier) cannot occur. The study of native HlyA, together with the nonlytic precursor pro-HlyA, and of different mutants demonstrates that although some nonlytic variants (e.g. pro-HlyA) exhibit very low levels of insertion, others (e.g. the nonlytic mutant HlyA H859N) insert even more strongly than the lytic wild type. These results show that insertion does not necessarily lead to membrane lysis, i.e. that insertion and lysis are not "coupled" phenomena. Millimolar levels of Ca(2+), which are essential for the lytic activity, cause an extra degree of insertion but only in the case of the lytic forms of HlyA.

Adsorption↗

PubMed2005

A new folding paradigm for repeat proteins.

The folding/unfolding transitions of a series of designed consensus tetratricopeptide repeat proteins are quantitatively described by the classical one-dimensional Ising model, which thus represents a new folding paradigm for repeat proteins. Moreover, for the first time for any protein, a theoretical model predicts the folding/unfolding transition midpoint and the width of the transition.

Amino Acid Motifs↗

PubMed2004

Protein design to understand peptide ligand recognition by tetratricopeptide repeat proteins.

Protein design aims to understand the fundamentals of protein structure by creating novel proteins with pre-specified folds. An equally important goal is to understand protein function by creating novel proteins with pre-specified activities. Here we describe the design and characterization of a tetratricopeptide (TPR) protein, which binds to the C-terminal peptide of the eukaryotic chaperone Hsp90. The design emphasizes the importance of both direct, short-range protein-peptide interactions and of long-range electrostatic optimization. We demonstrate that the designed protein binds specifically to the desired peptide and discriminates between it and the similar C-terminal peptide of Hsp70.

Amino Acid Sequence↗

PubMed2003

Asp-863 is a key residue for calcium-dependent activity of Escherichia coli RTX toxin alpha-haemolysin.

alpha-Haemolysin is a protein toxin secreted by pathogenic strains of Escherichia coli and requires sub-millimolar Ca(2+) for optimum lytic activity. As a member of the so-called RTX toxin family it contains a Gly-rich, Asp-rich Ca(2+)-binding domain, consisting of a series of nonapeptides repeated in tandem. Asp-863 is located immediately after the last-but-one nonapeptide. A mutant in which Asp-863 has been substituted by Gly displays a requirement for Ca(2+) that is 100-fold higher than the wild-type. Membrane lytic activity, as well as a conformational change revealed through an increase in intrinsic fluorescence, and the appearance of Ca(2+)-bound protein monomers resolvable by fast protein liquid chromatography, are all three dependent on Ca(2+) concentrations in the 2-20 mM range. Most RTX toxins have an Asp or Glu residue located at a position homologous to Asp-863, thus the key role of this residue for Ca(2+) requirements of alpha-haemolysin may be a general feature of this family of toxins.

Amino Acid Sequence↗

PubMed2003

A receptor-binding region in Escherichia coli alpha-haemolysin.

Escherichia coli alpha-hemolysin (HlyA) is a 107-kDa protein toxin with a wide range of mammalian target cells. Previous work has shown that glycophorin is a specific receptor for HlyA in red blood cells (Cortajarena, A. L., Goñi, F. M., and Ostolaza, H. (2001) J. Biol. Chem. 276, 12513-12519). The present study was aimed at identifying the glycophorin-binding region in the toxin. Data in the literature pointed to a short amino acid sequence near the C terminus as a putative receptor-binding domain. Previous sequence analyses of several homologous toxins that belong, like HlyA, to the so-called RTX toxin family revealed a conserved region that corresponded to residues 914-936 of HlyA. We therefore prepared a deletion mutant lacking these residues (HlyA Delta 914-936) and found that its hemolytic activity was decreased by 10,000-fold with respect to the wild type. This deletion mutant was virtually unable to bind human and horse red blood cells or to bind pure glycophorin in an affinity column. The peptide Trp914-Arg936 had no lytic activity of its own, but it could bind glycophorin reconstituted in lipid vesicles. Moreover, the peptide Trp914-Arg936 protected red blood cells from hemolysis induced by wild type HlyA. It was concluded that amino acid residues 914-936 constitute a major receptor-binding region in alpha-hemolysin.

Amino Acid Sequence↗

PubMed2002

His-859 is an essential residue for the activity and pH dependence of Escherichia coli RTX toxin alpha-hemolysin.

Escherichia coli alpha-hemolysin (HlyA) is a toxin protein that, in common with other members of the RTX family, contains a calcium-binding domain consisting of a number of Gly- and Asp-rich nonapeptides (17 in this case) repeated in tandem. Amino acid number 6 in these nonapeptides is almost invariably Asp, and occasionally Asn, but HlyA contains a His residue (number 859 in the chain) in position 6 of the last-but-one nonapeptide. HlyA mutants have been prepared, by site-directed mutagenesis, in which His-859 has been replaced by an Asn (H859N) or by Asp (H859D). HlyA exists in aqueous media in an aggregate-monomer equilibrium, but only the monomer containing bound Ca(2+) (HlyA.Ca) appears to be competent to achieve target membrane insertion and subsequent lysis. In mutant H859N, equilibrium appears to be shifted toward the aggregate, therefore the protein does not exchange Ca(2+) with the aqueous environment, no HlyA.Ca monomers are detected, and the protein lacks any membrane lytic activity. Mutant H859D in turn is almost indistinguishable from the wild-type regarding its calcium binding and membrane lytic activity, however, it differs significantly in its pH dependence. Wild-type HlyA activity decreases sigmoidally with pH, following rather closely the protonation curve of a His residue (apparent pK(a) approximately 6.5). With mutant H859D activity decreases almost linearly with pH and to a smaller extent. It can be concluded that His-859 plays a critical role in several aspects of HlyA activity, namely self-aggregation properties, calcium binding, hemolysis, and pH dependence.

Bacterial Proteins↗