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Biomedical subjects

M Saraste

Publications and source records attributed to M Saraste.

At least 19 recordsLinked to original sources

Does Vav bind to F-actin through a CH domain?

An actin-binding protein domain we call here 'calponin-homology' or CH is present in signalling proteins such as Vav which are involved in activation and inactivation of small G-proteins. Using profile methods, we have detected two repeats of this domain in the actin-binding region of alpha-actinin and related proteins. Based on this, we propose that CH domain in Vav and other signalling proteins is employed for association with filamentous actin, and that this function correlates with their control on the G-proteins Rac and Rho which are involved in the organization of cytoskeleton.

Actins

Molecular mechanism of the calcium-induced conformational change in the spectrin EF-hands.

Calcium is a universally employed cytosolic messenger in eukaryotic cells. Most of the proteins that bind signalling calcium are members of the calmodulin superfamily and share two or more helix-loop-helix motifs known as EF-hands. A model, based on structure comparison of different domains and supported by preliminary NMR data, has suggested that EF-hands involved in signal transduction undergo a major conformational change upon calcium binding from a 'closed' to an 'open' state allowing protein-protein interaction. We have determined the solution structures of the EF-hand pair from alpha-spectrin in the absence and in the presence of calcium. The structures are in the closed and open conformation respectively, providing a definite experimental proof for the closed-to-open model. Our results allow formulation of the rules which govern the movement induced by calcium. These rules may be generalized to other EF-hands since the key residues involved are conserved within the calmodulin family.

Amino Acid Sequence

Structure of the binding site for inositol phosphates in a PH domain.

Phosphatidylinositol bisphosphate has been found to bind specifically to pleckstrin homology (PH) domains that are commonly present in signalling proteins but also found in cytoskeleton. We have studied the complexes of the beta-spectrin PH domain and soluble inositol phosphates using both circular dichroism and nuclear magnetic resonance spectroscopy, and X-ray crystallography. The specific binding site is located in the centre of a positively charged surface patch of the domain. The presence of 4,5-bisphosphate group on the inositol ring is critical for binding. In the crystal structure that has been determined at 2.0 A resolution, inositol-1,4,5-trisphosphate is bound with salt bridges and hydrogen bonds through these phosphate groups whereas the 1-phosphate group is mostly solvent-exposed and the inositol ring has virtually no interactions with the protein. We propose a model in which PH domains are involved in reversible anchoring of proteins to membranes via their specific binding to phosphoinositides. They could also participate in a response to a second messenger such as inositol trisphosphate, organizing cross-roads in cellular signalling.

Amino Acid Sequence

Spectroscopic and mutagenesis studies on the CuA centre from the cytochrome-c oxidase complex of Paracoccus denitrificans.

Cytochrome-c oxidase contains an unusual copper centre (CuA) located in subunit II. This centre mediates one-electron transfer from cytochrome c to low-spin heme a. Recent spectroscopic and biochemical studies have shown that this centre is a valence delocalised dinuclear [Cu(+1.5)-Cu(+1.5)] centre. We have measured the absorption, EPR and variable-temperature magnetic circular dichroism spectra of the CuA-binding domain isolated from Paracoccus denitrificans cytochrome aa3. The EPR spectrum showed the following signals: gparallel = 2.18; gperpendicular = 2.03. gparallel exhibited a seven-line hyperfine splitting pattern, with an intensity ratio showing that the single unpaired electron interacted equally with two copper nuclei. The magnetic circular dichroism spectrum was identical to those from CuA in bovine heart cytochrome-c oxidase and centre A of nitrous-oxide reductase, showing the close structural similarity between the three centres. To identify the ligands of CuA, all the conserved putative ligands in the P. denitrificans CuA domain were substituted. Only five residues, Cys244, Cys248, His209, His252, and Met255, were required for correct assembly of the CuA centre. Replacement of Met255 caused protein misfolding. Hence, methionine may have a structural role for the folding of the protein rather than being a CuA ligand. Given that both copper ions must have identical coordination geometries, the number of possible structures is limited. Two models are proposed: one involves the thiolate side-chains of Cys244 and Cys248 bridging a pair of copper ions with one histidine coordinating each copper ion, and the other has terminal ligation of each copper ion by one cysteine and one histidine residue. In both models, the metal-metal distance can be sufficiently short to permit direct d-orbital overlap of the copper ions. The magnetic circular dichroism transitions at 475 nm and 525 nm are assigned to thiolate-to-copper charge-transfer processes polarised perpendicular to one another, although the magnetic circular dichroism intensities show that the excited states were heavily mixed with copper d-orbitals. These intensities can be interpreted in the thiolate bridged model in terms of transitions within a Cu2(SR)2 rhomb. In the model involving terminal cysteine ligation, exciton coupling of two thiolate-to-copper charge-transfer transitions of similar energy, polarised along the Cu-S bonds, would contribute two transitions perpendicular to one another. This requires that the cysteine ligands have a cis orientation relative to one another.(ABSTRACT TRUNCATED AT 400 WORDS)

Amino Acid Sequence

New archaebacterial genes coding for redox proteins: implications for the evolution of aerobic metabolism.

Archaebacterial respiratory chains are poorly understood at the molecular level. We have cloned and sequenced a cluster of five new genes from the archaebacterium Sulfolobus acidocaldarius, four of them coding for redox proteins: a Rieske iron-sulphur protein, a cytochrome b, a subunit II of cytochrome oxidase and a blue copper protein (sulfocyanin). The fifth gene codes for a hydrophobic protein with no homologue in the databases. The gene organization and biochemical data suggest that all four redox proteins probably form part of a membrane respiratory complex together with SoxM, a previously characterized catalytic subunit of cytochrome oxidase. A phylogenetic analysis of the new protein sequences gives support to the view that an elaborate aerobic respiratory chain was already present in the last common ancestor of all living organisms.

Aerobiosis

Electron transfer between cytochrome c and the isolated CuA domain: identification of substrate-binding residues in cytochrome c oxidase.

Subunit II of cytochrome c oxidase has a C-terminal domain that is exposed to aqueous solution on membrane surface and contains a copper center called CuA. The central part of the cytochrome c binding site is thought to reside in this domain. We have expressed the subunit II fragment of the Paracoccus denitrificans cytochrome c oxidase in a soluble form and studied its interaction with cytochrome c by stopped-flow spectroscopy. The oxidation of cytochrome c by the CuA domain follows monophasic kinetics, indicating the presence of a single kinetically competent binding site. In low ionic strength medium, the domain oxidizes Paracoccus cytochrome c-550 and horse mitochondrial cytochrome c at the rates of 1.5 x 10(6) and 3 x 10(5) M-1 s-1, respectively. The reaction rates are strongly dependent on ionic strength, which must reflect electrostatic interactions within the complex. The KD for the complex between the bacterial cytochrome c and the domain is 1.6 microM; i.e., it is similar to that between the mitochondrial cytochrome c and the intact oxidase, suggesting that both contain the same catalytically competent binding site. Using site-directed mutagenesis, we have identified five conserved residues of the CuA domain that are involved in the cytochrome c binding. Mutations of glutamine 148, glutamate 154, aspartate 206, aspartate 221, or glutamate 246 lead to a 35-85% decrease in the rate of cytochrome c oxidation. The simultaneous substitution of three invariant carboxylic acids (aspartate 206, aspartate 221, and glutamate 246) leads to a 95% decrease in the reaction rate. Conversely, the reaction can be enhanced by removing a positive charge (lysine 219) from the CuA domain.

Amino Acid Sequence

The C-terminal domain of alpha-spectrin is structurally related to calmodulin.

An alignment of amino acid sequences suggests that the spectrin domain, which contains two EF-hand calcium-binding motifs, is structurally related to calmodulin. It is possible to align approximately 160 residues at the C-terminus of alpha-spectrin with the entire calmodulin sequence. We have expressed this domain in Escherichia coli and purified it. Circular dichroic and nuclear magnetic resonance spectroscopy show that the protein is folded and mostly helical. The conformation of the protein, as monitored spectroscopically, is sensitive to calcium at 0.1-1.0 mM. Equilibrium dialysis shows that there are two binding sites within this domain, with affinities in the 0.5 mM range. The domain can be split into N-terminal and C-terminal halves which fold independently. Only the N-terminal subdomain binds calcium. These data suggest that the C-terminus of alpha-spectrin has a domain with a calmodulin fold and two calcium-binding sites. Sequence alignments suggest that the related domains in alpha-actinin, and possibly in dystrophin, may share the same calmodulin-like structure. However, only non-muscle alpha-actinins appear to have one or two EF-hand(s) with the calcium-binding consensus sequence, and a strict consensus is not found in the muscle alpha-actinins or dystrophins.

Amino Acid Sequence

Engineering membrane proteins.

Much of the research on integral membrane proteins mirrors that on soluble proteins; however, membrane protein engineering also has its own ends and means, many of which take advantage of the peculiar situation of membrane proteins, whose chains are distributed between one lipidic and two aqueous phases. Extramembrane loops have been shortened, cut, or elongated with segments forming proteolytic cleavage sites, foreign epitopes, extra transmembrane segments, or even whole proteins, with the aim of facilitating purification, biochemical/biophysical studies, or crystallogenesis. Transmembrane alpha-helices have been deleted, duplicated, exchanged, transported into a foreign context or replaced with synthetic peptides, in order to both understand their integration into, and assembly in, the membrane and unravel their functional role. Insertion of cysteine residues has been the basis for a great diversity of experiments, ranging from the exploration of secondary, tertiary and quaternary structures of the transmembrane region to the creation of anchoring points for reporter molecules. Chemical engineering--the synthesis of protein fragments or even of whole proteins--offers particularly exciting new prospects, given the small size of folding domains in alpha-helical membrane proteins. Membrane protein engineering is rapidly developing its own agenda of questions and tool chest of techniques.

Bacteriorhodopsins

Pleckstrin homology domains: a fact file.

Structures of three different pleckstrin homology domains have been determined within the past year. They have a common core consisting of a seven-stranded and strongly bent beta-sheet and a C-terminal alpha-helix that packs against the beta-sheet. Phosphatidylinositol 4,5-bisphosphate and related compounds specifically bind to pleckstrin homology domains, suggesting that the domain may be involved in reversible anchorage to membranes or in recognition of a second messenger, such as inositol 1,4,5-trisphosphate. Pleckstrin homology domains have also been suggested to bind to the G beta gamma complex, but direct evidence for this is missing.

Animals

Saline contrast and colour Doppler transoesophageal echocardiography in detecting a patent foramen ovale and right-to-left shunts in stroke patients.

A paradoxical embolism due to right-to-left shunt through a patent foramen ovale (PFO) can be responsible for stroke and other ischaemic cerebral events. We studied the usefulness of saline contrast transoesophageal echocardiography after the Valsalva manoeuvre in detecting PFO and right-to-left shunts in 28 adult patients without known reason for a recent stroke. The results were compared with conventional transthoracic colour Doppler and with transoesophageal colour Doppler techniques. A PFO was found in 24 patients (86%) of our selected study population, whereas in four patients no PFO was found. A PFO with left-to-right shunt could be diagnosed by transthoracic colour Doppler echocardiography in only one case. A PFO with left-to-right shunt was found by transoesophageal colour Doppler echocardiography in 17 patients (61%), but in only three of them was a right-to-left shunt detected, even after the Valsalva manoeuvre. In contrast, a PFO with right-to-left shunt could be detected in 21 patients (75%) by using saline contrast transoesophageal echocardiography with the Valsalva manoeuvre. However, the method was unable to detect three cases of PFO with only left-to-right shunt, which were detected by colour Doppler transoesophageal echocardiography. In conclusion, our results show that saline contrast transoesophageal echocardiography with the Valsalva manoeuvre greatly improves the echocardiographic detection of PFO with right-to-left shunts in stroke patients.

Adult

Free thyroid hormones and a third-generation TSH assay in the detection of hyperthyroidism during long-term thyroxine treatment in thyroid carcinoma patients.

We evaluated the value of serum-free thyroid hormone and thyrotropin (TSH) concentrations in the detection of peripheral hyperthyroidism during thyroxine suppression therapy. A total of 57 patients on a stable thyroxine dose and 70 controls participated in the study. Serum-free thyroxine (FT4), free triiodothyronine (FT3) and TSH were measured by immunoassays based on time-resolved fluorescence (Delfia). The assay for TSH was a modification of a third generation Delfia hTSH Ultra method. The patients were classified into euthyroid and hyperthyroid subgroups based on clinical signs and symptoms (Wayne index). Systolic time intervals (STI) were measured. The Wayne indices were higher among patients than controls (p < 0.0001). The STI results were similar in patients and controls. Only FT4 had the discriminatory power for classifying euthyroid and hyperthyroid patients according to discriminant analyses. The diagnostic value of FT4 was further assessed by calculating the area under the relative operating characteristic (ROC) curve. The area was 0.707 (SE 0.0918), which was significantly different from an area of 0.5, i.e. the area of a test of no value (p = 0.032). In conclusion, a high serum FT4 concentration indicates hyperthyroidism during long-term thyroxine treatment among thyroid carcinoma patients. Although the degree of TSH suppression can now be exactly monitored with new third generation TSH assays, hyperthyroidism cannot be defined using TSH concentration in thyroid carcinoma patients. Therefore, additional serum FT4 concentration assays are needed in the assessment of hyperthyroidism associated with TSH suppression therapy in thyroid carcinoma patients.

Adult

Characterization of the interaction of natural proline-rich peptides with five different SH3 domains.

The interaction of six different proline-rich peptides with five SH3 domains has been investigated by using spectroscopic techniques. These peptides correspond to natural sequences and have been implicated in the interaction of some SH3 domains with other proteins. We have determined the Kd values for all of the possible combinations between the peptides and the SH3 domains. Low specificity and low affinity (> 5 microM) are the most remarkable conclusions from these studies. None of the peptides tested here were found to bind with significant affinity to spectrin-SH3 or n-src-SH3. Abl-SH3 seems to be the most selective of the domains analyzed here, while Fyn-SH3 is the most promiscuous. CD and FTIR studies indicate that these peptides adopt to different extents a PPII-like structure in aqueous solution. However, analysis of the SH3 domain complexes with these peptides suggests that proline-rich peptides do not necessarily adopt an overall PPII structure over their entire length upon binding to the different SH3 domains.

Amino Acid Sequence

A second terminal oxidase in Sulfolobus acidocaldarius.

We previously found that the soxABCD operon encodes a quinol oxidase complex in Sulfolobus acidocaldarius and this enzyme was purified and characterized. In this study, we have used a cloning procedure based on the conservation of oxidase sequences and the polymerase chain reaction to isolate a new gene (soxM) encoding a subunit of another terminal oxidase. This terminal oxidase is a fusion between two central components of cytochrome oxidases, subunits I and III. soxM forms a transcriptional unit which is expressed under heterotrophic growth conditions. The corresponding protein was detected by direct protein sequencing in a preparation enriched with a cytochrome absorbing light at 562 nm. This preparation contains a terminal oxidase which is able to oxidize the artificial substrate N,N,N',N'-tetramethyl-p-phenylenediamine. This preparation also contains SoxC, a protein homologous to the mitochondrial cytochrome b, and a Rieske iron-sulphur center. We suggest that SoxM is the core component of a second terminal oxidase complex and that this complex may share a subunit (SoxC) with the SoxABCD complex.

Amino Acid Sequence

Mutagenesis of a gene encoding a cytochrome o-like terminal oxidase of Azotobacter vinelandii: a cytochrome o mutant is aero-tolerant during nitrogen fixation.

The amino acid sequence obtained by translating the nucleotide sequence of a 0.55 kb fragment, amplified from Azotobacter vinelandii chromosomal DNA by PCR, was 57% identical to part of the Escherichia coli cyoB gene, encoding subunit I of the cytochrome bo-type quinol oxidase. This fragment was mutated in vitro by insertion of a kanamycin-resistance cassette and introduced into the chromosome of A. vinelandii by homologous recombination. The mutant contained no spectrally detectable cytochrome o. However, in the stationary phase of growth, the level of the alternative oxidase (cytochrome bd) was 11-fold higher than in the wild-type strain. Respiration of the mutant was insensitive to chlorpromazine, an inhibitor thought to act specifically on cytochrome o. Cytochrome o-deficient mutants fixed nitrogen in air, clearly distinguishing the role of this oxidase from that of cytochrome bd, which is required for respiratory protection of oxygen-labile nitrogenase.

Amino Acid Sequence

Evolution of cytochrome oxidase, an enzyme older than atmospheric oxygen.

Cytochrome oxidase is a key enzyme in aerobic metabolism. All the recorded eubacterial (domain Bacteria) and archaebacterial (Archaea) sequences of subunits 1 and 2 of this protein complex have been used for a comprehensive evolutionary analysis. The phylogenetic trees reveal several processes of gene duplication. Some of these are ancient, having occurred in the common ancestor of Bacteria and Archaea, whereas others have occurred in specific lines of Bacteria. We show that eubacterial quinol oxidase was derived from cytochrome c oxidase in Gram-positive bacteria and that archaebacterial quinol oxidase has an independent origin. A considerable amount of evidence suggests that Proteobacteria (Purple bacteria) acquired quinol oxidase through a lateral gene transfer from Gram-positive bacteria. The prevalent hypothesis that aerobic metabolism arose several times in evolution after oxygenic photosynthesis, is not sustained by two aspects of the molecular data. First, cytochrome oxidase was present in the common ancestor of Archaea and Bacteria whereas oxygenic photosynthesis appeared in Bacteria. Second, an extant cytochrome oxidase in nitrogen-fixing bacteria shows that aerobic metabolism is possible in an environment with a very low level of oxygen, such as the root nodules of leguminous plants. Therefore, we propose that aerobic metabolism in organisms with cytochrome oxidase has a monophyletic and ancient origin, prior to the appearance of eubacterial oxygenic photosynthetic organisms.

Aerobiosis

Structure and evolution of cytochrome oxidase.

The structural features of cytochrome oxidases are reviewed in light of their evolution. The substrate specificity (quinol vs. cytochrome c) is reflected in the presence of a unique copper centre (CuA) in cytochrome c oxidases. In several lines of evolution, quinol oxidases have independently lost this copper. Also, the most primitive cytochrome c oxidases do not contain this copper, and electron entry takes place via c-type haems. These enzymes, exemplified by the rhizobial FixN complex, probably remind the first oxidases. They are related to the denitrification enzyme nitric oxide reductase.

Bacteria