PubMed Health⌕ Search

Biomedical subjects

A Galat

Publications and source records attributed to A Galat.

At least 19 recordsLinked to original sources
PubMed2006

Analysis of the Trypanosoma cruzi cyclophilin gene family and identification of Cyclosporin A binding proteins.

The Trypanosoma cruzi cyclophilin gene family comprises 15 paralogues whose nominal masses vary from 19 to 110 kDa, namely TcCyP19, TcCyP20, TcCyP21, TcCyP22, TcCyP24, TcCyP25, TcCyP26, TcCyP28, TcCyP29, TcCyP30, TcCyP34, TcCyP35, TcCyP40, TcCyP42 and TcCyP110. Under the conditions used, only some of the T. cruzi cyclophilin paralogue products could be isolated by affinity chromatography. The 15 paralogues were aligned with 495 cyclophilins from diverse organisms. Analyses of clusters formed by the T. cruzi cyclophilins with others encoded in various genomes revealed that 8 of them (TcCyP19, TcCyP21, TcCyP22, TcCyP24, TcCyP35, TcCyP40, TcCyP42 and TcCyP110) have orthologues in many different genomes whereas the other 7 display less-defined patterns of their sequence attributes and their classification to a specific group of cyclophilin's orthologues remains uncertain. Seven epimastigote cDNA clones encoding cyclophilin isoforms were further studied. These genes were found dispersed throughout the genome of the parasite. Amastigote and trypomastigote mRNAs encoding these 7 genes were also detected. We isolated 4 cyclosporin A-binding proteins in T. cruzi epimastigote extracts, which were identified by mass spectrometry as TcCyP19, TcCyP22, TcCyP28 and TcCyP40. Cyclosporin A-binding to these cyclophilins might be of importance to the mechanism of action of Cyclosporin A and its non-immunosuppressive analogues, whose trypanocidal effects were previously reported, and therefore, of potential interest in the chemotherapy of Chagas' disease.

Amino Acid Sequence↗
PubMed2000

Mammalian FKBP-25 and its associated proteins.

Soluble proteins from porcine brain were divided into two packs: (1) proteins which pass freely through CM52-cellulose, and (2) proteins retained on CM52. Each of these two packs of proteins was fractionated on preparative flat-bed isoelectrofocusing gel in the range of pH 2-12. Native FKBP-25 and its truncated forms were found among other proteins retained on CM52-cellulose. Immunoblotting with anti-FKBP-25 showed two bands in the range 27-30 kDa, one due to unmodified FKBP-25 and other due to FKBP-25 mixed with high-mobility group II protein (HMG-II). Selective immunostaining with anti-FKBP-25 antibodies of proteins which were not retained on CM52-cellulose showed several bands within the range of pI 7-5 and mass of 23 +/- 2 kDa. These fractions of proteins were next resolved on two-dimensional gels and immunostained with anti-FKBP-25 antibodies. Six proteins in the pI range 7-5 were detected. Edman degradation of alpha-chymotrypsin digests of the major spot suggests that it contains the GTP-binding protein Rab5 co-migrating with guanylyl kinase, whereas MALDI-TOF showed that a residual content of FKBP-25 may be also associated with these two proteins. A residual quantity of FKBP-25 was also associated with the phosphatidylethanolamine-binding protein which is abundant in the brain.

Alkaline Phosphatase↗
PubMed2000

Sequence diversification of the FK506-binding proteins in several different genomes.

Sequences of FK506-binding proteins (FKBPs) from four genomes of the following organisms were compared: the prokaryote Escherichia coli, the lower eukaryote Saccharomyces cerevisiae, the plant Arabidopsis thaliana, the nematode Caenorhabditis elegans and a composite of 14 unique FKBPs from two mammalian organisms Homo sapiens (man) and Mus musculus (domestic mouse). A singular FK506-like binding domain (FKBD) has about 12 kDa and occurs in the form of archetypal FKBP-12 and as a part of different proteins ranging in size from 13 to 135 kDa. Some organisms may contain a variable number of proteins which consist from two to four consecutively fused FKBDs. In the 12-kDa subgroup of archetypal FKBPs sequence identity (ID) varies from 100 to 83% (mammalian FKBPs-12), 75-50% in mammalian vs. invertebrate FKBPs-12, and fall to about 30% for pairwise sequence comparisons of mammalian and bacterial FKBPs-12 which suggests that their sequences are divergent. Multiple sequence alignment of FKBPs from the four genomes and a set of unique mammalian FKBPs does not contain any explicit consensus sequence but certain sequence positions have conserved physico-chemical characteristics. Variations of hydrophobicity and bulkiness in the multiple sequence alignment are nonsymmetrical because the physico-chemical properties of the aligned sequences changed during evolution. These variations at the sequence positions which are crucial for binding the immunosuppressive macrolide FK506 and peptidyl-prolyl cis/trans isomerase (PPIase) activity are small.

Amino Acid Sequence↗
PubMed1999

Variations of sequences and amino acid compositions of proteins that sustain their biological functions: An analysis of the cyclophilin family of proteins.

The sequences of the ubiquitous and phylogenetically diversified cyclophilin family of proteins were divided into six groups, namely, vertebrates, invertebrates, other metazoa, plants, fungi, and prokaryotes. These groups of sequences were aligned with the multiple sequence alignment program Clustal-W. The variations of amino acid substitutions and amino acid compositions for these six groups of cyclophilins were calculated using a novel suite of multiple-sequence alignment analysis routines. The cyclophilins from vertebrates can be divided for at least two distinct structural classes that differ from each other by a variable-length amino acid insert within the loop that links alpha-helix II and beta-strand III. A similar structural feature is also present in the other groups of cyclophilins, namely, those from invertebrates, other metazoa, plants, and fungi. The sequences of cyclophilins from fungi and prokaryotes are more diversified than those from vertebrates, and their alterations involve structures other than the amino acid inserts within the loops. Variations of the hydrophobicity and bulkiness of amino acid substitutions of the aligned sequences were calculated for each group of cyclophilins and for the alignment of all the sequences. The variations have clear asymmetry that may signify the need for modification of the physical properties of certain fragments of cyclophilins that are involved in interactions with various cellular components in the evolving environment.

Amino Acid Sequence↗
PubMed1999

Detection of polyglutamine expansion in a new acidic protein: a candidate for childhood onset schizophrenia?

Polyglutamine expansion (PGE) encoded by a CAG repeat underlies eight inherited neurodegenerative diseases, among which is Huntington's disease. CAG expansion has also been reported in schizophrenia, suggesting a role for PGE. To investigate the potential role of PGE as a candidate for schizophrenia, we searched for PGE in nuclear families comprising a patient affected by childhood onset schizophrenia (COS, a rare and severe form of the disease) as a variation of the candidate gene approach for identifying susceptibility genes. We tested lymphoblastoid cell lines from COS patients (n = 32) by Western blot analysis with 1C2, a monoclonal antibody that specifically recognizes long polyglutamines. Eight of 11 unrelated black American COS patients showed a 60-kDa (approximately) band indicative of PGE. A strong 60-kDa band (suggestive of a large PGE) was detected in two of the eight positive patients. A weaker 60-kDa band (suggestive of a smaller and non pathogenic PGE) was detected in some unaffected parents or sibs of these two COS patients, and in six other black American COS patients. The strong and weak PGE signals were found to correspond to two different proteins. Unrelated black Americans unaffected by COS (n = 38) were negative for the strong 60-kDa PGE signal. Healthy white Americans (n = 53) were negative for both the strong and weak 60-kDa PGE signals. Two-dimensional gel analysis suggested that the strong PGE signal corresponds to an acidic (pI 4 approximately) protein and resulted in a more precise estimation (52-57 kDa) of its relative mass. This protein appeared to be not represented in Genbank, as suggested by the exclusion of several candidate CAG repeats. Our data suggest that this acidic protein might be a candidate for COS.

Adolescent↗
PubMed1998

Divergent and common groups of proteins in glands of venomous snakes.

Protein contents of venom-producing glands from the sea-snake Laticauda colubrina (LC) and terrestrial Vipera Russelli (VR) were studied using high-resolution two-dimensional gels: isoelectric focusing followed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (IEF/SDS-PAGE) and nonequilibrium pH gradient electrophoresis (NEPHGE) followed by SDS-PAGE. Tentative identities of numerous proteins were established using their amino acid compositions and in certain cases the identities were verified by microsequencing of their N-terminals and internal fragments. As expected, we found several proteins known to be present in the venom of the respective snakes. These include numerous isoforms of phospholipase A2 (PLA2) in both snake glands, various neurotoxins in LC glands and factor IX/factor X-binding protein, hemorrhagic factor and coagulation factor X activating enzyme in Russell's viper glands (VR). Not unexpectedly, we also found a number of cell housekeeping proteins, cytoskeletal proteins, proteins that are necessary for folding, such as heat-shock proteins, protein disulfide-isomerase and peptidyl-prolyl cis/trans isomerases. Unexpectedly, however, the glands of Laticauda colubrina and Russell's viper include a large quantity of antihemorrhagic factor and inhibitor of PLA2, respectively, that have been previously described in snake plasma. The possible reason associated with the presence of these components in venom glands is discussed.

Animals↗
PubMed1997

Subunit of glycosylation-inhibiting factor is an abundant protein that binds to certain glycoproteins and sugars.

12 kDa subunit of glycosylation-inhibiting factor (GIF) is an abundant protein that can be isolated to homogeneity from different mammalian organs by successive application of the carboxymethylcellulose cation exchanger CM52, preparative flat-bed isoelectrofocusing and repeated application of CM52-cellulose. Several isoforms of the 12 kDa GIF subunit exist in mammalian tissues. Conformational stability of two isoforms of a 12 kDa porcine GIF subunit have been studied by CD. Conformation of the protein remains stable within the range 20 degrees to 60 degrees C. Over 60 degrees C the protein undergoes irreversible denaturation. The 12 kDa GIF subunit is not stable within the pH range 2 to 3, adopts quasi-native structure within the pH range 3.5 to 5 while it remains stable between the pHs 6 to 10. The 12 kDa GIF subunit strongly binds to CM52-cellulose from which it can be eluted at concentrations of NaCl higher than 0.6 M. The GIF subunit may also be eluted from the modified cellulose using certain glycoproteins and sugars. High abundance of the 12 kDa GIF subunit in different mammalian tissues and its capacity to bind certain glycoproteins and sugars may suggest that the protein might be involved in regulatory mechanisms of glycoprotein transport (chaperone for glycoproteins) and modulation of interactions between secreted glycoproteins and the cell surface receptors.

Amino Acid Sequence↗
PubMed1996

Proteins and their amino acid compositions: uniqueness, variability, and applications.

Amino acid compositions (AAC) of proteins were analyzed in terms of their uniqueness and variability. Using several measures of convergence between the AACs of randomly chosen proteins versus those stored in protein data banks, it was established that certain families of proteins have unique AACs despite the mutations of their sequences which were imposed in the process of evolution. AACs may be used to establish the identities of many proteins which were sorted through various chromatographic media prior to their fractionation on two-dimensional (2D) gels. Subfractionations of proteins markedly enhance the chances for proper identification of low-abundant proteins which rest inaccessible if the total protein extract of an organ is analyzed on 2D gels. Although the amino acid composition versus protein identity (AAC-PI) method allows identification with high confidence of unique proteins resolved on monodimensional SDS-PAGE (1D) gels and arrays of protein isoforms resolved on two-dimensional (2D) gels, selective immunoblotting is still a more robust method. Thus, in principle, the AAC-PI method may allow limiting the number of "unknown" spots on 2D gels which could be further investigated by microsequencing and/or mass spectroscopy. However, to resolve certain ambiguities inherently linked with protein identities derived only from their AACs, the AAC-PI method must be sometimes aided by microsequencing and immunoblotting, especially in the construction of high-resolution 2D maps of proteins. A suite of algorithms which form the AAC-PI method are described in detail.

Algorithms↗
PubMed1996

A note on circular-dichroic-constrained prediction of protein secondary structure.

Circular dichroic (CD) spectra of bovine immunosuppressant binding proteins FKBP12 and FKBP25, and cyclophilins (peptidylprolyl isomerases) A (bCyP-18) and B(bCyP-20), the immunophilins which selectively bind the clinically useful immunosuppressants FK506, rapamycin and cyclosporin A, respectively, were analysed using the singular-value-decomposition algorithm augmented by a simplified variable selection method. The differences between the CD-estimated values of alpha-helix, beta-structure and beta-turn and those predicted by the Chou-Fasman algorithm were minimized using the CD data as constraints of an algorithm which utilizes the method of hierarchical updating of quasi-equipotential peptide segments of the Chou-Fasman prediction. The method allows one to correct the Chou-Fasman prediction of secondary structures in globular proteins.

Amino Acid Isomerases↗
PubMed1996

A large-scale processing of kinetic data files with derivation of the inhibitory constant Ki: an application to proline isomerases.

An integral system of algorithms (file preprocessor + the adapted KORE program + the Powell non-linear least-squares minimizer) named KINMIN is described. This system was applied to simultaneously process a large number of kinetic data files for cis/trans isomerization of Xaa-Pro bonds in synthetic peptides catalysed by peptidylproline cis/trans isomerases which can be inhibited by nanomolar concentrations of the immunosuppressive compounds cyclosplorin-A, FK506 or rapamycin. The system allows preprocessing of kinetics data files and derives from them the first-order rate constants which are used to optimize the inhibitory constant Ki of each inhibitor. The KINMIN program may be also applied to derive Ki for other sets of enzymes and their inhibitors.

Algorithms↗
PubMed1995

Amino acid compositions of proteins and their identities.

A critical overview is given on the application of amino acid composition data for the establishment of the protein's identity (amino acids composition vs. protein identity, the AAC-PI method). Several criteria are used to measure the differences between the amino acid compositions of various proteins. The AAC-PI method unambiguously identifies proteins which belong to the families with a high phylogenetic conservancy of their sequences. The identification of pure proteins can be accomplished with a relatively high level of confidence. The AAC-PI method, however, sometimes needs the support of N-terminal or internal sequencing of proteins since, alone, it cannot distinguish whether the lack of finding a candidate protein in protein data bases is because the investigated amino acid composition corresponds to an unknown protein or its processed form or because it is a sum of at least two protein components, or whether it is due to other experimental errors. The identification of a few new proteins such as "arginine-rich protein", macrophage migration inhibitory factor (MIF) and the preformed neurotrophic factor present in the calf brain cytosol is also reported.

Algorithms↗
PubMed1994

A diversified family of 12-kDa proteins with a high amino acid sequence similarity to macrophage migration-inhibitory factor (MIF).

Two isoforms of a bovine-brain-derived 12-kDa protein (designated p12a and p12b) whose N-termini have a high amino acid sequence similarity with the glycosylation-inhibiting factor (GIF) and macrophage migration-inhibitory factor (MIF) were purified to homogeneity. The complete amino acid sequence of bovine p12a (pI 9.5) was determined by Edman degradation of the intact molecule and overlapping fragments generated by proteolytic cleavage. The p12a isoform has nine and ten conservative substitutions versus human GIF (hGIF) and human MIF (hMIF), respectively. Molecular filtration revealed that both isoforms of p12 exist as monomers in aqueous solution. Circular dichroism spectra indicate that both isoforms of p12 consist of 39 +/- 3% alpha helix, 23 +/- 3% beta structure and 15 +/- 3% beta turns. Although the N-terminal parts of p12a and p12b have weak amino acid sequence similarity with that of glutathione S-transferase (GST) neither isoform of p12 was bound to a GST-affinity gel nor had GST activity. Despite a high amino acid sequence similarity with human MIF neither of the p12 isoforms inhibited migration of the mouse monocyte-macrophage cells P338D1.

Amino Acid Sequence↗
PubMed1994

Cyclophilin-B is an abundant protein whose conformation is similar to cyclophilin-A.

Cyclophilin-B (bCyP-20) was isolated in a relatively high quantity from calf brain and spleen tissues consecutively applying weak cation exchange, chromatofocusing and strong cation exchange chromatographies. Edman degradation yielded the N-terminal sequence NH2-DEKKKGPKVTVK- VYFDLRIGDEDIGRVVIGLFGKTVPKTVDNFVAL. Bovine cyclophilin-B possesses the peptidylproline cis-trans isomerase activity which is inhibited by nM concentrations of CsA. bCyP-20 has a strong tendency to bind to cation exchangers including DNA and heparin. It could be released from DNA affinity column at concentrations of NaCl higher than 200 mM. Circular dichroism spectroscopy revealed that bovine cyclophilin-A (bCyP-18) and bCyP-20 in aqueous solution have similar conformations.

Amino Acid Isomerases↗
PubMed1993

Peptidylproline cis-trans-isomerases: immunophilins.

Two sequence-unrelated families of proteins possess peptidylproline cis-trans-isomerase activities (PPIase). PPIases are highly sequence conserved and multifunctional proteins which are present in many types of cells with a considerably divergent phylogenetic distribution. On the cellular level, PPIases occur in every compartment, both as free species and anchored to membranes. Diverse posttranslational modifications such as glycosylation, N-terminal modifications and phosphorylation constitute the additional functional features of PPIases. Folding, assembly and trafficking of proteins in the cellular milieu are regulated by PPIases. These enzymes accelerate the rate of in-vitro protein folding and they have the ability to bind proteins and act as chaperones. Some PPIases are coregulatory subunits of molecular complexes including heat-shock proteins, glucocorticoid receptors and ion channels. Secreted forms of PPIases are inflammatory and chemotactic agents for monocytes, eosinophils and basophils. The potent and clinically useful immunosuppressants CsA, FK506 or rapamycin bind with high affinities to PPIases (immunophilins). The binding criterion allows us to sort the PPIases for the following two superfamilies of proteins: the cyclophilins (CsA-binding proteins) and the FKBP (FK506/rapamycin-binding proteins). Although none of PPIases appeared to be essential for the viability of haploid yeast cells some of the immunophilin/immunosuppressant complexes are toxic both for yeast and mammalian cells. At least seven unlinked genes of cyclophilins and four unlinked genes of FKBP exist in human genomic DNA. Selected immunophilins regulate two different signalling pathways in lymphoid cells, namely the secretion of growth factors by stimulated T-cells and interleukin-2-induced T-cell proliferation. Moreover, selected FKBP mediate the cytotoxic effects of rapamycin in non-lymphoid cells. Accounts of the discovery of PPIases (immunophilins) and their functions are given in this review. A larger spectrum of proteins is analysed in relation to various signal-transduction pathways in lymphoid cells which involve immunophilins or their complexes with the immunosuppressants CsA, FK506 or rapamycin.

Amino Acid Isomerases↗
PubMed1993

Purification of macrophage migration inhibitory factor (MIF) from bovine brain cytosol.

Two isoforms of the macrophage migration inhibitory factor (MIF) have been isolated to homogeneity from bovine brain cytosol. In agreement with the cDNA sequence of their human counterpart, they both have an apparent molecular weight of 12 kDa and are characterized by the following N-terminal amino acid sequence NH2-PMFVVNTNVPRASVPDGLLSELTQQLAQATGKPPQYIAV-. CD spectra revealed that bovine MIF contains 42% (+/- 3%) alpha-helix and 21% (+/- 3%) beta-structure. CD-constrained prediction of the secondary structure assigned MIF to the alpha/beta-class of proteins.

Amino Acid Sequence↗
PubMed1993

On the localization of FKBP25 in T-lymphocytes.

Using polyclonal rabbit antibodies against bovine FKBP25, NEPHGE/SDS-PAGE and Western blotting we demonstrate that the rapamycin-specific immunophilin FKBP25 is present in T-lymphoma Jurkat cells. Subsequent fractionations of the soluble Jurkat cell proteins have revealed that FKBP25 predominantly occurs in the nuclear fraction. FKBP25 has the ability to bind to DNA. The FKBP25/DNA complex can be dissociated in the presence of a high salt concentration. FKBP12, which shares high amino acid sequence homology to the C-terminal domain of FKBP25, has no tendency to bind to DNA. CD-constrained predictions of the secondary structures in FKBP25 suggest that an amphipathic helix-loop-helix occurs in the N-terminal part of the protein and may account for its binding to DNA.

Amino Acid Sequence↗
PubMed1992

A rapamycin-selective 25-kDa immunophilin.

FKBP25, a previously uncharacterized 25-kDa FK506- and rapamycin-binding protein, was purified to homogeneity from calf thymus, brain, and spleen, and the sequence of a 215 amino acid (aa) 24-kDa C-terminal peptide was established. The N-terminal domain (101 aa) is unrelated to any known protein, is hydrophilic, and is predicted by circular dichroism spectroscopy to be largely alpha-helix. The C-terminal domain (114 aa) is homologous to FKBP12 and other FKBPs but has a potential nuclear targeting sequence and a unique insertion of seven amino acids in one of its loops. FKBP25 displays the rotamase activity characteristic of FKBPs; the activity is inhibited by the immunosuppressants rapamycin (Ki = 0.9 nM) and FK506 (Ki = 160 nM), but not cyclosporin A. The protein, its rapamycin selectivity, and the potential nuclear targeting sequence are discussed in terms of the structure of hFKBP12.

Amino Acid Sequence↗