Functional diversity and pharmacological profiles of the FKBPs and their complexes with small natural ligands.

From 5 to 12 FK506-binding proteins (FKBPs) are encoded in the genomes of disparate marine organisms, which appeared at the dawn of evolutionary events giving rise to primordial multicellular organisms with elaborated internal body plan. Fifteen FKBPs, several FKBP-like proteins and some splicing variants of them are expressed in humans. Human FKBP12 and some of its paralogues bind to different macrocyclic antibiotics such as FK506 or rapamycin and their derivatives. FKBP12/(macrocyclic antibiotic) complexes induce diverse pharmacological activities such as immunosuppression in humans, anticancerous actions and as sustainers of quiescence in certain organisms. Since the FKBPs bind to various assemblies of proteins and other intracellular components, their complexes with the immunosuppressive drugs may differentially perturb miscellaneous cellular functions. Sequence-structure relationships and pharmacological profiles of diverse FKBPs and their involvement in crucial intracellular signalization pathways and modulation of cryptic intercellular communication networks were discussed.

Conserved structural determinants in three-fingered protein domains.

The three-dimensional structures of some components of snake venoms forming so-called 'three-fingered protein' domains (TFPDs) are similar to those of the ectodomains of activin, bone morphogenetic protein and transforming growth factor-beta receptors, and to a variety of proteins encoded by the Ly6 and Plaur genes. The analysis of sequences of diverse snake toxins, various ectodomains of the receptors that bind activin and other cytokines, and numerous gene products encoded by the Ly6 and Plaur families of genes has revealed that they differ considerably from each other. The sequences of TFPDs may consist of up to six disulfide bonds, three of which have the same highly conserved topology. These three disulfide bridges and an asparagine residue in the C-terminal part of TFPDs are essential for the TFPD-like fold. Analyses of the three-dimensional structures of diverse TFPDs have revealed that the three highly conserved disulfides impose a major stabilizing contribution to the TFPD-like fold, in both TFPDs contained in some snake venoms and ectodomains of several cellular receptors, whereas the three remaining disulfide bonds impose specific geometrical constraints in the three fingers of some TFPDs.

Long-sarafotoxins: characterization of a new family of endothelin-like peptides.

Sarafotoxins (SRTXs) constitute a family of vasoactive peptides that were initially isolated from the venom of Atractaspis engaddensis, and that are structurally and functionally related to endothelins (ETs). Analysis of the venom of Atractaspis microlepidota microlepidota revealed several new SRTX molecules manifesting some new structural and functional characteristics. These novel SRTXs are longer by three amino acids than the previously described SRTXs, and are designated here "long-SRTXs". Six isoforms, derived from new poly-cistronic precursors, have been identified so far in the venom of this snake. One of these isoforms, designated SRTX-m, was chemically synthesized and its biological properties were studied. Our results show that SRTX-m induces toxicity in mice, mostly due to vasoconstriction, and also that it has a lower toxicity and potency than the more potent SRTX described up to now: sarafotoxin-b (SRTX-b) from A. engaddensis.

Function-dependent clustering of orthologues and paralogues of cyclophilins.

The 18 kDa archetypal cyclosporin-A binding protein, cyclophilin-A, has multiple paralogues in the human genome. Only 18 of those paralogues have been detected as mRNAs or proteins whose masses vary from 18 to 354 kDa, whereas the functional significance of the open reading frames (ORFs) encoding other paralogues of cyclophilin-A remains unknown. The genomes of Drosophila melanogaster, Caenorhabditis elegans, Arabidopsis thaliana, Schizosaccharomyces pombe, and Saccharomyces cerevisiae encode different numbers of the cyclophilin paralogues, some of which are orthologous to the human cyclophilins. A library of novel algorithms was developed and used for computation of the conservation levels for hydrophobicity and bulkiness profiles, and amino acid compositions (AACs) of 303 aligned sequences of cyclophilins. The majority of the paralogues and orthologues encoded in these 6 genomes differ considerably from each other. Some of the orthologues and paralogues have high correlation coefficients (CCFs) for pairwise compared hydrophobicity and bulkiness profiles, and whose AACs differ to a low degree. Convergence of these three properties of the polypeptide chain and apparent conservation of the typical sequence hallmarks and parameters allowed for the clustering of the functionally related orthologues and paralogues of the cyclophilins. The clustering method allowed for sorting out the cyclophilins into several distinct classes. Analyses of the overlapping clusters of sequences permitted delineation of some hypothetical pathways that might have led to the creation of certain paralogues of cyclophilins in the eukaryotic genomes.

A note on clustering the functionally-related paralogues and orthologues of proteins: a case of the FK506-binding proteins (FKBPs).

The expression patterns of 18 FK506-binding proteins (FKBPs) encoded in the human genome have been established whereas the functional significance of the numerous ORFs coding for FKBP-like sequences remains unknown. Nominal masses of the human FKBPs vary from 12 to 135 kDa. Some large FKBPs consist up to four repeats of the 12 kDa FK506-like binding domain (FKBD) whereas other large FKBPs contain one FKBD linked to different functional domains such as TPRs, leucine-zipper, calmodulin-binding domain etc. The genomes of other eukaryotic organisms, namely D. melanogaster, C. elegans, A. thaliana, S. pombe and S. cerevisiae encode different numbers of the FKBPs' paralogues some of which are orthologues to the human FKBPs. A library of novel algorithms was developed and used for computation of the level of conservation of the hydrophobicity and bulkiness profiles, and the amino acid compositions (AACs) of 247 aligned sequences of FKBPs. The pairwisely-compared hydrophobicity and bulkiness profiles for some combinations of the aligned sequences of the FKBDs yielded high values of the correlation coefficients (CCF). The AACs of some combinations of the aligned sequences of the FKBDs also differed to a low degree. The functionally-related orthologues and paralogues of the FKBPs were clustered by using the following criteria: 1 degrees apparent conservation of the crucial amino acid (AA) residues for peptidylprolyl cis/trans isomerase (PPIase) acitity and binding of some immunosuppressive drugs; 2 degrees convergence of the three mentioned above properties of the polypeptide chain; 3 degrees similarity in the sequence attributes pI and total hydrophobicity index (HI). The clustering method was used for setting up several hypotheses on the emergence of certain classes of the FKBPs in the eukaryotic kingdom.