Diagnosis and management of heart failure from hospital admission to discharge: A practical expert guidance

Heart failure (HF) has high event rates, mortality, and is challenging to manage in clinical practice. Clinical management is complicated by complex therapeutic strategies in a population with a high prevalence of comorbidity and general frailty. In the last four years, an abundance of research has become available to support multidisciplinary management of heart failure from within the hospital through to discharge and primary care as well as supporting diagnosis and comorbidity management. Within the hospital setting, recent evidence supports sacubitril-valsartan combination in frail, deteriorating or de novo patients with LVEF≤40%. Furthermore, new strategies such as SGLT2 inhibitors and vericiguat provide further benefit for patients with decompensating HF. Studies with tafamidis report major clinical benefits specifically for patients with ATTR cardiac amyloidosis, a remaining underdiagnosed and undertreated disease. New evidence for medical interventions supports his bundle pacing to reduce QRS width and improve haemodynamics as well as ICD defibrillation for non-ischemic cardiomyopathy. The Mitraclip reduces hospitalisations and mortality in patients with symptomatic, secondary mitral regurgitation and ablation reduces mortality and hospitalisations in patients with paroxysmal and persistent atrial fibrillation. In end-stage HF, the 2018 French Heart Allocation policy should improve access to heart transplants for stable, ambulatory patients and, mechanical circulatory support should be considered to avoid deteriorating on the waiting list. In the community, new evidence supports that improving discharge education, treatment and patient support improves outcomes. The authors believe that this review fills the gap between the guidelines and clinical practice and provides practical recommendations to improve HF management.

Ligand-Directed Modification of Active Matrix Metalloproteases: Activity-based Probes with no Photolabile Group

Activity-based probes enable discrimination between the active enzyme and its inactive or inactivated counterparts. Since metalloproteases catalysis is non-covalent, activity-based probes targeting them have been systematically developed by decorating reversible inhibitors with photo-crosslinkers. By exploiting two types of ligand-guided chemistry, we identified novel activity-based probes capable of covalently modifying the active site of matrix metalloproteases (MMPs) without any external trigger. The ability of these probes to label recombinant MMPs was validated in vitro and the identity of the main labelling sites within their S₃ ' region unambiguously assigned. We also demonstrated that our affinity probes can react with rhMMP12 at nanogram scale (that is, at 0.07 % (w/w)) in complex proteomes. Finally, this ligand-directed chemistry was successfully applied to label active MMP-12 secreted by eukaryote cells. We believe that this approach could be transferred more widely to many other metalloproteases, thus contributing to tackle their unresolved proteomic profiling in vivo.

Peptidylprolyl Isomerases as In Vivo Carriers for Drugs That Target Various Intracellular Entities

Analyses of sequences and structures of the cyclosporine A (CsA)-binding proteins (cyclophilins) and the immunosuppressive macrolide FK506-binding proteins (FKBPs) have revealed that they exhibit peculiar spatial distributions of charges, their overall hydrophobicity indexes vary within a considerable level whereas their points isoelectric (pIs) are contained from 4 to 11. These two families of peptidylprolyl cis/trans isomerases (PPIases) have several distinct functional attributes such as: (1) high affinity binding to some pharmacologically-useful hydrophobic macrocyclic drugs; (2) diversified binding epitopes to proteins that may induce transient manifolds with altered flexibility and functional fitness; and (3) electrostatic interactions between positively charged segments of PPIases and negatively charged intracellular entities that support their spatial integration. These three attributes enhance binding of PPIase/pharmacophore complexes to diverse intracellular entities, some of which perturb signalization pathways causing immunosuppression and other system-altering phenomena in humans.

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.

Common structural traits for cystine knot domain of the TGFβ superfamily of proteins and three-fingered ectodomain of their cellular receptors

The transforming growth factor-β (TGFβ) superfamily of proteins and their receptors are crucial developmental factors for all metazoan organisms. Cystine-knot (CK) motif is a spatial feature of the TGFβ superfamily of proteins whereas the extra-cellular domains (ectodomains) of their respective receptors form three-fingered protein domain (TFPD), both stabilized by tight cystine networks. Analyses of multiple sequence alignments of these two domains encoded in various genomes revealed that the cystines forming the CK and TFPD folds are conserved, whereas the remaining polypeptide patches are diversified. Orthologues of the human TGFβs and their respective receptors expressed in diverse vertebrates retain high sequence conservation. Examination of 3D structures of various TGFβ factors bound to their receptors have revealed that the CK and TFPD domains display several similar spatial traits suggesting that these two different protein folds might have been acquired from a common ancestor.

Molecular aspects of cyclophilins mediating therapeutic actions of their ligands

Cyclosporine A (CsA) is an immunosuppressive cyclic peptide that binds with a high affinity to 18 kDa human cyclophilin-A (hCyPA). CsA and its several natural derivatives have some pharmacological potential in treatment of diverse immune disorders. More than 20 paralogues of CyPA are expressed in the human body while expression levels and functions of numerous ORFs encoding cyclophilin-like sequences remain unknown. Certain derivatives of CsA devoid of immunosuppressive activity may have some potential in treatments of Alzheimer diseases, Hepatitis C and HIV infections, amyotrophic lateral sclerosis, congenital muscular dystrophy, asthma and various parasitic infections. Here, we discuss structural and functional aspects of the human cyclophilins and their interaction with various intra-cellular targets that can be under the control of CsA or its complexes with diverse cyclophilins that are selectively expressed in different cellular compartments. Some molecular aspects of the cyclophilins expressed in parasites invading humans and causing diseases were also analyzed.

On transversal hydrophobicity of some proteins and their modules

Hydrophobicity of proteins encoded in the genomes of diverse organisms was quantified using two novel concepts: (A) amino acid (AA) bulkiness-dependent hydrophobicity profiles and (B) spatial context of hydrophobicity distribution in AA triads. Both concepts were introduced into an algorithm that was used for extracting protein clusters from diverse genomic databases whose sequence attributes were similar to those in the multiple sequence alignment (MSA) of a given family of proteins. The sequences of the G protein-coupled receptors (GPCRs) encoded in different genomes were used as templates for testing the above concepts. The following sequence attributes were used for protein clustering: (A) sequence similarity scores (IDs); (B) amino acid composition (AAC); (C) hydrophobicity; (D) AA-bulkiness; and (E) alpha-helical propensity potentials. Diverse GPCRs display variable distributions of AA bulkiness-dependent buildups and declines in the hydrophobicity profiles that may be related to their function-dependent way of packing and allostery in the membrane. It is shown that intramolecular transversal nonbonded interactions between the TM segments in diverse GPCRs involve about 50% of hydrophobic atoms. Similar interaction networks exist between alpha-helices of tetratricopeptide (TPR) motifs-containing immunophilins and other proteins containing alpha-helical bundles.

The three-fingered protein domain of the human genome

Extracellular domains of some cellular receptors expressed in the organisms at different levels of development belong to three-fingered protein (TFP) fold. The Homo sapiens genome encodes at least 45 genes containing from one to three TFP domains (TFPDs), namely diverse paralogues of the Ly6 gene, CD59 and the receptors of activins, bone morphogenetic proteins, Mullerian inhibiting substance and transforming growth factor-beta. C4.4a and urokinase/plasminogen activatory receptor contain two and three TFPD repeats, respectively. These diverse proteins have a low overall sequence similarity with each other and their hydrophobicity levels vary to a considerable degree. It is suggested that sequence differentiation within the TFPD led to distinct groups of proteins whose attributes were optimized to fit both the physicochemical properties specific to their functional microenvironment and selective targeting of their highly diversified extracellular cofactors.

Functional drift of sequence attributes in the FK506-binding proteins (FKBPs)

Diverse members of the FK506-binding proteins (FKBPs) group and their complexes with different macrocyclic ligands of fungal origins such as FK506, rapamycin, ascomycin, and their immunosuppressive and nonimmunosuppressive derivatives display a variety of cellular and biological activities. The functional relatedness of the FKBPs was estimated from the following attributes of their aligned sequences: 1 degrees conservation of the consensus sequence; 2 degrees sequence similarity; 3 degrees pI; 4 degrees hydrophobicity; 5 degrees amino acid hydrophobicity and bulkiness profiles. Analyses of the multiple sequence alignments and intramolecular interaction networks calculated from a series of structures of the FKBPs revealed some variations in the interaction clusters formed by the AA residues that are crucial for sustaining peptidylprolyl cis/trans isomerases (PPIases) activity and binding capacity of the FKBPs. Fine diversification of the sequences of the multiple paralogues and orthologues of the FKBPs encoded in different genomes alter the intramolecular interaction patterns of their structures and allowed them to gain some selectivity in binding to diverse targets (functional drift).

Involvement of some large immunophilins and their ligands in the protection and regeneration of neurons: a hypothetical mode of action

The powerful immunosuppressive drugs such as FK506 and its derivatives induce some regeneration and protection of neurons from ischaemic brain injury and some other neurological disorders. The drugs form complexes with diverse FKBPs but apparently the FKBP52/FK506 complex was shown to be involved in the protection and regeneration of neurons. We used several different sequence attributes in searching diverse genomic databases for similar motifs as those present in the FKBPs. A Fortran library of algorithms (Par_Seq) has been designed and used in searching for the similarity of sequence motifs extracted from the multiple sequence alignments of diverse groups of proteins (query motifs) and the target motifs which are encoded in various genomes. The following sequence attributes were used in the establishment of the degree of convergence between: (A) amino acid (AA) sequence similarity (ID) of the query/target motifs and (B) their: (1) AA composition (AAC); (2) hydrophobicity (HI); (3) Jensen-Shannon entropy; and (4) AA propensity to form a particular secondary structure. The sequence hallmark of two different groups of peptidylprolyl cis/trans isomerases (PPIases), namely tetratricopetide repeat (TPR) motifs, which are present in the heat-shock cyclophilins and in the large FK506-binding proteins (FKBPs) were used to search various genomic databases. The Par_Seq algorithm has revealed that the TPR motifs have similar sequence attributes as a number of hydrophobic sequence segments of functionally unrelated membrane proteins, including some of the TMs from diverse G protein-coupled receptors (GPCRs). It is proposed that binding of the FKBP52/FK506 complex to the membranes via the TPR motifs and its interaction with some membrane proteins could be in part responsible for some neuro-regeneration and neuro-protection of the brain during some ischaemia-induced stresses.

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.

Molecular cloning and expression pattern of the Fkbp25 gene during cerebral cortical neurogenesis

Neocortical neurons are generated predominantly from the cells that proliferate in the ventricular zone of the telencephalon. In order to understand the nature of these expanding cortical neuronal progenitor cells, we selected by differential display some transcripts that were enriched in the telencephalon as compared to the more caudal regions (diencephalon/mesencephalon). This systematic screening revealed one of the differentially expressed transcripts, namely the Fkbp25 mRNA that encodes a member of the FK506 binding proteins (FKBPs). Northern blot analysis showed that the expression of the single 1.4kb Fkbp25 transcript reached a maximum level on embryonic day 11.5 at the start of cortical neurogenesis in the mouse and was followed by a weak basal expression in the adult brain. In the embryo, Fkbp25 gene was strongly expressed in the telencephalon ventricular zone but also in areas active in myogenesis (walls of the ventricle and the atrium) and chondrogenesis (the cartilage of the rib and the hindlimb). An increase in the transcript levels of the Fkbp25 gene was also observed during the two successive proliferation waves of the cerebellum development. Immunostaining on primary cultures of embryonic day 10.5 telencephalon stem cells showed that the Fkbp25 protein was present in the cytoplasm and nuclei of cells cultured for 6h but exclusively in the nuclei of the Tuj-1 immunoreactive neurons obtained after 3 days of culture (The sequence data reported here have been submitted to GenBank under accession no. AF135595.).

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.

Long-size isoelectricfocusing (IEF) in flexible silicone tubes: an application to semi-preparative fractionation of proteins

Soluble proteins extracted from porcine brains were subjected to a series of optional fractionation steps on various chromatographic media including a novel device for semi-preparative isoelectrofocusing (IEF) carried in a flexible silicone tube. The dimensions of the IEF granulated gel beds can be varied from 40 to 75 cm (length) and 0.4-1.6 cm (diameter) which are dependent on the protein's concentration. An average optimal focalisation time of proteins is dependent of the tube length, its diameter and complexity of proteins' mixtures but it is usually reached during 15,000-30,000 Vh. A series of sequential protein's fractionation techniques including semi-preparative IEF carried in the flexible silicone tube with the following dimensions: 75 cm in length and 1.6 cm in diameter permitted for observation and partial characterisation of several proteins whose expression levels are specifically high in the brain.

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.

Peptidylprolyl cis/trans isomerases (immunophilins): biological diversity--targets--functions

Information recovered from genome sequencing projects, multiple sequence alignments, structural analyses of PPIase and published records were used in deciphering the biological diversity, functions and targets of four groups of proteins encoded by dissimilar sets of sequences whose spatial representations exhibit peptidylprolyl cis/trans isomerase activity (PPIase). In the human genome there are encoded fifteen proteins whose segments have significant homology with the sequence of 12 kDa protein which is the target of the potent immunosuppressive macrolides FK506 or rapamycin. The 12 kDa archetype of the FK506-binding protein (FKBP), known as FKBP-12a, is an abundant intracellular protein whereas other FKBPs possessing from one to four FK506-like binding domains (FKBDs) have nominal masses varying from 13 to 135 kDa. The human genome contains at least sixteen genes encoding proteins comprising one cyclosporin-A (CsA) binding domain (CLD) called cyclophilins whose nominal masses vary from 17 to 324 kDa and multiple coding segments for small cyclophilins (17-19 kDa) whose transcription levels and functions remain unknown. The third group of PPIases encoded in the genome comprises two proteins (hPin1 and hParv14) where hPin1 is an important PPIase for cell cycle. The A. thaliana, C. elegans, D. melanogaster and S. cerevisiae genomes encode a less diverse spectrum of PPIases whereas the prokaryotic genomes contain from none to three cyclophilins, from none to four genes encoding FKBPs, one distant homologue of the Pin1 protein named parvulin and the fourth group of PPIases known as trigger factors. PPIases are discretely distributed to different cellular compartments and interact with a number of targets that control a range of cellular processes. Analyses of the sequence alignments of the two groups of PPIases, namely cyclophilins and FKBPs from diverse phyla, show that in each group their sequences diverge but the amino acid residues which form the PPIase activity site and macrolide binding cavity remain well conserved in the majority of them which suggests that the spatial structures and functions of each group of PPIases remain conserved.

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.

Exogenous myristic acid acylates proteins in cultured rat hepatocytes

Fatty acid acylation is a functionally important modification of proteins. In the liver, however, acylated proteins remain largely unknown. This work was aimed at investigating fatty acid acylation of proteins in cultured rat hepatocytes. Incubation of these cells with [9,10-3H] myristic acid followed by two-dimensional electrophoresis separation of the delipidated cellular proteins and autoradiography evidenced the reproducible and selective incorporation of radioactivity from the precursor into 18 well-resolved proteins in the 10--120 kDa range and the 4--7 pH range. Radiolabeling of these proteins resulted from covalent linkage to the precursor [9,10-3H] myristic acid or to its elongation product, palmitic acid. The majority of the covalent linkages between the proteins and the fatty acids were broken by base hydrolysis, which indicated that the linkage was of thioester or ester-type. Only one of the studied proteins was attached to myristic acid via an amide linkage which resisted the basic treatment but was broken by acid hydrolysis. After incubation with [9,10-3H] palmitic acid, only two proteins previously detected with myristic acid were radiolabeled. Finally, the identified acylated proteins may be grouped into two classes: proteins involved in signal transduction (the alpha subunit of a heterotrimeric G protein and several small G proteins) and cytoskeletal proteins (cytokeratins, actin).

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.

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.

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.

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.

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.

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.

Convergence of amino acid compositions of certain groups of protein aids in their identification on two-dimensional electrophoresis gels

The amino acid composition (AAC) versus the protein identity (PI) method was used for establishment of the identities of proteins from bovine brain and kidneys which were prefractionated on a CM52 cation exchanger and by preparative flat-bed isoelectric focusing. Established identities of proteins whose AACs converge with those of other members of their proper superfamily are reliable. Groups of convergent AACs can be extracted from protein databases using the standard root-mean-square rule (Rmsd) with measures the difference between the AAC of chosen protein versus those in the database. Convergence of AACs of proteins is dependent on several factors such as the upper limit of Rmsd, the limits of variations of molecular mass (m) and isoelectric point (pI), the number of proteins with similar AACs present in protein databases, and the domain structure of proteins. AACs of many proteins remain unique if the Rmsd is maintained within 1.5-1.0 with m +/- 3kDA and pI +/- 4. Certain groups of multidomain proteins have quasi-unique AACs only if the Rmsd is restrained to a value within 1.0 and 0.7. Convergence of AACs of certain groups of proteins may indicate that a common biological function exists for some members of each group. The AAC-PI method may become an additional search tool for protein functions.

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.

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.

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 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.