Deciphering function and mechanism of calcium-binding proteins from their evolutionary imprints

Calcium-binding proteins regulate ion metabolism and vital signalling pathways in all living organisms. Our aim is to rationalize the molecular basis of their function by studying their evolution using computational biology techniques. Phylogenetic analysis is of primary importance for classifying cognate orthologs; profile hidden Markov models (HMM) of individual subfamilies discern functionally relevant sites by conservation probability analysis; and 3-dimensional structures display the integral protein in context. The major classifications of calcium-binding proteins, viz. EF-hand, C2 and ANX, exhibit structural diversity in their HMM fingerprints at the subfamily level, with functional consequences for protein conformation, exposure of receptor interaction sites and/or binding to membrane phospholipids. Calmodulin, S100 and annexin families were characterized in Petromyzon marinus (sea lamprey) to document genome duplication and gene creation events during the key evolutionary transition to primitive vertebrates. Novel annexins from diverse organisms revealed calcium-binding domains with accessory structural features that define their unique molecular fingerprints, protein interactivity and functional specificity. These include the first single-domain, bacterial annexin in Cytophaga hutchinsonii, the 21 tetrad annexins from the unicellular protist Giardia intestinalis, an ancestor to land plant annexins from the green alga Ostreococcus lucimarinus, invertebrate octad annexins and a critical polymorphism in human ANXA7. Receptor docking models supported the hypothesis of a potential interaction between annexin and C2 domains as a propitious mechanism for ensuring membrane translocation during signal transduction.     

Reconstructing reticulate evolutionary histories of plants

Identifying signatures of hybridization in molecular data and distinguishing them from other causes of phylogenetic incongruence is important for evaluating the evolutionary significance of hybridization in plants. Consensus networks and supernetworks provide a means for doing this. In this review, we explain these methodologies, discuss their potential and illustrate their application with examples from the Brassicaceae.     

Inositolpolyphosphates and their binding proteins —a short review

Since 1983, when it was discovered that inositol 1,4,5-trisphosphate can act as second messenger to release Ca²⁺ from the endoplasmic reticulum, widespread research has focused on the phosphatidylinositol signalling transduction pathway and the host of inositolphosphates formed intracellularly after stimulation thereof. Although the polyphosphates, inositoltetrakisphosphate (InsP₄) and inositolhexakisphosphate (InsP₆), have received their share of attention, a definite physiological role has not been ascribed to them as yet. Different binding proteins for these two polyphosphates have been demonstrated, especially in brain tissue, indicating their possible importance in the cell.InsP₆ is known as one of nature's most powerful antioxidants and has already been demonstrated to possess the abilities to be of use in the industry as well as in the medical profession. As its natural actions are poorly understood and its possible side-effects have not been widely investigated, basic research regarding its cellular and subcellular activities is urgently called for.Recipient of Servier Investigator Award     

Spatial analysis of taxonomic and genetic patterns and their potential for understanding evolutionary histories

Aim The aim of this research is to develop and investigate methods for the spatial analysis of diversity based on genetic and taxonomic units of difference. We use monophyletic groups of species to assess the potential for these diversity indices to elucidate the geographical components of macro‐scaled evolutionary processes. Location The range occupied by Pultenaea species in temperate and sub‐tropical eastern Australia, extending from western South Australia (133° E–32° S) to Tasmania (146° E–43° S) to coastal central Queensland (148° E–20° S). Methods We applied a series of both spatially explicit and spatially implicit analyses to explore the nature of diversity patterns in the genus Pultenaea, Fabaceae. We first analysed the eastern species as a whole and then the phylogenetic groups within them. We delineated patterns of endemism and biotic (taxon) regions that have been traditionally circumscribed in biogeographical studies of taxa. Centres of endemism were calculated using corrected weighted endemism at a range of spatial scales. Biotic regions were defined by comparing the similarity of species assemblages of grid cells using the Jaccard index and clustering similar cells using hierarchical clustering. On the basis that genetically coherent areas were likely to be more evolutionary informative than species patterns, genetic indices of similarity and difference were derived. A matrix of similarity distances between taxa was generated based on the number of shared informative characters of two sections of trnL‐F and ndhF chloroplast nuclear regions. To identify genetically similar areas, we clustered cells using the mean genetic similarities of the species contained within each pair of cells. Measures of the mean genetic similarity of species in areas were delineated using a geographically local multi‐scalar approach. Resultant patterns of genetic diversity are interpreted in relation to theories of the evolutionary relationships between species and species groups. Results Centres of Pultenaea endemism were defined, those of clades 1 congruent with the spatially separated centres of clades 2 and 3. The taxonomic classification analysis defined cells with shared groups of species, which in some cases clustered when plotted in geographic space, defining biotic regions. In some instances the distribution of biotic regions was congruent with centres of endemism, however larger scale groupings were also apparent. In clade 1 one set of species was replaced by another along the extent of the range, with some connectivity between some geographically disjunct regions due to the presence of widespread species. In the combined analysis of clade 2 and 3 species the major biotic (taxonomic) groups with geographic coherence were defined by species in the respective clades, representing the geographic separation of these clades. However distinctive biotic regions within these main groupings of clades 2 and 3 were also apparent. Clustering cells using the mean genetic similarities of the species contained within each pair of cells indicated that some of the taxonomically defined biotic boundaries were the result of changes in composition of closely related species. This was most apparent in clades 1 and 2 where most cells were highly genetically similar. In clade 3 genetically distinct groups remained and were in part defined by sister taxa with disjunct distributions. Gradients in mean genetic similarity became more apparent from small to larger scales of analysis. At larger scales of analysis, regions of different levels of genetic diversity were delineated. Regions with highest diversity levels (lowest level of similarity) often represented regions where the ranges of phylogenetically distinctive species intergraded. Main conclusions The combined analysis of diversity, phylogeny and geography has potential to reveal macro‐scaled evolutionary patterns from which evolutionary processes may be inferred. The spatial genetic diversity indices developed in this study contribute new methods for identifying coherent evolutionary units in the landscape, which overcome some of the limitations of using taxonomic data, and from which the role of geography in evolutionary processes can be tested. We also conclude that a multiple‐index approach to diversity pattern analysis is useful, especially where patterns may be the result of a long history of different environmental changes and related evolutionary events. The analysis contributes to the knowledge of large‐scale diversity patterns of Pultenaea which has relevance for the assessment of the conservation status of the genus.     

IGF binding proteins and their functions

The insulin-like growth factor (IGF) binding proteins (IGFBPs) have several functions, including transporting the IGFs in the circulation, mediating IGF transport out of the vascular compartment, localizing the IGFs to specific cell types, and modulating both IGF binding to receptors and growth-promoting actions. The functions of IGFBPs appear to be altered by posttranslational modifications. IGFBP-3, -4, -5, and -6 have been shown to be glycosylated. Likewise all the IGFBPs have a complex disulfide bond structure that is required for maintenance of normal IGF binding. IGFBP-2, -3, -4, and -5 are proteolytically cleaved, and specific proteases have been characterized for IGFBP-3, -4, and -5. Interestingly, attachment of IGF-I or II to IGFBP-4 results in enhancement of proteolysis, whereas attachment of either growth factor to IGFBP-5 results in inhibition of proteolytic cleavage. Cleavage of IGFBP-3 results in the appearance of a 31 kDa fragment that is 50-fold reduced in its affinity for the IGF-I or IGF-II. In spite of the reduction in its affinity, this fragment is capable of potentiating the effect of IGF-I on cell growth responses; therefore, proteolysis may be a specific mechanism that alters IGFBP modulation of IGF actions. Other processes that result in a reduction in IGF binding protein affinity are associated with potentiation of cellular responses to IGF-I and -II. Specifically, the binding of IGFBP-3 to cell surfaces is associated with its ability to enhance IGF action and with a ten- to 12-fold reduction in its affinity for IGF-I and IGF-II. Likewise, binding of IGFBP-5 to extracellular matrix (ECM) results in an eightfold reduction in its affinity and a 60% increase in cell growth in response to IGF-I. Another post-translational modification that modifies IGFBP activity is phosphorylation. IGFBP-1, -2, -3, and -5 have been shown to be phosphorylated. Phosphorylation of IGFBP-1 results in a sixfold enhancement in its affinity for IGF-I and -II. Following this enhancement of IGFBP-1 affinity, this binding protein loses its capacity to potentiate IGF-I growth-promoting activity. Future studies using site-directed mutagenesis to modify these proteins should enable us to determine the effect of these posttranslational modifications on the ability of IGFBPs to modulate IGF biologic activity. © 1993 Wiley-Liss, Inc.     

Involvement of serum mannan binding proteins and mannose receptors in uptake of mannosylated liposomes by macrophages

The roles of serum mannan binding protein (MBP) and the mannose receptor in the cellular uptake of mannosylated liposomes (Man-liposomes) by macrophages were studied. Man-liposomes were prepared by incorporating cholesten-5-yloxy-N-(4-((1-imino-2-beta-D-thiomannosylethyl)amino)butyl)formamide (Man-C4-Chol) into small unilamellar long circulating liposomes consisting of cholesterol (Chol) and distearoyl phosphatidylcholine (DSPC). In the in vitro cellular uptake study with cultured mouse peritoneal macrophages, [(3)H]Man-liposomes were taken up to a great extent, whereas no significant uptake was observed for [(3)H]cholesterol and DSPC liposomes without Man-C4-Chol (Bare-liposomes). The uptake of [(3)H]Man-liposomes was dose- and temperature-dependent and inhibited by an excess of mannosylated bovine serum albumin, suggesting their specific uptake via membrane mannose receptor-mediated endocytosis. Furthermore, it was demonstrated that (111)In-MBP binds strongly to Man-liposomes based on the recognition of Man-C4-Chol and markedly enhanced their uptake by macrophages. These results are supported by confocal laser microscopic images. In addition, in vivo hepatic uptake of (111)In-MBP was enhanced by Man-liposomes. On the other hand, the uptake of Man-liposomes was significantly reduced by preincubation with serum and further with MBP-depleted serum suggesting inhibitory effects of serum proteins such as albumin on mannose receptor-mediated endocytosis. The involvement of serum-type MBP and membrane mannose receptors in the uptake of Man-liposomes is thus suggested.     

Substrate binding and enzyme function investigated by infrared spectroscopy

Protein conformational changes triggered by molecule binding are increasingly investigated by infrared spectroscopy often using caged compounds. Several examples of molecule-protein recognition studies are given, which focus on nucleotide binding to proteins. The investigation of enzyme mechanisms is illustrated in detail using the Ca(2+)-ATPase of the sarcoplasmic reticulum membrane as an example. It is shown that infrared spectroscopy provides valuable information on general aspects of enzyme function as well as on molecular details of molecule-protein interactions and the mechanism of catalysis.     

Glycoprotein G isoforms from some alphaherpesviruses function as broad-spectrum chemokine binding proteins

Mimicry of host chemokines and chemokine receptors to modulate chemokine activity is a strategy encoded by beta- and gammaherpesviruses, but very limited information is available on the anti-chemokine strategies encoded by alphaherpesviruses. The secretion of chemokine binding proteins (vCKBPs) has hitherto been considered a unique strategy encoded by poxviruses and gammaherpesviruses. We describe a family of novel vCKBPs in equine herpesvirus 1, bovine herpesvirus 1 and 5, and related alphaherpesviruses with no sequence similarity to chemokine receptors or other vCKBPs. We show that glycoprotein G (gG) is secreted from infected cells, binds a broad range of chemokines with high affinity and blocks chemokine activity by preventing their interaction with specific receptors. Moreover, gG also blocks chemokine binding to glycosaminoglycans, an interaction required for the correct presentation and function of chemokines in vivo. In contrast to other vCKBPs, gG may also be membrane anchored and, consistently, we show chemokine binding activity at the surface of cells expressing full-length protein. These alphaherpesvirus vCKBPs represent a novel family of proteins that bind chemokines both at the membrane and in solution.     

Evolution of EF-hand calcium-modulated proteins. II. Domains of several subfamilies have diverse evolutionary histories

Summary In the first report in this series we described the relationships and evolution of 152 individual proteins of the EF-hand subfamilies. Here we add 66 additional proteins and define eight (CDC, TPNV, CLNB, LPS, DGK, 1 F8, VIS, TCBP) new subfamilies and seven (CAL, SQUD, CDPK, EFH5, TPP, LAV, CRGP) new unique proteins, which we assume represent new subfamilies.The main focus of this study is the classification of individual EF-hand domains. Five subfamilies—calmodulin, troponin C, essential light chain, regulatory light chain, CDC31/caltractin-and three uniques—call, squidulin, and calcium-dependent protein kinase-are congruent in that all evolved from a common four-domain precursor. In contrast calpain and sarcoplasmic calcium-binding protein (SARC) each evolved from its own one-domain precursor. The remaining 19 subfamilies and uniques appear to have evolved by translocation and splicing of genes encoding the EF-hand domains that were precursors to the congruent eight and to calpain and to SARC.The rates of evolution of the EF-hand domains are slower following formation of the subfamilies and establishment of their functions. Subfamilies are not readily classified by patterns of calcium coordination, interdomain linker stability, and glycine and proline distribution. There are many homoplasies indicating that similar variants of the EF-hand evolved by independent pathways.Offprint requests to: R. H. Kretsinger     

Structure, function and evolutionary relationship of proteins containing a disintegrin domain.

Disintegrins are soluble integrin ligands from snake venoms that disrupt cell-matrix interactions. Recently, the nuclear magnetic resonance structures of two disintegrins were determined, providing provocative molecular insight into how a disintegrin may engage an integrin. In addition, it has recently been realized that disintegrins are derived from larger multifunctional proteins, and that there is a family of membrane-anchored, disintegrin domain-containing proteins that may promote important cell-cell interactions.     

Quantitative analysis of the binding affinity of poly(ADP-ribose) to specific binding proteins as a function of chain length

Poly(ADP-ribose) (PAR) is synthesized by poly(ADP-ribose) polymerases in response to genotoxic stress and interacts non-covalently with DNA damage checkpoint and repair proteins. Here, we present a variety of techniques to analyze this interaction in terms of selectivity and affinity. In vitro synthesized PAR was end-labeled using a carbonyl-reactive biotin analog. Binding of HPLC-fractionated PAR chains to the tumor suppressor protein p53 and to the nucleotide excision repair protein XPA was assessed using a novel electrophoretic mobility shift assay (EMSA). Long ADP-ribose chains (55-mer) promoted the formation of three specific complexes with p53. Short PAR chains (16-mer) were also able to bind p53, yet forming only one defined complex. In contrast, XPA did not interact with short polymer, but produced a single complex with long PAR chains (55-mer). In addition, we performed surface plasmon resonance with immobilized PAR chains, which allowed establishing binding constants and confirmed the results obtained by EMSA. Taken together, we developed several new protocols permitting the quantitative characterization of PAR–protein binding. Furthermore, we demonstrated that the affinity of the non-covalent PAR interactions with specific binding proteins (XPA, p53) can be very high (nanomolar range) and depends both on the PAR chain length and on the binding protein.     

Phylogenetic diversity as a window into the evolutionary and biogeographic histories of present-day richness gradients for mammals

Phylogenetic diversity (PD) captures the shared ancestry of species, and is increasingly being recognized as a valuable conservation currency. Regionally, PD frequently covaries closely with species richness; however, variation in speciation and extinction rates and/or the biogeographic history of lineages can result in significant deviation. Locally, these differences may be pronounced. Rapid recent speciation or high temporal turnover of lineages can result in low PD but high richness. In contrast, rare dispersal events, for example, between biomes, can elevate PD but have only small impact on richness. To date, environmental predictors of species richness have been well studied but global models explaining variation in PD are lacking. Here, we contrast the global distribution of PD versus species richness for terrestrial mammals. We show that an environmental model of lineage diversification can predict well the discrepancy in the distribution of these two variables in some places, for example, South America and Africa but not others, such as Southeast Asia. When we have information on multiple diversity indices, conservation efforts directed towards maximizing one currency or another (e.g. species richness versus PD) should also consider the underlying processes that have shaped their distributions.     

Titration calorimetry as a binding assay for lipid-binding proteins

Titration calorimetry has been evaluated as a method for obtaining binding constants and thermodynamic parameters for the cytosolic fatty acid- and lipid-binding proteins. An important feature of this method was its ability to accurately determine binding constants in a non-perturbing manner. The equilibrium was not perturbed, since there was no requirement ot separate bound and free ligand in order to obtain binding parameters. Also, the structure of the lipid-protein complex was not perturbed, since native ligands were used rather than non-native analogues. As illustrated for liver fatty acid-binding protein, the method distinguished affinity classes whose dissociation constants differed by an order of magnitude or less. It also distinguished endothermic from exothermic binding reactions, as illustrated for the binding of two closely related bile salts to ileal lipid-binding protein. The main limitations of the method were its relatively low sensitivity and the difficulty working with highly insoluble ligands, such as cholesterol or saturated longchain fatty acids. However, the signal-to-noise ratio was improved by manipulating the buffer conditions, as illustrated for oleate binding to rat intestinal fatty acid binding protein. Binding parameters are reported for oleate interactions with several wild-type and mutant lipid-binding proteins from intestine. Where possible, the binding parameters obtained from calorimetry were compared with results obtained from fluorescence and Lipidex binding assays of comparable systems.Abbreviations I-FABP recombinant (E. coli-derived) rat Intestinal Fatty Acid-Binding Protein - I-FABP (R106 Q) a mutant form of I-FABP in which arginine-106 has been replaced by glutamine - CRBP-II recombinant rat Cellular Retinol-Binding Protein - CRBP-II (Q109R) a mutant form of CRBP-II in which glutamine-109 has been replaced by arginine - L-FABP recombinant rat Liver Fatty Acid-Binding Protein - I-LBP recombinant rat Ileal Lipid-Binding Protein, n, lipid: protein molar binding stoichiometry - Kd and Ka dissociation and association constants for ligand binding, respectively - H enthalpy of binding - G Gibbs free energy of binding - S enthalpy of binding - T Temperature in °K     

CP43-like chlorophyll binding proteins: structural and evolutionary implications

CP43, encoded by the psbC gene, is a chlorophyll (Chl)-binding protein of Photosystem II (PSII), the water-splitting and oxygen-evolving enzyme of photosynthesis. CP47, encoded by psbB, a Chl-binding protein of PSII, is closely related to CP43. The Chl-binding six transmembrane helical unit typified by CP43, is also structurally related to the N-terminal domains of the PsaA and PsaB proteins of Photosystem I (PSI) as well as to the family of light-harvesting proteins encoded by cyanobacterial isiA genes and prochlorophyte pcb genes. Here we use recent structural information derived for PSII and PSI to review similarities and differences between the various members of the CP43-like class of light-harvesting proteins, exploring both functional and evolutionary implications.     

The function of inositol high polyphosphate binding proteins

The inositol phosphate metabolism network has been found to be much more complex than previously thought, as more and more inositol phosphates and their metabolizing enzymes have been discovered. Some of the inositol phosphates have been shown to have biological activities, but little is known about their signal transduction mechanisms except for that of inositol 1,4,5-trisphosphate. The recent discovery, however, of a number of binding proteins for inositol high polyphosphate [inositol 1,3,4,5-tetrakisphosphate (IP₄), inositol 1,3,4,5,6-pentakisphosphate, or inositol hexakisphosphate] enables us to speculate on the physiological function of these compounds. In this article we focus on two major issues: (1) the roles of inositol high polyphosphates in vesicular trafficking, especially exocytosis, and (2) pleckstrin homology domaincontaining IP4 binding proteins involved in the Ras signaling pathway.     

The biotin-thyroxin conjugate as a bifunctional ligand of binding proteins

The conjugate of the residue of vitamin H (biotin, Bt) with the hormone of thyroid gland thyroxin (T₄) was prepared by N-acylation of N-(3-aminopropyl)biotin amide with N-hydroxysuccinimide ester of N-acetyl thyroxin. The interactions of the Bt-T₄ conjugate with one or simultaneously with two binding proteins with affinity to Bt or T₄ in solution and on a solid phase were studied by electron spectroscopy, enzyme immunoassay, and computer modeling. Bt-T₄ was specifically fixed in the Bt-binding site of the streptavidin molecule via a large number of hydrogen bonds and hydrophobic interactions. The maximum of the streptavidin fluorescence shifted to a long-wave area and its intensity decreased as a result of complex formation. The degree of quenching of the protein emission was significantly higher than that of the streptavidin-Bt complex. Additional fluorescence quenching resulted from interactions which were sensitive to pH, ionic strength, and detergents and stabilized the position of the thyroxin part of the conjugate near Trp120 of streptavidin in its complex with Bt-T₄. The Bt-T₄ conjugate also formed a specific equimolar complex with T₄-binding human globulin (TBG) by the same mechanism as that for T₄. The Bt residue did not participate in the interactions which changed characteristics of the TBG fluorophores. The Bt-T₄ conjugate was bound to avidin on a solid phase in the solid phase enzyme immunoassay owing to its biotin function, whereas its thyroxin part was exposed to a solution and interacted with polyclonal antibodies to T₄. The intact T₄ competitively inhibited this interaction after its addition to the system. Bt-T₄ also exhibited its bifunctional activity in other immune analytic system. The conjugate bound streptavidin was labeled with Eu³⁺-chelate and subsequently formed a three component complex with participation of a monoclonal antibody to T₄ immobilized on a solid phase. Free T₄ inhibited the thyroxin function of the conjugate bound to the labeled streptavidin proportionally to its concentration in a sample of human blood serum. Parameters of the immunofluorescent analysis demonstrated that the streptavidin-Bt-T₄ complex was actively bound to the T₄-antibody, but had practically no interaction with serum T₄-binding proteins, including TBG. Probably, nonspecific interactions of the T₄ residue with streptavidin in its complex with Bt-T₄, along with steric factors, complicated penetration of thyroxin in this complex into active sites of TBG and other T₄-binding proteins of blood serum. The Bt-T₄ stable conjugate was synthesized according to a plain scheme and could be used as a bifunctional ligand of binding proteins in biochemical studies and immune analytical systems for medicinal diagnostics.