Structure and function insights garnered from in silico modeling of the thrombospondin type-1 domain-containing 7A antigen

The thrombospondin type-1 domain containing 7A (THSD7A) protein is known to be one of the antigens responsible for the autoimmune disorder idiopathic membranous nephropathy. The structure of this antigen is currently unsolved experimentally. Here we present a homology model of the extracellular portion of the THSD7A antigen. The structure was evaluated for folding patterns, epitope site prediction, and function was predicted. Results show that this protein contains 21 extracellular domains and with the exception of the first two domains, has a regular repeating pattern of TSP-1-like followed by F-spondin-like domains. Our results indicate the presence of a novel Trp-ladder sequence of WxxxxW in the TSP-1-like domains. Of the 21 domains, 18 were shown to have epitope binding sites as predicted by epitopia. Several of the F-spondin-like domains have insertions in the canonical TSP fold, most notably the coiled coil region in domain 4, which may be utilized in protein-protein binding interactions, suggesting that this protein functions as a heparan sulfate binding site.     

Phylogenetic relationships and evolution of Crassulaceae inferred from matK sequence data

Chloroplast gene matK sequence data were used to estimate the phylogeny of 112 species of Crassulaceae sampled from 33 genera and all six recognized subfamilies. Our analyses suggest that five of six subfamilies recognized in the most recent comprehensive classification of the family are not monophyletic. Instead, we recovered a basal split in Crassulaceae between the southern African CRASSULA: clade (Crassuloideae) and the rest of the family (Sedoideae). These results are compatible with recent studies of cpDNA restriction site analyses. Within Sedoideae, four subclades were also recovered: KALANCHOE:, Leucosedum, Acre, and AEONIUM:; evidence also exists for a TELEPHIUM: clade and SEMPERVIVUM: clade. The genus SEDUM: is highly polyphyletic with representatives spread throughout the large Sedoideae clade. Sympetaly and polymerous flowers have arisen multiple times in Crassulaceae and thus are not appropriate characters upon which to base subfamilial limits, as has been done in the past. One floral character, haplostemy, appears to be confined to the well-supported CRASSULA: clade. Our analyses suggest a southern African origin of the family, with subsequent dispersal northward into the Mediterranean region. From there, the family spread to Asia/eastern Europe and northern Europe; two separate lineages of European Crassulaceae subsequently dispersed to North America and underwent substantial diversification. Our analyses also suggest that the original base chromosome number in Crassulaceae is x = 8 and that polyploidy has played an important role in seven clades. Three of these clades are exclusively polyploid (SEMPERVIVUM: clade and two subclades within the KALANCHOE: and AEONIUM: clades), whereas four (Crassula, Telephium, Leucosedum, and ACRE: clades) comprise both diploid and polyploid taxa. Polyploidy is particularly rampant and cytological evolution especially complex in the ACRE: clade.     

Negative regulation of epidermal growth factor signaling by selective proteolytic mechanisms in the endosome mediated by cathepsin B

We have investigated the relevant protease activity in rat liver, which is responsible for most of the receptor-mediated epidermal growth factor (EGF) degradation in vivo. EGF was sequentially cleaved by endosomal proteases at a limited number of sites, which were identified by high performance liquid chromatography and mass spectrometry. EGF proteolysis is initiated by hydrolysis at the C-terminal Glu(51)-Leu(52) bond. Three additional minor cleavage sites were identified at positions Arg(48)-Trp(49), Trp(49)-Trp(50), and Trp(50)-Glu(51) after prolonged incubation. Using nondenaturating immunoprecipitation and cross-linking procedures, the major proteolytic activity was identified as that of the cysteine protease cathepsin-B. The effect of injected EGF on subsequent endosomal EGF receptor (EGFR) proteolysis was further evaluated by immunoblotting. Using endosomal fractions prepared from EGF-injected rats and incubated in vitro, the EGFR was lost with a time course superimposable with the loss of phosphotyrosine content. The cathepsin-B proinhibitor CA074-Me inhibited both in vivo and in vitro the endosomal degradation of the EGFR and increased the tyrosine phosphorylation states of the EGFR protein and the molecule SHC within endosomes. The data, therefore, describe a unique pathway for the endosomal processing of internalized EGF receptor complexes, which involves the sequential function of cathepsin-B through selective degradation of both the ligand and receptor.     

Interdependency of sequence and positional specificities for cysteine proteases of the papain family

The specificity of cysteine proteases is characterized by the nature of the amino acid sequence recognized by the enzymes (sequence specificity) as well as by the position of the scissile peptide bond (positional specificity, i.e., endopeptidase, aminopeptidase, or carboxypeptidase). In this paper, the interdependency of sequence and positional specificities for selected members of this class of enzymes has been investigated using fluorogenic substrates where both the position of the cleavable peptide bond and the nature of the sequence of residues in P2-P1 are varied. The results show that cathepsins K and L and papain, typically considered to act strictly as endopeptidases, can also display dipeptidyl carboxypeptidase activity against the substrate Abz-FRF(4NO2)A and dipeptidyl aminopeptidase activity against FR-MCA. In some cases the activity is even equal to or greater than that observed with cathepsin B and DPP-I (dipeptidyl peptidase I), which have been characterized previously as exopeptidases. In contrast, the exopeptidase activities of cathepsins K and L and papain are extremely low when the P2-P1 residues are A-A, indicating that, as observed for the normal endopeptidase activity, the exopeptidase activities rely heavily on interactions in subsite S2 (and possibly S1). However, cathepsin B and DPP-I are able to hydrolyze substrates through the exopeptidase route even in absence of preferred interactions in subsites S2 and S1. This is attributed to the presence in cathepsin B and DPP-I of specific structural elements which serve as an anchor for the C- or N-terminus of a substrate, thereby allowing favorable enzyme-substrate interaction independently of the P2-P1 sequence. As a consequence, the nature of the residue at position P2 of a substrate, which is usually the main factor determining the specificity for cysteine proteases of the papain family, does not have the same contribution for the exopeptidase activities of cathepsin B and DPP-I.     

Aplysia californica mediated cyclisation of novel 3'-modified NAD+ analogues: a role for hydrogen bonding in the recognition of cyclic adenosine 5'-diphosphate ribose

Cyclic ADP-ribose mobilizes intracellular Ca2+ in a variety of cells. To elucidate the nature of the interaction between the C3' substituent of cADP-ribose and the cADPR receptor, three analogues of NAD+ modified in the adenosine ribase (xyloNAD+ 3'F-xyloNAD+ and 3'F-NAD+ were chemically synthesised from D-xylose and adenine starting materials. 3'F-NAD+ was readily converted to cyclic 3'F-ADP ribose by the action of the cyclase enzyme derived from the mollusc Aplysia californica. XyloNAD+ and 3'F-xyloNAD+ were cyclised only reluctantly and in poor yield to afford unstable cyclic products. Biological evaluation of cyclic 3'F-ADP ribose for calcium release in sea urchin egg homogenate gave an EC(50) of 1.5+/-0.5 microM. This high value suggests that the ability of the C3' substituent to donate a hydrogen bond is crucial for agonism.     

Adult and embryonic blood and endothelium derive from distinct precursor populations which are differentially programmed by BMP in Xenopus

Blood and blood vessels develop in close association in vertebrate embryos and loss-of-function mutations suggest common genetic regulation. By the criteria of co-expression of blood and endothelial genes, and lineage tracing of progeny, we locate two distinct populations of progenitors for blood and endothelial cells in developing Xenopus embryos. The first population is located immediately posterior to the cement gland during neurula stages and gives rise to embryonic blood and vitelline veins in the anterior ventral blood island (aVBI), and to the endocardium of the heart. The second population resides in the dorsal lateral plate mesoderm, and contains precursors of adult blood stem cells and the major vessels. Both populations differentiate into endothelial cells in situ but migrate to new locations to differentiate into blood, suggesting that their micro-environments are unsuitable for haematopoietic differentiation. Both require BMP for their formation, even the Spemann organiser-derived aVBI, but individual genes are affected differentially. Thus, in the embryonic population, expression of the blood genes, SCL and GATA2, depend on BMP signalling while expression of the endothelial gene, Xfli1, does not. By contrast, Xfli1 expression in the adult, DLP population does require BMP. These results indicate that both adult and the anterior component of embryonic blood in Xenopus embryos derive from populations of progenitors that also give rise to endothelial cells. However, the two populations give rise to distinct regions of the vasculature and are programmed differentially by BMP.