Homology modeling of nematode Caenorhabditis elegans CED3 protein-inhibitor complex.

CED3 protein, the product of a gene necessary for programmed cell death in the nematode Caenorhabditis elegans, is related to a highly specific cysteine protease family i.e., caspases. A tertiary-structural model has been constructed of a complex of the CED3 protein with tetrapeptide-aldehyde inhibitor, Ac-DEVD-CHO. The conformation of CED3 protein active site and the general binding features of inhibitor residues are similar to those observed in other caspases. The loop segment (Phe380-Pro387) binds with the P4 Asp in a different fashion compared to caspase-3. The comparative modeling of active sites from caspase-3 and CED3 protein indicated that although these enzymes require Asp at the position P4, variation could occur in the binding of this residue at the S4 subsite. This model allowed the definition of substrate specificity of CED3 protein from the structural standpoint and provided insight in designing of mutants for structure-function studies of this classical caspase homologue.

Predicted three-dimensional structural models of venom serine protease inhibitors and their interactions with trypsin and chymotrypsin.

Three homology models of trypsin and chymotrypsin inhibitor polypeptides from snake venom of Naja naja naja and Leaf-nosed viper in the unbound state and in complex with trypsin and chymotrypsin were built based on homology to bovine pancreatic trypsin inhibitor (BPTI). These venom inhibitors belong to the Kunitz-type inhibitor family, which is characterized by a distinct tertiary fold with three-conserved disulfide bonds. The general folding pattern in these trypsin and chymotrypsin inhibitor homology models is conserved when compared to BPTI. The respective orientations of the inhibitors bound to trypsin/chymotrypsin are similar to that of BPTI bound to bovine trypsin/chymotrypsin. The principal binding loop structure of the inhibitors fills the active site of enzymes in a substrate-like conformation and forms a series of independent main-chain and side-chain interactions with enzymes. In order to provide the possible fingerprints for molecular recognition at the enzyme-inhibitor interface, a detailed theoretical analysis of the interactions between the principal binding loop of these inhibitors and active site of trypsin/chymotrypsin is performed based on available crystal structural, site-directed mutagenetic, kinetic, and sequence analysis studies. Despite the variations present at different positions of the principal binding loop of trypsin and chymotrypsin inhibitor models from Leaf-nosed viper and cobra Naja naja naja, respectively (designated as LnvTI and NCI), there are favorable subsite binding interactions which are expected to exhibit equally potent inhibitory activity as BPTI. On the contrary, significant mutations at several secondary specificity positions in the Naja naja naja trypsin inhibitor (designated as NTI) are likely to affect different inhibitor-enzyme-subsites interactions. This may explain the observed increased inhibitory activity of this polypeptide on a structural basis.

Pharmacological effects of the leaf-nosed viper snake (Eristocophis macmahoni) venom and its HPLC fractions.

Crude venom from Eristocophis macmahoni was demonstrated to exert a potent inhibition of human blood platelet aggregation mediated by adenosine diphosphate (ADP), platelet activating factor (PAF) and arachidonic acid (AA). The venom caused lysis of the platelets, however, the red blood cells were not lysed by the venom. Substantial oedema was produced upon injection of the venom into the rat hind paw. Contrarily, the intraperitoneal injection of the venom to the rats caused an inhibition of the carrageenin-induced rat paw oedema. However, an 100% lethality within 24 h was observed with a dose of 40 mg/kg body weight. The venom was fractionated by reverse phase high pressure liquid chromatography (HPLC) and the fractions were analyzed for their effect on ADP-induced platelet aggregation. The fraction eluted at 15.5 min (20% acetonitrile concentration) exhibited an inhibitory effect of several-fold greater potency than that of the crude venom. Fractions eluted at 18.5 min (25.4% acetonitrile concentration) and onward showed a proaggregatory but insignificant effect. It is suggested that although the venom contains pro aggregatory components, inhibition of platelet aggregation seems to be its predominant activity.

Purification and primary structure of low molecular mass peptides from scorpion (Buthus sindicus) venom.

The primary structures of four low molecular mass peptides (Bs 6, 8, 10 and 14) from scorpion Buthus sindicus were elucidated via combination of Edman degradation and matrix-assisted laser desorption ionization mass spectrometry. Bs 8 and 14 are cysteine-rich, thermostable peptides composed of 35-36 residues with molecular weights of 3.7 and 3.4 kDa, respectively. These peptides show close sequence homologies (55-78%) with other scorpion chlorotoxin-like short-chain neurotoxins (SCNs) containing four intramolecular disulfide bridges. Despite the sequence variation between these two peptides (37% heterogeneity) their general structural organization is very similar as shown by their clearly related circular dichroism spectra. Furthermore, Bs6 is a minor component, composed of 38 residues (4.1 kDa) containing six half-cystine residues and having close sequence identities (40-80%) with charybdotoxin-like SCNs containing three disulfide bridges. The non-cysteinic, bacic and thermolabile Bs10 is composed of 34 amino acid residues (3.7 kDa), and belongs to a new class of peptides, with no sequence resemblance to any other so far reported sequence isolated from scorpions. Surprisingly, Bs10 shows some limited sequence analogy with oocyte zinc finger proteins. Results of these studies are discussed with respect to their structural similarities within the scorpion LCNs, SCNs and other biologically active peptides.

Primary structure of hemoglobin from cobra Naja naja naja.

Cobra snake Naja naja naja hemoglobin shows four bands on Triton electrophoresis. We present the primary structure of one alpha and one beta chain. The separation of polypeptide chains was achieved by ion exchange chromatography on carboxymethyl cellulose column. The amino acid sequence was established by automatic Edman degradation of the native chains and tryptic and hydrolytic peptides in a gas-phase sequencer. The structural data are compared with those of human and other reptile hemoglobins and reveal not only large variations from human but within reptiles. The amino acid exchanges involve several subunit contacts and heme binding sites. This is the first study on the hemoglobin of a land snake. There are only two amino acid sequences of sea snake hemoglobin (Microcephalophis gracilis gracilis and Liophis miliaris) reported in the literature.

Three-dimensional model and quaternary structure of the human eye lens protein gamma S-crystallin based on beta- and gamma-crystallin X-ray coordinates and ultracentrifugation.

A 3-dimensional model of the human eye lens protein gamma S-crystallin has been constructed using comparative modeling approaches encoded in the program COMPOSER on the basis of the 3-dimensional structure of gamma-crystallin and beta-crystallin. The model is biased toward the monomeric gamma B-crystallin, which is more similar in sequence. Bovine gamma S-crystallin was shown to be monomeric by analytical ultracentrifugation without any tendency to form assemblies up to concentrations in the millimolar range. The connecting peptide between domains was therefore built assuming an intramolecular association as in the monomeric gamma-crystallins. Because the linker has 1 extra residue compared with gamma B and beta B2, the conformation of the connecting peptide was constructed by using a fragment from a protein database. gamma S-crystallin differs from gamma B-crystallin mainly in the interface region between domains. The charged residues are generally paired, although in a different way from both beta- and gamma-crystallins, and may contribute to the different roles of these proteins in the lens.

Characterization of two platelet aggregation inhibitor-like polypeptides from viper venom.

Two polypeptides, eristocophins I and II, have been characterized from leaf-nosed viper (Eristocophis macmahoni) venom. They contain 10 half-Cys residues of a total of 61/62 residues, have 72% residue identity, and exhibit similarities to platelet aggregation inhibitors and segments of adhesive proteins. Eristocophin I contains the sequence Arg-Gly-Asp, known to inhibit fibrinogen interaction with the platelet receptor. Eristocophin II has Met instead of Arg in this sequence, and an adjacent Trp-Asn-Asp segment. The latter is also typical of adhesive proteins, thus linking two potentially functional segments in one molecule. Exchanges are maximal in these segments, suggesting that the polypeptides exhibit functional divergence with isoform differences in important regions.

Purification and characterization of two highly different group II phospholipase A2 isozymes from a single viperid (Eristocophis macmahoni) venom.

Two phospholipase A2 isozymes have been purified from leaf-nosed viper by gel permeation chromatography followed by reverse-phase HPLC and cation-exchange FPLC. Both enzymes contain seven pairs of half-cystine, typical of group II phospholipase A2. Surprisingly large differences, affecting both N- and C-terminal regions, exist between the two isozymes purified from the same snake venom. Exchanges occur at no less than 27 of 121 positions (22%), suggesting the possible existence of two genes for phospholipase A2. The residue identity with the enzymes from other Viperidae species is also low, only 44-48%, indicating extensive variations of this protein structure at large. Functionally, the present isozymes do not possess the cationic regions ascribed to myotoxicity and anti-coagulant effects of the enzyme.

Extensive multiplicity of the miscellaneous type of neurotoxins from the venom of the cobra Naja naja naja and structural characterization of major components.

A multiplicity of miscellaneous type neurotoxins were detected in the venom of the cobra Naja naja naja by use of reverse-phase HPLC and FPLC. The primary structures of major forms were determined, giving 4 novel structures. All four contain 62-65 residues, with 10 half-cystine residues and resemble the miscellaneous type of toxins from other Naja species. Differences within the species are extensive, exchanges occur at 27 positions, giving only 58% residue identity between all forms. However, the differences are largely limited to 3 regions corresponding to structurally important loops where two functional residues participating in receptor binding are exchanged. The four miscellaneous neurotoxins now characterized, together with the minor components of the miscellaneous type, the minimally four neurotoxins reported before, and other related toxins, indicate the existence of an extensive toxin gene multiplicity.

Primary structure of hemoglobin alpha-chain from cuckoo (Eudynamys scolopaceae, cuculiformes).

The complete amino acid sequence of the alpha A-chain of major hemoglobin component from Cuckoo (Eudynamys scolopaceae) is presented. Separation of the polypeptide subunits was achieved by ion exchange chromatography in the presence of 8 M urea. The sequence was studied by automatic Edman degradation of the native chain and its tryptic fragments in a gas-phase sequencer. Comparison with other avian hemoglobins shows residues alpha 21, alpha 30, alpha 96, alpha 110, and alpha 114 as being specific to Cuckoo. The functional significance of these is discussed.

Primary structure and functional properties of cobra (Naja naja naja) venom Kunitz-type trypsin inhibitor.

A trypsin inhibitor from the venom of the cobra Naja naja naja has been isolated by a single step of reverse-phase high-performance liquid chromatography. The protein strongly inhibits trypsin (Ki = 3.5 pM). The primary structure was determined by peptide analysis of the [14C]carboxymethylated inhibitor. The 57-residue polypeptide chain belongs to the family of Kunitz-type inhibitors, and exhibits 42% residue identity with bovine pancreatic trypsin inhibitor. The structure shows only 70% identity with the corresponding peptide from the Capa cobra (Naja nevia), establishing that the inhibitor molecule exhibits extensive variations. Functionally, a basic residue at position P3' correlates with strong inhibition.

Purification and characterization of a chymotrypsin Kunitz inhibitor type of polypeptide from the venom of cobra (Naja naja naja).

A chymotrypsin Kunitz inhibitor type of polypeptide has been isolated from the venom of Naja naja naja by reverse phase HPLC and cation exchange FPLC. It is present in a considerably lower amount than that of the corresponding trypsin inhibitor. The primary structure, determined by sequence analysis of the whole molecule and its tryptic peptides, has 57 residues with an apparent molecular mass of 6.2 kDa. The main contact site with the protease (P1) has a Phe, showing the specificity of the inhibitor. Of residues considered functionally important in Kunitz-type inhibitors, Gly-36 is replaced by Ser in a segment of weak contacts with the protease.

Characterization of a cytotoxin-like basic protein from the cobra (Naja naja naja) venom.

A cytotoxin-like basic protein has been isolated from the venom of the nominate race of cobra (Naja naja naja from Pakistan) by a single step of high-performance liquid chromatography. The primary structure was determined and consists of 62 amino acid residues in a single polypeptide chain. It is highly similar to that of the cytotoxin-like basic proteins isolated from other Naja species, but differs in two of the SS-loop structures from that of cytotoxins.

Characterization of two different peptides from the venom of the scorpion Buthus sindicus.

Two disulfide-rich, low-molecular mass peptides (approximately 3 kDa and approximately 4 kDa) have been isolated from Buthus sindicus venom using ion-exchange and reverse-phase HPLC. Peptide I has 35 residues with 8 half-cystine residues and is clearly related to four-disulfide core proteins of the neurophysin type and to toxins of other scorpion species (55-63% residue identity). Peptide II, present in low yield, has 28 residues with 6 half-cystine residues and a structure largely dissimilar from that of peptide I and other characterized toxins, although probably still a member of the disulfide core peptide type. Consequently, scorpion venom contains, in addition to toxins characterized before, toxin-like compounds with distant relationships.

Characterization of a heterogeneous camel milk whey non-casein protein.

A milk protein, occurring in the whey fraction, has been characterized from camel milk. Determination of the primary structure reveals the existence of two related types of chain with residue differences in at least the N-terminal region. A fragment representing an N-terminal part of the protein was also recovered (heterogeneous at the same positions). The absence of cysteine residues in the protein shows that no disulphide bridges are present. The pattern of fragments and a parent protein resembles that for casein and its fragments, showing that fragments and a multiplicity of forms may be typical for different milk proteins.

A camel milk whey protein rich in half-cystine. Primary structure, assessment of variations, internal repeat patterns, and relationships with neurophysin and other active polypeptides.

The amino acid sequence of a recently isolated camel milk protein rich in half-cystine has been determined by peptide analyses. The 117-residue protein has 16 half-cystine residues, concluded to correspond to disulfide bridges and suggesting a tight conformation of the molecule. Comparisons of the structure with those of other proteins reveal several interesting relationships. The camel protein is clearly homologous with a previously reported rat whey phosphoprotein of possible importance for mammary gland growth regulation, and with a mouse protein of probable relationship to neurophysins. The camel, rat and mouse proteins may represent species variants from a rapidly evolving gene. Residue identities in pairwise comparisons are 40% for the camel/rat proteins and 33% for the camel/mouse proteins, with 38 positions conserved in all three forms. The camel protein also reveals an internal repeat pattern similar to that for the other two proteins. The homology between the three milk whey proteins has wide implications for further relationships. Thus, previously noticed similarities, involving either of the milk proteins, include limited similarities to casein phosphorylation sites for the camel protein, to neurophysins in repeat and half-cystine patterns for the mouse and rat proteins, and to an antiprotease for the rat protein. These similarities are reinforced by the camel protein structure and the recognition of the three whey proteins as related. Finally a few superficial similarities with the insulin family of peptides and with some other peptides of biological importance are noticed. Combined, the results relate the camel protein in a family of whey proteins, and extend suggestions of relationships with some binding proteins.

A small camel-milk protein rich in cysteine/half-cystine.

A small protein (Mr about 14 000) rich in cysteine/half-cystine has been isolated from camel milk by exclusion chromatography and reverse-phase high-performance liquid chromatography. The N-terminal amino acid sequence shows a region with several positional identities with alpha and beta-caseins, which however lack cysteine residues; positions 16-20 are identical and involve the serine residues that have been found to be phosphorylated in beta-caseins.

Hemoglobins, XXXVIII. Amino acid sequence of a dimeric hemoglobin (erythrocruorin), component VI from Chironomus thummi thummi (CTT VI).

The dimeric hemoglobin CTT VI (Erythrocruorin) was isolated from the hemolymph of the larvae of Chironomus thummi thummi. The globin from CTT VI was subjected to trypsin, limited trypsin and cyanogen bromide digestion. For elucidation of the sequence in the C-terminal region, cleavage with Staphylococcus aureus V8 protease was also carried out. The peptides were separated by gel and ion-exchange chromatography. The handling of some large fragments was facilitated by maleylation and subsequent ion-exchange chromatography with conservation of the maleyl groups. The amino acid sequence was determined by automatic Edman degradation. The order of the peptides was provided by overlaps, but in two cases by homology only (for residues 98 and 99, and 109 and 110). The hemoglobin consists of 2 x 147 amino acids with a molecular weight of 32411. The sequence of CTT VI is compared with a monomeric (CTT III) and a dimeric hemoglobin (CTT II beta) and the human alpha-chains. The structural differences are discussed.