Phospholipases A2: a dendrogram from a distance matrix based on size and hydrophobicity of the residues in their homologous sequences

A distance matrix was obtained from aligned homologous sequences of 32 phospholipases A2 (EC 3.1.1.4) (24 from Elapid and 5 from Viperid venoms, and 3 from amammals), on the basis of the quantities Dij which are defined from a two-dimensional vector representation of the amino acid residues (dimensions: size and hydrophobicity). These Dij quantities were proposed in a previous paper (Ventura, M.M., (1989), An. Acad. brasil. Ci., 61:215). A dendrogram was constructed from this distance matrix empoying, for cluster analysis, the unweighted pair-group using arithmetic averages. Two groups of phospholipases A2: a) Elapid venom enzymes together with the three mammalian pancreatic enzymes (bovine, equine and porcine), and b) Viper venom enzymes (Crotalus, Trimeresurus and Bitis enzymes) can be well distinguished in the topology of the dendrogram. The Elapid group of enzymes in divided into two subgroups: a) Naja, Hemachatus and Bungarus venom enzymes, and b) Notechis, Laticauda, Enhydrina pancreatic phospholipases A2 and the enzymes from Naja, Hemachatus and Bungarus. These results are similar to those reported by Dufton and Hider (Eur. J. Biochem., 137:545 (1983)) which were obtained from the distance matrix based on minimum mutation distance between 25 selected residue positions in the pairwise compared sequences

Secondary structure of soybean trypsin inhibitor (Kunitz): a study by infrared spectroscopy

The infrared spectrum (amide I'region) of Kunitz soybean trypsin inhibitor (SBTI) was obtained in D2O solution and resolved into Gaussian componentes. A prominent broad band centered at 1643 cm -1 is shown on the unresolved spectrum, which is usually assigned to N-deuterated peptide groups in an unordered structure, since SBTI is known to be devoid of alfa-helix by CD and X-ray crystallographic studies. In addition, shoulders are evident at 1632 cm**-1 and 1676 cm**-1, which correspond probably to the v(PI,0) and v(O,pi) components assigned to an antiparallel chain ß-pleated sheet structure. Parameters (maximum absorptivity, wavenumber at the maximum of the band, and half-width at the band at half-height) for the four Gaussian component bands (in which the amide I' band was resolved) are given. A crude estimation of 4% is obtained for antiparallel ß-sheet in SBTI, i.e., this protein would be practically devoid of such a ß-structure. Notwithstanding the fact that this results is apparently in agreement with the far-UV CD spectrum (data reported in the literature), the predominant conformation class found in SBTI has been demonstrated to be approximate ß-sheet structures, with a small amount of regular sheet

Do snake venom cytoloxins eschibit amphiphilicity?

It is suggested, on the basis of the structural information available from the literature, that the molecules of cobramine B and homologous cytotoxins, in contrast to snake venom neurotoxins, are amphiphilic in the sense that they are composed of a predominantly hydrophobic multi-stranded ß-sheet and other regions sharply hydrophilic. It is possible that the direct lytic activity of snake venom cytotoxins is due, at least in part, to their amphiphathy

Phylogenetic relationships of snake venom toxic proteins

Two kinds of distance matrices have been formed from minimum mutational distances and absolute hydrophobicity differences obtained by comparison of aligned homologous sequences of 56 toxins from venom os snakes belonging to 7 genera. Phylogenetic trees were constructed from these distance matrices, employing the unweighted pair-group method using arthmetic averages (UPGMA). The Pearson product-moment correlation coefficient has been used to estimate the agreement between the original distance matrix and that obtained directly from the dendrogram. For al these procedures the set of computer programs PHYTREE (written in BASIC for micro-computer, and available from the author) has been used

Structural similarity in Bowman-Birk type protease inhibitors based on hydrophobicity

The degree of similarity in the three-dimensional structures of thirteen legume Bowman-Birk type protease inhibitors has been examined on the basis of the patterns of hydrophobicity found in their amino acid sequences, following the procedure described by Sweet & Eisenberg (1983). In the group of such double-headed protease inhibitors two sub-groups are distinguished presenting high structural similarity among their respective members and low similarity between them. Phylogenetic trees have been constructed from hydrophobicity difference and minimum mutational distance matrices, respectively

The complete amino acids sequence of the Vigna unguiculata (L.) Walp. seed trypsin and chymotrypsin inhibitor

Foi determinado em nosso Laboratório a seqüência completa de aminoácidos de um inhbidor de tripsina e quimotripsina, "double-headed", denominado abreviadamente BTCI, purificado de feijäo caupi Vigna unguiculata (L.) Walp.cv."Seridó". Os peptídeos trípticos e quimiotrípticos foram seqüenciados pelos métodos manuais de Edman-Gray, de Edman-Chang (N-terminais) e de carboxypeptidases (C-terminais). É a seguinte a seqüência de aminoácidos do BTCI: Ser Gly-His-Glx-Asx-Ser-Thr-Asx-Glx-Ala-Ser-Glx-Ser-Ser-Lys-Pro-Cys-Cys-Arg-Glx-Cys-Ala-Cys-Thr-Lys-Ser-Ile-Pro-Pro-Glx-Cys-Arg-Cys-Ser-Asx-Val-Arg-Leu-Asn-Ser Cys-His-Ser-Ala-Cys-Lys-Ser-Cys-Thr=Phe-Ser-Ile-Pro-Ala-Glx-Xys-Phe-Cys-Gly=Asx-Ile-Asx-Asx-Phe-Cys=Tyr-Lys-Pro-Cys-Lys-Ser-Ser-His-Ser-Asx-Asx-Asx-Asx0Trp-Asn. BTCI apresenta alto grau de homologia como vários outros inibidores da família Bowman-Birk

Trypsin and chymotryosin inhinitor of Vigna unguiculata seeds - involvement of tyrosyls in its interaction with proteases

When trypsin and chymotrypsin inhibitor of Vigna unguiculata seeds (black-eyed pea trypsin and chymotrypsin inhibitor, BTCI) combines with ß-trysin, 4.0, 1.5, 5.0, 5.8, and 6.6 tyrosyl residues are shield from reaction with N-acetylimidazole, at reagent/protein molar ratios of 60, 120, 200, 350 and 500, respectively. This may result from the presence of tyrosyl residues in the zone of contact between enzyme and inhibitor. In the interaction of BTCI and alpha-chymotrypsin, only 0.6 tyrosyl residues are shielded from the reaction with N-acetylimidazole, at a 500-fold reagent molar excess