Location and volume of the active site of chymotrypsin.

The active site of chymotrypsin molecule (approximated by a sphere with radius of 20 A) was taken as the largest cavity on the enzyme surface. The volume inside the approximating sphere is sufficient for placement of 95% of non-hydrogen atoms of the enzyme. The active site cavity is localized in a spherical sector with solid angle of 80 degrees whose axis passes through the CB-atom of the Ser195 residue.

Conformational analysis of the biologically active RGD-containing anti-adhesive peptide cyclo(ArgGlyAspPhe-D-val).

Using theoretical conformational analysis, the RGD-peptide with anti-adhesive activity cyclo(ArgGlyAspPhe-D-Val) was studied. Random sampling was used to search the conformational space of the allowed torsional angles of the main chain of the molecule. Among 900 stable conformers with different folding of the cyclic moiety of the peptide, only those were selected which corresponded to low-energy conformers of the model linear tripeptide AcAlaGlyAspNHMe.

Conformational analysis of the biologically active cyclic analog of beta-casomorphin H-Tyr-cyclo[D-OrnPheProGly].

A biologically active analog of beta-casomorphin, H-Tyr-cyclo[D-OrnPheProGly], was studied by theoretical conformational analysis. Random sampling was used to search the conformational space of allowed dihedral angles. Among 53 low-energy conformers with different folding of the peptide cyclic moiety, only those were selected which correspond to the low-energy area of the model linear tripeptide Ac-D-AlaAlaPro-NHMe.

The significant conservative and variable regions of the homologous protein sequences.

A method of identification of significant conservative and variable regions in homologous protein sequences is presented. A set of aligned homologous sequences is divided into two groups consisting of m and n most related sequences. Each pair of sequences from different group is compared using unitary similarity matrix.

Conservative and variable regions of homologous snake phospholipases A2 sequences: prediction of the taxon-specific peptides structure.

Homologous amino acid sequences of phospholipases A2 (PLA2) of snakes belonging to the families Elapidae, Viperidae, and Colubridae were considered in order to study the conservative and variable regions location. The PLA2 sequences were divided into two groups (taxons) according to the phylogenetic tree reconstructed from the pair similarity matrix. Results of the intergroup comparison were plotted to facilitate the identification of significant conservative and variable regions.