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.
View Article and Find Full Text PDFBiochemistry (Mosc)
September 2000
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.
View Article and Find Full Text PDFBiochemistry (Mosc)
September 1999
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.
View Article and Find Full Text PDFJ Biomol Struct Dyn
June 1992
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.
View Article and Find Full Text PDFHomologous 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.
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