Computational Biology The Serine Protease Active Site - Essay Example

Chymotrypsin belongs to the trypsin family of serine proteases and is usually secreted in inactive form (zymogen) in the small intestine. The structure of chymotrypsin was elucidated via the X-ray crystallography.Below is the structure of chymotrypsinogen (see Error: Reference source not found) The active site is the catalytic unit of an enzyme. The determination of the three-dimensional structure of chymotrypsin by X-ray crystallography was the basis of greater insight into the mechanism of action of serine proteases.

The Swiss-PDB Viewer software available at http://spdbv.vital-it.ch/disclaim.html was used to manipulate the coordinates of chymotrypsin and subtilisin serine proteases retrieved from the protein data bank (PDB available at www.rcsb.org). The catalytic site of most srine peptidaeses including chymotrypsin is composed of a catalytic traid of serine, histidine and aspartic acid residues. The ezyme the experimnt dealt with are are serine proteases and they have been known to exhibit similar spatial arrangements.

However, the residues of the enzymes may adopt different order in the amino acid sequence. Catalytic triad is composed of Ser195 on one side and Asp102 and His57 on the other side inside the active site cleft. An extensive hydrogen bonding network exists in the triad for instance Nδ1-H of His57 and Oδ1 of Asp102 and also between OH of Ser195 and the Nε2-H of His57. However in the event that His57 is protonated the latter bond is lost (Hedstrom, 2002). Figure 8: The positions of the backbone nitrogens are shown; the residues are Ser195 and Gly193 and the distances from these nitrogens to the peptide carbonyl oxygen.

This brings the two residues closer for interactions to occur The catalytic triad in subtilisin contains residues 32, 64 and 221; the oxyanion hole comprises the side chain of Asn155 and the backbone NH of Ser 221; the mouth of the specificity