Trypsin works to cleave peptide chains at the carboxyl site of amino acids. Its role is to hydrolyze proteins. More specifically, trypsin uses the histidine residue as a base to activate serine protease making it a better nucleophile. The histidine then acts as an acid which donates the proton from the nitrogen to the peptide leaving group. This information came from the paper by Radisky,Evette S., Lee, Justin M., Karen Lu, Chia-Jung and Koshland, Jr. Daniel E.You may include any references to papers as in: the use of JSmol in Proteopedia [1] or to the article describing Jmol [2] to the rescue.
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Structural highlights
Trypsin's selectively binds only positively charged residues such as Arg and Lys because the GLY 216 and 226 residues allows for the larger residues to fit in the pocket and are preferential because they stabilize the negative charge on the aspartic acid. The main transition state of interest of interest is the which forms when the peptide bond of the newly bound substrate complex (as a tetrahedral intermediate) is cleaved yielding a carbonyl group on SER 195. The involves the residues SER 195, HIS 57, Asp 102 and GLY 193 in which the trypsin substrate forms a stable tetrahedral intermediate upon the formation of H-bonds located in what is known as the "oxyanion hole" which is located between SER 195 and GLY 193. This preferential binding of the enzyme-substrate complex of the acyl-enzyme intermediate is responsible for much of the catalytic efficiency of serine proteases.
