Three-dimensional model coenzyme

In our initial research on semisynthetic enzymes, we examined briefly the modification of the serine proteinase a-chymotrypsin, perhaps the best understood of the proteolytic enzymes. A logical choice as a residue for alkylation in the active site of a-chymotrypsin is His-57. However, an examination of a three-dimensional model (Lab Quip) of chymotrypsin in which coenzyme analogs were covalently attached to His-57 suggested strongly that such modifications would block completely the enzyme s active site region and that the probability of new reactions being catalyzed by the modified enzyme would be low. Another possible site of modification of chymotrypsin that could be considered was Met-192. This residue, located on the periphery of the... 

Once an enzyme or receptor has been identified, ideally it should be isolated and characterized. A three-dimensional structure is very useful and can be determined from X-ray crystallography, NMR or by some other means which may include computer-assisted molecular modeling. The mechanism for the normal catalytic activity of the enzyme should be understood. This includes knowing the natural substrates, any natural inhibitors, and any coenzyme requirements. An i n vitro assay method must be developed to quantitatively test the effectiveness of potential inhibitors. At this point molecular modeling techniques can be used in the design process. 

As discussed previously (Section IV), residues 245-280 of bovine GDH display sequence homology with the residues comprising the coenzyme binding domain of the dehydrogenases of known three-dimensional structure and sequence. Moreover, the three residues to which a functional role has been attributed are all conserved in GDH and those residues, believed to lie facing the /3-pleated sheet regions, are either identical or functionally conserved in GDH when compared to other dehydrogenases. It seems likely, therefore, that residues 245-280 of bovine GDH comprise a portion of the adenylate subsite within the active site for coenzyme [subsite II in the Cross and Fisher model 309)]. 

When designing models of coenzymes it is important to examine the structure of the corresponding enzymes. The three-dimensional structure of horse liver alcohol dehydrogenase has been resolved at 0.24 nm resolution by the group of C. I. Branden from Uppsala (280) and has been correlated to a number of physical and chemical studies in solution. The active enzyme has a molecular weight of 80,000 and is a dimer of two identical subunits. 

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