Computation of enzyme-substrate specificity. 1981

D F DeTar

The present study reports the development of a new procedure for teh theoretical computation of enzyme-substrate specificities. The immediate goal has been to identify experimental data with which computations may be effectively compared, examine the underlying theoretical principles, and demonstrate feasibility. The experimental systems treated are hydrolyses catalyzed by chymotrypsin of Ac-Trp-NH2, of Ac-Phe-NH2, and of the Hein-Niemann "locked" substrate derived from phenylalanine; this may be designated as Lock-HN-OCH3. For Trp and Phe, the L enantiomers are substrates while the D enantiomers are inhibitors, thus indicating differences of 7 kcal/mol or more in delta delta G (D-L). For the "locked" substrate, the D enantiomer is the better substrate and delta delta G (D-L) is -4 to -6 kcal/mol. We have used molecular mechanics to compute steric energies of models for the transition state for these hydrolyses and have been able to reproduce the experimental delta delta G values surprisingly well even with a relatively primitive model. The differences in computed steric energies are not due to any one major term but are rather the consequences of summations of a large number of small terms. The new method shows promise of developing into a useful probe for the quantitative study of biochemical systems.

UI MeSH Term Description Entries
D007700 Kinetics The rate dynamics in chemical or physical systems.
D010649 Phenylalanine An essential aromatic amino acid that is a precursor of MELANIN; DOPAMINE; noradrenalin (NOREPINEPHRINE), and THYROXINE. Endorphenyl,L-Phenylalanine,Phenylalanine, L-Isomer,L-Isomer Phenylalanine,Phenylalanine, L Isomer
D011485 Protein Binding The process in which substances, either endogenous or exogenous, bind to proteins, peptides, enzymes, protein precursors, or allied compounds. Specific protein-binding measures are often used as assays in diagnostic assessments. Plasma Protein Binding Capacity,Binding, Protein
D011487 Protein Conformation The characteristic 3-dimensional shape of a protein, including the secondary, supersecondary (motifs), tertiary (domains) and quaternary structure of the peptide chain. PROTEIN STRUCTURE, QUATERNARY describes the conformation assumed by multimeric proteins (aggregates of more than one polypeptide chain). Conformation, Protein,Conformations, Protein,Protein Conformations
D002918 Chymotrypsin A serine endopeptidase secreted by the pancreas as its zymogen, CHYMOTRYPSINOGEN and carried in the pancreatic juice to the duodenum where it is activated by TRYPSIN. It selectively cleaves aromatic amino acids on the carboxyl side. Alpha-Chymotrypsin Choay,Alphacutanée,Avazyme
D004798 Enzymes Biological molecules that possess catalytic activity. They may occur naturally or be synthetically created. Enzymes are usually proteins, however CATALYTIC RNA and CATALYTIC DNA molecules have also been identified. Biocatalyst,Enzyme,Biocatalysts
D000595 Amino Acid Sequence The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION. Protein Structure, Primary,Amino Acid Sequences,Sequence, Amino Acid,Sequences, Amino Acid,Primary Protein Structure,Primary Protein Structures,Protein Structures, Primary,Structure, Primary Protein,Structures, Primary Protein
D001665 Binding Sites The parts of a macromolecule that directly participate in its specific combination with another molecule. Combining Site,Binding Site,Combining Sites,Site, Binding,Site, Combining,Sites, Binding,Sites, Combining
D013329 Structure-Activity Relationship The relationship between the chemical structure of a compound and its biological or pharmacological activity. Compounds are often classed together because they have structural characteristics in common including shape, size, stereochemical arrangement, and distribution of functional groups. Relationship, Structure-Activity,Relationships, Structure-Activity,Structure Activity Relationship,Structure-Activity Relationships
D013379 Substrate Specificity A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts. Specificities, Substrate,Specificity, Substrate,Substrate Specificities

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