Understanding Enzyme-Substrate Complex and Inhibition Mechanisms in Biochemistry

1. Enzymes Part II M.F.Ullah, Ph.D ShowketH.Bhat, PhD COURSE TITLE: BIOCHEMISTRY 1 COURSE CODE: BCHT 201 PLACEMENT/YEAR/LEVEL: 2nd Year/Level 4, 1st Semester

2. The Enzyme-Substrate Complex • These reversible reaction steps represent the steps in an enzyme catalyzed reaction • The first step involves formation of an enzyme-substrate complex, E-S • E-S* is the transition state • E-P is the enzyme-product complex

3. Enzyme-Substrate Complex Details • The part of the enzyme combining with the substrate is the active site • Active sites characteristics include: • Pockets or clefts in the surface of the enzyme • R groups at active site are called catalytic groups • Shape of active site is complimentary to the shape of the substrate • The enzyme attracts and holds the enzyme using weak noncovalent interactions • Conformation of the active site determines the specificity of the enzyme

4. The Transition State and Product Formation How does the enzyme promote a faster chemical reaction? • As the substrate interacts with the enzyme, its shape changes and this new shape is less energetically stable • This transition state has features of both substrate and product and falls apart to yield product, which dissociates from the enzyme

5. Possible Types of Transition State Changes • The enzyme might put “stress” on a bond facilitating bond breakage

6. The enzyme might bring two reactants into close proximity and maintain proper orientation.

7. Inhibitors of Enzyme Activity • Chemicals can bind to enzymes and eliminate or drastically reduce catalytic activity • Classify enzyme inhibitors on the basis of reversibility and competition. • Irreversible inhibitorsbind tightly to the enzyme and thereby prevent formation of the E-S complex. • Reversible competitive inhibitorsoften structurally resemble the substrate and bind at the normal active site • Reversible noncompetitiveinhibitors usually bind at someplace other than the active site. • Binding is weak and thus, inhibition is reversible

8. Irreversible Inhibitors • react with specific type of enzyme functional group (e.g., Ser-OH, or Cys-SH, or His imidazole) on any enzyme/proteinIrreversible enzyme inhibitors bind very tightly to the enzyme • Binding of the inhibitor to one of the R groups of a amino acid in the active site • This binding may block the active site binding groups so that the enzyme-substrate complex cannot form • Alternatively, an inhibitor may interfere with the catalytic group of the active site eliminating catalysis • Irreversible inhibitors include: • Arsenic • Snake venom • Nerve gas

9. Mechanism of Nerve gas- A potent neurotoxin

10. Reversible, Competitive Inhibitors • Reversible, competitive enzyme inhibitors are also called structural analogs • Molecules that resemble the structure and charge distribution of a natural substance for an enzyme • Resemblance permits the inhibitor to occupy the enzyme active site • Once inhibitor is at the active site, no reaction can occur and the enzyme activity is inhibited • Inhibition is competitive because the inhibitor and the substrate compete for binding to the active site • Degree of inhibition depends on the relative concentrations of enzyme and inhibitor

11. Reversible, Competitive Inhibitors

12. Reversible, Noncompetitive Inhibitors • Reversible, noncompetitive enzyme inhibitors bind to R groups of amino acids or to the metal ion cofactors • This binding is weak • Enzyme activity is restored when the inhibitor dissociates from the enzyme-inhibitor complex • These inhibitors: • Do not bind to the active site • Do modify the shape of the active site once bound elsewhere in the structure