BIOC lecture 10

Active site

Has specific amino side chains projecting into itBind substrates via several weak interactionsDetermine specificity of reaction

Weak bonds are advantageous

Many weak interactions ensure specificity reversability: - several bonds are required for substrate binding - Weak bonds only form if the relevant atoms are precisely positioned- it is easy to break weak bonds

Ionic bonds

make use of charged side chains (Asp, Glu, Arg, Lys)

Hydrogen bonds - directional, stable

Side chain or backbone O and N atoms can often act as hydrogen bonds donors and acceptors

Van der Waals interactions

between any protein and substrate atoms in close proximity; weakest of the interactions

Covalent bonds

relatively rare; much stronger than the other bonds

Enzymes geometic and stereopecifity

Provided the shape of the active site is asymmetric, the enzyme can distinguish between identical groups on the substrate

Lock and key

Shape of the substrate and the conformation of the active site are complementary to one another

Induced-fit model

The enzyme undergoes a conformational change upon binding to the substrate. The shape of the active site becomes complementary to the shape of the substrate only after the substrate binds to the enzyme

How is ΔGo lowered?

1. Ground state destabilisation2. Transition state stabilisation3. Alternate reaction pathway with a different lower energy transition state1 and 2 can be achieved the same way: by having an active site that has shape/charge complementarity to the TS, not the substrate

Catalytic mechanisms (5)

1. preferential binding of the transition state2. proximity and orientation effects3. acid -base catalysis4. metal ion catalysis5. covalent catalysis

Preferential binding of the transition state

prediction: an enzyme should bind the transition state more tightly than it binds the substrateProblem: transition states are transient and cannot be isolated. need to design and synthesis an analogue

Transition state analogues as drugs - lipitor

Lipitor= powerful cholesterol-loweing drugInhibit HMG-CoA reductase (biosynthetic pathway for cholesterol)Transition state analogue inhibitors of reaction

Transition state analogues as drugs

Make ideal enzyme inhibitorsEnalapril and Aliskiren lower BPStains lower serum cholesterolProtease inhibitors are AIDS drugsJuvenile hormone esterase is a pesticide targetTamiflu is an inhibitor of influenza neuraminidase

Proximity and orientation effects

For two molecules to react the need to be close together and in the right orientation

Acid-base catalysis

Involves H+ transfer

Acid base catalysis - Histadine

particularly suitable to these types of interactionspKa is 6.5 (close to physiological pH)Depending on the environment of the active site His can donate or accept a proton

Metal ion catalysis

At least a third of enzymes require metal ions for catalytic activity. These metals provide:- substrate orientation (due to specific coordination geometrics)- Ability to act as Lewis acids (e- acceptors( to polarise H2O or other functional groups- sites for e- transfer (ox and red reactions)

Hexokinase using Mg2+ as a cofactor

Mg2+ ion balances negative charge of the transition state

Covalent catalysis

involves the formation of a reactive short lived intermediate, which is covalently attached to the enzyme