This animation shows the crystal structure of porcine malate dehydrogenase (MDH) as refined by Birktoft and colleagues.  By clicking on the button below you should be able to make out secondary, tertiary and quaternary elements of structure. Can you? 

The MDH quaternary struture can be seen to be formed as a dimer of two monomers (tertiary structure) shown in green and gray. Within each monomer, the secondary structural elements of a-helices and b-pleated sheets should also be visible.  

Now cast your mind back to the practical session MDL1-3.  Did the enzyme require anything in addition to the substrate malate in order to catalyze a reaction?

There is an NAD⁺ molecule bound within each subunit.  Clicking on the button below should highlight them.

NAD⁺ can be dispaced from the enzyme by disruption of the hydrogen bonds which defines NAD⁺ as a co-factor, rather than a prosthetic group (Metabolism lectures 2 and 3).

Question:

Treatment of MDH with cyanide results in oxidation of -SH groups away from the active site and the subsequent inhibition of enzyme function.  Do you think this is likely to be competitive or non- competitive inhibition?  

What will happen to the values for K_M and Vmax for the enzyme? 

(Please try to reflect on the problem and scroll down for the solution only when you have attempted the question). 

Solution

Cyanide does not resemble the substrate and exerts its effects well away from the active site.  It is therefore a non-competitive inhibitor of MDH and as such will have no effect on K_M  (remember this value tells us about the affinity of the enzyme for substrate).  However, Vmax will be appreciably reduced as the enzymes activity is hampered by the inhibitor.

Jmol: an open-source Java viewer for chemical structures in 3D. 

http://www.jmol.org