Introduction to Enzyme and Coenzyme Chemistry - E-Library Home

48 Chapter 3
Examination of protein structure in solution by nuclear magnetic resonance
(NMR) spectroscopy has revealed that there is a signiWcant amount of internal
motion in a protein, on a timescale of 1–10 ns. Such internal motion could
transmit kinetic energy from a distant part of the protein to the active site in
order to assist in catalysis. It has been proposed that dynamic Xuctations in the
protein structure are used by enzymes to organise the enzyme–substrate complex
into a reactive conformation.
The role of protein dynamics in enzyme catalysis is therefore a topic of
considerable interest. Selection of enzyme catalysts by ‘directed evolution’ has
revealed, in a number of cases, that amino acid residues distant from active sites
can have a dramatic eVect on enzyme activity. Replacement of Gly-120 to
valine in dihydrofolate reductase (see Figure 3.22) disrupts the internal motion
of a protein loop, and so interferes with the conversion of the ternary complex
to the reactive conformation, hence this step becomes partially rate-limiting,
reducing the rate of hydride transfer 500-fold. Thus, protein dynamics may
have an important role to play in enzyme catalysis.
Figure 3.22 Structure of dihydrofolate reductase (PDB Wle 1DDS), showing Gly-120 and
the loop whose internal motion is implicated in catalysis. Gly-120 and the FG loop
involving Gly-120 are shown in red; the bound inhibitor (methotrexate) at the active site is shown
in black.