M. Cascella, C. Micheletti, U. Rothlisberger and P. Carloni
Evolutionarily Conserved Functional Mechanics across Pepsin-like
and Retroviral Aspartic Proteases fluctuations on enzymatic activity
J. Am. Chem. Soc. 127
3734-3742 (2005)
Link to online article.
ABSTRACT
The biological function of the aspartic protease from
HIV-1 has recently been related to the conformational flexibility of
its structural scaffold. Here, we use a multistep strategy to
investigate whether the same mechanism affects the functionality in
the pepsin-like fold. (i) We identify the set of conserved residues by
using sequence-alignment techniques. These residues cluster in three
distinct regions: near the cleavage-site cavity, in the four -sheets
cross-linking the two lobes, and in a solvent-exposed region below the
long -hairpin in the N-terminal lobe. (ii) We elucidate the role
played by the conserved residues for the enzymatic functionality of
one representative member of the fold family, the human -secretase, by
means of classical molecular dynamics (MD). The conserved regions
exhibit little overall mobility and yet are involved into the most
important modes of structural fluctuations. These modes influence the
substratecatalytic aspartates distance through a relative rotation of
the N- and C-terminal lobes. (iii) We investigate the effects of this
modulation by estimating the reaction free energy at different
representative substrate/ enzyme conformations. The activation free
energy is strongly affected by large-scale protein motions, similarly
to what has been observed in the HIV-1 enzyme. (iv) We extend our
findings to all other members of the two eukaryotic and retroviral
fold families by recurring to a simple, topology-based, energy
functional. This analysis reveals a sophisticated mechanism of
enzymatic activity modulation common to all aspartic proteases. We
suggest that aspartic proteases have been evolutionarily selected to
possess similar functional motions despite the observed fold
variations.