MD trajectories for "Kinetic barrier to enzyme inhibition is manipulated by dynamical local interactions in E. coli DHFR"

Dihydrofolate reductase (DHFR) is an important drug target and a highly studied model
protein for understanding enzyme dynamics. DHFR’s crucial role in folate synthesis renders it
an ideal candidate to understand protein function and protein evolution mechanisms. In this
study, to understand how a newly proposed DHFR inhibitor, 4’-deoxy methyl trimethoprim
(4’-DTMP), alters evolutionary trajectories, we studied interactions that lead to its superior
performance over trimethoprim (TMP). To elucidate the inhibition mechanism of 4’-DTMP,
we first confirmed, both computationally and experimentally, that the relative binding free
energy cost for the mutation of TMP and 4’-DTMP are the same, pointing to the origin of the
characteristic differences to be kinetic rather than thermodynamic. We then employed an
interaction-based analysis by focusing first on the active site, then on the whole enzyme. We
confirmed that the polar modification in 4’-DTMP induces additional local interactions with
the enzyme, particularly the M20 loop. These changes are propagated to the whole enzyme as
shifts in the hydrogen bond networks. To shed light on the allosteric interactions, we support
our analysis with network-based community analysis and show that segmentation of the loop
domain of the inhibitor-bound DHFR must be avoided by a successful inhibitor.