Conformational Freedom in Tight Binding Enzymatic Transition-State Analogues

Transition-state analogues of bacterial
5′-methylthioadenosine/S-adenosylhomocysteine
nucleosidases (MTANs) disrupt quorum-sensing
pathways in Escherichia coli and Vibrio cholerae, demonstrating the potential to limit pathogenicity without placing
bacteria under intense selective pressure that leads to antibiotic
resistance. Despite the similarity of the crystal structures of E. coli MTAN (EcMTAN) and V. cholerae MTAN (VcMTAN) bound
to DADMe-Immucillin-A transition-state (TS) analogues, EcMTAN demonstrates femtomolar affinity for BuT-DADMe-Immucillin-A
(BDIA) whereas VcMTAN possesses only picomolar affinity.
Protein dynamic interactions are therefore implicated in this inhibitor
affinity difference. We conducted molecular dynamics simulations of
both EcMTAN and VcMTAN in complex
with BDIA to explore differences in protein dynamic architecture.
Simulations revealed that electrostatic and hydrophobic interactions
with BDIA are similar for both enzymes and thus unlikely to account
for the difference in inhibitor affinity. The EcMTAN–BDIA
complex reveals a greater flexibility and conformational freedom of
catalytically important atoms. We propose that conserved motions related
to the EcMTAN transition state correlate with the
increased affinity of BDIA for EcMTAN. Transition-state
analogues permitting protein motion related to formation of the transition
state are better mimics of the enzymatic transition state and can
bind more tightly than those immobilizing catalytic site dynamics.