Atomistic Simulations of the Mechanisms of the Poorly Catalytic Mitochondrial Chaperone Trap1: Insights into the Effects of Structural Asymmetry on Reactivity

The mitochondrial
chaperone Trap1 is an ATPase protein that oversees
the correct folding of client proteins and exhibits altered activity
and/or expression levels in certain cancers. By inducing extensive
structural rearrangements, ATP cleavage is essential for Trap1 to
fulfill its task; at the same time, Trap1’s sluggish ATP turnover
represents one of the control switches through which its conformational
cycle and inter-residue cross-talk signals mediating it can be subtly
tuned. Remarkably, hydrolysis requires Trap1 to adopt a distinctive
asymmetric “closed” homodimeric conformation wherein
the ATP bound to the “buckled” protomer (Buc) is preferentially cleaved, while hydrolysis in the “straight”
protomer (Str) remains unfavored. However, molecular
links between asymmetry and Trap1’s characteristic reactivity
remain elusive, due to intrinsic mechanistic complexity and its protomers’
active site similarity. To address this issue, we herein report a
detailed computational investigation of Trap1’s potential ATPase
mechanisms. Through classical molecular dynamics (MD) simulations
we monitor how frequently ATP and nucleophilic water WatNuc can attain reactive poses within Buc and Str. Semiempirical hybrid quantum mechanical–molecular
mechanical (QM/MM) MD simulations coupled to umbrella sampling and
benchmarked with density functional theory calculations are then used
to sample reaction free energy barriers within each protomer for two
possible hydrolytic pathways. Enzyme-assisted hydrolysis, featuring
a metaphosphate-like transition state and a catalytic glutamate deprotonating WatNuc, is found to be favored in
both protomers over substrate-assisted hydrolysis. However, we also
find that WatNuc’s sequestration
by another water molecule WatTyr bound to a vicinal tyrosine is far rarer in Buc, proving
that such a rare sequestration lowers reaction barriers for the enzyme-assisted
pathway. We thus identify the (biologically significant) tyrosine
as the main mediator favoring ATP hydrolysis in Buc over Str. Our improved model for Trap1 reactivity is experimentally
and structurally consistent and should further aid in the development
of selective modulators of the protein’s activities.