Dissecting the Effect of Temperature on Hyperthermophilic Pf2001 Esterase Dimerization by Molecular Dynamics

Pf2001 esterase (Pf2001) from Pyrococcus
furiosus has hyperthermophilic properties and exerts
a biocatalytic function
in a dimeric state. Crystal structures revealed that the structural
rearrangement of the cap domain is responsible for the Pf2001 dimer
formation. However, the details of the cap domain remodeling and the
effects of temperature on the dimerization process remain elusive
at the molecular level, taking into account that experimental methods
are difficult to capture the dynamic process of dimerization to some
extent. Herein, four dimer models based on the monomeric crystal structure
(PDB ID: 5G59) were constructed to investigate the conformational
transition details and temperature effects in the dimerization by
conventional molecular dynamics and accelerated molecular dynamics
simulations. Our simulation results indicate that the monomer undergoes
a conformational change into a “preparatory state” at
high temperatures, which is more favorable for its transformation
into a stable dimer. The subsequent free energy landscape analysis
further identifies four intermediate states (from separated state
to dimeric state) and discloses that a more accessible α-helix
driven by stronger hydrophobic interactions induces a rearrangement
of the cap domain, displaying a “tic-tac-toe” activation
feature that is important for stabilizing the dimer interface and
facilitating the formation of hydrophobic pockets. In addition, the
electrostatic potential surface analysis illustrates that the weaker
electrostatic repulsion (Lys and Arg) in the dimer interface at high
temperatures is also a key factor for dimer stabilization. Altogether,
our results can provide molecular-level insight into the dimer formation
process of hyperthermophilic esterase and would be useful to understand
the enzymatic specificity of α/β-hydrolase.