A Computationally Efficient Method to Generate Plausible Conformers for Ensemble Docking and Binding Free Energy Calculations

TL;DR

This paper introduces a fast computational method to generate plausible protein conformers for accurate docking and binding energy calculations.

Contribution

A novel mixed-resolution approach combining normal mode analysis and restrained MD simulations to generate reliable conformers for ensemble docking.

Findings

Truncated conformers of TIM showed comparable binding energies to intact structures.

100 ns simulations were sufficient for accurate binding affinity estimation.

Species-specific binding dynamics were observed at the TIM dimer interface.

Abstract

This study presents
a computationally efficient approach to generate
plausible protein conformers for ensemble docking to enable evaluations
of interactions between ligand and protein for ranking the docked
ligands according to their binding affinities. Two binding regions
of triose phosphate isomerase (TIM), its catalytic site with DHAP
( TIM), and its dimer interface
with 3PG (TIM) involving
flexible loops were investigated as case studies. The binding sites
of the apo and holo forms were modeled at the atomistic scale (high
resolution) while the remaining structure was coarse-grained (low
resolution) leading to a mixed-resolution description of the protein.
The slowest three normal modes related to the functional dynamics
of TIM were obtained using the Anisotropic Network Model and employed
to derive 36 conformers of the truncated high-resolution regions by
assessing six deformation parameters in both directions of the harmonic
motions. Through energy minimization and docking calculations in Glide,
optimal extents of deformation were identified. The docked truncated
structures were then subjected to independent molecular dynamics (MD)
simulations to confirm the interactions of the ligands in the binding
sites. To prevent the disintegration of the truncated structure, different
buffer zones and harmonic restraints were assessed to finally decide
on four distinct zones with restraints of 0, 25, 35, and 50 kcal/mol·Å2. Each conformer underwent 900 ns-long simulations across
three replicates reaching a total simulation time of 15.2 μs.
Binding free energy calculations were conducted using the MM-GBSA
approach using the first 50, first 100, first 200, and 300 ns intervals,
which pointed out that 100 ns-long simulations were sufficient to
estimate the binding affinities for TIM. Results consistently indicated
comparable binding energies between the intact and truncated TIM structures
underscoring the approach’s reliability, where the truncated
conformers also offered varying binding site geometries yielding favorable
interactions. Comparative docking at the dimer interface of and TIM further highlighted species-specific
binding dynamics, affirming the methodology’s applicability
for diverse biological questions and establishing a computationally
efficient approach to estimate binding free energy values even for
supramolecular assemblages.

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