Dimerization energetics of the G‐protein coupled bile acid receptor TGR5 from all‐atom simulations

Abstract

We describe the first extensive energetic evaluation of GPCR dimerization on the atomistic level by means of potential of mean force (PMF) computations and implicit solvent/implicit membrane end‐point free energy calculations (MM‐PBSA approach). Free energies of association computed from the PMFs show that the formation of both the 1/8 and 4/5 interface is energetically favorable for TGR5, the first GPCR known to be activated by hydrophobic bile acids and neurosteroids. Furthermore, formation of the 1/8 interface is favored over that of the 4/5 interface. Both results are in line with our previous FRET experiments in live cells. Differences in lipid‐protein interactions are identified to contribute to the observed differences in free energies of association. A per‐residue decomposition of the MM‐PBSA effective binding energy reveals hot spot residues specific for both interfaces that form clusters. This knowledge may be used to guide the design of dimerization inhibitors or perform mutational studies to explore physiological consequences of distorted TGR5 association. Finally, we characterized the role of Y111, located in the conserved (D/E)RY motif, as a facilitator of TGR5 interactions. The types of computations performed here should be transferable to other transmembrane proteins that form dimers or higher oligomers as long as good structural models of the dimeric or oligomeric states are available. Such computations may help to overcome current restrictions due to an imperfect energetic representation of protein association at the coarse‐grained level. © 2019 Wiley Periodicals, Inc.

Recent Developments in Free Energy Calculations for Drug Discovery

“…Additionally, GPCR dimerization is also studied with the TGR5 system through PMF computations using umbrella sampling and MM-PBSA. Computational results corroborate experimental FRET experiments in revealing residue hot spots at the 1/8 interface for dimerization inhibitors to target ( Waschenbach et al, 2020 ). The mechanism of opioid pain suppression is examined through simulation of fentanyl with the Gluoeobacter violaceus ligand-gated ion channel.…”

Substrate Access Mechanism in a Novel Membrane-Bound Phospholipase A of Pseudomonas aeruginosa Concordant with Specificity and Regioselectivity

“…63−65 We probed for the convergence of our PMFs by comparing PMFs generated from increasing lengths of US simulations and found that US times of ∼300 ns are needed to yield PMF differences below chemical accuracy. 66 Finally, we validated our PMF computations by comparing the computed absolute binding free energy of DLPG to PlaF for the most preferred access mode to an estimate of the experimental binding free energy. The PMFs revealed that tail-first access through T2 is the most preferred method for DLPG and 2LMG.…”

“…Applying US along pathways identified by sMD simulations or targeted simulations , has been shown to be an effective method of computing PMF. Moreover, the choice of an appropriate reaction coordinate is essential for this approach. − We probed for the convergence of our PMFs by comparing PMFs generated from increasing lengths of US simulations and found that US times of ∼300 ns are needed to yield PMF differences below chemical accuracy . Finally, we validated our PMF computations by comparing the computed absolute binding free energy of DLPG to PlaF for the most preferred access mode to an estimate of the experimental binding free energy.…”

Substrate access mechanism in a novel membrane-bound phospholipase A of Pseudomonas aeruginosa concordant with specificity and regioselectivity

“…Moreover, the choice of an appropriate reaction coordinate is essential for this approach [63][64][65]. We probed for the convergence of our PMFs by comparing PMFs generated from increasing lengths of US simulations and found that US times of ~300 ns are needed to yield PMF differences below chemical accuracy [66]. Finally, we validated our PMF computations by comparing the computed absolute binding free energy of DLPG to PlaF for the most preferred access mode to an estimate of the experimental binding free energy.…”