Molecular Dynamics Simulations Reveal Complex Structural Transitions in G Protein-Coupled Receptors

Core Concepts

Multiple walker supervised molecular dynamics (mwSuMD) can efficiently simulate complex structural transitions in G protein-coupled receptors, including ligand binding, receptor activation, G protein coupling, and receptor heterodimerization.

Abstract

The content describes the development and application of a novel computational method, multiple walker supervised molecular dynamics (mwSuMD), to study complex structural transitions in G protein-coupled receptors (GPCRs).
The key highlights and insights are:

mwSuMD was validated on the dynamic docking and unbinding of the vasopressin peptide to its receptor V2R, showing improved performance compared to the original SuMD method, especially with shorter time windows.

mwSuMD was able to simulate the binding of the stimulatory G protein (Gs) to the β2-adrenergic receptor (β2AR) and the inhibitory G protein (Gi) to the adenosine A1 receptor (A1R), capturing key interactions not observed in experimental structures.

mwSuMD simulated the complete activation process of the glucagon-like peptide-1 receptor (GLP-1R), from the binding of the small molecule agonist PF06882961 to the receptor, the conformational transition to the active state, and the subsequent binding and activation of the Gs protein, including the GDP release.

mwSuMD was used to model the heterodimerization between the adenosine A2A receptor (A2AR) and the dopamine D2 receptor (D2R), and the binding of the heterobivalent ligand compound 26 to the preformed heterodimer.

The results demonstrate that mwSuMD can efficiently address complex GPCR structural transitions, including ligand binding, receptor activation, G protein coupling, and receptor heterodimerization, without the need for energetic biases, providing valuable insights into GPCR pharmacology and function.

Stats

The RMSD of AVP Cα atoms to the cryo-EM structure 7DW9 was 3.80 ± 0.52 Å during a classic (unsupervised) equilibrium MD simulation of the X-ray AVP:V2R complex.
The minimum RMSD of AVP to the cryo-EM structure 7DW9 obtained with mwSuMD was 3.85 Å.
The RMSD of Gsα to the experimental Gs:β2AR complex (PDB 3NS6) reached values close to 5 Å during the mwSuMD simulations.
The RMSD of Giα (residues 243-355) to the A1R experimental complex (PDB 6D9H) reached 4.82 Å during the mwSuMD simulation, while a 1000-ns classic MD simulation did not produce a productive engagement.

Quotes

"mwSuMD can address, without or with limited energetic bias, complex binding processes such as G protein selectivity and homo- and heterodimerization that are intrinsically linked to the dynamics of the protein and out of reach of classic MD."
"Remarkably, the dissociation of AVP from V2R was simulated much more rapidly by mwSuMD than by SuMD, suggesting it is an efficient tool for studying the dissociation of ligands from GPCRs."
"To our knowledge, this is the first time the whole sequence of events leading from an inactive GPCR to the GDP release is simulated. Remarkably, this was obtained without biasing the simulations with external energy."

Key Insights Distilled From

Hidden GPCR structural transitions addressed by multiple walker supervised molecular dynamics (mwSuMD)

by Deganutti,G.... at www.biorxiv.org 10-27-2022

https://www.biorxiv.org/content/10.1101/2022.10.26.513870v3

Deeper Inquiries

How could mwSuMD be further improved or combined with other computational methods to provide a more comprehensive understanding of GPCR structural dynamics and function

mwSuMD can be enhanced and complemented with other computational methods to offer a more comprehensive understanding of GPCR structural dynamics and function. One approach could involve integrating mwSuMD with enhanced sampling techniques like metadynamics or Markov State Models (MSMs). By combining mwSuMD with metadynamics, the exploration of complex energy landscapes and rare events in GPCR dynamics could be further accelerated. Metadynamics introduces an energy potential to overcome barriers, allowing for the sampling of transitions that might be challenging to capture with mwSuMD alone. Additionally, coupling mwSuMD with MSMs could provide a detailed kinetic model of GPCR conformational changes, shedding light on the timescales of different structural transitions. MSMs can help in identifying key metastable states and transition pathways, offering a more detailed picture of GPCR dynamics over longer timescales.

What are the potential limitations or caveats of the mwSuMD approach, and how could they be addressed in future studies

While mwSuMD is a powerful tool for studying GPCR structural transitions, there are potential limitations and caveats that should be considered. One limitation is the reliance on predefined metrics for supervision, which may not always capture the full complexity of GPCR dynamics. To address this, future studies could explore the use of machine learning algorithms to adaptively select relevant metrics during simulations, allowing for a more dynamic and responsive approach. Another caveat is the need for accurate force fields and parameterization, especially for non-standard ligands or lipid modifications. Continual refinement and validation of force fields through comparison with experimental data can help mitigate this limitation. Additionally, the interpretation of mwSuMD results should be done cautiously, considering the inherent simplifications and approximations made in the simulations. Collaborations between computational and experimental researchers can help validate and refine the findings from mwSuMD simulations.

Given the insights provided by mwSuMD simulations, what new experimental studies could be designed to validate the computational findings and further elucidate the mechanisms of GPCR activation and signaling

The insights gained from mwSuMD simulations open up new avenues for experimental studies to validate and expand on the computational findings regarding GPCR activation and signaling. One experimental approach could involve site-directed mutagenesis studies to verify the key residues and interactions identified in the simulations. By selectively mutating these residues and observing the impact on GPCR function, researchers can confirm the role of specific amino acids in ligand binding, receptor activation, and G protein coupling. Functional assays measuring downstream signaling pathways, such as cAMP production or calcium mobilization, can provide further validation of the predicted mechanisms of GPCR activation. Moreover, structural biology techniques like cryo-electron microscopy and X-ray crystallography can be employed to capture the dynamic conformations of GPCRs and their complexes with ligands and G proteins, corroborating the structural transitions observed in mwSuMD simulations. Collaborative efforts between computational and experimental teams are essential to bridge the gap between simulation predictions and experimental observations in GPCR research.