Differences between G-Protein-Stabilized Agonist-GPCR Complexes and their Nanobody-Stabilized Equivalents

Area of Science:

• Biochemistry
• Structural Biology
• Pharmacology

Background:

• Protein nanobodies (intracellular binding partners, IBPs) are utilized as stabilizers for G-protein-coupled receptors (GPCRs) to facilitate crystallization in active conformations.
• Understanding the structural and functional implications of using IBPs versus native G-proteins is crucial for accurate drug design.

Purpose of the Study:

• To investigate the similarities and differences between GPCR-agonist ternary complexes formed with G-proteins and those formed with IBPs using computational simulations.
• To elucidate how IBPs influence agonist binding modes within GPCR ternary complexes.

Main Methods:

• Molecular dynamics (MD) simulations were employed.
• Metadynamics enhanced sampling techniques were utilized to explore conformational landscapes.

Main Results:

• Significant differences in agonist binding modes were observed between GPCR-G-protein and GPCR-IBP ternary complexes for two out of three receptors studied.
• Intracellular binding partners (IBPs) can modulate the binding affinity and mode of agonists to GPCRs.

Conclusions:

• The use of IBPs for GPCR crystallization can alter agonist binding modes compared to native G-protein interactions.
• These IBP-induced alterations necessitate a re-evaluation of drug design strategies targeting GPCRs, considering the specific intracellular binding partner used during structural studies.