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bioRxiv · 10.1101/2025.06.26.661669

Constant-pH simulation of the human β2 adrenergic receptor inactivation

Ballabio, F.·Capelli, R.
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Abstract

Understanding the molecular basis of pH-dependent G protein-coupled receptor (GPCR) signaling is crucial for comprehending physiological regulation and drug design. Here, we investigate the human {beta}2 adrenergic receptor ({beta}2AR), a prototypical GPCR whose function is sensitive to pH conditions. Employing extensive constant-pH molecular dynamics simulations, we provide a detailed atomistic characterization of {beta}2AR inactivation across physiologically relevant pH values (4-9). Our simulations reveal that {beta}2AR inactivation is closely linked to protonation events at critical residues, notably E2686x30 involved in the ionic lock formation. Furthermore, we find that inactivation occurs without direct sodium binding to the ion-binding pocket around residue D792x50. Instead, sodium ions predominantly interact with D1133x32, effectively blocking deeper entry toward the traditional binding site. These results challenge existing mechanistic models and highlight the necessity of accurately modeling electrostatics in GPCR simulations. Our findings underscore the potential of constant-pH methodologies to advance the understanding of GPCR dynamics, influencing both fundamental biology and therapeutic strategies.

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Ballabio, F., Capelli, R.. 2025-06-29. Constant-pH simulation of the human β2 adrenergic receptor inactivation. https://doi.org/10.1101/2025.06.26.661669

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