Intrinsic Dynamics and Causality in Correlated Motions Unraveled in Two Distinct Inactive States of Human β₂-Adrenergic Receptor

Abstract

The alternative inactive state of the human β 2adrenergic receptor originally exposed in molecular dynamics simulations was investigated using various analysis tools to evaluate causality between correlated residue-pair fluctuations and suggest allosteric communication pathways. A major conformational shift observed in the third intracellular loop (ICL3) displayed a novel inactive state, featuring an inaccessible G protein binding site blocked by ICL3 and an expanded orthosteric ligand binding site. Residue-based meansquare fluctuation and stiffness calculations revealed a significant mobility decrease in ICL3, which induced a mobility increase in the remaining loop regions. This indicates conformational entropy loss in one mobile region being compensated by residual intermolecular motions in other mobile regions. Moreover, the extent of significantly correlated motions decreased, and correlations that once existed between transmembrane helices shifted toward regions with increased mobility. Conditional time-delayed cross-correlation analysis identified distinct driver−follower relationship profiles. Prior to its packing, freely moving ICL3 was markedly driven by transmembrane helix-8 whereas once packed, ICL3 controlled future fluctuations of nearby helices. Moreover, two transmembrane helices, (H5 and H6), started to control future fluctuations of a remote site, the extracellular loop, ECL2. This clearly suggests that allosteric coupling between extra-and intracellular parts intensified, in agreement with the receptor's well recognized feature, which is the inverse proportionality between activity and the degree of coupling.

The nuclear receptor LRH-1 discriminates between ligands using distinct allosteric signaling circuits

“…Activating ligands induce coordinated, productive motions with residues in helix 7 and AFB, attenuating signaling to the AF-H. Tif2 communicates via coordinated motions or destabilizing fluctuations depending on ligand status. Both types of allosteric communication have been reported in other systems (30)(31)(32)(33)(34)(35).…”

The nuclear receptor LRH‐1 discriminates between ligands using distinct allosteric signaling circuits

“…Tif2 communicates via coordinated motions or destabilizing fluctuations depending on ligand status. Both types of allosteric communication have been reported in other systems (Galdadas et al, 2021; Koehler et al, 2020; Kumar et al, 2020; Schulze et al, 2016; Sogunmez & Akten, 2019; Whitford et al, 2008).…”

Distinctive communication networks in inactive states of β2‐adrenergic receptor: Mutual information and entropy transfer analysis

“…ICL3 apparently displayed a dual character in Phase I, as its remaining residues from 230 5.69 to 259 6.21 appeared as major source sites. In our previous work by Sogunmez and Akten, 19 conditional time‐delayed cross‐correlation (CTC) analysis revealed a similar dual character for ICL3. Another important entropy source that appeared in Figure 5B was observed on H8, which was also encountered in our previous CTC analysis as the region with the highest driving capability among others in Phase I.…”

“…The highest decrease in MI was observed for three major loop regions, ICL2, ECL2, and ICL3 upon shifting to Phase II. Interestingly, H8 the small appendage of H7, which is known to play a key role in receptor activation 39 and was observed to drive the future dynamics of the receptor, 19 lost its communication with the lower part of H1 in Phase II.…”

“…This was a direct consequence of multiple hydrogen bonds created between ICL3 and the receptor core. For an in‐depth investigation of the distinctive character of the receptor's dynamics, a time‐delayed cross‐correlation analysis of atomic fluctuations was conducted to identify potential sites in driver‐follower correspondences 19 . Each inactive state displayed a unique driver‐follower relationship in addition to an increased amount of coupling in the new inactive state where two transmembrane helices, H5 and H6, which are key sites for communication pathway, started to control ECL2 at a remote site of the receptor.…”