The Approach of Conformational Chimeras to Model the Role of Proline‐Containing Helices on GPCR Mobility: the Fertile Case of Cys‐LTR1

Abstract

The homology modeling of GPCRs has benefitted vastly from the availability of some resolved structures, which allow the generation of many reliable GPCR models. However, the dynamic behavior of such receptors has been only minimally examined in silico, although several pieces of evidence have highlighted some conformational switches that can orchestrate the activation mechanism. Among such switches, Pro-containing helices play a key role in determining bending in TM helices and thereby the width of the TM bundle. The approach proposed herein involves the generation of a set of possible models (conformational chimeras) by exhaustively combining the two main conformations (straight and bent) that a Pro-containing helix can assume. This approach was validated by generating conformational chimeras for the Cys-LTR1 receptor, which is involved in contractile and inflammatory processes. The generated chimeras were then used for docking a small set of representative ligands. The results revealed the flexibility mechanisms of Cys-LTR1, showing how the docked agonists vary their stabilizing interactions, shifting from the open to closed state, and how the examined antagonists are able to block the receptor in an open and inactive conformation, thus behaving as inverse agonists. This study emphasizes the promising potential of chimera modeling, confirms the key role of proline residues in receptor activation, and suggests that docking results can be improved by considering the often-overlooked flexibility of receptors.

Helix kinks are equally prevalent in soluble and membrane proteins

“…These two distributions are very similar. There are a similar number of helices with maximum angles <20 in the two datasets, and the two distributions peak at the same angle (10 ). A few more membrane helices than soluble helices have angles between 20 and 30 , and a few more soluble helices than membrane helices have maximum angles above 50 .…”

“…Disruptions of α‐helices (frequently referred to as kinks) are known to occur in many proteins . It has been claimed that these are much less frequent in soluble protein helices than membrane protein helices, and that those in transmembrane helices are linked to function . The majority of previous research has concentrated on kinks in transmembrane helices, but there is little comparable research into soluble helix kinks.…”

Toward an Understanding of Agonist Binding to Human Orexin-1 and Orexin-2 Receptors with G-Protein-Coupled Receptor Modeling and Site-Directed Mutagenesis

“…43−51 They offer a way to sample different functional substates of the GPCRs 40,52,53 and for the rationalization of its ligand binding and functional effects. 39,54−60 However, when using this approach, one is often unsure of the relevance of all the substates sampled. To help prioritize the analysis of the sampled substates, we developed a new protein pairwise similarity method (ProS) to compare and visualize the structural data generated in an MD run and to cluster the GPCR substructures sampled.…”

Enhancing the Reliability of GPCR Models by Accounting for Flexibility of Their Pro‐Containing Helices: the Case of the Human mAChR1 Receptor

“…In a recent study, we showed that the structural effects of the Pro‐containing transmembrane helices can be simulated by generating the so‐called conformational chimeras, namely GPCR models in which the possible conformations of the Pro‐containing helices are exhaustively combined. These chimeras were found to account for receptor flexibility and were applied to explore ligand recognition by the human Cys‐LTR1 receptor 7…”