An Ensemble-Based Protocol for the Computational Prediction of Helix–Helix Interactions in G Protein-Coupled Receptors using Coarse-Grained Molecular Dynamics

Abstract

The accurate identification of the specific points of interaction between G protein-coupled receptor (GPCR) oligomers is essential for the design of receptor ligands targeting oligomeric receptor targets. A coarse-grained molecular dynamics computer simulation approach would provide a compelling means of identifying these specific protein–protein interactions and could be applied both for known oligomers of interest and as a high-throughput screen to identify novel oligomeric targets. However, to be effective, this in silico modeling must provide accurate, precise, and reproducible information. This has been achieved recently in numerous biological systems using an ensemble-based all-atom molecular dynamics approach. In this study, we describe an equivalent methodology for ensemble-based coarse-grained simulations. We report the performance of this method when applied to four different GPCRs known to oligomerize using error analysis to determine the ensemble size and individual replica simulation time required. Our measurements of distance between residues shown to be involved in oligomerization of the fifth transmembrane domain from the adenosine A2A receptor are in very good agreement with the existing biophysical data and provide information about the nature of the contact interface that cannot be determined experimentally. Calculations of distance between rhodopsin, CXCR4, and β1AR transmembrane domains reported to form contact points in homodimers correlate well with the corresponding measurements obtained from experimental structural data, providing an ability to predict contact interfaces computationally. Interestingly, error analysis enables identification of noninteracting regions. Our results confirm that GPCR interactions can be reliably predicted using this novel methodology.

Computational Modeling of Realistic Cell Membranes

“…Such approaches require a high-throughput approach to obtain statistically relevant results. 478,479 The ability to predict packing of TM helices has paved the way for CG modeling studies of self-assembly of larger protein complexes, in particular, protein complexes in which the interface is formed by single TM helices. 480−482 For instance, in a joint experimental/modeling effort, van den Boogaart et al 483 revealed the molecular organization of syntaxin clusters and showed that syntaxin clustering is mediated by electrostatic interactions with the strongly anionic lipid phosphatidylinositol-4,5-bisphosphate (PIP2).…”

G protein-coupled receptor-receptor interactions give integrative dynamics to intercellular communication

“…-Molecular dynamics and coarse-grained simulations are one of the most versatile and widely applied computational techniques for the study of membrane proteins (Almeida et al, 2017), as they consider the tertiary structure of the studied proteins and can implement an energy landscape to estimate the molecular interactions, also accounting for the role of the lipid microenvironment. Such methods have also been used to study of GPCR dimerization and oligomerization (Fanelli et al, 2013;Jonas et al, 2015;Altwaijri et al, 2017). Examples include the study of rhodopsin dimer (Filizola et al, 2006) and simulations of vasopressin receptor oligomerization (Witt et al, 2008) and of the mGluR 2 -5-HT 2A heterodimeric complex (Bruno et al, 2009).…”

“…Examples include the study of rhodopsin dimer (Filizola et al, 2006) and simulations of vasopressin receptor oligomerization (Witt et al, 2008) and of the mGluR 2 -5-HT 2A heterodimeric complex (Bruno et al, 2009). A structural characterization of the human A 2A adenosine receptor homodimer was very recently provided (Altwaijri et al, 2017) using a new coarse-grained approach to molecular dynamics simulations, specifically developed for identifying helix-helix interactions in GPCR.…”

Hit-to-lead and lead optimization binding free energy calculations for G protein-coupled receptors

“…There is an urgent need for approaches and tools that permit the prediction of rapid, accurate and reliable properties of systems across science as a whole. We have a longstanding interest in the development of in silico methodologies able to predict values computationally that agree with and therefore may replace experimental measurements [ 1 – 4 ]. Here, we focus our efforts on a subject of global importance in computational biomedicine: the accurate prediction of protein–small molecule binding affinities.…”