Dimensionality Reduction-Based Analysis of the Molecular Dynamics of G Protein-Coupled Receptors

G-protein coupled receptors (GPCRs) are the most abundant and varied family of transmembrane proteins. Beyond their basic biological functions, they are of relevance to pharmacology, as they are involved in a variety of human pathologies. Molecular dynamics (MD) are a reliable and effective simulation technique that allows us to investigate and examine the structure and activity that shape biomolecular energy systems. In this article, Dimensionality Reduction (DR) methods are used to explore protein trajectories by generating different data abstractions with the objective of finding the best simplified representation of such proteins. For that, these methods are applied to publicly available data from a GPCR MD database. The protein abstractions generated by several DR methods applied to the inactive, intermediate, and active conformational states of the GPRC MD simulations are compared through their entropy quantification and visual representation. In addition, experiments involve three types of MD data representation, namely the 3D position of amino acids, the distances between the helices of the molecules, and the dihedral angles representing the torsion angles of Psi and Phi of each amino acid. The reported results show how some of the DR methods capture the smooth temporal evolution of the GPCR representations and their state transitions.