A Computational Study on GPCR Activation Mechanisms: Insights from Adrenaline Binding and G-Protein Dissociation

Abstract

GPCRs are the most prominent family of membrane proteins that serve as major targets for one-third of the drugs produced. A detailed understanding of the molecular mechanism of drug-induced activation and inhibition of GPCRs is crucial for the rational design of novel therapeutics. The binding of the neurotransmitter adrenaline to the β2-adrenergic receptor (β2AR) is known to induce a flight or fight cellular response, but much remains to be understood about binding-induced dynamical changes in β2AR and adrenaline. In Chapter 3, we examine the potential of mean force (PMF) for the unbinding of adrenaline from the orthosteric binding site of β2AR and the associated dynamics using umbrella sampling and molecular dynamics (MD) simulations. The calculated PMF reveals a global energy minimum, which corresponds to the crystal structure of β2AR-adrenaline complex, and a meta-stable state in which the adrenaline is moved slightly deeper into the binding pocket with a different orientation compared to that in the crystal structure. The orientational and conformational changes in adrenaline during the transition between these two states and the underlying driving forces of this transition are also explored. Based on clustering of MD configurations and machine learning-based statistical analyses of time series of relevant collective variables, the structures and stabilizing interactions of these two states of the β2AR-adrenaline complex are also investigated. In Chapter 4, the PMF of G-Protein dissociation, and GDP dissociation are studied. In order to study the entire GPCR activation pathway, models have been constructed for 3 different states (inactive, intermediate, and active states) of the G-Protein-β2AR complex. The results suggest that the binding of GDP to G-Protein favours G-Protein dissociation from β2AR. In summary, the findings enhance our understanding of GPCR activation and the advancement of new therapies aimed at GPCRs by offering comprehensive insights into conformational changes, energetics, and critical residues involved. The methodologies and discoveries presented in this study establish the groundwork for an automated process to explore ligand dynamics and interactions between drugs and GPCRs, thereby facilitating future research endeavors in this domain.