The role of ion and proton transfer for the activation of GPCRs
Lead Research Organisation:
University of Dundee
Department Name: School of Life Sciences
Abstract
Cell surface receptors are membrane proteins that transmit ligand binding information from the extracellular side into signalling pathways within the cell, with G-protein coupled receptors (GPCRs) being their largest and most important superfamily. Due to their importance, they have evolved into the most varied and abundant class of membrane proteins, and they represent the majority of current drug targets. However, how they transmit signals across the cell membrane remains poorly understood.
In this project, we will investigate how GPCRs trigger signal transduction on the intracellular side of the cell by binding ligands on their extracellular surface. It has recently been found that Na+ ions bind to a universally conserved site in the middle of class-A GPCRs, halfway across the membrane domain [1]. Mutations around this site either severely disrupt signalling or lead to constitutive activity, independent of ligand binding, in the majority of these proteins. A major feature of the ion binding site is a titratable, conserved aspartate residue.
We will use atomistic molecular dynamics simulations on the microsecond timescale, pKa and empirical valence bond calculations to study the role of ion binding and ion movements within GPCRs for their activation and how these transitions are linked to proton transfer and protonation changes of the key residues [see, e.g., 2]. Moreover, we will investigate the role of the conserved polar residues that form a hydrated channel into the protein and line the ion binding site for human disease and signalling specificity [3]. This will be achieved by using large-scale human gene variation data and evaluating them by advanced bioinformatic sequence analysis methods.
References:
1. Katritch, Vsevolod, et al. "Allosteric sodium in class A GPCR signaling." Trends in biochemical sciences 39 (2014): 233-244.
2. Vickery, Owen N., et al. "Structural mechanisms of voltage sensing in G protein-coupled receptors." Structure 24 (2016): 997-1007.
3. Vickery, Owen N., Jan-Philipp Machtens, and Ulrich Zachariae. "Membrane potentials regulating GPCRs: insights from experiments and molecular dynamics simulations." Current opinion in pharmacology 30 (2016): 44-50.
In this project, we will investigate how GPCRs trigger signal transduction on the intracellular side of the cell by binding ligands on their extracellular surface. It has recently been found that Na+ ions bind to a universally conserved site in the middle of class-A GPCRs, halfway across the membrane domain [1]. Mutations around this site either severely disrupt signalling or lead to constitutive activity, independent of ligand binding, in the majority of these proteins. A major feature of the ion binding site is a titratable, conserved aspartate residue.
We will use atomistic molecular dynamics simulations on the microsecond timescale, pKa and empirical valence bond calculations to study the role of ion binding and ion movements within GPCRs for their activation and how these transitions are linked to proton transfer and protonation changes of the key residues [see, e.g., 2]. Moreover, we will investigate the role of the conserved polar residues that form a hydrated channel into the protein and line the ion binding site for human disease and signalling specificity [3]. This will be achieved by using large-scale human gene variation data and evaluating them by advanced bioinformatic sequence analysis methods.
References:
1. Katritch, Vsevolod, et al. "Allosteric sodium in class A GPCR signaling." Trends in biochemical sciences 39 (2014): 233-244.
2. Vickery, Owen N., et al. "Structural mechanisms of voltage sensing in G protein-coupled receptors." Structure 24 (2016): 997-1007.
3. Vickery, Owen N., Jan-Philipp Machtens, and Ulrich Zachariae. "Membrane potentials regulating GPCRs: insights from experiments and molecular dynamics simulations." Current opinion in pharmacology 30 (2016): 44-50.
Organisations
People |
ORCID iD |
| Ulrich Zachariae (Primary Supervisor) | |
| Neil Thomson (Student) |