Computational Studies of Charge in G Protein Coupled Receptors

Abstract

Electrostatic interactions play significant roles in the functioning of almost all proteins, and thus have a significant impact on biological phenomena at the molecular level. At the epicenter of these interactions are amino acids that are electrically charged and thus participate in interactions involving proteins. The G protein-coupled receptors (GPCRs) comprise the largest known class of transmembrane receptors and are important in mediating an extremely diverse array of signal transduction pathways. The distribution of charged residues carrying ionizable groups was studied by creating a dataset of GPCRs using homology modeling. This dataset was used to study the distribtuion of charged residues, with particular emphasis on the transmembrane elements of GPCRs, in an attempt to correlate locations with significant amounts of charge to functional sites. Calculations of pKa were used to assess functionality of such residues; there was no conclusive evidence that these amino acids are functional. Ionizable groups localized to the transmembrane region of GPCRs were divided into two groups - high frequency residues and low frequency residues. After verifying that high frequency residues represented well known charged residues conserved throughout GPCRs, the residues having low frequencies were selected for pKa calculations. The Finite Difference Poisson Boltzmann (FDPB) and Finite Difference Debye Huckel (FD/DH) methods were used calculate shifts in pKa values for a series of residues, so that their charge state could be predicted, and each residue location was queried in literature for functional annotations. Few of the selected residues had annotations, suggesting perhaps that the scale of the dataset should be increased.

Date of Award	3 Jan 2014
Original language	English
Awarding Institution	The University of Manchester
Supervisor	James Warwicker (Supervisor) & Robin Curtis (Supervisor)