An accurate representation of protein structures, in addition to conformational dynamics and allosteric coupling, is critical to understanding protein function. Protein structures are only useful if they are accurate (i.e., close to the "true" structure) and, equally importantly, can be shown to be accurate. Unlike X-ray crystal structures, validating NMR structures has been largely an unresolved problem. Recently, we have developed a method called ANSURR (Fowler et al., Nature Communications 2020, Cell Reports 2021), which measures the accuracy of NMR protein structures by comparing the random coil index [RCI] (which relies on experimental backbone chemical shifts) against the local rigidity predicted by mathematical rigidity theory calculated from NMR structures. We will introduce the method and report on large-scale ANSURR analysis of NMR structures in the PDB. We have also developed algorithms from mathematical rigidity theory that provide a mechanical interpretation of allosteric signaling in protein structures. These algorithms predict if a perturbation of rigidity at one site of the protein can propagate across a network and, in turn, cause a change in rigidity at a second distant site, resulting in allosteric transmission. We will highlight a few applications of rigidity theory allosteric methods on G-Protein Coupled Receptors (GPCRs): how ligands trigger allosteric changes that propagate to functionally important regions; the role of beta-gamma subunit in G proteins as critical facilitators of allostery within the ternary complex with adenosine A2AR; the role of differentiated allosteric pathways in GPCR promiscuity and selectivity in A2AR in the presence of different G protein subtypes.
Fowler N., Sljoka A. and Williamson MP, A method for validating the accuracy of NMR protein structures, Nature Communications, 11, 6321, 2020.
Fowler N., Sljoka A. and Williamson M., The Accuracy of NMR structures in Protein Data Bank, Structure, 2021.
Huang S.K., Pandey A., Tran D.T., Villanueva N.L., Kitao A., Sunahara R.K., Sljoka A and Prosser R.S., Delineating the conformational landscape of the adenosine A2A receptor during G protein coupling, Cell, 2021.
Huang, S.K., Picard, LP., Rahmatullah, R.S.M. et al. Sljoka, A. and Prosser S.R. Mapping the conformational landscape of the stimulatory heterotrimeric G protein. Nat Struct Mol Biol (2023).