Elucidating allosteric regulations by means of computer simulations

Challenges of allosteric regulation

Protein conformational dynamics is often regulated by allosteric effectors, ligands that produce a structural change in the target in a region distant from their binding site. Allosteric regulations, although widespread in biology, are still difficult to determine both from the experimental and computational sides.

Our methodology

Our co-founder Prof. Modesto Orozco and his team from the Institute of Biomedical Research (IRB) Barcelona have combined multiscale molecular calculations, free-energy methods and coevolutionary information to investigate and quantify the allosteric interactions of adenylyl cyclase (AC) with G proteins, a classic example of allosteric regulation that has long escaped in-depth molecular comprehension.

The objective of this investigation was to efficiently explore the functional conformational landscape of AC with and without the allosteric effector bound using computational tools. To observe functional transitions at an atomistic level, coevolutionary information, multiscale molecular simulations, and free-energy methods were combined to interrogate and quantify the allosteric regulation of functional changes in protein complexes. Results indicate that AC regulation relies on a rather simple ON/OFF regulation of its functional dynamics. Binding of G proteins to AC alters the conformational free-energy landscape following a population-shift paradigm. AC populates two main conformational ensembles with all the existing experimental structures falling into just one of these ensembles. Notably, AC shifts from one ensemble to the other depending on which G protein it binds to. If an inhibitory G protein is complexed with AC, the conformational population is shifted to closed and inactive configurations. Interestingly, protein dynamics allowed to obtain the pathway of signal transduction and allosteric communication in AC, connecting several conformational communities:

Pathways of signal transduction and allosteric communication
Pathways of signal transduction and allosteric communication in AC from community network analysis. Gαs and Gαi correspond to stimulatory and inhibitory Gα proteins, respectively.

Future applications

The methodology used in this work can be applied to elucidate other allosteric regulations and therefore explain cellular processes that are not yet completely understood, which can further lead to important applications in both pharmaceutical and biotechnological industries. At Nostrum Biodiscovery we are able to apply these techniques for clients interested in protein allosteric regulation.

Probing allosteric regulations with coevolution-driven molecular simulations