Real-time observation of ligand-induced allosteric transitions in a PDZ domain

TL;DR

This study combines transient infrared spectroscopy and molecular dynamics to observe ligand-induced allosteric transitions in the PDZ2 domain across nanoseconds to microseconds, revealing how free energy landscape remodeling underpins allostery.

Contribution

It demonstrates real-time observation of allosteric transitions in a PDZ domain using a novel ligand-switching approach coupled with spectroscopy and simulations.

Findings

Allosteric transitions occur over a broad timescale from nanoseconds to microseconds.

Subtle shifts in populations of well-defined states drive conformational changes.

Allostery involves remodeling of the protein's free energy landscape.

Abstract

While allostery is of paramount importance for protein regulation, the underlying dynamical process of ligand (un)binding at one site, resulting time evolution of the protein structure, and change of the binding affinity at a remote site is not well understood. Here the ligand-induced conformational transition in a widely studied model system of allostery, the PDZ2 domain, is investigated by transient infrared spectroscopy accompanied by molecular dynamics simulations. To this end, an azobenzene derived photoswitch is linked to a peptide ligand in a way that its binding affinity to the PDZ2 domain changes upon switching, thus initiating an allosteric transition in the PDZ2 domain protein. The subsequent response of the protein, covering four decades of time ranging from $\sim$1~ns to $\sim$10~$\mu$s, can be rationalize by a remodelling of its rugged free energy landscape, with ver subtle shifts in the populations of a small number of structurally well defined states. It is proposed that structurally and dynamically driven allostery, often discussed as limiting scenarios of allosteric communication, actually go hand-in-hand, allowing the protein to adapt its free energy landscape to incoming signals.