Conformational Changes in Protein Binding Processes

Abstract

Ligand-protein and protein-protein binding processes play a crucial role in biological systems. They are often associated with conformational changes that induce effects such as signal transmission or allostery. To structurally and energetically explore the interplay between induced fit, conformational selection, and allostery, we performed molecular dynamics simulations of three selected proteins.As a first system, we choose the cAMP binding process at the potassium channel MloK1. The obtained free energy differences between the two main protein conformations, an open and a closed state, reveal that the process is best described by an induced fit mechanism. We found that the binding affinity is mainly caused by the conformational change.Next, we explored the structural determinants of allostery of the export protein CRM1. This ring-shaped protein plays a crucial role in the nucleocytoplasmic transport of macromolecules. We investigated what structural features and how the binding of RanGTP and cargo proteins determine the overall conformation. We found that the enforced rearrangement of a key helix due to RanGTP binding changes the stability of the overall conformation. This induces a global conformational change, which in turn causes a local conformational change in the cargo binding site. The link between global and local conformation leads to cooperative binding.Third, we investigated the influence of ligand binding on the dimerisation of nitrate reductase. This enzyme is a key player in nitrogen fixation and binds a molybdenum containing cofactor in its active centre. We identified key motions caused by the cofactor binding, and suggest how these motions might be coupled to dimerisation.Overall our simulations underline and explain how subtle free energy changes due to ligand/protein binding can change the overall protein free energy landscape thus causing conformational changes, which are key to the protein function.