Molecular dynamics study of monomeric chorismate mutase shows large reduction in conformational diversity of loops upon binding of the transition state analog

Abstract

In this in silico study, we investigated the structure and dynamics of the molten globule enzyme, monomeric chorismate mutase, which catalyzes the conversion of chorismate to prephenate despite its molten globule state. The primary aim was to understand how the enzyme stabilizes the transition state of the reaction while maintaining its molten globule characteristics. Using the transition state analog (TSA) from the NMR structure (PDB code 2GTV), molecular dynamics simulations revealed multiple hydrogen bonds between three of the enzyme's helices and the TSA. Specific residues that formed stable hydrogen bonds with the TSA were identified as potential mutation targets. Furthermore, the binding of the TSA significantly reduced the entropy of the enzyme and led to the rigidification of the backbone dihedrals across all helices. The flexibility of the loop connecting helices 1 and 2, was also analyzed, showing reduced conformational diversity upon TSA binding. Structural differences between the apo and TSA-bound forms were noted, with helices 3 and 4 exhibiting altered helicity, including a kink in helix 3 and unravelling in helix 4. Despite its molten globule nature, monomeric chorismate mutase can stabilize the TSA through hydrogen bonds involving charged residues, which are essential for maintaining the helix bundle structure. This study highlights the importance of local structural dynamics and entropy changes in enzyme catalysis, offering insights into how molten globule states can support efficient enzymatic activity.