Asymmetric Behavior of Thymidylate Synthase Dimer Subunits in Denaturating Solvent Observed with Molecular Dynamics

Filip Leonarski,Andrzej Leś,Monika Świniarska

doi:10.1155/2015/389018

Abstract

A molecular dynamics simulations of the thymidylate synthase denaturation in chaotrope solvents (urea, guanidinium hydrochloride) were performed on 600 ns timescale. It appeared that this dimeric enzyme undergoes partial unfolding asymmetrically. It was shown also that urea is a better denaturant in the MD condition, as compared to guanidinium chloride. The unfolding occurs first at the external helices (AA 88-118) and follows by the AA 188-200 region. The present results correspond to the suggested in the literature activity of thymidylate synthase through a half-the-site mechanism.

Highlights

The thymidylate synthase enzyme has been studied experimentally for a long time due to its unique role as an agent catalyzing reductive methylation of dUMP using 5,10methylenetetrahydrofolate as a cofactor [1]
General observation from Root Mean Square Deviation (RMSD) measurements (Figure 1) is that the protein in water remains stable, so it can be taken as a reference for chaotrope simulations
In this work we have shown that denaturation of a relatively large protein, like thymidylate synthase, in adverse solvent conditions, might be observed in molecular dynamics simulations on hundreds of nanosecond timescales (0.5 μs)

Summary

Introduction

The thymidylate synthase enzyme has been studied experimentally for a long time due to its unique role as an agent catalyzing reductive methylation of dUMP using 5,10methylenetetrahydrofolate as a cofactor [1]. A distinctive feature of thymidylate synthase is that it is the sole de novo source of thymidylate in a cell, which makes it the target protein in various types of chemotherapies [2,3,4]. Thymidylate synthase (TS) is a dimeric enzyme. There is an interesting feature of TS. Two structurally equivalent active sites of TS display apparent functional nonequivalence suggesting TS to be a half-the-sites activity enzyme [5]. The principle of half-the-site reactivity was established by Levitzki and coworkers [6] summarizing the discoveries in the late

Methods

Results

Conclusion