QM/MM simulations provide insight into the mechanism of bioluminescence triggering in ctenophore photoproteins.

Reza H Sajedi,Reza Khodarahmi,Majid Taghdir,Hossein Naderi-Manesh,Ammar Mohseni,Zaiddodine Pashandi,Maryam Molakarimi,Michael W Parker,Michael A Gorman

doi:10.1371/journal.pone.0182317

Abstract

Photoproteins are responsible for light emission in a variety of marine ctenophores and coelenterates. The mechanism of light emission in both families occurs via the same reaction. However, the arrangement of amino acid residues surrounding the chromophore, and the catalytic mechanism of light emission is unknown for the ctenophore photoproteins. In this study, we used quantum mechanics/molecular mechanics (QM/MM) and site-directed mutagenesis studies to investigate the details of the catalytic mechanism in berovin, a member of the ctenophore family. In the absence of a crystal structure of the berovin-substrate complex, molecular docking was used to determine the binding mode of the protonated (2-hydroperoxy) and deprotonated (2-peroxy anion) forms of the substrate to berovin. A total of 13 mutants predicted to surround the binding site were targeted by site-directed mutagenesis which revealed their relative importance in substrate binding and catalysis. Molecular dynamics simulations and MM-PBSA (Molecular Mechanics Poisson-Boltzmann/surface area) calculations showed that electrostatic and polar solvation energy are +115.65 and -100.42 kcal/mol in the deprotonated form, respectively. QM/MM calculations and pKa analysis revealed the deprotonated form of substrate is unstable due to the generation of a dioxetane intermediate caused by nucleophilic attack of the substrate peroxy anion at its C3 position. This work also revealed that a hydrogen bonding network formed by a D158- R41-Y204 triad could be responsible for shuttling the proton from the 2- hydroperoxy group of the substrate to bulk solvent.

Highlights

Photoproteins are responsible for light emission in many marine taxa, notably in the coelenterate family
Mechanism of bioluminescence triggering in ctenophore photoproteins using quantum mechanics/molecular mechanics (QM/MM) simulations of obelin and aequorin
Since uncertainty still largely exists about the catalytic mechanism in the ctenophore family, we investigated the binding mode of coelenterazine, in protonated (2-hydroperoxy) and deprotonated (2-peroxy anion) states, to berovin through induced fit docking (IFD) and molecular dynamics (MD) simulations

Summary

Introduction

Photoproteins are responsible for light emission in many marine taxa, notably in the coelenterate family. Ca2+-regulated photoproteins contain a 2-hydroperoxy coelenterazine chromophore which is tightly but non-covalently bound to the apoprotein. Binding of Ca2+ to the EF-hands cause conformational changes resulting in oxidative decarboxylation of coelenterazine and returning the excited coelenteramide to its ground state [1]. This mechanism causes light to be emitted in the blue range of the spectrum [2, 3]

Methods

Results

Conclusion