Modeling Chemical Reactions by QM/MM Calculations: The Case of the Tautomerization in Fireflies Bioluminescent Systems

Abstract

In less than half a century, the hybrid QM/MM method has become one of the most used technique to model molecules embedded in a complex environment. A well-known application of the QM/MM method is for biological systems. Nowadays, one can understand how enzymatic reactions work or compute spectroscopic properties, like the wavelength of emission. Here, we have tackled the issue of modeling chemical reactions inside proteins. We have studied a bioluminescent system, fireflies, and deciphered if a keto-enol tautomerization is possible inside the protein. The two tautomers are candidates to be the emissive molecule of the bioluminescence but no outcome has been reached. One hypothesis is to consider a possible keto-enol tautomerization to treat this issue, as it has been already observed in water. A joint approach combining extensive MD simulations as well as computation of key intermediates like TS using QM/MM calculations is presented in this publication. We also emphasize the procedure and difficulties met during this approach in order to give a guide for this kind of chemical reactions using QM/MM methods.

Exploring the Possibility of Excited State Keto‐Enolate Transformation of the Oxyluciferin‐Luciferase Complex with QM/MM Free Energy Simulations

“…Although no reference for relative stability between keto and enolate form in protein is available, these results are consistent with the ones obtained in vacuum or in DMSO . A similar trend was also obtained between phenolate‐keto and phenolate‐enol forms in protein …”

“…For example, acidic enol formation through protonation on the keto group by a lysine residue displayed a ∼60 kcal/mol of energy barrier . Keto‐enol tautomerization reaction based on a 5‐centered model including AMP and water also presented 50–80 kcal/mol of barriers depending on the adopted transition state structures . Compared to these, the 37 kcal/mol barrier that we have obtained here is much smaller.…”

“…Song and Rhee examined the possibility of forming an enol species through protonation of the keto oxygen by nearby lysine residue and concluded that the barrier is too high for both direct and water‐bridged pathways . Navizet and co‐workers modeled the 5‐center tautomerization pathway including AMP and water molecule and also concluded that the tautomerization is unlikely . A recent experimental study also supported the same conclusion that the phenolate‐keto form is the only plausible emitter .…”

Effect of Protein Conformation and AMP Protonation State on Fireflies’ Bioluminescent Emission

“…QM/MM calculations have been performed using a QM/MM coupling scheme [46] between Gaussian09 [47] and Tinker [48]. The B3LYP functional and the 6-311G(2d,p) basis set were selected, as their suitability for this chromophore has been previously reported [25,26,49,50]. Nevertheless, a benchmark with the CAM-B3LYP and M062X functional has been done, showing similar trends (Table S1).…”

“…Regarding the active site, different amino acids close to oxyluciferin could be sensitive to pH changes, as well as AMP which lies close to oxyluciferin once it is produced in the second catalytic reaction. Moreover, different chemical forms are possible for oxyluciferin, interconverted by tautomerization reactions or protonation/deprotonation of hydroxyl groups (phenol or enol groups) [25,26,27].…”