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Theoretical study on bioluminescence mechanism of firefly luciferase-oxyluciferin system

Title
Theoretical study on bioluminescence mechanism of firefly luciferase-oxyluciferin system
Authors
송창익
Date Issued
2011
Publisher
포항공과대학교
Abstract
The main purpose of the study is to elucidate the underlying mechanism of firefly bioluminescence. The results will be helpful in broadening our understanding on general aspects of bioluminescence. In general, a methodology which can describe the excited state dynamics more efficiently and reliably will be developed. That approach can possibly be adopted to wider range of luminescent systems where the excited state consideration is natural and essential. First, construction of force field parameters of the oxyluciferin molecule on its electronic ground and excited states is presented. Several new approaches are introduced for more reliable parameterization: argon-scanning, Hessian matching, and constrained-group parameterization. The Ar-scanning approach is for fitting Lennard-Jones parameters so that the constructed force field can mimic the changes in ab initio energy of oxyluciferin-argon pair at various argon positions. The Hessian matching procedure is to closely reproduce the second derivative matrix of the bonded interaction terms of the force field functions, in comparison with the quantum chemically obtained results. The constrained-group algorithm is applied for both of these approaches to enable an automated atom-type-based parameterization. For complete description of the force field of the oxyluciferin molecule, we have also adopted the second order perturbatively corrected one-particle density matrices to obtain the atomic partial charges within the conventional framework of the restrained electrostatic potential fit. With the availability of the full force field parameter sets, the differences in condensed-phase dynamics on the two states can be investigated. As a simple demonstration, molecular dynamics simulations of aqueous oxyluciferin solution have been performed. The surrounding water structures for the two cases are analyzed by inspecting both the static solvent distribution functions as well as time variation of solvent-solute interaction. The contributions of charge-charge and dispersive interactions toward the solvation dynamics are also discussed. Second, dynamics of the firefly luciferase-oxyluciferin complex both in its electronically ground and excited states are studied using various theoretical approaches. By mimicking the physiological conditions with realistic models of the chromophore oxyluciferin, the enzyme luciferase, and solvating water molecules, and by performing real time simulations with molecular dynamics technique on the model surfaces, we reveal that the local chromophore-surrounding interaction patterns differ rather severely in the two states. Due to the protein presence, the solvation dynamics of water around the chromophore is also peculiar and shows widely different time scales on the two terminal oxygen atoms. In addition, simulations of the emission with the quantum-mechanics/molecular-mechanics (QM/MM) approach show a close relationship between the emission color variation and the environmental dynamics, mostly through electrostatic effects from the chromophore-surrounding interaction. We also discuss the importance of considering time scales of the luminescence and the dynamics of the interaction.
URI
http://postech.dcollection.net/jsp/common/DcLoOrgPer.jsp?sItemId=000001094020
http://oasis.postech.ac.kr/handle/2014.oak/1174
Article Type
Thesis
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