The Effect of Protein Conformational Flexibility on the Electronic Properties of a Chromophore

Abstract

In this paper we address the question of how a protein environment can modulate the absorption spectrum of a chromophore during a molecular dynamics simulation. The effect of the protein is modeled as an external field acting on the unperturbed eigenstates of the chromophore. Using a first-principles method recently developed in our group, we calculated the perturbed electronic energies for each frame and the corresponding wavelength absorption during the simulation. We apply this method to a nanosencond timescale molecular dynamics simulation of the light-harvesting peridinin-chlorophyll-protein complex from Amphidinium carterae, where chlorophyll was selected among the chromophores of the complex for the calculation. The combination of this quantum-classical calculation with the analysis of the large amplitude motions of the protein makes it possible to point out the relationship between the conformational flexibility of the environment and the excitation wavelength of the chromophore. Results support the idea of the existence of a correlation between protein conformational flexibility and chlorophyll electronic transitions induced by light.

The role of Arginine 38 in horseradish peroxidase enzyme revisited: A computational investigation

“…Recent literature (18)(19)(20) has shown that, under native conditions, biomacromolecules should be considered as an ensemble of conformational states rather than as a single static picture, being subject to thermal fluctuations and conformational transitions which might play a key-role in fine tuning the biological activity. Similar conclusion was drawn in our previous paper (15), where it was found that after an exothermic and mechanically hindered proton transfer (from H 2 O 2 to His42), the reaction pocket at room temperature is in equilibrium between two conformations, differing essentially for the His42 position, and Cpd0 formation is therefore characterized by a large entropic contribution.…”

Electronic properties of formaldehyde in water: a theoretical study

“…This clearly limits the theoretical investigation to rather static information excluding the coupling between electronic properties and molecular motions, which can be essential for spectroscopic properties and chemical reactions. In this Letter, we perform a computational study of formaldehyde in water, using the recently introduced perturbed matrix method (PMM) [5,6] to obtain formaldehyde vertical excitation energy from molecular dynamics (MD) simulation data. This simple molecule has been extensively studied with a variety of quantum chemical procedures [7][8][9][10] and hence it is very suited for evaluating PMM accuracy, compared to other approaches.…”

Conformational and Electronic Properties of a Microperoxidase in Aqueous Solution: A Computational Study

“…The application of PMM provides rather good results for reproducing complicated observables such as the absorbtion spectrum of a highly fluctuating molecule in solution. However, unlike the heme in protein environment, [16,17] the relative ground-excited states electronic properties of MMP-5 in aqueous solution are not modulated by the conformational fluctuations of the molecular environment. This observation plausibly indicates some intrinsic differences emerging when this species is within its natural environment and when it is in aqueous solution.…”

“…[16,17] In fact when we were dealing with an enzyme, the solvent field had only a limited and indirect role concerning the perturbation of the transitions. More precisely, the solvent was normally found to play the role of modulating the fluctuation of the protein whose field is, on the other hand, mainly responsible for the perturbation.…”

“…In this respect, we have recently proposed [14,15] and successfully applied [16][17][18] a new computational approach, perturbed matrix method (PMM), particularly designed, through the combination of molecular dynamics (MD) simulations and quantum-chemical calculations, to address the electronic properties of complex molecular systems such as MMP-5. Herein, with the use of this theoretical-computational approach, we will try to address the study of aqueous MMP-5 essentially focussing on two basic questions: what does the MMP-5 structure look like, that is, the conformational features of the polypeptide chains in aqueous solution?…”