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

Riccardo Spezia ^*, Massimiliano Aschi , Alfredo Di Nola ^*, Marilena Di Valentin , Donatella Carbonera  and Andrea Amadei 

^* Dipartimento di Chimica, Università di Roma "La Sapienza", 00185 Rome, Italy; Dipartimento di Chimica, Ingegneria Chimica e Materiali, Università de l'Aquila, 67010 l'Aquila, Italy; Dipartimento di Chimica-Fisica, Università di Padova, 35131 Padua, Italy; and Dipartimento di Scienze e Tecnologie Chimiche, Università di Roma "Tor Vergata", 00133 Rome, Italy

Correspondence: Address reprint requests to Dr. A. Amadei, Tel.: +39-06-72594905; Fax: +39-0672594328; E-mail: andrea.amadei{at}uniroma2.it.

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.

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