title: 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.
authors.affiliation: Dipartimento di Chimica, Università di Roma La Sapienza, Italy.
authors.forename: Riccardo
authors.initials: R
authors.lastname: Spezia
authors.forename: Massimiliano
authors.initials: M
authors.lastname: Aschi
authors.forename: Alfredo Di
authors.initials: AD
authors.lastname: Nola
authors.forename: Marilena Di
authors.initials: MD
authors.lastname: Valentin
authors.forename: Donatella
authors.initials: D
authors.lastname: Carbonera
authors.forename: Andrea
authors.initials: A
authors.lastname: Amadei
mesh_terms: D000818:Animals; D002338:Carotenoids / Q000737:chemistry* / Q000528:radiation effects*; D002734:Chlorophyll / Q000737:chemistry* / Q000528:radiation effects*; D000077194:Chlorophyll A; D003198:Computer Simulation; D004141:Dinoflagellida / Q000737:chemistry; D004563:Electrochemistry / Q000379:methods; D004735:Energy Transfer; D008027:Light; D045342:Light-Harvesting Protein Complexes / Q000737:chemistry / Q000528:radiation effects; D046911:Macromolecular Substances; D008958:Models, Molecular; D009038:Motion; D010777:Photochemistry / Q000379:methods; D011487:Protein Conformation; D015800:Protozoan Proteins / Q000737:chemistry* / Q000528:radiation effects*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D013223:Statistics as Topic; D013329:Structure-Activity Relationship
chemical_list: D045342:Light-Harvesting Protein Complexes; D046911:Macromolecular Substances; D015800:Protozoan Proteins; C073227:peridinin chlorophyll-a protein, Dinophyceae; D002734:Chlorophyll; D002338:Carotenoids; D000077194:Chlorophyll A