Tyrosine absorption spectroscopy: Backbone protonation effects on the side chain electronic properties

• Published in: Journal of computational chemistry 2018-08, Vol.39 (22), p.1747-1756
• Main Authors: Del Galdo, Sara, Mancini, Giordano, Daidone, Isabella, Zanetti Polzi, Laura, Amadei, Andrea, Barone, Vincenzo
• Format: Article
• Language: English
• Subjects: Absorption spectra; Absorption spectroscopy; Backbone; Chains; Chromophores; Computer simulation; Electronic spectra; Embedding; Environmental effects; force field refinement; Molecular dynamics; Perturbed Matrix Method; Protonation; Quantum mechanics; semiclassical computational spectroscopy; Spectrum analysis; Tyrosine; Variations
• ISSN: 0192-8651; 1096-987X
• DOI: 10.1002/jcc.25351

The UV–vis spectrum of Tyrosine and its response to different backbone protonation states have been studied by applying the Perturbed Matrix Method (PMM) in conjunction with molecular dynamics (MD) simulations. Herein, we theoretically reproduce the UV–vis absorption spectrum of aqueous solution of Tyrosine in its zwitterionic, anionic and cationic forms, as well as of aqua‐p‐Cresol (i.e., the moiety that constitutes the side chain portion of Tyrosine). To achieve a better accuracy in the MD sampling, the Tyrosine Force Field (FF) parameters were derived de novo via quantum mechanical calculations. The UV–vis absorption spectra are computed considering the occurring electronic transitions in the vertical approximation for each of the chromophore configurations sampled by the classical MD simulations, thus including the effects of the chromophore semiclassical structural fluctuations. Finally, the explicit treatment of the perturbing effect of the embedding environment permits to fully model the inhomogeneous bandwidth of the electronic spectra. Comparison between our theoretical–computational results and experimental data shows that the used model captures the essential features of the spectroscopic process, thus allowing to perform further analysis on the strict relationship between the quantum properties of the chromophore and the different embedding environments. © 2018 Wiley Periodicals, Inc. Tyrosine UV–vis spectroscopy is an important tool to study protein response to environmental changes. Thus, a deep understanding of the effects of the embedding environment on the Quantum properties of the chromophore is crucial. These effects may be described using Perturbed Matrix Method (PMM). Herein, we theoretically reproduce the absorption spectrum of aqueous solution of Tyrosine in its zwitterionic, anionic and cationic conditions by applying the PMM procedure in conjunction with molecular dynamics simulations.