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

Journal of Computational Chemistry
Sara Del GaldoVincenzo Barone

Abstract

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 pe...Continue Reading

References

Feb 1, 1968·Proceedings of the Society for Experimental Biology and Medicine·C C Shepard, E Ribi
Dec 1, 1993·Proteins·A AmadeiH J Berendsen
Sep 15, 1988·Physical Review A: General Physics·A D Becke
Apr 1, 2003·Journal of Computational Chemistry·Maurizio CossiVincenzo Barone
Jan 11, 2007·The Journal of Chemical Physics·Giovanni BussiMichele Parrinello
Mar 5, 2009·The Journal of Chemical Physics·Andrea AmadeiMassimiliano Aschi
Jun 28, 2014·Science·Alex Rodriguez, Alessandro Laio
Jul 16, 2014·The Journal of Physical Chemistry. B·Louise H FornanderBengt Nordén
Oct 14, 2014·Wiley Interdisciplinary Reviews. Computational Molecular Science·Kestutis AidasHans Agren
Nov 10, 2015·Physical Chemistry Chemical Physics : PCCP·Sara Del GaldoAndrea Amadei
Nov 26, 2015·Journal of Chemical Theory and Computation·Javier CerezoFabrizio Santoro
Mar 10, 2009·Journal of Chemical Theory and Computation·Vincenzo BaroneFabrizio Santoro
Sep 1, 2007·Journal of Chemical Theory and Computation·Ivo Cacelli, Giacomo Prampolini
Oct 7, 2016·Physical Chemistry Chemical Physics : PCCP·Sara Del Galdo, Andrea Amadei
Oct 21, 2016·Physical Chemistry Chemical Physics : PCCP·Massimiliano AschiAndrea Amadei
Sep 22, 2017·Journal of Chemical Theory and Computation·Oliver Carrillo-ParramonVincenzo Barone

❮ Previous
Next ❯

Citations

Sep 15, 2018·Physical Chemistry Chemical Physics : PCCP·Laura Zanetti-PolziAndrea Amadei
Aug 1, 2020·Frontiers in Chemistry·Sara Del GaldoVincenzo Barone
Mar 24, 2020·Journal of Physics. Condensed Matter : an Institute of Physics Journal·Cristina PuzzariniVincenzo Barone

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.