AutoCAD 2014

The Photoactive Yellow Protein

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Photoactive Yellow Protein (PYP) is a small globular protein that activate negative phototaxis in purple sulphur bacterium Ectothiorhodospira halophila. The photosensitive component of PYP is a 4-hydroxycynnamic acid, also known as p-coumaric acid (pCA), chromophore covalently bound through a thioester linkage to the sole cysteine of the protein. To better understand the role of the environment in the absorption and emission properties and on the dynamics of the PYP chromophore, different experimental and theoretical studies have been addressed to reduced model chromophores.
We investigated the room temperature ground and excited state properties of different PYP modelchromophores both in vacuo and in water solution by means of QM/MM simulations. Four different molecular models of the PYP chromophore were considered: pCA-n (neutral p-coumaric acid in vacuo), pCA-a (anionic p-coumaric acid in vacuo), TMpCA-a (thio-methyl p-coumaric acid in vacuo), and TMpCA-a-sol (thio-methyl p-coumaric acid in QM/MM water solution). The absorption spectra can be calculated by averaging snapshots from ab initio MD both in vacuo and in QM/MM solution (see figure below).



                                                The calculated absorption spectra during ab initio molecular dynamics symulations of PYP
                                            chromophore models in vacuo and in solution. pCA-n/a (neutral/anionic pcoumaric acid in gas phase),
                                                             TMpCA-a (anionic thio-methyl pCA in gas phase and in solution)

In a similar manner, the absorption spectra of the full PYP protein in solution can be calculated and compared with the available experimental results. 
On the basis of these computer simulations we are investigating at the molecular level the interplay between absorption spectra, molecular geometries and solvent (or protein) environment in the Photoactive Yellow Protein and in its synthetic chromophore analogues.



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