Sandbox 206: Difference between revisions

==== The Chromophore ====

Chromophores almost always arise in one of two forms: conjugated pi systems and metal complexes. In our case, the chromophore is a conjugated pi-bond system. In this type of chromophores, the electrons jump between energy levels that are extended pi orbitals, created by a series of alternating single and double bonds, often in aromatic systems.<ref>http://www.chemguide.co.uk/analysis/uvvisible/theory.html#top</ref>.   

The residues surrounding the Venus chromophore are similar to those surrounding the chromophore of EYFP. Electron density studies of Venus show an 11° angle between the planes of the chromophore and Tyr203, while the same angle measured in EYFP is 11.5–12.3°, making the plane of the Venus chromophore slightly more parallel than that of EYFP.  

This small difference may account for a minor change in the absorption spectrum of Venus rela- tive to EYFP, as seen at a pH range of 4.6–8.6 and a 50 mM NaCl concentration. Although the position of the main absorp- tion maximum remains unchanged (516 nm) in both Venus and EYFP, a smaller peak resulting from the neutral (protonated) chromophore is shifted in Venus by 20 nm producing a peak at 413 nm versus 393 nm in EYFP. The slightly more parallel orientation of the aromatic rings of Tyr66 and Tyr203 might also help improve the π-π interaction, thus reducing the excited state energy of the neutral chromophore. If this is the case, we can hypothesize that at lower pH, which is favorable to chro- mophore protonation, the angle between the rings would be smaller than 11°.