title: Electronic circular dichroism of fluorescent proteins: a computational study.
abstract: The electronic circular dichroism (ECD) properties of the green fluorescent protein and other fluorescent proteins have been calculated with density functional theory. The influence of different embedding models on the ECD signal of the chromophore has been investigated by modeling the protein environment by the polarizable continuum model (QM/PCM), by the polarizable embedding model (PE-QM/MM), by treating the minimal environment quantum mechanically at the same footing as the chromophore (QM/QM), and by adding the remaining part of the protein by means of PCM (QM/QM/PCM). The rotatory strength is found to be more sensitive than the oscillatory strength to changes in the geometry of the chromophore and its surroundings and to the type of embedding model used. In general, explicit embedding of the surrounding protein (PE-QM/MM or QM/QM) induces an increase in the rotatory strength of the chromophore. Explicit inclusion of the whole protein through polarizable embedding is found to be an affordable embedding model that gives the correct sign of the rotatory strength for all fluorescent proteins. PCM is useful as a first approximation to protein environment effects, but as a rule seems to underestimate the rotatory strength.
authors: Faculty of Chemistry, University of Warsaw , Pasteura 1, 02-093 Warszawa, Poland.
authors: Anna
authors: A
authors: Pikulska
authors: Arnfinn Hykkerud
authors: AH
authors: Steindal
authors: Maarten T P
authors: MT
authors: Beerepoot
authors: Magdalena
authors: M
authors: Pecul
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry; D002942:Circular Dichroism; D003198:Computer Simulation; D049452:Green Fluorescent Proteins / Q000737:chemistry*; D006860:Hydrogen Bonding; D008164:Luminescent Proteins / Q000737:chemistry; D008956:Models, Chemical; D011789:Quantum Theory; D014867:Water / Q000737:chemistry
chemical_list: D001426:Bacterial Proteins; C485182:Cyan Fluorescent Protein; D008164:Luminescent Proteins; C413663:fluorescent protein 583; C054562:yellow fluorescent protein, Bacteria; D014867:Water; D049452:Green Fluorescent Proteins