title: Computational study of the absorption spectra of green fluorescent protein mutants.
abstract: In this work, we present a theoretical study of the relationship between molecular structure and the red-shift in absorption spectra of S65G and S65T green fluorescent protein (GFP) mutants. To identify the effects of the protein environment, we combined results from molecular dynamics (MD) simulations and quantum mechanics/molecular mechanics calculations to obtain structural properties, and applied time-dependent density functional theory to calculate the excitation energies. By using results from the MD simulations, we were able to provide a systematic analysis of the structural details that may effect the red-shift in the absorption spectra when taking into account temperature effects. Furthermore, a detailed study of hydrogen bonding during the MD simulations demonstrated differences between S65G and S65T, for example, regarding hydrogen bonding with Glu222. An analysis of the absorption spectra for different forms of the chromophore emphasized the dominance of the anionic forms in solution for the S65G and S65T GFP mutants.
authors.affiliation: Air Force Research Laboratory, Materials and Manufacturing Directorate, 3005 Hobson Way, Wright-Patterson Air Force Base, OH 45433-7702, USA.
authors.forename: Soumya S
authors.initials: SS
authors.lastname: Patnaik
authors.forename: Steven
authors.initials: S
authors.lastname: Trohalaki
authors.forename: Rajesh R
authors.initials: RR
authors.lastname: Naik
authors.forename: Morley O
authors.initials: MO
authors.lastname: Stone
authors.forename: Ruth
authors.initials: R
authors.lastname: Pachter
mesh_terms: D003198:Computer Simulation; D005453:Fluorescence; D049452:Green Fluorescent Proteins / Q000737:chemistry* / Q000235:genetics* / Q000378:metabolism; D006860:Hydrogen Bonding; D008958:Models, Molecular; D015394:Molecular Structure; D050505:Mutant Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D009154:Mutation / Q000235:genetics; D012694:Serine / Q000235:genetics / Q000378:metabolism; D013053:Spectrophotometry
chemical_list: D050505:Mutant Proteins; D049452:Green Fluorescent Proteins; D012694:Serine