title: Fluorescent protein barrel fluctuations and oxygen diffusion pathways in mCherry.
abstract: Fluorescent proteins (FPs) are valuable tools as biochemical markers for studying cellular processes. Red fluorescent proteins (RFPs) are highly desirable for in vivo applications because they absorb and emit light in the red region of the spectrum where cellular autofluorescence is low. The naturally occurring fluorescent proteins with emission peaks in this region of the spectrum occur in dimeric or tetrameric forms. The development of mutant monomeric variants of RFPs has resulted in several novel FPs known as mFruits. Though oxygen is required for maturation of the chromophore, it is known that photobleaching of FPs is oxygen sensitive, and oxygen-free conditions result in improved photostabilities. Therefore, understanding oxygen diffusion pathways in FPs is important for both photostabilites and maturation of the chromophores. In this paper, we use molecular dynamics calculations to investigate the protein barrel fluctuations in mCherry, which is one of the most useful monomeric mFruit variant. We employ implicit ligand sampling to determine oxygen pathways from the bulk solvent into the mCherry chromophore in the interior of the protein. We also show that these pathways can be blocked or altered and barrel fluctuations can be reduced by strategic amino acid substitutions.
authors.affiliation: Department of Physics, Florida International University, Miami, Florida 33199, USA. chapagap@fiu.edu
authors.forename: Prem P
authors.initials: PP
authors.lastname: Chapagain
authors.forename: Chola K
authors.initials: CK
authors.lastname: Regmi
authors.forename: William
authors.initials: W
authors.lastname: Castillo
mesh_terms: D004058:Diffusion; D005453:Fluorescence; D008164:Luminescent Proteins / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D016297:Mutagenesis, Site-Directed; D050505:Mutant Proteins / Q000737:chemistry* / Q000378:metabolism*; D010100:Oxygen / Q000737:chemistry / Q000378:metabolism; D038761:Photobleaching; D015202:Protein Engineering; D017434:Protein Structure, Tertiary; D000097573:Red Fluorescent Protein
chemical_list: D008164:Luminescent Proteins; D050505:Mutant Proteins; D010100:Oxygen; D000097573:Red Fluorescent Protein