title: Analysis of the unfolding process of green fluorescent protein by molecular dynamics simulation.
abstract: Molecular dynamics simulation of the enforced stretching of circularly permuted green fluorescent protein (cpGFP) was performed to observe the detailed process of unfolding of beta-sheets in cpGFP and to clarify the structural change arising from the force. The simulation using the generalized Born method with original force field parameters enabled us to observe the unfolding process of the entire region of the protein and to clarify atom motion of the individual domain during the stretching. The force required for the stretching of cpGFP was estimated from the differential of the computed potential energy. A prominent rise in force appeared three times during the stretching. The amplitude and the position of these three peaks were consistent with the observation in atomic force microscopy (AFM) experiments. Further, the movements of atoms involved in each peak were shown to be closely related to the dissociation of hydrogen bonds. Additional simulations for the unfolding process of titin and spectrin also gave satisfactory interpretation of the results of previous AFM experiments. The difference in the enforced stretching process between cpGFP and wild-type GFP was further discussed through the MD simulation.
authors.affiliation: Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 263-8522, Japan.
authors.forename: Yoshihiro
authors.initials: Y
authors.lastname: Hisatomi
authors.forename: Daisuke
authors.initials: D
authors.lastname: Katagiri
authors.forename: Saburo
authors.initials: S
authors.lastname: Neya
authors.forename: Masahiko
authors.initials: M
authors.lastname: Hara
authors.forename: Tyuji
authors.initials: T
authors.lastname: Hoshino
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D003198:Computer Simulation; D049452:Green Fluorescent Proteins / Q000737:chemistry*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D017510:Protein Folding; D017433:Protein Structure, Secondary; D013816:Thermodynamics
chemical_list: D049452:Green Fluorescent Proteins