Abstract
The molecular modeling of structural forms of the green fluorescent protein (GFP) with the Ser65Thr single-site mutation was performed by the quantum mechanics/molecular mechanics (QM/MM) method. Two model systems were constructed based on the crystallographic structure from the Protein Data Bank (PDB entry code 1EMA.) The model systems differ in the initial protonation state of the side chain of the amino acid residue Glu222 near the chromophore. The atomic coordinates of the protein macromolecule corresponding to the equilibrium geometric configurations were determined by total energy minimization using the QM/MM method within the density functional theory approximation PBE0/cc-pVDZ for the quantum subsystem that consists of the chromophore, a water molecule, and the side chains of Arg96, Glu222, and Ser205, and with the parameters of the AMBER force field for the molecular mechanics subsystem. In the analysis of the results, particular attention was given to the hydrogen bond redistribution in the chromophore-containing region of the protein caused by a change in the protonation state of the chromophore. The results obtained from the model containing the initially protonated side chain of Glu222 suggest a new interpretation of the photophysical processes in the green fluorescent protein.
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Disclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.