Parameterizing Fluorescent Protein Chromophores For Molecular Dynamics Simulations
Dr. Brent Krueger
Fluorescent proteins (FPs) are important to many studies of protein function, and we plan to examine them in the future using molecular dynamics (MD) simulations. Before running MD, fluorescent protein chromophore parameters must be determined that are consistent with the latest version of the Cornell et al. force field (1995, J. Am. Chem. Soc.), ff14SB (Maier et al., 2015, JTCC.) along with the generalized AMBER force field (Wang et al., 2004, J. Comput Chem.). Parameterization was carried out using quantum mechanical calculations to determine the optimized geometry and electrostatic potential of each chromophore. The restrained electrostatic potential (RESP) charge fitting procedure was used to derive atomic charges. All other parameters (Lennard-Jones, Bond length, Bond Angle, Dihedral Angles) were assigned by analogy to pre-existing force field parameters. Complete MD parameters are presented for the chromophores of six common FPs: EGFP, mCherry, DsRed, EBFP, EYFP, and ECFP.
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