Parameterization of Fluorescent Protein Chromophores

Student Author(s)

Dalton Blood

Faculty Mentor(s)

Dr. Brent Krueger

Document Type


Event Date



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 Cornell et al. force field (1995, J. Am. Chem. Soc.) and its variants (ff99, ff99SB, ff99bsc, ff14SB, etc), along with the generalized AMBER force field (GAFF; Wang et al., 2004, J. Comput Chem.) commonly used in AMBER. 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 interactions) 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.


This research was funded by NSF- RUI award #CHE-1058981, and computational resources were provided through NSF-MRI award #CHE-1039925 through the Midwest Undergraduate Computational Chemistry Consortium (MU3C).

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