Molecular dynamics (MD) simulations have been broadly applied to a wide variety of problems in which detailed intermolecular interactions impact equilibrium structures and structural dynamics. They can also provide through sampling of relevant structural space, allowing MD simulations to connect directly to experimental observables. The utility of these simulations relies on well-developed force field parameters. In this talk, I will present a set of MD parameters developed for six commonly-used fluorescent proteins: EGFP, EBFP, ECFP, EYFP, DsRed, and mCherry. The development was conducted in a modular fashion with particular emphasis on consistency across the six chromophores, and with the goal of making it relatively easy to extend these parameters to other fluorescent protein chromophores. The parameters are consistent with the Cornell (Cornell et al., <i>J. Am. Chem. Soc.</i>, 1995, 117, 5179-5197) family of AMBER force fields including ff14SB, ff19SB, and GAFF. The parameters themselves will be described as well as our suggested procedure for developing parameters for other fluorescent proteins.

Modeling fluorescent proteins: Molecular dynamics parameters for six fluorescent protein chromophores

Fall 2022 abstracts, posters, and presentations will launch in mid-September.

ACS Fall 2022

The official archive and repository for all ACS Meetings & Expositions abstracts and select posters or presentations.