Molecular dynamics study of chemically engineered green fluorescent protein mutants: Comparison of intramolecular fluorescence resonance energy transfer rate

Felicity L. Mitchell, Filipp Frank, Gabriel E. Marks, Miho Suzuki, Kenneth T. Douglas, Richard A. Bryce

    Research output: Contribution to journalArticlepeer-review

    Abstract

    Because of its unusual spectroscopic properties, green fluorescent protein (GFP) has become a useful tool in molecular genetics, biochemistry and cell biology. Here, we computationally characterize the behavior of two GFP constructs, designed as bioprobes for enzymatic triggering using intramolecular fluorescence resonance energy transfer (FRET). These constructs differ in the location of an intramolecular FRET partner, an attached chemical chromophore (either near an N-terminal or C-terminal site). We apply the temperature replica exchange molecular dynamics method to the two flexible constructs in conjunction with a generalized Born implicit solvent model. The calculated rate of FRET was derived from the interchromophore distance, R, and orientational factor, k 2. In agreement with experiment, the construct with the C-terminally attached dye was predicted to have higher energy transfer rate than observed for the N-terminal construct. The molecular basis for this observation is discussed. In addition, we find that the orientational factor, k 2, deviates from the commonly assumed value, the implications of which are also considered. © 2009 American Chemical Society.
    Original languageEnglish
    Pages (from-to)28-39
    Number of pages11
    JournalProteins: Structure, Function and Bioinformatics
    Volume75
    Issue number1
    DOIs
    Publication statusPublished - Apr 2009

    Keywords

    • FRET
    • GFP
    • Replica exchange molecular dynamics

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