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Molecular dynamics study of chemically engineered green fluorescent protein mutants: Comparison of intramolecular fluorescence resonance energy transfer rate
Author(s) -
Mitchell Felicity L.,
Frank Filipp,
Marks Gabriel E.,
Suzuki Miho,
Douglas Kenneth T.,
Bryce Richard A.
Publication year - 2009
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.22218
Subject(s) - förster resonance energy transfer , intramolecular force , fluorescence , green fluorescent protein , chromophore , chemistry , molecular dynamics , fluorescent protein , biophysics , chemical physics , photochemistry , computational chemistry , stereochemistry , biochemistry , physics , biology , quantum mechanics , gene
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, κ 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, κ 2 , deviates from the commonly assumed value, the implications of which are also considered. Proteins 2009. © 2008 Wiley‐Liss, Inc.