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Molecular dynamics simulations of enhanced green fluorescent proteins: Effects of F64L, S65T and T203Y mutations on the ground‐state proton equilibria
Author(s) -
Nifosì R.,
Tozzini V.
Publication year - 2003
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.10335
Subject(s) - chromophore , green fluorescent protein , fluorescence , molecular dynamics , chemistry , protonation , hydrogen bond , ground state , proton , spectroscopy , fluorescence spectroscopy , molecule , photochemistry , chemical physics , computational chemistry , atomic physics , physics , ion , biochemistry , organic chemistry , quantum mechanics , gene
Molecular dynamics simulations with the Amber force field are carried out to study two mutants of the green fluorescent protein (GFP), namely EGFP (F64L/S65T) and T203Y‐EGFP (E 2 GFP). Those variants display an opposite equilibrium between the structural A and B states, associated with neutral and anionic protonation forms of the chromophore. Configurations of those two states are simulated for each variant and the energetics of their equilibrium in the two mutants is studied by evaluating the change in the relative free energy of A and B states (Δ G AB ) upon T203Y mutation. The resulting ΔΔ G AB agrees with the value inferred from absorption measurements. A comparison of the hydrogen bond network around the chromophore rationalizes the different population of state A and B in EGFP and E 2 GFP. On the basis of structural and energetic considerations, a mechanism for destabilization of the neutral chromophore in S65T mutants is proposed. Simulations of the B state of the S65T variant and of WT GFP are also performed for comparison and to test the force field parameters of the chromophore derived for the present calculations. Possible paths of proton transfer leading to nonfluorescent states of the chromophore are discussed in light of the photodynamical behavior of GFP, as revealed by fluorescence correlation spectroscopy and single‐molecule experiments. Proteins 2003;51:378–389. © 2003 Wiley‐Liss, Inc.