A molecular mechanics and database analysis of the structural preorganization and activation of the chromophore-containing hexapeptide fragment in green fluorescent protein

Journal of Biomolecular Structure & Dynamics
B R BranchiniM Zimmer

Abstract

We propose that heterologous posttranslational chromophore formation in green fluorescent protein (GFP) occurs because the chromophore-forming amino acid residues 65SYG67 are preorganized and activated for imidazolinone ring formation. Based on extensive molecular mechanical conformational searching of the precursor hexapeptide fragment (64FSYGVQ69), we suggest that the presence of low energy conformations characterized by short contacts (approximately 3 A) between the carbonyl carbon of Ser65 and the amide nitrogen of Gly67 accounts for the initial step in posttranslational chromophore formation. Database searches showed that the tight turn required to establish the key short contact is a unique structural motif that is rarely found, except in other FSYG tetrapeptide sequences. Additionally, ab initio calculations demonstrated that an arginine side chain can hydrogen bond to the carbonyl oxygen of Ser65, activating this group for nucleophilic attack by the nearby lone pair of the Gly67 amide nitrogen. We propose that GFP chromophore-formation is initiated by a unique combination of conformational and electronic enhancements, identified by computational methods.

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Citations

Jan 22, 1998·Current Opinion in Structural Biology·G N Phillips
Mar 24, 2016·Journal of Molecular Biology·Patricia S LanganAndrew R M Bradbury
Oct 15, 2011·The Journal of Physical Chemistry. a·Shahnawaz RafiqGurunath Ramanathan
Dec 18, 2019·Journal of the American Chemical Society·Soumit ChatterjeePeter Karuso
Nov 23, 2021·Biochemistry·Justin NwaforTanya L Schneider

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