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Fluorophore Conformation in Green Fluorescent Protein: A Quantum Mechanics/Molecular Mechanics Study

Published online by Cambridge University Press:  15 March 2011

Steven Trohalaki ,
Soumya S. Patnaik  and
Ruth Pachter
Steven Trohalaki
Affiliation:
The Anteon Corporation, 5100 Springfield Pike, Dayton, OH 45431-1231
Soumya S. Patnaik
Affiliation:
The Anteon Corporation, 5100 Springfield Pike, Dayton, OH 45431-1231
Ruth Pachter
Affiliation:
Air Force Research Laboratory, Materials & Manufacturing Directorate, Wright-Patterson Air Force Base, OH 45433-7702
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Abstract

Green Fluorescent Protein (GFP) is a widely used fluorescent marker exhibiting two excitation peaks – a strong peak at 398 nm and a second at 475 nm, with the fluorescence at ca. 510 nm. Its molecular structure consists of a β-barrel composed of 11 β-strands and a central helix containing the fluorophore. Two different forms of the fluorophore – a protonated/neutral fluorophore and a de-protonated/anionic fluorophore – are thought to be responsible for the two distinct spectroscopic states. Notably, the isolated fluorophore in solution is efficiently quenched. Conformational flexibility within the protein cavity is an implicitly important factor that governs the photochemistry of GFP. However, the literature contains accounts of studies that reach conflicting conclusions, claiming that either the fluorophore's barrier to internal rotation is negligibly small or that the protein cavity is not complementary to a planar fluorophore. In this work, we calculate the torsional potential of one of the two exocyclic bonds that connect the two rings in the fluorophore, taking into account its immediate environment by applying a quantum mechanics/molecular mechanics method, with the ultimate aim of evaluating the protein-environment effects on the fluorescence.

Type
Research Article
Information
MRS Online Proceedings Library (OPL) , Volume 826: Symposium V – Proteins as Materials , 2004 , V2.5
Copyright
Copyright © Materials Research Society 2004

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