Published on Web 03/23/2006
Simulating FRET from Tryptophan: Is the Rotamer Model Correct? Frank R. Beierlein,† Olaf G. Othersen,† Harald Lanig,† Siegfried Schneider,‡ and Timothy Clark*,† Contribution from the Computer-Chemie-Centrum, Friedrich-Alexander-UniVersita¨t Erlangen-Nu¨rnberg, Na¨gelsbachstrasse 25, 91052 Erlangen, Germany, and Institut fu¨r Physikalische und Theoretische Chemie, Friedrich-Alexander-UniVersita¨t Erlangen-Nu¨rnberg, Egerlandstrasse 3, 91058 Erlangen, Germany Received December 12, 2005; E-mail:
[email protected] Abstract: We present a computational model study designed to simulate the results of time-resolved fluorescence spectra of tryptophan in proteins. In such measurements, the occurrence of more than one fluorescence lifetime is generally attributed to the existence of several tryptophan rotamers and/or structural conformations of the protein structure. The protein system we chose for this initial study is the tetracycline repressor (TetR), an interesting model system for the investigation of the mechanisms of transcriptional regulation. Fluorescence resonance energy transfer (FRET) from tryptophan to tetracycline is frequently observed in complexes of the TetR with the antibiotic tetracycline. We use a combined classical/quantum mechanical approach to model the structure and the spectroscopic properties of the TetR-tetracycline complex. A classical molecular dynamics simulation provides input geometries for semiempirical quantum mechanical/molecular mechanical (QM/MM) single-point configuration interaction (CI) calculations, which are used to calculate tryptophan vertical absorption and fluorescence energies and intensities as well as relative FRET rate constants. These rate constants together with the Einstein coefficients for spontaneous emission and an assumed rate for nonradiative deactivation allow us to simulate fluorescence decay curves with and without FRET and for the entire ensemble as well as for individual rotamers. Our results indicate that the classical “rotamer model”, used to explain the multiexponential fluorescence-decay curves of timeresolved tryptophan emission spectra, can be extended to systems with FRET acceptors present in the protein matrix but that the interpretation of the fitted lifetimes is different to that usually used.
Introduction
Tetracycline (Tc) and its derivatives form a family of widely used broad-spectrum antibiotics that show bacteriostatic activity against Gram-positive and Gram-negative bacteria and other infective pathogens such as ricketsiae, mycoplasms, viruses, and protozoans. The tetracycline repressor/operator (TetR/tetO) system is a regulatory switch in the most important resistance mechanism of Gram-negative bacteria against the tetracycline class of antibiotics. When tetracycline enters the bacterial cell, it forms a chelate complex with divalent metal ions, mostly Mg2+. Under physiological conditions, the metal cation is chelated by the deprotonated 1,3-keto-enol group O11/O12of the zwitteranionic tetracycline molecule (Chart 1).1-5 † ‡
Computer-Chemie-Centrum. Institut fu¨r Physikalische und Theoretische Chemie.
(1) Saenger, W.; Orth, P.; Kisker, C.; Hillen, W.; Hinrichs, W. Angew. Chem. 2000, 112, 2122-2133. (2) Saenger, W.; Orth, P.; Kisker, C.; Hillen, W.; Hinrichs, W. Angew. Chem., Int. Ed. 2000, 39, 2042-2052. (3) Hinrichs, W.; Fenske, C. In Tetracyclines in Biology, Chemistry and Medicine; Nelson, M., Hillen, W., Greenwald, R. A., Eds.; Birkha¨user Verlag: Basel, Boston, Berlin, 2001; pp 107-123. (4) Othersen, O. G.; Beierlein, F.; Lanig, H.; Clark, T. J. Phys. Chem. B 2003, 107, 13743-13749. (5) Othersen, O. G.; Lanig, H.; Clark, T. J. Med. Chem. 2003, 46, 55715574. 5142
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Chart 1. Structure of the Physiologically Active Tetracycline-Magnesium Complex1-3 a
a The red line shows the orientation of the transition dipole of the first intense absorption in the BCD chromophore.
The expression of the protein responsible for the resistance, the tetracycline antiporter (TetA), is under tight transcriptional control of TetR. TetA is an intrinsic membrane transport protein that acts as an antiporter across the cell membrane and couples the efflux of the [TcMg]+ complex with the uptake of H+. In the absence of Tc, homodimeric TetR binds specifically to two operator sequences of the DNA (tetO) and thus prevents the expression of the genes tetA and tetR, i.e., the genes coding 10.1021/ja058414l CCC: $33.50 © 2006 American Chemical Society
Simulating FRET: Is the Rotamer Model Correct?
itself and the TetA protein. Two molecules of the [TcMg]+ complex bind to the TetR binding sites. This induces a cascade of allosteric conformational changes in the TetR protein, which result in an increased center-to-center separation of the DNArecognition helices (from 36.6 Å in the operator complex to 39.6 Å after inducer binding).1-3 These conformational changes lead to the dissociation of the TetR/DNA complex. One of the most useful spectroscopic techniques for the analysis of biopolymers in action and interaction uses fluorescence resonance energy transfer (FRET).6-13 This nonradiative energy transfer from a donor (D) to an acceptor (A) chromophore was first described by Theodor Fo¨rster in 1948.6,7 The basic requirements for FRET are sufficient overlap of the donor emission spectrum and the absorption spectrum of the acceptor, proximity of donor and acceptor (D-A separation 10-100 Å), and an almost parallel orientation of their transition dipoles. Because of its strong distance dependency, FRET is frequently used to examine molecular distances in biological macromolecules (“spectroscopic ruler”13), an important technique for the observation of molecular interactions and conformational changes (e.g., protein folding) with high spatial (1-10 nm) and time (
