Alanine

ABSTRACT The helix tilt and rotational orientation of the transmembrane segment of M2, a 97-residue protein from the Influenza A virus that forms H^sup +^-selective ion channels, have been determined by attenuated total reflection site-specific infrared dichroism using a novel labeling approach. Triple C-deuteration of the methyl group of alanine in the transmembrane domain of M2 was used, as such modification shifts the asymmetric and symmetric stretching vibrations of the methyl group to a transparent region of the infrared spectrum. Structural information can then be obtained from the dichroic ratios corresponding to these two vibrations. Two consecutive alanine residues were labeled to enhance signal intensity. The results obtained herein are entirely consistent with previous site-specific infrared dichroism and solid-state nuclear magnetic resonance experiments, validating C-deuterated alanine as an infrared structural probe that can be used in membrane proteins. This new label adds to the previously reported ^sup 13^C==^sup 18^O and C-deuterated glycine as a tool to analyze the structure of simple transmembrane segments and will also increase the feasibility of the study of polytopic membrane proteins with site-specific infrared dichroism.

INTRODUCTION

The use of structural data obtained from site-specific infrared dichroism (SSID) (Arkin et al., 1997) as a restraint for molecular dynamics protocols is an emerging method that has been applied to the study of the structure of various transmembrane helical bundles (Kukol and Arkin, 1999, 2000; Kukol et al., 1999; Torres et al., 2000). This technique relies upon the ability to selectively measure the infrared absorption of a particular mode in the peptide. The dichroic ratio obtained using polarized light can then be related to the orientation of the transition dipole moment and this in turn to the bond orientation of the particular chromophore.

This work was supported by a grant from the Biotechnology and Biological Sciences Research Council and the Wellcome Trust to ITA.

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Jaume Torres* and Isaiah T. Arkin^

*Cambridge Centre for Molecular Recognition, Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, United Kingdom; and ^The Alexander Silberman Institute of Life Sciences, Department of Biological Chemistry, The Hebrew University, Givat-Ram, Jerusalem, 91904, Israel

Address reprint requests to Isaiah T. Arkin, The Alexander Silberman Institute of Life Sciences, Department of Biological Chemistry, The Hebrew University, Givat-Ram, Jerusalem, 91904, Israel. Tel.: 972-2-658-- 4329; Fax: 972-2-658-4329; E-mail: arkin@cc.huji.ac.il.

Copyright Biophysical Society Feb 2002
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