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The N-terminal domain (IF2N) of bacterial translation initiation factor IF2 is connected to the conserved C-terminal domains by a flexible linker

¹ Department of Molecular Biology, University of Aarhus, Aarhus, Denmark
² Department of Chemistry and Biochemistry, Institute for Cellular and Molecular Biology, University of Texas, Austin, Texas 78712, USA

Reprint requests to: David W. Hoffman, Department of Chemistry and Biochemistry, Institute for Cellular and Molecular Biology, 1 University Station A5300, University of Texas, Austin, TX 78712-0165, USA; e-mail: dhoffman{at}mail.utexas.edu; fax: (512) 471-8696; or Hans Uffe Sperling-Petersen, Department of Molecular Biology, University of Aarhus, Gustav Wieds Vej 10c, DK8000 Aarhus C, Denmark; e-mail: husp{at}biobase.dk; fax +45 86182812.

Bacterial translation initiation factor IF2 is a multidomain protein that is an essential component of a system for ensuring that protein synthesis begins at the correct codon within a messenger RNA. Full-length IF2 from Escherichia coli and seven fragments of the protein were expressed, purified, and characterized using nuclear magnetic resonance (NMR) and circular dichroism (CD) methods. Interestingly, resonances of the 6 kD IF2N domain located at the extreme N terminus of IF2 can be clearly identified within the NMR spectra of the full-length 97-kD protein. ¹⁵N NMR relaxation rate data indicate that (1) the IF2N domain is internally well ordered and tumbles in solution in a manner that is independent of the other domains of the IF2 protein, and (2) the IF2N domain is connected to the C-terminal regions of IF2 by a flexible linker. Chemical shifts of resonances within the isolated IF2N domain do not significantly differ from those of the corresponding residues within the context of the full-length 97-kD protein, indicating that IF2N is a structurally independent unit that does not strongly interact with other regions of IF2. CD and NMR data together provide evidence that Domains I–III of IF2 have unstructured and flexible regions as well as substantial helical content; CD data indicate that the helical content of these regions decreases significantly at temperatures above 35°C. The features of structurally well-ordered N- and C-terminal domains connected by a flexible linker with significant helical content are reminiscent of another translation initiation factor, IF3.

Keywords: translation initiation; initiation factor; IF2; IF2N domain; NMR; circular dichroism; molecular dynamics

Abbreviations: CD, circular dichroism • DTT, dithiothreitol • IF, initiation factor • IF2N, IF2 N-terminal • NMR, nuclear magnetic resonance • PDB, Protein Data Bank • 1-D, one-dimensional • 2-D, two-dimensional • 3-D, three-dimensional

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