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Conversation 11: No. 1

category image Volume: Conversation 11
Issue Number 1
May 2000
ISBN 0-940030-80-2

Aromatic Ring Currents at a Protein Surface: Use of 1H-NMR Chemical Shifts to Refine the Structure of a Naked β Sheet

The naked β sheet, a newly recognized motif of protein structure, exhibits ordered surfaces in the absence of a conventional hydrophobic core. A model is provided by an archaeal Zn ribbon homologous to eukaryotic RNA polymerase II subunit 9 (RPB9). This subunit, which regulates transcriptional start-site selection and downstream pausing, contains Zn 2+-binding motifs similar to those of general transcription factors TFIIB and TFIIS. Interestingly, distance-geometry yields two models of the archaeal Zn ribbon differing in the orientation of a conserved tyrosine side chain on the well-ordered surface of the naked β-sheet. The models are equally consistent with conventional restraints and otherwise contain indistinguishable structural features, including a tetrahedral Cys4 Zn2+-binding sites, four antiparallel β-strands, and disordered loop. Due to the change in tyrosine orientation and correlated changes in the configuration of neighboring side chains, the two models predict inequivalent patterns of aromatic ring-current shifts. The observed secondary shifts of adjoining resonances are shown to be consistent with one model but not the other. In the consistent model the surface of the β-sheet contains successive aromatic edge-to-face contacts in accord with semi-classical and ab initio potentials. We speculate that the aromatic-rich surface of the hyperthermophilic RPB9 domain contributes its thermodynamic stability and provides a nucleic-acid-binding site in the eukaryotic and archaeal transcriptional machinery. The present study demonstrates how the reduced dimensionality of a surface can lead to ambiguities in the interpretation of nuclear Overhauser enhancements. The results illustrate the utility of chemical shifts at such a surface in the cross-validation of a high-resolution solution structure.

Bing Wang1a
Alan S. Stern2
Michael A. Weissb

1Departments of Chemistry and Biochemistry & Molecular Biology
Center for Molecular Oncology
924 E. 57th Street
The University of Chicago
Chicago, IL 60637-5419
2Rowland Institute for Science
100 Edwin Land Blvd.
Cambridge, MA 02142
aPresent address:
SmithKline Beecham Pharmaceuticals
709 Swedeland Road
King of Prussia, Pennsylvania 19406
bPresent address:
Department of Biochemistry
Case-Western Reserve University
School of Medicine
Cleveland, OH 44106-4935

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