title: Aromatic Ring Currents at a Protein Surface: Use of (1)H-NMR Chemical Shifts to Refine the Structure of a Naked β Sheet.
abstract: Abstract   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 Cys(4) Zn(2+)-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.
authors.affiliation: a      Departments of Chemistry and Biochemistry & Molecular Biology, Center for Molecular Oncology, 924 E. 57th Street   ,  The University of Chicago   ,    Chicago   ,    IL   ,    60637-5419.
authors.forename: B
authors.initials: B
authors.lastname: Wang
authors.forename: A S
authors.initials: AS
authors.lastname: Stern
authors.forename: M A
authors.initials: MA
authors.lastname: Weiss
mesh_terms: D000595:Amino Acid Sequence; D001665:Binding Sites; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D008969:Molecular Sequence Data; D017433:Protein Structure, Secondary