Three-dimensional structure of the weakly associated protein homodimer SeR13 using RDCs and paramagnetic surface mapping

Hsiau Wei Lee, Greg Wylie, Sonal Bansal, Xu Wang, Adam W. Barb, Megan A. Macnaughtan, Asli Ertekin, Gaetano T. Montelione, James H. Prestegard

Research output: Contribution to journalArticle

14 Scopus citations

Abstract

The traditional NMR-based method for determining oligomeric protein structure usually involves distinguishing and assigning intra- and intersubunit NOEs. This task becomes challenging when determining symmetric homo-dimer structures because NOE cross-peaks from a given pair of protons occur at the same position whether intra- or intersubunit in origin. While there are isotope-filtering strategies for distinguishing intra from intermolecular NOE interactions in these cases, they are laborious and often prove ineffectual in cases of weak dimers, where observation of intermolecular NOEs is rare. Here, we present an efficient procedure for weak dimer structure determination based on residual dipolar couplings (RDCs), chemical shift changes upon dilution, and paramagnetic surface perturbations. This procedure is applied to the Northeast Structural Genomics Consortium protein target, SeR13, a negatively charged Staphylococcus epidermidis dimeric protein (Kd 3.4 ± 1.4 mM) composed of 86 amino acids. A structure determination for the monomeric form using traditional NMR methods is presented, followed by a dimer structure determination using docking under orientation constraints from RDCs data, and scoring under residue pair potentials and shape-based predictions of RDCs. Validation using paramagnetic surface perturbation and chemical shift perturbation data acquired on sample dilution is also presented. The general utility of the dimer structure determination procedure and the possible relevance of SeR13 dimer formation are discussed. Published by Wiley-Blackwell.

Original languageEnglish (US)
Pages (from-to)1673-1685
Number of pages13
JournalProtein Science
Volume19
Issue number9
DOIs
StatePublished - Sep 2010

Keywords

  • Homo-oligomer
  • NMR
  • Paramagnetic relaxation
  • Residual dipolar coupling
  • Weak dimer

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology

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    Lee, H. W., Wylie, G., Bansal, S., Wang, X., Barb, A. W., Macnaughtan, M. A., Ertekin, A., Montelione, G. T., & Prestegard, J. H. (2010). Three-dimensional structure of the weakly associated protein homodimer SeR13 using RDCs and paramagnetic surface mapping. Protein Science, 19(9), 1673-1685. https://doi.org/10.1002/pro.447