posters 5th Asia-Pacific NMR Symposium 2013

How reliable are pseudocontact shifts induced in proteins and ligands by mobile paramagnetic tags? A modelling study (#202)

Dmitry Shishmarev 1 , Gottfried Otting 1
  1. John Curtin School of Medical Research, Australian National University, Canberra, ACT, Australia

Paramagnetic metal ions with a non-zero anisotropic component of the magnetic susceptibility tensor (Δχ tensor) induce pseudocontact shifts (PCSs) and residual dipolar couplings (RDCs) in proteins, yielding valuable restraints in structural studies. In particular, studies of ligands that bind to the protein tagged with the metal ion are of great interest in fragment-based drug design. To create easy-to-interpret PCSs, the metal ion must be attached to the protein in a rigid manner. Most existing methods for the site-specific attachment of a metal tag, however, result in tethers with residual flexibility.

We present model calculations that attempt to quantify how much the quality of the ∆χ tensor is compromised by mobility of the metal-binding tag.1 Assuming that the protein can be approximated by a sphere and the tag is attached by a single tether, the results show that a single effective ∆χ tensor can describe PCSs and RDCs of the protein spins reasonably well even in the presence of substantial tag mobility, while the quality of the PCS prediction for a ligand attached to the surface of the protein is much poorer. Nonetheless, PCS prediction for the ligand can be significantly improved by using an effective ∆χ tensor that is fitted to the PCSs of only those protein spins that are located near the ligand-binding site. PCSs arising from paramagnetic metal tags can thus be used to extract valuable structural information even if the tag is flexible.

The simulations also show that the magnitude of the effective ∆χ tensor depends on the main orientation of the metal complex relative to the protein, so that the effective ∆χ tensor can be larger or smaller than the real ∆χ tensor associated with the metal ion. Therefore, magnitude of the effective ∆χ tensor cannot be used to quantify the degree of the tag flexibility.

  1. Shishmarev D, Otting G (2013) J Biomol NMR 56:203-215