Paper Citing NAMD - Abstract
Zhang, Yixuan; Deng, Lu; Kitova, Elena N.; Klassen, John S.
Dissociation of Multisubunit Protein-Ligand Complexes in the Gas Phase. Evidence for Ligand Migration
JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY, 24:1573-1583, OCT 2013
The results of collision-induced dissociation (CID) experiments performed on gaseous protonated and deprotonated ions of complexes of cholera toxin B subunit homopentamer (CTB5) with the pentasaccharide (beta-D-Galp-(1 -> 3)-beta-D-GalpNAc-(1 -> 4)[alpha-D-Neu5Ac-(2 -> 3)]-beta-D-Galp-(1 -> 4)-beta-D-Glcp (GM1)) and corresponding glycosphingolipid (beta-D-Galp-(1 -> 3)-beta-D-GalpNAc-(1 -> 4)[alpha-D-Neu5Ac-(2 -> 3)]-beta-D-Galp-(1 -> 4)-beta-D-Glcp-Cer (GM1-Cer)) ligands, and the homotetramer streptavidin (S-4) with biotin (B) and 1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine-N-(biotinyl) (Btl), are reported. The protonated (CTB5 + 5GM1)(n+) ions dissociated predominantly by the loss of a single subunit, with the concomitant migration of ligand to another subunit. The simultaneous loss of ligand and subunit was observed as a minor pathway. In contrast, the deprotonated (CTB5 + 5GM1)(n-) ions dissociated preferentially by the loss of deprotonated ligand; the loss of ligand-bound and ligand-free subunit were minor pathways. The presence of ceramide (Cer) promoted ligand migration and the loss of subunit. The main dissociation pathway for the protonated and deprotonated (S-4 + 4B)(n+/-) ions, as well as for deprotonated (S-4 + 4Btl)(n-) ions, was loss of the ligand. However, subunit loss from the (S-4 + 4B)(n+) ions was observed as a minor pathway. The (S-4 + 4Btl)(n+) ions dissociated predominantly by the loss of free and ligand-bound subunit. The charge state of the complex and the collision energy were found to have little effect on the relative contribution of the different dissociation channels. Thermally-driven ligand migration between subunits was captured in the results of molecular dynamics simulations performed on protonated (CTB5 + 5GM1)(15+) ions (with a range of charge configurations) at 800 K. Notably, the migration pathway was found to be highly dependent on the charge configuration of the ion. The main conclusion of this study is that the dissociation pathways of multisubunit protein-ligand complexes in the gas phase depend, not only on the native topology of the complex, but also on structural changes that occur upon collisional activation.
