Mass spectrometry locates local and allosteric conformational changes that occur on cofactor binding

Beveridge, Rebecca and Migas, Lukasz G. and Payne, Karl A. P. and Scrutton, Nigel S. and Leys, David and Barran, Perdita E. (2016) Mass spectrometry locates local and allosteric conformational changes that occur on cofactor binding. Nature Communications, 7 (1). pp. 1-9. ISSN 2041-1723

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    Abstract

    Fdc1 is a decarboxylase enzyme that requires the novel prenylated FMN cofactor for activity. Here, we use it as an exemplar system to show how native top-down and bottom-up mass spectrometry can measure the structural effect of cofactor binding by a protein. For Fdc1Ubix, the cofactor confers structural stability to the enzyme. IM–MS shows the holo protein to exist in four closely related conformational families, the populations of which differ in the apo form; the two smaller families are more populated in the presence of the cofactor and depopulated in its absence. These findings, supported by MD simulations, indicate a more open structure for the apo form. HDX-MS reveals that while the dominant structural changes occur proximal to the cofactor-binding site, rearrangements on cofactor binding are evident throughout the protein, predominantly attributable to allosteric conformational tightening, consistent with IM–MS data.