Deuterium Exchange Mass Spectrometry as a Probe of Protein Kinase Activation. Analysis of Wild-Type and Constitutively Active Mutants of MAP Kinase Kinase-1

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Abstract
Wild-type and constitutively active mutants of human MAP kinase kinase-1 (MKK1) were analyzed by deuterium exchange mass spectrometry using a protocol that minimized loss of deuterium during analysis due to back exchange. The observed peptides accounted for 335 out of 393 residues. Not counting overlap peptides, three peptides showed decreased exchange in constitutively active compared to wild-type MKK1 and nine showed increased exchange. Backbone amides in which exchange rates decreased upon kinase activation were observed near the regulatory phosphorylation sites Ser218 and Ser222 and the adjacent β9 strand. These decreases are consistent with electrostriction or reduced solvent access due to domain closure or formation of new hydrogen or salt bonds around the catalytic cleft and within the activation lip. Increased exchange upon activation was observed within six peptides derived from helix C and the five-stranded β sheet from the N-proximal lobe of the conserved kinase domain and in one peptide located at the interface between the N- and C-proximal lobes. Two amides that underwent increased exchange were specifically localized between residues 68 and 69 in β1 and 140 and 142 in β5. These residues probably form contacts with each other on opposite sites of the β sheet as well as with helix C. These increases appeared to represent localized fluctuations, rather than rigid body rearrangements, suggesting that MKK1 activation requires enhanced flexibility within the N-proximal lobe, perhaps to accommodate ATP binding, phosphotransfer, or ADP release.