Integrated solid/solution NMR assignment allows mapping dynamics and ligand binding in a 134 kDa enzyme

Abstract

Understanding enzyme function requires characterizing not only static structure but also dynamics and ligand interactions. NMR spectroscopy provides this insight at atomic resolution, yet for large proteins the difficulty of resonance assignment has largely confined such studies to systems below[~] 50 kDa, or to observing only methyl groups. Here we present an integrated magic-angle spinning (MAS) and solution NMR study of the 134 kDa tetrameric malate dehydrogenase from Ignicoccus islandicus (IiMDH), an enzyme of particular interest as an evolutionary intermediate between allosteric lactate dehydrogenases and non-allosteric malate dehydrogenases. By combining high-dimensional (up to 4D) MAS NMR experiments on sedimented protein with solution NMR, we achieved 92% backbone heavy-atom assignment and 91% assignment of all Ile-{delta}1, Leu-{delta}1/-{delta}2, Val-{gamma}1/-{gamma}2, Met-{varepsilon} and Thr-{gamma} methyl groups. Building on these assignments, MAS NMR 15N rotating-frame relaxation (R1p) measurements revealed pronounced microsecond-timescale backbone dynamics in functionally critical regions, including the catalytic loop and the mobile surface loop. Complementary methyl-axis order parameters from solution NMR identified additional flexible sites in the hydrophobic core. Chemical shift perturbation experiments upon addition of the substrate analogue oxamate, monitored via backbone 1H-15N TROSY, revealed both active-site contacts and rearrangements of helices a2F and a3G, regions implicated in allosteric signal transmission. The integrated approach demonstrated here exploits the distinct strengths of MAS and solution NMR, and provides a comprehensive view of structure, dynamics, and substrate interactions in a large oligomeric enzyme that would not be accessible by either technique alone.