Characterizing Methyl-Bearing Side Chain Contacts and Dynamics Mediating Amyloid β Protofibril Interactions Using 13Cmethyl-DEST and Lifetime Line Broadening

Many details pertaining to the formation and interactions of protein aggregates associated with neurodegenerative diseases are invisible to conventional biophysical techniques. We recently introduced N-15 dark-state exchange saturation transfer (DEST) and N-15 lifetime line-broadening to study solution backbone dynamics and position-specific binding probabilities for amyloid beta (A beta) monomers in exchange with large (2-80 MDa) protofibrillar A beta aggregates. Here we use C-13(methyl) DEST and lifetime line-broadening to probe the interactions and dynamics of methyl-bearing side chains in the A beta-protofibril-bound state. We show that all methyl groups of A beta 40 populate direct-contact bound states with a very fast effective transverse relaxation rate, indicative of side-chain-mediated direct binding to the protofibril surface. The data are consistent with position-specific enhancements of C-13(methyl)-R-2(tethered) values in tethered states, providing further insights into the structural ensemble of the protofibril-bound state.