Explicit models of motions to analyze NMR relaxation data in proteins

Nuclear Magnetic Resonance (NMR) is a tool of choice to characterize molecular motions. In biological macromolecules, pico- to nanosecond motions, in particular, can be probed by nuclear spin relaxation rates, which depend on the time fluctuations of the orientations of spin interaction frames. For the past 40 years, relaxation rates have been successfully analyzed using the Model-Free (MF) approach, which makes no assumption on the nature of motions and reports on the effective amplitude and timescale of the motions. However, obtaining a mechanistic picture of motions from this type of analysis is difficult at best, unless complemented with molecular dynamics (MD) simulations. In spite of their limited accuracy, such simulations can be used to obtain the information necessary to build explicit models of motions designed to analyze NMR relaxation data. Here, we present how to build such models, suited in particular to describe motions of methyl-bearing protein side chains and compare them with the MF approach. We show on synthetic data that explicit models of motions are more robust in the presence of rotamer jumps which dominate the relaxation in methyl groups of protein side chains. We expect this work to motivate the use of explicit models of motion to analyze MD and NMR data. Published under an exclusive license by AIP Publishing.

Automated summary

Nuclear Magnetic Resonance (NMR) is a useful tool for studying molecular motions. The Model-Free (MF) approach has been widely used to analyze NMR relaxation rates, but complementing it with molecular dynamics (MD) simulations is necessary to obtain a mechanistic understanding of the motions. This paper demonstrates how to build explicit models of methyl-bearing protein side chain motions and compares them with the MF approach.