Similarities and Differences among Protein Dynamics Studied by Variable Temperature Nuclear Magnetic Resonance Relaxation

Understanding and
describing the dynamics of proteins is one of
the major challenges in biology. Here, we use multifield variable-temperature
NMR longitudinal relaxation (R1) measurements to determine
the hierarchical activation energies of motions of four different
proteins: two small globular proteins (GB1 and the SH3 domain of α-spectrin),
an intrinsically disordered protein (the C-terminus of the nucleoprotein
of the Sendai virus, Sendai Ntail), and an outer membrane protein
(OmpG). The activation energies map the motions occurring in the side
chains, in the backbone, and in the hydration shells of the proteins.
We were able to identify similarities and differences in the average
motions of the proteins. We find that the NMR relaxation properties
of the four proteins do share similar features. The data characterizing
average backbone motions are found to be very similar, the same for
methyl group rotations, and similar activation energies are measured.
The main observed difference occurs for the intrinsically disordered
Sendai Ntail, where we observe much lower energy of activation for
motions of protons associated with the protein–solvent interface
as compared to the others. We also observe variability between the
proteins regarding side chain 15N relaxation of lysine
residues, with a higher activation energy observed in OmpG. This hints
at strong interactions with negatively charged lipids in the bilayer
and provides a possible mechanistic clue for the “positive-inside”
rule for helical membrane proteins. Overall, these observations refine
the understanding of the similarities and differences between hierarchical
dynamics in proteins.