SRLS Analysis of ¹⁵N-¹H NMR Relaxation from the Protein S100A1: Dynamic Structure, Calcium Binding, and Related...

We report on amide (N-H) NMR relaxation from the protein S100A1 analyzed with the slowly relaxing local structure (SRLS) approach. S100A1 comprises two calcium-binding "EF-hands" (helix-loop-helix motifs) connected by a linker. The dynamic structure of this protein, in both calcium-free and calcium-bound form, is described as the restricted local N-H motion coupled to isotropic protein tumbling. The restrictions are given by a rhombic potential, u (∼10 kT), the local motion by a diffusion tensor with rate constant D₂ (∼10⁹ s^-1), and principal axis tilted from the N-H bond at angle β (10-20°). This parameter combination provides a physically insightful picture of the dynamic structure of S100A1 from the N-H bond perspective. Calcium binding primarily affects the C-terminal EF-hand, among others slowing down the motion of helices III and IV approximately 10-fold. Overall, it brings about significant changes in the shape of the local potential, u, and the orientation of the local diffusion axis, β. Conformational entropy derived from u makes an unfavorable entropic contribution to the free energy of calcium binding estimated at 8.6 ± 0.5 kJ/mol. The N-terminal EF-hand undergoes moderate changes. These findings provide new insights into the calcium-binding process. The same data were analyzed previously with the extended model-free (EMF) method, which is a simple limit of SRLS. In that interpretation, the protein tumbles anisotropically. Locally, calcium binding increases ordering in the loops of S100A1 and conformational exchange (R_ex) in the helices of its N-terminal EF-hand. These are very unusual features. We show that they most likely stem from problematic data-fitting, oversimplifications inherent in EMF, and experimental imperfections. R_ex is shown to be mainly a fit parameter. By reanalyzing the experimental data with SRLS, which is largely free of these deficiencies, we obtain-as delineated above-physically-relevant structural, kinetic, geometric, and binding information.