The relation of the X-ray B-factor to protein dynamics: insights from recent dynamic solid-state NMR data

Abstract

In addressing the potential use of B-factors derived from X-ray scattering data of proteins for the understanding the (functional) dynamics of proteins, we present a comparison of B-factors of five different proteins (SH3 domain, Crh, GB1, ubiquitin and thioredoxin) with data from recent solid-state nuclear magnetic resonance experiments reflecting true (rotational) dynamics on well-defined timescales. Apart from trivial correlations involving mobile loop regions and chain termini, we find no significant correlation of B-factors with the dynamic data on any of the investigated timescales, concluding that there is no unique and general correlation of B-factors with the internal reorientational dynamics of proteins.

Site‐Resolved Backbone and Side‐Chain Intermediate Dynamics in a Carbohydrate‐Binding Module Protein Studied by Magic‐Angle Spinning NMR Spectroscopy

“…Generally, R 2 values for all resolved residues (loops and β‐sheet) are higher compared with the values obtained for resolved β‐sheet residues alone. This result supports the conclusions stated above from previous studies48, 62 that no explicit correlation exists between order parameters and X‐ray B‐factors. We find that Cα carbons exhibit the lowest correlation (R 2 of 0.08 and 0.02 for all residues and β‐sheet residues, respectively), whereas Cβ carbons have the highest R 2 values (R 2 of 0.33 and 0.11).…”

“…It is less established that B‐factors and NMR parameters are correlated. In fact, in a recent paper by Reichert et al 62. it has been shown that for various NMR dynamic timescale measurements, extracted for a variety of proteins studied by MAS NMR spectroscopy, there is a poor correlation between B‐factor values and NMR dynamic measurements of backbone nitrogen atoms.…”

Peptide Modulation of Class I Major Histocompatibility Complex Protein Molecular Flexibility and the Implications for Immune Recognition*

“…Although B-factors are impacted by model error and lattice imperfections and report more on static disorder within the crystalline environment as opposed to motions in solution (33,34), we reasoned that an analysis of a large number of pMHC complexes would allow some of these limitations to be circumvented.…”

The G‐Protein‐Coupled Neuropeptide Y Receptor Type 2 is Highly Dynamic in Lipid Membranes as Revealed by Solid‐State NMR Spectroscopy

“…[8,14] Such conformational switching is the functionally most relevant dynamic mode of GPCRs. [10,15] A second dynamic mode involves local fluctuations in the backbone and the side chain in thermodynamic equilibrium. [10,15] These can occur as local fluctuations as well as correlated motions of entire secondary structure units.…”