Cross-Correlated Motions in Azidolysozyme

Abstract

The changes in the local and global dynamics of azide-labelled lysozyme compared with that of the wild type protein are quantitatively assessed for all alanine residues along the polypeptide chain. Although attaching -N3 to alanine residues has been considered to be a minimally invasive change in the protein it is found that depending on the location of the alanine residue, the local and global changes in the dynamics differ. For Ala92, the change in the cross-correlated motions are minimal, whereas attaching -N3 to Ala90 leads to pronounced differences in the local and global correlations as quantified by the cross-correlation coefficients of the Cα atoms. We also demonstrate that the spectral region of the asymmetric azide stretch distinguishes between alanine attachment sites, whereas changes in the low frequency, far-infrared region are less characteristic.

Local Hydration Control and Functional Implications Through S-Nitrosylation of Proteins: Kirsten Rat Sarcoma Virus (K-RAS) and Hemoglobin (Hb)

“…The RMSD for the overall structure of cis-K-RASNO was stable throughout the trajectory at ∼1.5 Å. These findings are also consistent with previous work on the dynamics of azide (N 3 – ) attached to alanine residues in lysozyme, for which simulations on the 100 ns time scale found stable structures of the modified proteins. , It should, however, be mentioned that the focus of the present work is on the local water dynamics, which is expected to converge on the 10 ns time scale, and not on the global changes of the protein structure which may require considerably longer sampling times.…”