Lysine side-chain dynamics derived from 13C-multiplet NMR relaxation studies on di- and tripeptides

Abstract

13C NMR relaxation data have been used to determine dipolar auto- and cross-correlation times for the di- and tripeptides GK, KG, and GKG, primarily to analyze lysine side-chain motional dynamics. In general, correlation times are largest for backbone positions and decrease on going through the lysine side chain, consistent with the idea of increased mobility at C delta and C episilon methylenes. Correlation times, however, vary with the peptide ionization state. In the zwitterionic state of GK, for example, both auto- and cross-correlation times are at their maximum values, indicating reduced internal motions probably resulting from intramolecular electrostatic interactions. Modifying the charge state increases motional fluctuations. Activation energies determined from the temperature dependence of CH rotational autocorrelation times at neutral pH are approximately equal for glycine and lysine C alpha and lysine C beta and C gamma positions (4.1 +/- 0.2 to 4.5 +/- 0.2 kcal/mol) and tend to decrease slightly for lysine C delta and C epsilon (3.8 +/- 0.2 to 4.3 +/- 0.2 kcal/mol). The sign of lysine side-chain cross-correlations could not be explained by using any available rotational model, including one parameterized for multiple internally restricted rotations and anisotropic overall tumbling. Molecular and stochastic dynamics calculations were performed to obtain insight into correlated internal rotations and coupled overall tumbling and internal motions. Relatively strong correlations were found for i,i+1 backbone and lysine side-chain internal bond rotations. Stochastic dynamics calculations were more successful at explaining experimentally observed correlation times. In the fully charged state, a preferred conformation was detected with an all-trans lysine side chain.

Motional dynamics of residues in a β‐hairpin peptide measured by 13C‐NMR relaxation

“…4) as noted for V5 and G7. Because this tendency also has been observed for motions in a lysine side chain (Mikhailov et al, 1995), it may be that positive rotational correlations of adjacent bonds is the norm, at least in some structures. Daragan and Mayo (1996b) reported that, in P-strands, c$,$ rotations are positively correlated and, in this hairpin peptide, YIO is located within a /?-strand of a short P-sheet (Ramirez-Alvarado et al, 1996).…”

Molecular Motion of Spin Labeled Side Chains in α-Helices: Analysis by Variation of Side Chain Structure

“…Purification with flash column chromatography (hexane/EtOAc) yielded 12b as a yellow oil 24 mg (42%). IR (Nujol) ν max 2970 cm -1 , 2920 cm (22), 166 (64), 83 (51), 67 (42), 55(53), 41(100).…”

Deuterium Spin Probes of Side-Chain Dynamics in Proteins. 2. Spectral Density Mapping and Identification of Nanosecond Time-Scale Side-Chain Motions

“…The meaning of the best-fit order parameters S f 2 extracted from fits using the LS-2 and -3 models in cases where slow side-chain dynamics is present is discussed below. Theoretical treatments which draw the connection between the model-free parameters and more fundamental quantities describing side-chain torsional dynamics have been presented in a number of recent papers. − …”