What Drives 15N Spin Relaxation in Disordered Proteins? Combined NMR/MD Study of the H4 Histone Tail

Abstract

Backbone ( 15 N) NMR relaxation is one of the main sources of information on dynamics of disordered proteins. Yet, we do not know very well what drives 15 N relaxation in such systems, i.e., how different forms of motion contribute to the measurable relaxation rates. To address this problem, we have investigated, both experimentally and via molecular dynamics simulations, the dynamics of a 26-residue peptide imitating the N-terminal portion of the histone protein H4. One part of the peptide was found to be fully flexible, whereas the other part features some transient structure (a hairpin stabilized by hydrogen bonds). The following motional modes proved relevant for 15 N relaxation. 1) Sub-picosecond librations attenuate relaxation rates according to S 2 $0.85-0.90. 2) Axial peptide-plane fluctuations along a stretch of the peptide chain contribute to relaxation-active dynamics on a fast timescale (from tens to hundreds of picoseconds). 3) 4/j backbone jumps contribute to relaxation-active dynamics on both fast (from tens to hundreds of picoseconds) and slow (from hundreds of picoseconds to a nanosecond) timescales. The major contribution is from polyproline II (PPII) 4 b transitions in the Ramachandran space; in the case of glycine residues, the major contribution is from PPII 4 (b) 4 rPPII transitions, in which rPPII is the mirror-image (right-handed) version of the PPII geometry, whereas b geometry plays the role of an intermediate state. 4) Reorientational motion of certain (sufficiently long-lived) elements of transient structure, i.e., rotational tumbling, contributes to slow relaxation-active dynamics on $1-ns timescale (however, it is difficult to isolate this contribution). In conclusion, recent advances in the area of force-field development have made it possible to obtain viable Molecular Dynamics models of protein disorder. After careful validation against the experimental relaxation data, these models can provide a valuable insight into mechanistic origins of spin relaxation in disordered peptides and proteins.

Sequence-dependent correlated segments in the intrinsically disordered region of ChiZ

“…Similar to ChiZ1-64, sequence-specific backbone dynamics has been reported on a number of other IDPs using NMR, some in combination with MD simulations (38, 48-50, 53, 55, 71, 72). Whereas stable secondary structures such as a-helices and b-hairpins can certainly lead to slow backbone dynamics (38,48,50,53), as demonstrated here for ChiZ1-64, interaction networks, in particular those mediated by charged and aromatic residues, can lead to the formation of correlated segments, which can have slow dynamics even when the backbone remains disordered. We propose correlated segment as a defining feature for the conformation and dynamics of IDPs.…”

“…In several MD simulation studies, the CNH(t) correlation functions were fitted to a sum of exponentials, but either the fitting parameters or the trajectories used for the fitting had to be adjusted in order to reach agreement with experimental data (46)(47)(48)(49)(50)(51). It is thus notable that, using the AMBER14SB (52) / TIP4PD (43) force field and without adjusting CNH(t), Kämpf et al (53) were able to reproduce experimental relaxation data for the 26-residue N-terminal fragment of histone H4. In NMR and MD studies in which CNH(t) was fitted to a sum of exponentials, 3 or 4 exponentials were typically used, and the time constants ranged from a few ps to 10 ns.…”

Sequence-Dependent Correlated Segments in the Intrinsically Disordered Region of ChiZ

“…In several MD simulation studies, the C NH ( τ ) correlation functions were fitted to a sum of exponentials, but either the fitting parameters or the trajectories used for the fitting had to be adjusted in order to reach agreement with the experimental data [ 46 , 47 , 48 , 49 , 50 , 51 ]. It is thus notable that, using the AMBER14SB [ 52 ]/TIP4PD [ 43 ] force field and without adjusting C NH ( τ ), Kämpf et al [ 53 ] were able to reproduce experimental relaxation data for the 26-residue N-terminal fragment of histone H4. In NMR and MD studies in which C NH ( τ ) was fitted to a sum of exponentials, three or four exponentials were typically used, and the time constants ranged from a few ps to 10 ns.…”

Heterogeneous dynamics in partially disordered proteins

“…15 For disordered proteins, canonical force fields predict too condensed conformational ensembles and calculated NMR parameters often disagree with experiments. [18][19][20][21][22] Attempts to overcome these issues have been made by reweighting the conformational ensembles 23 or rescaling the timescales to reproduce the experimentally measured NMR spin relaxation times. 22,24 While these approaches can be useful in the interpretation of individual experiments, they cannot be generally applied for proteins with heterogeneous dynamics in complex environments, such as membrane bound disordered linkers.…”