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

ABSTRACT: Backbone (¹⁵N) NMR relaxation is one of the main sources of information on dynamics of disordered proteins. Yet, we do not know very well what drives ¹⁵N 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 ¹⁵N relaxation. 1) Sub-picosecond librations attenuate relaxation rates according to S² ?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) ?/? 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) ? ? transitions in the Ramachandran space; in the case of glycine residues, the major contribution is from PPII ? (?) ? rPPII transitions, in which rPPII is the mirror-image (right-handed) version of the PPII geometry, whereas ? 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.

SUBMITTER: Kampf K

PROVIDER: S-EPMC6302223 | biostudies-literature | 2018 Dec

REPOSITORIES: biostudies-literature

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

Kämpf Kerstin K Izmailov Sergei A SA Rabdano Sevastyan O SO Groves Adam T AT Podkorytov Ivan S IS Skrynnikov Nikolai R NR

Biophysical journal 20181120 12

Backbone (15N) NMR relaxation is one of the main sources of information on dynamics of disordered proteins. Yet, we do not know very well what drives 15N 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 ...[more]

PMID: 30527335

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Project description:Clays, hydrous aluminous phyllosilicates, have a significant impact on the interpretation of physical measurements and properties of porous media. In particular, the presence of paramagnetic and/or ferromagnetic ions like iron, nickel, and magnesium in clays can complicate the analysis of nuclear magnetic resonance (NMR) data for porous media characterization. This is due to the internal magnetic field gradient induced by the clay minerals. In this study, we aim to investigate the impact of clay content on spin-spin relaxation time (T 2), which is strongly influenced by the pore surface chemistry. Seven rock core plugs, characterized with variable clay content, were used for this purpose. The clay mineralogy and volume were determined by means of quantitative evaluation of minerals by scanning electron microscopy (QEMSCAN). The T 2 relaxation time was measured using a Carr-Purcell-Meiboom-Gill (CPMG) sequence with variable echo spacing (T E). The maximum percentage difference in dominant T 2 values (MRDT 2) between shortest and longest echo spacing was subsequently correlated with clay content obtained from QEMSCAN. Our results show that the reduction in T 2 distribution with increasing echo time T E is more significant in samples characterized by higher clay contents. The MRDT 2 was found to be strongly correlated with clay content. An analytical equation is presented expressing MRDT 2 as a function of clay content providing a quick and non-destructive approach for clay content estimation. Moreover, the MRDT 2-clay content relationship showed a nonlinear behavior: MRDT 2 increases drastically as the clay content increases up to 15%, beyond which the rate of MRDT 2 change with clay content diminishes. This behavior could be attributed to the clay distribution. At higher clay contents (above 15%), it is more likely for clay to form clusters (structural clays), which will not significantly increase the clay surface in contact with the pore fluid. Further, experimental data suggests that ignoring the impact of clay on internal magnetic gradients and T 2 signal may result in considerable underestimation of the actual pore size distribution.

Dataset Information

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

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

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