Combining molecular and spin dynamics simulations with solid-state NMR: a case study of amphiphilic lysine-leucine repeat peptide aggregates

Abstract

Interpreting dynamics in solid-state molecular systems requires characterization of the potentially heterogeneous environmental contexts of molecules. In particular, the analysis of solid-state NMR (ssNMR) data to elucidate molecular dynamics involves modeling the restriction to overall tumbling by neighbors, as well as the concentrations of water and buffer. In this exploration of the factors that influence motion, we utilize atomistic molecular dynamics (MD) trajectories of peptide aggregates with varying hydration to mimic an amorphous solid-state environment, and predict ssNMR relaxation rates. We also account for spin diffusion in multiply spin-labeled (up to 19 nuclei) residues, with several models of dipolar-coupling networks. The framework serves as a general approach to determine essential spin couplings affecting relaxation, benchmark MD force fields, and reveal the hydration-dependence of dynamics in a crowded environment. We demonstrate the methodology on a previously characterized amphiphilic 14-residue lysine-leucine repeat peptide, LKα14 (Ac-LKKLLKLLKKLLKL-c), which has an α-helical secondary structure and putatively forms leucine-burying tetramers in the solid state. We measure R₁ relaxation rates of uniformly ¹³C-labeled, and site-specific ²H-labeled leucines in the hydrophobic core of LKα14 at multiple hydration levels. Studies of 9 and 18 tetramer bundles reveal that: (a) for the incoherent component of ¹³C relaxation, nearest-neighbor spin interactions dominate, while ¹H-¹H interactions have minimal impact; (b) AMBER ff14SB dihedral barriers for the leucine Cγ - C_δ bond (“methyl rotation barriers”) must be lowered by a factor of 0.7 to better match the ²H data; (c) proton-driven spin diffusion (PDSD) explains some of the discrepancy between experimental and simulated rates for the C_β and Cα nuclei; and (d) ¹³C relaxation rates are mostly underestimated in the MD simulations at all hydrations, and the discrepancies identify likely motions missing in the 50 ns MD trajectories.

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ORCID for Ilya Kuprov: orcid.org/0000-0003-0430-2682

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