Combining Molecular and Spin Dynamics Simulations with Solid-State NMR: A Case Study of Amphiphilic Lysine-Leucine Repeat Peptide Aggregates.

Interpreting dynamics in solid-state molecular systems requires characterization of the potentially heterogeneous environmental contexts of molecules. In particular, the analysis of solid-state nuclear magnetic resonance (ssNMR) data to elucidate molecular dynamics (MD) 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 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 the 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 the following: (a) for the incoherent component of 13C relaxation, the nearest-neighbor spin interactions dominate, while the 1H-1H interactions have minimal impact; (b) the AMBER ff14SB dihedral barriers for the leucine Cγ-Cδ bond ("methyl rotation barriers") must be lowered by a factor of 0.7 to better match the 2H data; (c) proton-driven spin diffusion explains some of the discrepancy between experimental and simulated rates for the Cß 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.

Solid state deuterium NMR study of LKα14 peptide aggregation in biosilica.

In nature, organisms including diatoms, radiolaria, and marine sponges use proteins, long chain polyamines, and other organic molecules to regulate the assembly of complex silica-based structures. Here, the authors investigate structural features of small peptides, designed to mimic the silicifying activities of larger proteins found in natural systems. LKα14 (Ac-LKKLLKLLKKLLKL-C), an amphiphilic lysine/leucine repeat peptide with an α-helical secondary structure at polar/apolar interfaces, coprecipitates with silica to form nanospheres. Previous 13C magic angle spinning studies suggest that the tetrameric peptide bundles that LKα14 is known to form in solution may persist in the silica-complexed form, and may also function as catalysts and templates for silica formation. To further investigate LKα14 aggregation in silica, deuterium solid-state nuclear magnetic resonance (2H ssNMR) was used to establish how leucine side-chain dynamics differ in solid LKα14 peptides isolated from aqueous solution, from phosphate-buffered solution, and in the silica-precipitated states. Modeling the 2H ssNMR line shapes probed the mechanisms of peptide preaggregation and silica coprecipitation. The resulting NMR data indicates that the peptide bundles in silica preserve the hydrophobic interior that they display in the hydrated solid state. However, NMR data also indicate free motion of the leucine residues in silica, a condition that may result from structural deformation of the aggregates arising from interactions between the surface lysine side chains and the surrounding silica matrix.

Synthesis with structural and electronic characterization of homoleptic Fe(II)- and Fe(III)-fluorinated phenolate complexes.

Four Fe(III) compounds and one Fe(II) compound containing mononuclear, homoleptic, fluorinated phenolate anions of the form [Fe(OAr)(m)](n-) have been prepared in which Ar(F) = C(6)F(5) and Ar' = 3,5-C(6)(CF(3))(2)H(3): (Ph(4)P)(2)[Fe(OAr(F))(5)], 1, (Me(4)N)(2)[Fe(OAr(F))(5)], 2, {K(18-crown-6)}(2)[Fe(OAr(F))(5)], 3a, {K(18-crown-6)}(2)[Fe(OAr')(5)], 3b, and {K(18-crown-6)}(2)[Fe(OAr(F))(4)], 6. Two dinuclear Fe(III) compounds have also been prepared: {K(18-crown-6)}(2)[(OAr(F))(3)Fe(µ(2)-O)Fe(OAr(F))(3)], 4, and {K(18-crown-6)}(2)[(OAr(F))(3)Fe(µ(2)-OAr(F))(2)Fe(OAr(F))(3)], 5. These compounds have been characterized with UV-vis spectroscopy, elemental analysis, Evans method susceptibility, and X-ray crystallography. All-electron, geometry-optimized DFT calculations on four [Ti(IV)(OAr)(4)] and four [Fe(III)(OAr)(4)](-) species (Ar = 2,3,5,6-C(6)Me(4)H, C(6)H(5), 2,4,6-C(6)Cl(3)H(2), C(6)F(5)) with GGA-BP and hybrid B3LYP basis sets demonstrated that, under D(2d) symmetry, π donation from the O 2p orbitals is primarily into the d(xy) and d(z(2)) orbitals. The degree of donation is qualitatively consistent with expectations based on ligand Brønsted basicity and supports the contention that fluorinated phenolate ligands facilitate isolation of nonbridged homoleptic complexes due to their reduced π basicity at oxygen.