Studying the Conformation of a Silaffin-Derived Pentalysine Peptide Embedded in Bioinspired Silica using Solution and Dynamic Nuclear Polarization Magic-Angle Spinning NMR

Abstract

Smart materials are created in nature at interfaces between biomolecules and solid materials. The ability to probe the structure of functional peptides that engineer biogenic materials at this heterogeneous setting can be facilitated tremendously by use of DNP-enhanced solid-state NMR spectroscopy. This sensitive NMR technique allows simple and quick measurements, often without the need for isotope enrichment. Here, it is used to characterize a pentalysine peptide, derived from a diatom's silaffin protein. The peptide accelerates the formation of bioinspired silica and gets embedded inside the material as it is formed. Two-dimensional DNP MAS NMR of the silica-bound peptide and solution NMR of the free peptide are used to derive its secondary structure in the two states and to pinpoint some subtle conformational changes that the peptide undergoes in order to adapt to the silica environment. In addition, interactions between abundant lysine residues and silica surface are identified, and proximity of other side chains to silica and to neighboring peptide molecules is discussed.

Atom Probe Tomography for 3D Structural and Chemical Analysis of Individual Proteins

“…At present, we cannot ascertain that the protein retains its exact functional structure after the sol–gel process. As the water is exchanged for silica, it is reasonable to expect at least minor conformational changes in response, for instance rearrangements of hydrophilic amino acid side chains. However, silica‐encapsulated enzymes can reportedly retain their catalytic activity and even remain entirely unperturbed, as evident from solid‐state NMR studies …”

Biosilica and bioinspired silica studied by solid-state NMR

“…In cases where the solid support is transparent, Confocal Laser Scanning Microscopy has been applied [61][62][63]: the homogeneity of the adsorption of the enzyme has a profound influence on the activity of the composite [64,65]. In case the matrix is inorganic, like for biosilica, the protein can be localized by high-resolution TEM [66,67], or by secondary electron emission analysis in SEM. In operando characterization of the catalyst (i.e.…”

“…Some of us have applied a DNP-based approach to the structural characterization of the pentalysine peptide PL12 (KAAKLFKPKASK) derived from Thalassiosira pseudonana. [67] PL12 is able to accelerate the silica condensation from silicic acid and 1 H- 29 Si correlation experiments were used to probe proximity between silica and the lysine sidechains ( Figure 4). By means of NMR it is possible to study the conformation of the peptide, however, the dilution of the sample in the silica matrix makes this approach lengthy beyond applicability.…”

“…For Ser 11, the value for the largest population is given in the chart. Reprinted with permission from reference[67]. Copyright 2015 American Chemical Society.…”

Biofunctionalization of Nano Channels by Direct In‐Pore Solid‐Phase Peptide Synthesis

“…Here, solid‐state NMR can provide important information on the structural composition of these organic/inorganic hybrids . Accordingly a number of studies focused on the understanding of natural diatoms by using solid‐state NMR methods including DNP‐assisted solid‐state NMR . However, it is still hard to obtain detailed information on the structural composition of these materials due to their complexity and the low concentration of the organic compounds on the silica surface, which lead to overlapping of signals in solid‐state NMR.…”