Base Dynamics in the I Protein Binding Site.

Protein-DNA interactions play an important role in numerous biological functions within the living cell. In many of these interactions, the DNA helix is significantly distorted upon protein-DNA complex formation. The I restriction-modification system is one such system, where the methylation target is flipped out of the helix when bound to the methyltransferase.

Backbone Structure of Diatom Silaffin Peptide R5 in Biosilica Determined by Combining Solid-State NMR with Theoretical Sum-Frequency Generation Spectra.

Silaffin peptide R5 is key for the biogenesis of silica cell walls of diatoms. Biosilification by the R5 peptide has potential in biotechnology, drug development, and materials science due to its ability to precipitate stable, high fidelity silica sheets and particles. A true barrier for the design of novel peptide-based architectures for wider applications has been the limited understanding of the interfacial structure of R5 when precipitating silica nanoparticles.

Binding of Dipeptides to Fatty Acid Membranes Explains Their Colocalization in Protocells but Does Not Select for Them Relative to Unjoined Amino Acids.

Dipeptides, which consist of two amino acids joined by a peptide bond, have been shown to have catalytic functions. This observation leads to fundamental questions relevant to the origin of life. How could peptides have become colocalized with the first protocells? Which structural features would have determined the association of amino acids and peptides with membranes? Could the association of dipeptides with protocell membranes have driven molecular evolution, favoring dipeptides over individual amino acids? Using pulsed-field gradient nuclear magnetic resonance, we find that several prebiotic amino acids and dipeptides bind to prebiotic membranes.

Studies of Dynamic Binding of Amino Acids to TiO Nanoparticle Surfaces by Solution NMR and Molecular Dynamics Simulations.

Adsorption of biomolecules onto material surfaces involves a potentially complex mechanism where molecular species interact to varying degrees with a heterogeneous material surface. Surface adsorption studies by atomic force microscopy, sum frequency generation spectroscopy, and solid-state NMR detect the structures and interactions of biomolecular species that are bound to material surfaces, which, in the absence of a solid-liquid interface, do not exchange rapidly between surface-bound forms and free molecular species in bulk solution. Solution NMR has the potential to complement these techniques by detecting and studying transiently bound biomolecules at the liquid-solid interface.

Trimethylation of the R5 Silica-Precipitating Peptide Increases Silica Particle Size by Redirecting Orthosilicate Binding.

The unmodified R5 peptide from silaffin in the diatom Cylindrotheca fusiformis rapidly precipitates silica particles from neutral aqueous solutions of orthosilicic acid. A range of post-translational modifications found in R5 contribute toward tailoring silica morphologies in a species-specific manner. We investigated the specific effect of R5 lysine side-chain trimethylation, which adds permanent positive charges, on silica particle formation.