Statistical and energetic analysis of hydrogen bonds in short and long peptide nanotapes/nanofibers using molecular dynamics simulations

Abstract

• Evaluation of the stability of peptide nanomaterials via molecular dynamics. • Importance of hydrogen bonds in fiber/tape-like peptide nanomaterials. • Structural analysis using NVT and NPT ensemble in molecular dynamics simulations. In this work, we performed fully atomistic classical molecular dynamics simulations to characterize the structural and energetic interaction of peptide nanoribbons/nanofibers with different lengths. The nanostructures are formed by peptides used in the release of bioactive molecules and tissue regeneration, composed of lysine (K), serine (S) and leucine (L), in the following sequence K 2 (SL) 6 K 2 . The simulations were performed and analyzed in isobaric-isothermal (NPT) and isovolumetric-isothermal (NVT) ensembles. Our results evaluate how these nanostructures are stabilized by the hydrogen bonds (HB) between the peptides. In general, the average number of these HBs is between 5 and 6 HBs per peptide in the nanostructure, with a lifetime that can reach up to 2.2 ns and a cut-off energy of about 23 kJ/mol. All analyzes are considered in structures with lengths varying from 6 to 18 nm which represents a careful study of tape/fiber simulations.