Design and Characterization of pH-Responsive DGEA-Derived Peptide Scaffolds: A Comprehensive Molecular Dynamics Simulation Study

Abstract

Peptide-based, functionally active, stimuli-responsive biomaterials hold immense potential for diverse biomedical applications. Functionally active motifs of extracellular matrix (ECM) proteins, when conjugated with self-assembling peptides (SAP) or polymers, demonstrate significant promise in the development of such bioactive scaffolds. However, synthesis complexity, high associated costs, limited functionality, and potential immune responses present significant challenges. This study explores collagen-I-derived DGEA motif-based SAPs, incorporating modifications such as salt bridge pairing, charged and polar residues, hydrophobic residues, amyloidogenic sequences, and non-ECM motifs, to develop stimuli-responsive, functionally active scaffolds. Extensive molecular dynamics (MD) simulations, totaling 16.7 μs, were conducted on 20 systematically designed peptide systems. These simulations also characterized the stimuli-responsive properties of the peptides, focusing on pH and temperature responsiveness. Among the 20 designs, three peptide systems─DGEA-SBD, DGEA-SBE (salt-bridge modifications), and DGEA-F4 (with hydrophobic residue addition at the C-terminus)─successfully formed large, stable, and bioactive scaffolds. These systems exhibited enhanced aggregation (greater than 90%) and improved interpeptide hydrogen bonding (more than 30 bonds) while maintaining the accessibility of functional motifs (60-70% availability) compared to the unmodified DGEA motif. Notably, the DGEA-SBD and DGEA-SBE peptides showed a transition from small, unstable, uneven gel-like structures to large, stable, uniform, and functionally active scaffolds as the pH shifted from 3.0 to physiological pH. Comprehensive MD simulation studies demonstrated that these designed peptides exhibit increased aggregation and enhanced interpeptide hydrogen bonding while retaining their functional activity under various physiological conditions, highlighting their promising potential for biomedical applications.

Keywords: DGEA motif; molecular dynamics simulations; pH responsive biomaterial; scaffold design; self-assembled peptides.