Journal Article Epublish
PubMed: 42509748 DOI: 10.3390/biom16070954
Temperature Replica-Exchange Molecular Dynamics Reveals a Heterogeneous Recognition-Compatible Ensemble of the Laminin-Derived Peptide CDPGYIGSR.
Biomolecules 16(7)
Authors: Carmen Di Giovanni, Antonio Lavecchia
Affiliations
- Department of Pharmacy, "Drug Discovery Laboratory", University of Naples "Federico II", 80131 Naples, Italy.
Abstract
The laminin-derived nonapeptide CDPGYIGSR contains the bioactive YIGSR motif, historically associated with inhibition of tumor cell adhesion, invasion, angiogenesis, and laminin-receptor-mediated cell responses. Although these activities have often been attributed to the 37/67 kDa laminin receptor/RPSA axis, the molecular identity and organization of the laminin-binding receptor system remain debated. This uncertainty makes it essential to define the intrinsic conformational preferences of CDPGYIGSR in solution before assigning a unique receptor-bound structure. In this study, temperature replica-exchange molecular dynamics (T-REMD) simulations in explicit solvent are employed to characterize the solution conformational ensemble of CDPGYIGSR. Free energy landscape analysis, clustering, and structural descriptors reveal a predominant compact bend-like backbone arrangement, together with alternative low-lying conformational states within a heterogeneous ensemble. Rather than assuming a single bioactive conformation, the conformational ensemble is analyzed in terms of structural features that are consistent with available NMR observations and reported structure-activity relationships. Importantly, the most populated conformations in solution do not necessarily correspond to the bioactive state upon receptor binding. Instead, a subset of conformations sharing common structural motifs, including a central backbone bend and specific residue exposure patterns, may represent states compatible with receptor recognition. These results provide an ensemble-based structural framework that connects simulation-derived conformational motifs with available NMR observations and structure-activity data, supporting a recognition-compatible ensemble model in which compact preorganized states may contribute to receptor binding.
MeSH
Cells, Solutions, Laminin, Temperature