Conformational requirement on peptides to exert laminin's activities and search for protein segments with laminin's activities

Abstract

The human laminin alpha3 chain LG4 module has biological activities of cell adhesion, heparin binding, migration, and neurite outgrowth. The authors had previously identified that the active site of this protein is in residues 1411-1429 (amino-acid sequence = KNSFMALYLSKGRLVFALG called A3G756) and that a three-amino-acid sequence KGR in A3G756 is crucial for exerting the activities. An experiment has shown that a cyclo-hEF3A peptide (a cyclic analog of A3G756) exhibits stronger activities than a linear-hEF3A peptide (a linearized peptide of the cyclo-hEF3A peptide). This experiment implies that adopting a loop conformation may be important for exerting the activities. In this study, the authors first computed the solution structures of the cyclo-hEF3A and linear-hEF3A peptides by molecular dynamics simulations. The obtained conformational ensembles consisted of a variety of conformations, which is a usual property of short peptides in solution. The ensembles involved a fraction where the peptide adopted beta-hairpins and KGR was located at the hairpin head. If there are protein segments that adopt beta-hairpins similar to those sampled from the simulation and have the KGR sequence at the hairpin head, these segments may have some activities. Then, the authors searched a database for segments satisfying these requirements and detected six functional segments. Three of them had laminin's activity, and the remaining three had activities similar to laminin's activities. Analyses on the conformational ensembles of cyclo- and linear-hEF3A peptides suggest that not only the KGR position in the hairpin but also the inter-strand packing is important for exerting laminin's activities.

Structural Study of Cell Attachment Peptide Derived from Laminin by Molecular Dynamics Simulation

“…In our previous studies [ 35 , 36 ], we performed simulated annealing [ 49 ] to investigate the structure for the global minimum of potential energy state of EF1 and EF2 peptides derived from the LG4 modules of laminin α1 and 2 chains. The results of simulated annealing show that hairpin-like structures were found for EF1, but not for EF2.…”