Computational study of pH-dependent membrane insertion of pHLIP peptides
The pH (low) insertion peptide (pHLIP) belongs to a family of transmembrane peptides, with the ability to insert in membrane cells dependent on how acidic is their vicinity, such as in tumoral cells, thus working as an efficient tumor-specific biomarker. However, wt-pHLIP pH -dependent membrane insertion has not been fully explored at the molecular level. Also, since the peptide accumulates in the kidneys in considerable amounts, due to their naturally acidic extracellular pH, it is urgent to improve peptide specificity by delimiting the pH range of insertion.
The constant-pH molecular dynamics (CpHMD) method proved to be capable in sampling protonation states of titrable residues of both wt-pHLIP and L16H variant, while also revealing important structural details about the peptide-membrane equilibria. Furthermore, our work produced remarkable results by predicting detailed and accurate pKa profiles of the residues. Moreover, the L16H variant was able to establish a pH range of insertion, despite being too large for in vivo studies and therapeutic purposes. For the future, we aim to improve sampling quality, using a pH replica exchange (pHRE) methodology, for better system description and pKa prediction. Additionally, we will design new pHLIP sequences mutated with cationic residues, as to narrow down the pH range of insertion and evaluate their validity for clinical applications.