Final Activity Report Summary - PENETRATING PEPTIDES (Cell penetrating peptides: Modelling transmembrane insertion)
Cell-penetrating peptides (CPPs) have recently attracted much attention because of their apparent ability to penetrate cell membranes in an energy independent manner. In this project, molecular dynamics simulation techniques were used to study the interaction of two CPPs, i.e. penetratin and the Transactivator of transcription (TAT) peptide with Dipalmitoyl phosphatidylcholine (DPPC) and Dioleylphosphatidylcholine (DOPC) phospholipid bilayers, shedding light on the mechanisms via which these peptides might cross biological membranes.
The simulations suggested that the peptides might enter the cell through micropinocytosis. Multiple peptides were observed to induce large deformations in the lipid bilayer in the form of deep grooves, which enclosed aggregated peptides. This structure persisted for the time scale of the simulations, equal to hundreds of nanoseconds. No spontaneous pore formation was observed during the simulations. However, pore formation could be induced in simulations where an external potential was used to pull a single penetratin or TAT peptide into the membrane.
Using umbrella sampling techniques the free energy of inserting a single peptide into a DPPC bilayer was estimated to be approximately 75 kJ/mol-1 in the case of penetratin and approximately 120 kJ/mol-1 in the case of TAT peptide, suggesting that penetratin was more likely to translocate spontaneously through the membrane than TAT peptide. It was also evident that penetration of single peptides would require a timescale of at least seconds to minutes.
In addition, the work illustrated the extent to which the results of such simulations could be dependent on initial conditions, extent of equilibration, size of the system and conditions under which the simulations were performed.
The simulations suggested that the peptides might enter the cell through micropinocytosis. Multiple peptides were observed to induce large deformations in the lipid bilayer in the form of deep grooves, which enclosed aggregated peptides. This structure persisted for the time scale of the simulations, equal to hundreds of nanoseconds. No spontaneous pore formation was observed during the simulations. However, pore formation could be induced in simulations where an external potential was used to pull a single penetratin or TAT peptide into the membrane.
Using umbrella sampling techniques the free energy of inserting a single peptide into a DPPC bilayer was estimated to be approximately 75 kJ/mol-1 in the case of penetratin and approximately 120 kJ/mol-1 in the case of TAT peptide, suggesting that penetratin was more likely to translocate spontaneously through the membrane than TAT peptide. It was also evident that penetration of single peptides would require a timescale of at least seconds to minutes.
In addition, the work illustrated the extent to which the results of such simulations could be dependent on initial conditions, extent of equilibration, size of the system and conditions under which the simulations were performed.