Membrane adsorption, folding, insertion and translocation of synthetic trans-membrane peptides.
Spontaneous membrane adsorption, folding and insertion of the synthetic WALP16 and KALP16 peptides was studied by computer simulations starting from completely extended conformations. The peptides were simulated using an unmodified all-atom force field in combination with an efficient Monte Carlo sampling algorithm. The membrane is represented implicitly as a hydrophobic zone inside a continuum solvent modelled using the generalized Born theory of solvation. The method was previously parameterized to match insertion energies of hydrophobic side chain analogs into cyclohexane and no parameters were optimized for the present simulations. Both peptides rapidly precipitate out of bulk solution and adsorb to the membrane surface. Interfacial folding into a helical conformation is followed by membrane insertion. Both the peptide conformations and their location in the membrane are strongly temperature dependent. The temperature dependent behaviour can be summarized by fitting to a four-state model, separating the system into folded and unfolded conformers, which are either inserted into the membrane or located at the interfaces. As the temperature is lowered the dominant peptide conformation of the system changes from unfolded surface bound configurations to folded surface bound states. Folded trans-membrane conformers represent the dominant configuration at low temperatures. The analysis allows direct estimates of the free energies of peptide folding and membrane insertion. In the case of WALP the quality of the fit is excellent and the thermodynamic behaviour is in good agreement with expected theoretical consideration. For KALP the fit is more problematic due to the large solvation energies of the charged lysine residues.
Ulmschneider
Martin B
MB
Department of Biochemistry, University of Oxford, Oxford, UK. martin@ulmschneider.com
Ulmschneider
Jakob P
JP
D000327:Adsorption; D000465:Algorithms; D000595:Amino Acid Sequence; D003198:Computer Simulation; D008051:Lipid Bilayers; D008565:Membrane Proteins / Q000138:chemical synthesis / Q000737:chemistry*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009010:Monte Carlo Method; D010455:Peptides / Q000138:chemical synthesis / Q000737:chemistry; D011487:Protein Conformation; D017510:Protein Folding; D017433:Protein Structure, Secondary; D013816:Thermodynamics
D008051:Lipid Bilayers; D008565:Membrane Proteins; D010455:Peptides