Thermodynamics of peptide insertion and aggregation in a lipid bilayer.
A variety of biomolecules mediate physiological processes by inserting and reorganizing in cell membranes, and the thermodynamic forces responsible for their partitioning are of great interest. Recent experiments provided valuable data on the free energy changes associated with the transfer of individual amino acids from water to membrane. However, a complete picture of the pathways and the associated changes in energy of peptide insertion into a membrane remains elusive. To this end, computational techniques supplement the experimental data with atomic-level details and shed light on the energetics of insertion. Here, we employed the technique of umbrella sampling in a total 850 ns of all-atom molecular dynamics simulations to study the free energy profile and the pathway of insertion of a model hexapeptide consisting of a tryptophan and five leucines (WL5). The computed free energy profile of the peptide as it travels from bulk solvent through the membrane core exhibits two minima: a local minimum at the water-membrane interface or the headgroup region and a global minimum at the hydrophobic-hydrophilic interface close to the lipid glycerol region. A rather small barrier of roughly 1 kcal mol (-1) exists at the membrane core, which is explained by the enhanced flexibility of the peptide when deeply inserted. Combining our results with those in the literature, we present a thermodynamic model for peptide insertion and aggregation which involves peptide aggregation upon contact with the membrane at the solvent-lipid headgroup interface.
Babakhani
Arneh
A
Department of Chemistry & Biochemistry, and Howard Hughes Medical Institute, University of California at San Diego, 9500 Gilman Drive, MC 0365 La Jolla, California 92093-0365, USA. ababakha@mccammon.ucsd.edu
Gorfe
Alemayehu A
AA
Kim
Judy E
JE
McCammon
J Andrew
JA
D000465:Algorithms; D003198:Computer Simulation; D006860:Hydrogen Bonding; D007930:Leucine / Q000737:chemistry; D008051:Lipid Bilayers / Q000737:chemistry*; D008958:Models, Molecular; D009842:Oligopeptides / Q000737:chemistry*; D011485:Protein Binding; D013816:Thermodynamics; D014357:Trypsin / Q000737:chemistry
D008051:Lipid Bilayers; D009842:Oligopeptides; D014357:Trypsin; D007930:Leucine