Molecular Dynamics Simulation of a Transmembrane Peptide.

VILLARREAL MA; MONTICH GG

Buenos Aires.

Congreso; XIV International Biophysics Congress; 2002

Molecular dynamics simulation <!-- @page { size: 8.27in 11.69in; margin: 0.79in } P { margin-bottom: 0.08in } --> We present a molecular dynamics simulation of the peptide Ac-K2-(LA)12-K2-amide (LA)12 in a DPPC membrane in the liquid-crystalline phase. The (LA)12 and related peptides has been extensively used as an experimental model of intramembrane domains of transmembrane proteins. The experimental information available for the (LA)12-DPPC system include infrared spectroscopy, circular dichroism, 1H NMR, and calorimetry. This information is used to setup and validate the simulations. A simulation of 10 ns long of a system containing the peptide (initially in the -helix conformation), 124 lipids, and 3600 water molecules is performed in the NVT ensemble. The stability of the -helix conformation of peptide is analyzed in terms of rms deviations and the breaking of the intramolecular hydrogen bonds. They shown that the -helix is highly stable and adopt a tilted orientation with respect to the membrane normal. The deuterium order parameters of the aliphatic chains of the lipids, and the local density of the different groups are calculated as a function of the distance from the peptide. They reveal a major order of the lipid chains and an increased density in the vicinity of the peptide.