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Biophys. J. BioFAST: First Published January 22, 2008. doi:10.1529/biophysj.107.112805
© 2008 by the Biophysical Society.

A more recent version of this article appeared on May 1, 2008.
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BIOPHYSICAL THEORY AND MODELING

Distribution of Amino Acids in a Lipid Bilayer from Computer Simulations

Justin L MacCallum 1, W.F. Drew Bennett 1 and D. Peter Tieleman 1*

1 University of Calgary

* To whom correspondence should be addressed. E-mail: tieleman{at}ucalgary.ca.

Submitted on May 14, 2007
Revised on June 27, 2007
Accepted on 4 December 2007


  Abstract
We have calculated the distribution in a lipid bilayer of small molecules mimicking 17 natural amino acids in atomistic detail by molecular dynamics simulation. For Lys, Arg, Glu, and Asp we considered both charged and uncharged forms. The results give detailed insight in the molecular basis of the preferred location and orientation of each side chain as well the preferred charge state for ionizable residues. Partitioning of charged and polar side chains is accompanied by water defects connecting the side chains to bulk water. These water defects dominate the energetic of partitioning, rather than simple partitioning between water and a hydrophobic phase. Lys, Glu, and Asp become uncharged well before reaching the center of the membrane, but Arg may be either charged or uncharged at the center of the membrane. Phe has a broad distribution in the membrane but Trp and Tyr localize strongly to the interfacial region. The distributions are useful for the development of coarse-grained and implicit membrane potentials for simulation and structure prediction. We discuss the relationship between the distribution in membranes, bulk partitioning to cyclohexane, and several amino acid hydrophobicity scales.

Key Words: free energy calculation, hydrophobicity scale, implicit potentials, membrane protein structure, pKa calculation, partitioning




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Copyright © 2008 by the Biophysical Society.