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Position-resolved free energy of solvation for amino acids in lipid membranes from molecular dynamics simulations.
Stockholm University.
Stockholm University.ORCID iD: 0000-0002-2734-2794
2008 (English)In: Proteins: Structure, Function, and Genetics, ISSN 0887-3585, E-ISSN 1097-0134, Vol. 70, no 4, 1332-44 p.Article in journal (Refereed) Published
Abstract [en]

Studies of insertion and interactions of amino acids in lipid membranes are pivotal to our understanding of membrane protein structure and function. Calculating the insertion cost as a function of transmembrane helix sequence is thus an important step towards improved membrane protein prediction and eventually drug design. Here, we present position-dependent free energies of solvation for all amino acid analogs along the membrane normal. The profiles cover the entire region from bulk water to hydrophobic core, and were produced from all-atom molecular dynamics simulations. Experimental differences corresponding to mutations and costs for entire segments match experimental data well, and in addition the profiles provide the spatial resolution currently not available from experiments. Polar side-chains largely maintain their hydration and assume quite ordered conformations, which indicates the solvation cost is mainly entropic. The cost of solvating charged side-chains is not only significantly lower than for implicit solvation models, but also close to experiments, meaning these could well maintain their protonation states inside the membrane. The single notable exception to the experimental agreement is proline, which is quite expensive to introduce in vivo despite its hydrophobicity--a difference possibly explained by kinks making it harder to insert helices in the translocon.

Place, publisher, year, edition, pages
2008. Vol. 70, no 4, 1332-44 p.
National Category
Biophysics Bioinformatics and Systems Biology Theoretical Chemistry
URN: urn:nbn:se:kth:diva-82623DOI: 10.1002/prot.21629ISI: 000253567400023PubMedID: 17876818OAI: diva2:498458
QC 20120214Available from: 2012-02-12 Created: 2012-02-12 Last updated: 2012-02-14Bibliographically approved

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Lindahl, Erik
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