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Modeling Protein–Micelle Systems in Implicit Water
journal contribution
posted on 2015-06-25, 00:00 authored by Rodney
E. Versace, Themis LazaridisSeveral
membrane proteins and numerous membrane-active peptides
have been studied in detergent micelles by solution NMR. However,
the detailed structure of these complexes remains unknown. We propose
a modeling approach that treats the protein and detergent in atomistic
detail and the solvent implicitly. The model is based on previous
work on dodecylphosphocholine micelles, adapted for use with the CHARMM36
force field and extended to sodium dodecyl sulfate micelles. Solvation
parameters were slightly adjusted to reproduce experimental data on
aggregation numbers and critical micelle concentrations. To test the
approach, several membrane-active peptides and three β-barrel
membrane proteins were subjected to molecular dynamics simulations
in the presence of a large number of detergent molecules. Their experimentally
determined secondary structure was maintained and the RMSD values
were less than 2 Å. Deformations were commonly observed in the
N or C termini. The atomistic view of the protein–micelle systems
that this approach provides could be useful in interpreting biophysical
experiments carried out in the presence of detergent.
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Keywords
C terminipresenceImplicit WaterSeveral membrane proteinsRMSD valuesCHARMM 36 force fielddetergent moleculessolution NMRmodeling approachatomistic detailaggregation numberspeptidesodium dodecyl sulfate micellesSolvation parameters2 Å. Deformationsatomistic viewdodecylphosphocholine micellesdynamics simulationsdetergent micellesmicelle concentrations
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