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Modeling Protein-Micelle Systems in Implicit Water.

Rodney E Versace¹, Themis Lazaridis¹

¹Department of Chemistry, The City College of New York, 160 Convent Avenue, New York, New York 10031, United States.

The Journal of Physical Chemistry. B

|June 3, 2015

Summary

This study introduces a new atomistic modeling approach for membrane proteins and peptides in detergent micelles. The method accurately predicts structures, aiding in the interpretation of biophysical experiments.

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Area of Science:

Biophysics
Computational Biology
Structural Biology

Background:

Solution NMR studies membrane proteins and peptides in detergent micelles.
Detailed structures of these protein-detergent complexes remain largely unknown.

Purpose of the Study:

To develop an atomistic modeling approach for protein-detergent complexes.
To enable detailed structural analysis of membrane proteins and peptides in micelles.

Main Methods:

Developed a CHARMM36-based model for dodecylphosphocholine and sodium dodecyl sulfate micelles.
Employed implicit solvent and adjusted solvation parameters.
Performed molecular dynamics simulations on peptides and beta-barrel membrane proteins.

Main Results:

Maintained experimentally determined secondary structures.
Achieved root-mean-square deviation (RMSD) values below 2 Å.
Observed common deformations in N or C termini of proteins.

Conclusions:

The atomistic modeling approach provides detailed views of protein-micelle systems.
This method can aid in interpreting biophysical experiments involving detergents.