Membrane Protein Simulations Using AMBER Force Field and Berger Lipid Parameters
Arnau Cordomí1, Gianluigi Caltabiano1, Leonardo Pardo1
1Laboratori de Medicina Computacional, Unitat de Bioestadística, Facultat de Medicina, Universitat Autònoma de Barcelona , 08193 Bellaterra, Spain.
Journal of Chemical Theory and Computation
|November 24, 2015
Summary
The AMBER99SB and Berger force fields are compatible for membrane protein simulations. This combination accurately models protein and membrane structures, offering reliable free energy estimations.
Area of Science:
- Computational chemistry
- Biophysics
- Molecular dynamics simulations
Background:
- AMBER force fields are widely used for protein simulations but lack specific lipid parameters.
- This limitation hinders their application in membrane protein simulations.
Purpose of the Study:
- To assess the compatibility of Berger's united-atom lipid parameters with AMBER force fields for membrane protein simulations.
- To evaluate the performance of AMBER99SB/Berger and OPLS-AA/Berger force field combinations.
Main Methods:
- Computed free energies of solvation and transfer for amino acid side-chains using thermodynamic integration.
- Performed molecular dynamics simulations of three membrane proteins (β2 adrenergic G protein-coupled receptor, Aquaporin-1, Omp32) in a POPC lipid bilayer.
Main Results:
- Demonstrated compatibility between AMBER99SB and Berger force fields.
- Showed reliable free energy estimations and accurate descriptions of membrane and protein structural properties.
- The AMBER99SB/Berger combination outperformed OPLS-AA/Berger in certain aspects.
Conclusions:
- The AMBER99SB/Berger force field combination is a reliable choice for membrane protein simulations.
- This combination merges the strengths of AMBER99SB (ligand parametrization, secondary structure) with validated Berger lipid parameters.
