Outer membrane proteins: comparing X-ray and NMR structures by MD simulations in lipid bilayers

Area of Science:

• Structural biology
• Biophysics
• Computational biology

Background:

• Bacterial outer membrane proteins (OmpA, OmpX, PagP) are crucial for cell structure and function.
• X-ray diffraction and NMR spectroscopy are key techniques for determining protein structures.
• Understanding protein dynamics is essential for elucidating biological mechanisms.

Purpose of the Study:

• To compare the conformational dynamics of bacterial outer membrane proteins derived from X-ray versus NMR structures.
• To assess the influence of starting structure quality on molecular dynamics (MD) simulation stability and mobility.
• To identify dominant motions and their localization within these proteins.

Main Methods:

• Multiple molecular dynamics (MD) simulations (7 x 15 ns) of OmpA, OmpX, and PagP in a DMPC lipid bilayer.
• Calculation of root mean square deviation (RMSD) to assess conformational drift and simulation stability.
• Analysis of root mean square fluctuations (RMSF) to determine residue mobility.
• Principal component analysis (PCA) to identify dominant protein motions.

Main Results:

• Starting structure quality primarily affects the simulation stability of the transmembrane beta-barrel domain.
• NMR-based simulations generally show higher protein mobility compared to X-ray-based simulations.
• Dominant motions, captured by the first two eigenvectors, are concentrated in extracellular loops and PagP's N-terminal alpha-helix.
• While motion magnitudes are similar, directions of dominant motions show poor correlation between X-ray and NMR simulations due to limited sampling.

Conclusions:

• NMR-derived structures may provide a more dynamic representation of bacterial outer membrane proteins in simulations.
• The choice of starting structure significantly impacts the interpretation of protein dynamics from MD simulations.
• Further simulations are needed to fully capture the directional dynamics of these proteins.