Force field impact and spin-probe modeling in molecular dynamics simulations of spin-labeled T4 lysozyme.
Several attempts have been made to compute electron paramagnetic resonance (EPR) spectra of biomolecules, using motional models or simulated trajectories to describe dynamics. Ideally, the simulated trajectories should capture "fast" (picosecond) snapshots of spin-probe rotations accurately, while being lengthy enough to ensure a proper Fourier integration of the time-domain signal. It is the interplay of the two criteria that poses computational challenges to the method. In this context, an analysis of the spin-probe and protein conformational sampling and equilibration, with different force fields and with explicit solvent, may be a useful attempt. The present work reports a comparative study of the effect of the molecular dynamics (MD) force field on conformational sampling and equilibration in two spin-labeled T4 lysozyme (T4L) variants, N40C and K48C. Ensembles of 10x 3 ns-trajectories per variant and per force field (OPLS/AMBER and AMBER99) are analyzed for a reliable assessment of convergence and sampling. It is found that subtle site-dependent differences in spin-probe rotations and torsions are more readily captured in the AMBER99 trajectories than in the OPLS/AMBER simulations. On the other hand, sampling and equilibration are found to be better with the OPLS/AMBER force field at equal trajectory lengths.
Stoica
Ileana
I
National Research Council of Canada, Biotechnology Research Institute, 6100 Royalmount Avenue, Montréal, QC, H4P 2R2, Canada. istoica@physics.cornell.edu
D017122:Bacteriophage T4 / Q000201:enzymology*; D003198:Computer Simulation; D004578:Electron Spin Resonance Spectroscopy / Q000379:methods*; D008958:Models, Molecular; D009038:Motion; D009113:Muramidase / Q000737:chemistry*; D020125:Mutation, Missense; D012399:Rotation; D013113:Spin Labels; D014102:Torsion Abnormality
D013113:Spin Labels; D009113:Muramidase