Importance of long-time simulations for rare event sampling in zinc finger proteins.
Molecular dynamics (MD) simulation methods have seen significant improvement since their inception in the late 1950s. Constraints of simulation size and duration that once impeded the field have lessened with the advent of better algorithms, faster processors, and parallel computing. With newer techniques and hardware available, MD simulations of more biologically relevant timescales can now sample a broader range of conformational and dynamical changes including rare events. One concern in the literature has been under which circumstances it is sufficient to perform many shorter timescale simulations and under which circumstances fewer longer simulations are necessary. Herein, our simulations of the zinc finger NEMO (2JVX) using multiple simulations of length 15, 30, 1000, and 3000 ns are analyzed to provide clarity on this point.
a Department of Physics , Wake Forest University , Winston-Salem , NC 27109 , USA.
Ryan
R
Godwin
b Department of Cancer Biology , Wake Forest University Health Sciences , Winston-Salem , NC 27107 , USA.
William
W
Gmeiner
a Department of Physics , Wake Forest University , Winston-Salem , NC 27109 , USA.
Freddie R
FR
Salsbury
D006801:Humans; D051550:I-kappa B Kinase / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D011487:Protein Conformation; D016335:Zinc Fingers
C491731:IKBKG protein, human; D051550:I-kappa B Kinase
NEMO; molecular dynamics; zinc finger