Chaos in protein dynamics

摘要: MD simulations, currently the most detailed description of dynamic evolution proteins, are based on repeated solution a set differential equations implementing Newton's second law. Many such systems known to exhibit chaotic behavior, i.e., very small changes in initial conditions amplified exponentially and lead vastly different, inherently unpredictable behavior. We have investigated response protein fragment an explicit solvent environment perturbations atomic positions (10−3–10−9 A). Independent starting conformation (native-like, compact, extended), perturbed dynamics trajectories deviated rapidly, leading conformations that differ by approximately 1 A RMSD within 1–2 ps. Furthermore, introducing perturbation more than ps before significant conformational transition leads loss trajectories. present evidence observed behavior reflects physical properties system rather numerical instabilities calculation discuss implications for models folding use as tool analyze pathways. Proteins 29:417–425, 1997. © 1997 Wiley-Liss, Inc.