Chaos in protein dynamics.
MD simulations, currently the most detailed description of the dynamic evolution of proteins, are based on the repeated solution of a set of differential equations implementing Newton's second law. Many such systems are known to exhibit chaotic behavior, i.e., very small changes in initial conditions are amplified exponentially and lead to vastly different, inherently unpredictable behavior. We have investigated the response of a protein fragment in an explicit solvent environment to very small perturbations of the atomic positions (10(-3)-10(-9) A). Independent of the starting conformation (native-like, compact, extended), perturbed dynamics trajectories deviated rapidly, leading to conformations that differ by approximately 1 A RMSD within 1-2 ps. Furthermore, introducing the perturbation more than 1-2 ps before a significant conformational transition leads to a loss of the transition in the perturbed trajectories. We present evidence that the observed chaotic behavior reflects physical properties of the system rather than numerical instabilities of the calculation and discuss the implications for models of protein folding and the use of MD as a tool to analyze protein folding pathways.
Braxenthaler
M
M
Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, Rockville, USA.
Unger
R
R
Auerbach
D
D
Given
J A
JA
Moult
J
J
D001426:Bacterial Proteins / Q000737:chemistry; D003198:Computer Simulation; D008958:Models, Molecular; D017711:Nonlinear Dynamics; D009716:Numerical Analysis, Computer-Assisted; D010455:Peptides / Q000737:chemistry; D011487:Protein Conformation; D011489:Protein Denaturation; D017510:Protein Folding; D012260:Ribonucleases / Q000737:chemistry
D001426:Bacterial Proteins; D010455:Peptides; D012260:Ribonucleases; C019760:Bacillus amyloliquefaciens ribonuclease