Estimates for the potential accuracy required in realistic protein folding simulations and structure recognition experiments.
BACKGROUND
We have recently addressed the problem of the potential accuracy required for protein folding simulations using a combination of theoretical considerations and lattice model simulations. In the present study, we combine the previously developed theoretical formalism with the law of corresponding states proposed recently by Onuchic, Wolynes and collaborators and obtain estimates for the potential accuracy required for computational studies of a small helical protein.


RESULTS
Our estimates suggest that effective energies of interaction between amino acid residues could be measured with an error around +/- 330 cal mol-1 for a resulting inaccurate potential still appropriate for structure recognition experiments, where the native conformation must remain the global energy minimum. For an ab initio folding simulation, where the energy of the native conformation must be sufficient to balance the entropy of the denatured state at a temperature at which the dynamics of the system are fast, the permissible error depends on the simulation temperature and can be as high as +/- 120 cal mol-1.


CONCLUSIONS
The results indicate that potentials do not need to be extremely accurate in order to be useful in computational studies. Results from different groups can be interpreted as an indication that available potentials are too inaccurate for ab initio simulations but not far from the permissive limit required for structure recognition.
de Araújo
A F
AF
Biophysics Program, Brandeis University, Waltham, MA 02254, USA.
Pochapsky
T C
TC
D003198:Computer Simulation; D008956:Models, Chemical; D017510:Protein Folding; D015203:Reproducibility of Results; D013816:Thermodynamics