Abstract:

Distance geometry and molecular dynamics are currently employed in determining molecular structures with interatomic distances from NMR NOESY experiment. Because of the flexibility of peptide, distances obtained from NMR are usually not sufficient to confine its structure. Both distance geometry and molecular dynamics will bias in the conformational space at this circumstance. Constraint Monte Carlo simulated annealing was established to solve this problem. Distance constraints were included into the ECEPP/2 force field by introducing a harmonic energy term. Conformational analysis of a pentapeptide with eight interatomic distances from NMR was carried out as a test. By comparison of the 100 conformers obtained from constraint simulated annealing and the 100 conformers from distance geometry calculation, it was found that constraint simulated annealing can cover the outcomes of distance geometry and at the same time give more con-formers fitting to the experimental data. The result shows that constraint Monte-Carlo simulated annealing is more valid in constructing peptide structures from NMR distances than currently employed methods when no sufficient distances from NMR are available.

Key words: Simulated annealing, Conformation, Peptide