Atomistic Brownian dynamics simulation of peptide phosphorylation

We report the implementation of an all-atom Brownian dynamics simulation mo del of peptides using the constraint algorithm LINCS. The algorithm has bee n added as a part of UHBD. It uses adaptive time steps to achieve a balance between computational speed and stability. The algorithm was applied to st udy the effect of phosphorylation on the conformational preference, of the peptide Gly-Ser-Ser-Ser. We find that the middle serine residue experiences considerable conformational change from the C-7eq to the alpha (R) structu re upon phosphorylation. NMR (3)J coupling constants were also computed fro m the Brownian trajectories using the Karplus equation. The calculated (3)J results agree reasonably well with experimental data for phosphorylated pe ptide but less so for doubly charged phosphorylated one.