Article
Atomistic Brownian Dynamics Simulation of Peptide Phosphorylation
Journal of the American Chemical Society
(2001)
Abstract
We report the implementation of an all-atom Brownian dynamics simulation model of peptides using the constraint algorithm LINCS. The algorithm has been 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 study 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) structure upon phosphorylation. NMR (3)J coupling constants were also computed from the Brownian trajectories using the Karplus equation. The calculated (3)J results agree reasonably well with experimental data for phosphorylated peptide but less so for doubly charged phosphorylated one.
Disciplines
Publication Date
January 9, 2001
DOI
10.1021/ja010190t
Citation Information
Shen T, Wong Cf and McCammon Ja. "Atomistic Brownian Dynamics Simulation of Peptide Phosphorylation" Journal of the American Chemical Society Vol. 123 Iss. 37 (2001) p. 9107 - 9111 Available at: http://works.bepress.com/chung-wong/47/