Atomistic Brownian Dynamics Simulation of Peptide Phosphorylation

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 st...

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Bibliographic Details
Published in:Journal of the American Chemical Society 2001-09, Vol.123 (37), p.9107-9111
Main Authors: Shen, Tongye, Wong, Chung F, McCammon, J. Andrew
Format: Article
Language:English
Subjects:
Algorithms
Computer Simulation
Models, Biological
Models, Chemical
Models, Molecular
Oligopeptides - chemistry
Oligopeptides - metabolism
Phosphorylation
Protein Conformation
Thermodynamics
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Summary: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 7e q to the αR 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.
ISSN:0002-7863
1520-5126
DOI:10.1021/ja010190t