Atomistic Brownian Dynamics Simulation of Peptide Phosphorylation

Shen T; Wong Cf; McCammon Ja; Chung Wong

doi:10.1021/ja010190t

Atomistic Brownian Dynamics Simulation of Peptide Phosphorylation

Shen T, Wong Cf, McCammon Ja, Chung Wong

University of Missouri-St. Louis

Research output: Contribution to journal › Article › peer-review

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.

Original language	American English
Journal	Journal of the American Chemical Society
Volume	123
DOIs	https://doi.org/10.1021/ja010190t
State	Published - Jan 9 2001

Disciplines

Atomic, Molecular and Optical Physics
Inorganic Chemistry

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title = "Atomistic Brownian Dynamics Simulation of Peptide Phosphorylation",

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. ",

author = "Shen T and Wong Cf and McCammon Ja and Chung Wong",

note = "J Am Chem Soc. 2001 Sep 19;123(37):9107-11. Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.; Research Support, U.S. Gov't, P.H.S.",

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doi = "10.1021/ja010190t",

language = "American English",

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T1 - Atomistic Brownian Dynamics Simulation of Peptide Phosphorylation

AU - T, Shen

AU - Cf, Wong

AU - Ja, McCammon

AU - Wong, Chung

N1 - J Am Chem Soc. 2001 Sep 19;123(37):9107-11. Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S.; Research Support, U.S. Gov't, P.H.S.

PY - 2001/1/9

Y1 - 2001/1/9

N2 - 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.

AB - 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.

UR - https://www.ncbi.nlm.nih.gov/pubmed/11552818

U2 - 10.1021/ja010190t

DO - 10.1021/ja010190t

M3 - Article

VL - 123

JO - Journal of the American Chemical Society

JF - Journal of the American Chemical Society

ER -

Atomistic Brownian Dynamics Simulation of Peptide Phosphorylation

Abstract

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