Atomistic Brownian dynamics simulation of peptide phosphorylation

T Shen; C F Wong; J A McCammon

doi:10.1021/ja010190t

Atomistic Brownian dynamics simulation of peptide phosphorylation

J Am Chem Soc. 2001 Sep 19;123(37):9107-11. doi: 10.1021/ja010190t.

Authors

T Shen¹, C F Wong, J A McCammon

Affiliation

¹ Department of Physics, Howard Hughes Medical Institute, University of California San Diego, La Jolla, CA 92093-0365, USA. tshen@ucsd.edu

PMID: 11552818
DOI: 10.1021/ja010190t

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.

Publication types

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.

MeSH terms

Algorithms*
Computer Simulation
Models, Biological
Models, Chemical*
Models, Molecular
Oligopeptides / chemistry*
Oligopeptides / metabolism
Phosphorylation
Protein Conformation
Thermodynamics

Substances

Oligopeptides