AMBER force-field parameters for phosphorylated amino acids in different protonation states: phosphoserine, phosphothreonine, phosphotyrosine, and phosphohistidine
Top Cited Papers
- 21 October 2005
- journal article
- Published by Springer Science and Business Media LLC in Journal of Molecular Modeling
- Vol. 12 (3), 281-289
- https://doi.org/10.1007/s00894-005-0028-4
Abstract
We report a consistent set of AMBER force-field parameters for the most common phosphorylated amino acids, phosphoserine, phosphothreonine, phosphotyrosine, and phosphohistidine in different protonation states. The calculation of atomic charges followed the original restrained electrostatic potential fitting procedure used to determine the charges for the parm94/99 parameter set, taking α-helical and β-strand conformations of the corresponding ACE-/NME-capped model peptide backbone into account. Missing force-field parameters were taken directly from the general AMBER force field (gaff) and the parm99 data set with minor modifications, or were newly generated based on ab initio calculations for model systems. Final parameters were validated by geometry optimizations and molecular-dynamics simulations. Template libraries for the phosphorylated amino acids in Leap format and corresponding frcmod parameter files are made available.Keywords
This publication has 22 references indexed in Scilit:
- Development of the force field parameters for phosphoimidazole and phosphohistidineJournal of Computational Chemistry, 2004
- Development and testing of a general amber force fieldJournal of Computational Chemistry, 2004
- The origins of protein phosphorylationNature, 2002
- How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules?Journal of Computational Chemistry, 2000
- Direct Effects of Phosphorylation on the Preferred Backbone Conformation of Peptides: A Nuclear Magnetic Resonance StudyBiophysical Journal, 1999
- The MIDI! basis set for quantum mechanical calculations of molecular geometries and partial chargesTheoretical Chemistry Accounts, 1996
- Application of the multimolecule and multiconformational RESP methodology to biopolymers: Charge derivation for DNA, RNA, and proteinsJournal of Computational Chemistry, 1995
- Structural Consequences of Histidine Phosphorylation: NMR Characterization of the Phosphohistidine Form of Histidine-Containing Protein from Bacillus subtilis and Escherichia coliBiochemistry, 1994
- A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP modelThe Journal of Physical Chemistry, 1993
- Comparison of simple potential functions for simulating liquid waterThe Journal of Chemical Physics, 1983