AMBER force-field parameters for phosphorylated amino acids in different protonation states: phosphoserine, phosphothreonine, phosphotyrosine, and phosphohistidine

被引：0
作者：
Nadine Homeyer
Anselm H. C. Horn
Harald Lanig
Heinrich Sticht
机构：
[1] Friedrich-Alexander-Universität Erlangen-Nürnberg,Abteilung für Bioinformatik, Institut für Biochemie
[2] Computer-Chemie-Centrum,undefined
来源：
Journal of Molecular Modeling | 2006年 / 12卷
关键词：
AMBER; Parameters; Phosphorylated amino acids; Force field; Restrained electrostatic potential;
D O I：
暂无
中图分类号：
学科分类号：
摘要：
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.
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页码：281 / 289
页数：8
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