An AMBER/DYANA/MOLMOL phosphorylated amino acid library set and incorporation into NMR structure calculations
An AMBER/DYANA/MOLMOL phosphorylated amino acid library set and incorporation into NMR structure calculations
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DOI：
10.1007/s10858-005-1199-0
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发表时间：
2005-09-01
影响因子：
2.7
通讯作者：
Legge, GB
中科院分区：
文献类型：
--
作者：
Craft, JW;Legge, GB
使用核磁共振(核磁共振)确定蛋白质结构需要使用分子动力学程序，该程序结合了核磁共振实验数据和隐含的原子数据。每种氨基酸类型的原子参数都编码在结构计算程序(如Dyana和Amber)使用的库中。然而，这些程序或分子可视化程序MOLMOL中只包含少数非标准氨基酸文库集。我们的实验室正在使用核磁共振方法计算多肽和蛋白质的磷酸化和非磷酸化状态。为了计算化学上正确的结构，我们扩展了这些程序可用的分子库，包括修饰的氨基酸磷酸丝氨酸、磷酸苏氨酸和磷酸酪氨酸。
Protein structure determination using Nuclear Magnetic Resonance (NMR) requires the use of molecular dynamics programs that incorporate both NMR experimental and implicit atomic data. Atomic parameters for each amino acid type are encoded in libraries used by structure calculation programs such as DYANA and AMBER. However, only a few non-standard amino acid library sets are included in these programs or the molecular visualization program MOLMOL. Our laboratory is calculating the phosphorylated and non-phosphorylated states of peptides and proteins using NMR methods. To calculate chemically correct structures, we have extended the available molecular libraries for these programs to include the modified amino acids phosphoserine, phosphothreonine, and phosphotyrosine.