Relationship between chemical shift value and accessible surface area for all amino acid atoms
Relationship between chemical shift value and accessible surface area for all amino acid atoms
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DOI：
10.1186/1472-6807-9-20
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发表时间：
2009-04-02
影响因子：
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通讯作者：
Rieping, Wolfgang
中科院分区：
文献类型：
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作者：
Vranken, Wim F.;Rieping, Wolfgang
背景：从NMR实验中获得的化学位移是确定二级甚至三级蛋白质结构的重要工具。化学位移数据的主要存储库是BioMagResBank，它提供了具有此类信息的NMR-STAR文件。然而，由于原子和链命名的差异以及序列编号的变化，将此信息与PDB中非骨架原子的可用坐标数据联系起来并非易事。我们在这里描述了一组一致的化学位移和坐标数据的分析，其中，我们专注于每个原子的溶剂可及表面积（阿萨）之间的关系，在报告的坐标和它们报告的化学位移值中。数据可在http://www.ebi.ac.uk/pdbe/docs/NMR/shiftAnalysis/index.html.Conclusion上在线获得：与溶剂可访问的原子相比，每个原子阿萨为零的原子具有显著更大的化学位移分散度，并且通常具有不同的化学位移分布。在较高的每原子阿萨的情况下，化学位移值也趋向于无规卷曲值。每个原子的阿萨，虽然不是化学位移的决定因素，因此提供了一种直接将化学位移信息与原子坐标相关联的方法。
Background: Chemical shifts obtained from NMR experiments are an important tool in determining secondary, even tertiary, protein structure. The main repository for chemical shift data is the BioMagResBank, which provides NMR-STAR files with this type of information. However, it is not trivial to link this information to available coordinate data from the PDB for non-backbone atoms due to atom and chain naming differences, as well as sequence numbering changes.Results: We here describe the analysis of a consistent set of chemical shift and coordinate data, in which we focus on the relationship between the per-atom solvent accessible surface area (ASA) in the reported coordinates and their reported chemical shift value. The data is available online on http://www.ebi.ac.uk/pdbe/docs/NMR/shiftAnalysis/index.html.Conclusion: Atoms with zero per-atom ASA have a significantly larger chemical shift dispersion and often have a different chemical shift distribution compared to those that are solvent accessible. With higher per-atom ASA, the chemical shift values also tend towards random coil values. The per-atom ASA, although not the determinant of the chemical shift, thus provides a way to directly correlate chemical shift information to the atomic coordinates.