Updated restraint dictionaries for carbohydrates in the pyranose form.
Updated restraint dictionaries for carbohydrates in the pyranose form.
复制标题
更新的碳水化合物形式的碳水化合物的约束词典。
DOI：
10.1107/s2059798322001103
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发表时间：
2022-04-01
期刊：
影响因子：
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通讯作者：
Agirre J
中科院分区：
文献类型：
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作者：
Atanasova M;Nicholls RA;Joosten RP;Agirre J
已使用CCP 4中发布的最新方法生成了吡喃糖形式碳水化合物的新抑制词典。新的约束允许用户在优化过程中保持吡喃糖苷模型处于最低能量构象。在大分子结构精化期间使用约束字典来封装分子内连接性和几何信息。这些字典允许先前确定的“理想”值的功能，如键长，角度和扭转被用作约束目标。在细化过程中，约束影响模型采用与先前观察一致的构象。这在精制糖基化蛋白质的晶体结构时尤其重要，因为它们的分辨率往往比非糖基化蛋白质的分辨率差。吡喃糖苷，在所有形式的蛋白质糖基化中占压倒性多数的组分，经常在晶体结构中显示构象错误。虽然这些缺陷中的许多通常与模型构建有关，但细化问题也可能源于次优约束字典。为了避免随后的误解，并提高质量的所有吡喃糖单糖条目在CCP4 MPEG4图书馆，新的字典与改进的环扭转约束，坐标反映最低能量的环褶皱和更新的几何形状已经产生和评估。这些新字典现在是CCP4 MPEG4 Library的一部分，并将随CCP4 8.0版本发布。
New restraint dictionaries for carbohydrates in the pyranose form have been produced using the latest methods as released in CCP4. The new restraints allow users to keep pyranoside models in their lowest energy conformation during refinement. Restraint dictionaries are used during macromolecular structure refinement to encapsulate intramolecular connectivity and geometric information. These dictionaries allow previously determined ‘ideal’ values of features such as bond lengths, angles and torsions to be used as restraint targets. During refinement, restraints influence the model to adopt a conformation that agrees with prior observation. This is especially important when refining crystal structures of glycosylated proteins, as their resolutions tend to be worse than those of nonglycosylated proteins. Pyranosides, the overwhelming majority component in all forms of protein glycosylation, often display conformational errors in crystal structures. Whilst many of these flaws usually relate to model building, refinement issues may also have their root in suboptimal restraint dictionaries. In order to avoid subsequent misinterpretation and to improve the quality of all pyranose monosaccharide entries in the CCP4 Monomer Library, new dictionaries with improved ring torsion restraints, coordinates reflecting the lowest-energy ring pucker and updated geometry have been produced and evaluated. These new dictionaries are now part of the CCP4 Monomer Library and will be released with CCP4 version 8.0.