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首页> 外文期刊>Acta crystallographica.Section D Biological crystallography. >Factors correlating with significant differences between X-ray structures of myoglobin
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Factors correlating with significant differences between X-ray structures of myoglobin

机译：相关因素有显著差异x射线结构之间的肌红蛋白

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摘要

Validation of general ideas about the origins of conformational differences in proteins is critical in order to arrive at meaningful functional insights. Here, principal component analysis (PCA) and distance difference matrices are used to validate some such ideas about the conformational differences between 291 myoglobin structures from sperm whale, horse and pig. Almost all of the horse and pig structures form compact PCA clusters with only minor coordinate differences and outliers that are easily explained. The 222 whale structures form a few dense clusters with multiple outliers. A few whale outliers with a prominent distortion of the GH loop are very similar to the cluster of horse structures, which all have a similar GH-loop distortion apparently owing to intermolecular crystal lattice hydrogen bonds to the GH loop from residues near the distal histidine His64. The variations of the GH-loop coordinates in the whale structures are likely to be owing to the observed alternative intermolecular crystal lattice bond, with the change to the GH loop distorting bonds correlated with the binding of specific 'unusual' ligands. Such an alternative intermolecular bond is not observed in horse myoglobins, obliterating any correlation with the ligands. Intermolecular bonds do not usually cause significant coordinate differences and cannot be validated as their universal cause. Most of the native-like whale myoglobin structure outliers can be correlated with a few specific factors. However, these factors do not always lead to coordinate differences beyond the previously determined uncertainty thresholds. The binding of unusual ligands by myoglobin, leading to crystal-induced distortions, suggests that some of the conformational differences between the apo and holo structures might not be 'functionally important' but rather artifacts caused by the binding of 'unusual' substrate analogs. The causes of P6 symmetry in myoglobin crystals and the relationship between crystal and solution structures are also discussed.
机译：验证的一般观念的起源在蛋白质构象差异为了到达意义至关重要功能的见解。分析(PCA)和距离差矩阵用于验证一些这样的想法291肌红蛋白构象之间的差异从抹香鲸结构,马和猪。几乎所有的马和猪的结构形式紧凑的PCA集群只有轻微的坐标很容易的差异和异常值解释说。密集的集群与多个异常值。鲸鱼与突出的畸变异常值GH循环非常类似于集群的马结构,都有一个类似的GH-loop显然是由于分子间扭曲晶格氢键的GH循环从远端组氨酸His64附近的残留。GH-loop坐标的变化可能是由于鲸鱼结构观察替代分子间水晶晶格,改变GH循环扭曲了债券相关的绑定特定的“不寻常”的配体。分子间键没有观察到马肌红蛋白,消灭任何相关性配体。造成重大协调差异和无法验证的普遍原因。大多数的本土一样鲸鱼肌红蛋白结构可以与一些特定的异常值的因素。导致协调差异超出了之前确定的阈值的不确定性。绑定不寻常的肌红蛋白配体的领先表明crystal-induced扭曲一些构象之间的差异apo和整体结构可能不是“功能重要”而是工件绑定造成的“不寻常”的衬底类似物。水晶和水晶和之间的关系解决方案的结构进行了讨论。

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