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首页> 外文期刊>Acta crystallographica.Section D. Biological crystallography >Protein flexibility: coordinate uncertainties and interpretation of structural differences
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Protein flexibility: coordinate uncertainties and interpretation of structural differences

机译：蛋白质的灵活性:协调和不确定性结构差异的解释

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摘要

Valid interpretations of conformational movements in protein structures determined by X-ray crystallography require that the movement magnitudes exceed their uncertainty threshold. Here, it is shown that such thresholds can be obtained from the distance difference matrices (DDMs) of 1014 pairs of independently determined structures of bovine ribonuclease A and sperm whale myoglobin, with no explanations provided for reportedly minor coordinate differences. The smallest magnitudes of reportedly functional motions are just above these thresholds. Uncertainty thresholds can provide objective criteria that distinguish between true conformational changes and apparent 'noise', showing that some previous interpretations of protein coordinate changes attributed to external conditions or mutations may be doubtful or erroneous. The use of uncertainty thresholds, DDMs, the newly introduced CDDMs (contact distance difference matrices) and a novel simple rotation algorithm allows a more meaningful classification and description of protein motions, distinguishing between various rigid-fragment motions and nonrigid conformational deformations. It is also shown that half of 75 pairs of identical molecules, each from the same asymmetric crystallo-graphic cell, exhibit coordinate differences that range from just outside the coordinate uncertainty threshold to the full magnitude of large functional movements. Thus, crystallization might often induce protein conformational changes that are comparable to those related to or induced by the protein function.
机译：有效的解释构象运动在蛋白质结构由x射线晶体学要求的运动大小超过其阈值的不确定性。在这里,它是表明这种阈值从不同的距离矩阵(摘要)的1014双独立决定结构的牛核糖核酸酶A和精子鲸鱼的肌红蛋白,没有提供解释据说小坐标差异。据说最小大小的功能运动只是以上这些阈值。不确定的阈值可以提供目标标准区分真实的构象变化和明显的“噪音”,显示,一些以前的解释蛋白质坐标变化归因于外部条件或突变可能怀疑或错误的。DDMs,新引进CDDMs(接触距离差别矩阵)和一个简单的小说旋转算法允许一个更有意义的蛋白质的分类和描述动作,区分不同rigid-fragment运动和非刚性的构象变形。一半的75对相同的分子,每个从相同的不对称crystallo-graphic细胞,表现出协调差异范围从城外坐标不确定性满级的阈值大功能动作。经常引起蛋白质构象的变化与相关或引起的吗蛋白质的功能。

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