Eisenberg D, Bowie J U, Lüthy R, Choe S
Department of Chemistry and Biochemistry, UCLA 90024.
Faraday Discuss. 1992(93):25-34.
In the method of 3D (three-dimensional) profiles, each residue position in a protein is characterized by its environment and is represented by a row of 20 numbers in a table, the profile. These numbers are the statistical preferences (called 3D-1D scores) of each of the 20 amino acids for this environment. A profile is computed from the coordinates of a protein model, and it gives a score S for any amino acid sequence folded as the model. To date 3D profiles have found three applications. The first is to identify other protein sequences which are folded in the same general pattern as the structure from which the profile was prepared. These are sequences which have high scores for the profile computed from the model. The second is to assess the validity of protein models, however determined. Correct models are found to give profiles that have high scores for their own amino acid sequences, and incorrect models are found to have lower scores. The example of the X-ray structure determination of diphtheria toxin is discussed. The third application is to assess which is the stable oligomeric state of a folded protein. Several examples suggest that the highest profile score for a sequence is achieved when the protein is aggregated into its most stable oligomeric state.
在三维（3D）轮廓方法中，蛋白质中的每个残基位置都由其环境来表征，并由一个表格（即轮廓）中的一行20个数字来表示。这些数字是20种氨基酸中每一种在该环境下的统计偏好（称为3D-1D分数）。一个轮廓是根据蛋白质模型的坐标计算得出的，它会为任何按照该模型折叠的氨基酸序列给出一个分数S。到目前为止，3D轮廓已经有了三种应用。第一种是识别其他以与制备该轮廓的结构相同的大致模式折叠的蛋白质序列。这些序列对于根据该模型计算出的轮廓具有高分。第二种是评估蛋白质模型的有效性，无论其是如何确定的。发现正确的模型为其自身的氨基酸序列给出的轮廓具有高分，而错误的模型得分较低。文中讨论了白喉毒素X射线结构测定的例子。第三种应用是评估折叠蛋白的稳定寡聚状态是哪一种。几个例子表明，当蛋白质聚集到其最稳定的寡聚状态时，序列的轮廓得分最高。
