Interatomic Distances Chi-Squared Test

Models <i>in silico</i> were developed using Molecular Modelling Pro Plus, version 6.22, and ChemSite, version 5.10, produced by ChemSW (Accelrys Inc., San Diego, USA), as described in <i>Methods</i>. For EPL001’s ₉KEFNNI₁₄, nine atoms were selected from side chains and two from the peptide backbone, thus: a = nitrogen in the side-chain of K9; b = delta carbon in E; c = hydroxyl oxygen in the side-chain of E; d = beta carbon in F; e = gamma carbon of F; f = peptide bond carbon of I; g = delta carbon of I; h = gamma carbon of N13; i = nitrogen of the side-chain of N13; j = peptide bond carbon of N12, k = nitrogen of side-chain of N12. This permitted 46 measurements, each atom to every other atom: a-b, a-c etc. Distances between the same atoms were calculated for KEFNNI as a free peptide, with comparisons reducing in number for free EFNNI through free FNNI to free NNI. The peptide MKPVFNNI has also been modelled. A chi-squared test was used, with measurements from the EPL001 model in silico representing Expected (E) and measurements from the modelled free peptides as Observed (O). Chi-squared values were calculated on the basis of (O-E)²/E. dof = degrees of freedom.本研究采用ChemSW公司（Accelrys公司，美国圣地亚哥）推出的分子建模专业版6.22（Molecular Modelling Pro Plus）与ChemSite 5.10版，构建计算机模拟（in silico）模型，具体方法如《方法》（Methods）部分所述。针对EPL001的第9至14位残基肽段₉KEFNNI₁₄，从其侧链选取9个原子、肽主链选取2个原子，具体定义如下：a为第9位赖氨酸（K）的侧链氮原子；b为谷氨酸（E）的δ碳原子；c为谷氨酸（E）侧链的羟基氧原子；d为苯丙氨酸（F）的β碳原子；e为苯丙氨酸（F）的γ碳原子；f为异亮氨酸（I）的肽键碳原子；g为异亮氨酸（I）的δ碳原子；h为第13位天冬酰胺（N）的γ碳原子；i为第13位天冬酰胺（N）的侧链氮原子；j为第12位天冬酰胺（N）的肽键碳原子；k为第12位天冬酰胺（N）的侧链氮原子。由此可生成46组原子间距测量值，覆盖所有两两原子组合（如a-b、a-c等）。针对游离态KEFNNI肽计算对应原子间的距离，后续依次针对游离态EFNNI、游离态FNNI及游离态NNI开展相同计算时，可比较的组数逐渐减少。肽段MKPVFNNI同样完成了计算机建模。本研究采用卡方检验（chi-squared test），将EPL001计算机模拟模型的测量值作为期望频数（E），建模得到的游离态肽段测量值作为观测频数（O）。卡方值按照(O-E)²/E公式计算得出，dof即自由度（degrees of freedom）。

搜集汇总

背景与挑战

背景概述

该数据集基于分子建模软件对肽EPL001的原子间距离进行测量，并通过卡方检验比较其在结合状态与自由状态下的结构差异，以支持免疫学相关研究。数据集包含46个原子间距离测量值，涉及多个肽变体的分析，并采用CC BY 4.0许可证开放共享。