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Research Article

基于结构的蛋白质-肽亲和数据集及其非冗余基准:在计算肽学中的潜在应用

卷 31, 期 26, 2024

发表于: 06 November, 2023

页: [4127 - 4137] 页: 11

弟呕挨: 10.2174/0929867331666230908102925

价格: $65

摘要

背景：多肽在多种细胞功能中起着至关重要的作用，并通过与多种蛋白质的相互作用参与许多生物过程，在过去的几十年里，它也被开发为一类有前途的治疗药物，用于靶向可药物蛋白质。了解蛋白质-肽相互作用(PpIs)的结构和亲和力之间的内在联系对于计算肽学领域具有相当大的价值，例如指导蛋白质-肽对接计算，开发蛋白质-肽亲和力评分函数，以及为特定蛋白质受体设计肽配体。 目的：我们尝试创建一个数据源，将PpI结构与亲和力关联起来。 方法：通过全面调查整个蛋白质数据库(PDB)数据库以及本体丰富的文献信息，我们手动策划了一个基于结构的蛋白质-肽亲和数据集PpIDS，该数据集收集了350多个PpI复合物样品，这些样品具有实验测量的结构和亲和数据。将数据集进一步简化为一个由102个剔除样本组成的非冗余基准，即PpI[S/ A]BM，该基准只选择结构可靠、功能多样、进化非同源的样本。 结果：收集到的结构用x射线晶体学或溶液核磁共振在高分辨率水平上进行了解析，而沉积的亲和力通过解离常数(即Kd值)来表征，Kd值是蛋白质和肽之间分子间相互作用强度的直接生物物理测量，范围从亚纳摩尔到毫摩尔。set/benchmark中的PpI样品根据其肽配体的二级结构，任意分为α-螺旋、部分α-螺旋、结合形成的β-片、自折叠形成的β-链、混合等不规则类型，共分为6类。此外，我们还根据它们的生物学功能和结合行为对这些PpI进行了分类。 结论：

关键词: 基于结构的蛋白质-肽亲和数据集，蛋白质-肽相互作用，数据调查，基准，复杂结构，结合亲和，计算肽学。

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