本文旨在通过研究已知的复合物来了解纳米抗体-蛋白质对的结合策略。刚体蛋白-配体对接程序产生几种复合物,叫做诱饵,哪些是形状互补性得分高的优秀候选人,静电相互作用,去溶剂化,埋藏表面积,和伦纳德-琼斯的潜力。然而,对应于原生结构的诱饵是未知的。我们从单域抗体数据库中研究了36个纳米抗体-蛋白质复合物,sd-AbDB,http://www。sdab-db.ca/.对于每个结构,使用ZDOCK软件的快速傅里叶变换算法生成大量诱饵。根据目标蛋白质-纳米抗体相互作用能对诱饵进行排名,通过使用Dreiding力场计算,秩1具有最低的相互作用能。在36个蛋白质数据库(PDB)结构中,25个真实结构被预测为等级1。其余结构中的11个需要纳米抗体相对于蛋白质的Nangstrom大小的刚体平移以匹配给定的PDB结构。翻译后,所有复合物的Dreiding相互作用(DI)能量均降低并变为1级。在一个案例中,需要刚体旋转以及纳米体的平移来匹配晶体结构。我们使用了蒙特卡罗算法,该算法随机平移和旋转诱饵的纳米体,并计算DI能量。结果表明,刚体平移和DI能量足以确定ZDOCK创建的诱饵的正确结合位置和姿势。对sd-AbDB的调查表明,每个纳米抗体与其伴侣蛋白至少产生一个盐桥,这表明盐桥的形成是纳米抗体-蛋白质识别的重要策略。基于对36种晶体结构的分析和现有文献的证据,我们提出了一套可用于纳米抗体设计的原则。
This paper aims to understand the binding strategies of a nanobody-protein pair by studying known complexes. Rigid body protein-ligand docking programs produce several complexes, called decoys, which are good candidates with high scores of shape complementarity, electrostatic interactions, desolvation, buried surface area, and Lennard-Jones potentials. However, the decoy that corresponds to the native structure is not known. We studied 36 nanobody-protein complexes from the single domain antibody database, sd-Ab DB, http://www.sdab-db.ca/. For each structure, a large number of decoys are generated using the Fast Fourier Transform algorithm of the software ZDOCK. The decoys were ranked according to their target protein-nanobody interaction energies, calculated by using the Dreiding Force Field, with rank 1 having the lowest interaction energy. Out of 36 protein data bank (PDB) structures, 25 true structures were predicted as rank 1. Eleven of the remaining structures required Ångstrom size rigid body translations of the nanobody relative to the protein to match the given PDB structure. After the translation, the Dreiding interaction (DI) energies of all complexes decreased and became rank 1. In one case, rigid body rotations as well as translations of the nanobody were required for matching the crystal structure. We used a Monte Carlo algorithm that randomly translates and rotates the nanobody of a decoy and calculates the DI energy. Results show that rigid body translations and the DI energy are sufficient for determining the correct binding location and pose of ZDOCK created decoys. A survey of the sd-Ab DB showed that each nanobody makes at least one salt bridge with its partner protein, indicating that salt bridge formation is an essential strategy in nanobody-protein recognition. Based on the analysis of the 36 crystal structures and evidence from existing literature, we propose a set of principles that could be used in the design of nanobodies.