Alphafold2 models of 47G4 (Hu19) scFv dimers and of VLVL dimers

Alphafold2 models of 47G4 (Hu19) scFv dimers show a variety of swapped VH-VL structures. Alphafold2 dimers models of scFvs formed from VH and VL domains tend to swap to form diabodies with long linkers as for short linkers. The 47G4 scFv used in this study uses a VL-to-VH scFv construct with a long linker (see sequence in Figure 1) See Supplement files for: The 5 best Alphafold2 models of a predicted 47G4 (Hu19) scFv dimer, using the sequence in Figure 1. In PDB format. The 5 models are ranked by AF2 in files: ranked_0...4.pdb The 5 models can be compared by superimposition of the VL domain of chain A: in iCn3D using an iCn3D PNG image file. To see the models and analyze them in 3D, invoke iCn3D with the link: https://www.ncbi.nlm.nih.gov/Structure/icn3d/full.html ; open “iCn3D PNG image file” using the file: 5models_Hu19_scFv_AF2_icn3d_loadable.png Alphafold2 models for 47G4 (Hu19) VL-VL dimers In PDB format. The 25 models are ranked by AF2 in files: Hu19-VLVL-AF2-ranked_0…24.pdb Only one out of 25 models offers an inverted interface but offers lower confidence. All other present the canonical interface. List of PDB structures containing VL-VL quaternary interfaces (PDB accessed on 10/11/2021) See file: PDB-Igs-VLVL-asu+bu-with-over-10contacts.xls The file represents PDB structures that contain contacting VL domains with more than 10 arbitrary contacts in either the first biological Unit (BU) or asymmetric unit (ASU). Both BU and ASU are used as both may contain valid dimers, as in the the inverted VLVL dimer structure (7JO8) Some iCn3D links are provided in the excel file to look and analyze a number of structures. Some links compare 7JO8 to 1REI, or other VLVL parallel vs antiparallel dimer such as 1LVE vs 5LVE. VLVL based diabody models: canonical and inverted A model predicted by Alphafold2 version 2.0 for the 47G4 (Hu19) scFv dimer, using the sequence in Figure 1. Supplement file in PDB format: Hu19-VLVL-diabody-model.pdb Model building of a scFv dimer using the observed VLVL dimer (7JO8) Hu19-inverted VLVL-diabody-model.pdb Both models compared: VLVLDIAB_VLINVDIAB_icn3d_loadable.png Where no link is specified, PDBids can be directly loaded in iCn3D using the link https://www.ncbi.nlm.nih.gov/Structure/icn3d/full.html针对47G4（Hu19）单链抗体可变区片段（single-chain variable fragment, scFv）二聚体的阿尔法折叠2（AlphaFold2）模型，呈现出多种VH-VL交换结构。由重链可变区（variable heavy chain, VH）与轻链可变区（variable light chain, VL）构成的scFv所形成的AlphaFold2二聚体模型，无论连接肽（linker）长短，均易发生交换并形成双体抗体（diabody）。本研究中使用的47G4 scFv采用VL到VH方向的scFv构建体，带有长连接肽（序列参见图1）。补充文件包含：基于图1序列预测得到的47G4（Hu19）scFv二聚体的Top5 AlphaFold2模型，格式为蛋白质数据库（Protein Data Bank, PDB）格式。这5个模型由AlphaFold2（简称AF2）进行打分排序，对应文件为ranked_0…4.pdb。可通过对A链VL结构域进行叠合来比较这5个模型：可借助iCn3D的PNG图像文件完成该操作。若要在3D环境中查看并分析模型，请通过以下链接启动iCn3D：https://www.ncbi.nlm.nih.gov/Structure/icn3d/full.html，随后加载文件5models_Hu19_scFv_AF2_icn3d_loadable.png作为"iCn3D PNG image file"。针对47G4（Hu19）VL-VL二聚体的AlphaFold2模型，格式为PDB格式。25个模型由AF2打分排序，对应文件为Hu19-VLVL-AF2-ranked_0…24.pdb。25个模型中仅1个呈现反向界面，但置信度较低；其余模型均采用经典界面。包含VL-VL四级界面的PDB结构列表（PDB数据获取于2021年11月10日），对应文件为PDB-Igs-VLVL-asu+bu-with-over-10contacts.xls。该文件收录了在首个生物学单元（biological unit, BU）或不对称单元（asymmetric unit, ASU）中，VL结构域间存在超过10个非特异性接触的PDB结构。BU与ASU均可用于分析，因为二者均可能包含合法的二聚体，例如反向VL-VL二聚体结构7JO8。该Excel文件中提供了若干iCn3D链接，用于查看与分析多个结构。部分链接可用于对比7JO8与1REI，或是对比其他VL-VL平行二聚体与反平行二聚体，例如1LVE与5LVE。基于VL-VL的双体抗体模型：经典型与反向型。本研究通过AlphaFold2 2.0版本，基于图1序列预测得到47G4（Hu19）scFv二聚体模型，对应的PDB格式补充文件为Hu19-VLVL-diabody-model.pdb。利用已观测到的VL-VL二聚体（7JO8）构建的scFv二聚体模型，对应文件为Hu19-inverted VLVL-diabody-model.pdb。两个模型的对比文件为VLVLDIAB_VLINVDIAB_icn3d_loadable.png。若未指定链接，可直接通过以下链接在iCn3D中加载PDB编号：https://www.ncbi.nlm.nih.gov/Structure/icn3d/full.html