Mandal C, Kingery B D, Anchin J M, Subramaniam S, Linthicum D S
Department of Veterinary Pathobiology, Texas A&M University, College Station 77843, USA.
Nat Biotechnol. 1996 Mar;14(3):323-8. doi: 10.1038/nbt0396-323.
Immunoglobulin (Ig) amino acid sequences are highly conserved and often have sequence homology ranging from 70 to 95%. Antigen binding fragments (Fab), variable region fragments (Fv), and single chain Fv (scFv) of more than 50 myeloma proteins and monoclonal antibodies (mAb) have been crystallized and display a high degree of structural similarity. Based on this observation, several homology modeling approaches have been developed for the prediction of Fab and Fv structures prior to their experimental determination. We have extracted features from existing Ig sequences, 44 known Fab and Fv structures to create an automated AntiBody structure GENeration (ABGEN) algorithm for obtaining structural models of antibody fragments. ABGEN utilizes a homology based scaffolding technique, and includes the use of invariant and strictly conserved residues, structural motifs of known Fab, canonical features of hypervariable loops, torsional constraints for residue replacements and key inter-residue interactions. The validity of the ABGEN algorithm has been tested using a five-fold cross validation with the existing Fab structures. Molecular mechanics and dynamics methods have been implemented with ABGEN models to accurately predict two Fab structures of anti-sweetener antibodies prior to crystallographic determinations.
免疫球蛋白（Ig）的氨基酸序列高度保守，序列同源性通常在70%至95%之间。50多种骨髓瘤蛋白和单克隆抗体（mAb）的抗原结合片段（Fab）、可变区片段（Fv）和单链Fv（scFv）已被结晶，并显示出高度的结构相似性。基于这一观察结果，已经开发了几种同源建模方法，用于在通过实验确定Fab和Fv结构之前对其进行预测。我们从现有的Ig序列、44种已知的Fab和Fv结构中提取特征，以创建一种自动抗体结构生成（ABGEN）算法，用于获取抗体片段的结构模型。ABGEN利用基于同源性的支架技术，包括使用不变和严格保守的残基、已知Fab的结构基序、高变环的典型特征、残基替换的扭转约束以及关键的残基间相互作用。ABGEN算法的有效性已通过对现有Fab结构进行五重交叉验证进行了测试。分子力学和动力学方法已应用于ABGEN模型，以在晶体学测定之前准确预测抗甜味剂抗体的两种Fab结构。
