Crystal Structure and Computational Modeling of the Fab Fragment from a Protective Anti-Ricin Monoclonal Antibody
Crystal Structure and Computational Modeling of the Fab Fragment from a Protective Anti-Ricin Monoclonal Antibody
复制标题
DOI：
10.1371/journal.pone.0052613
复制
发表时间：
2012-12-19
期刊：
影响因子：
3.7
通讯作者：
Pincus, Seth H.
中科院分区：
文献类型：
--
作者：
Zhao, Zhiyu;Worthylake, David;Pincus, Seth H.
背景：许多抗体的晶体结构已被解决。已经开发了结构建模程序，其利用该信息基于其序列预测抗体的3-D结构。由于自我参考的问题，这些预测的准确性和实用性只能进行测试时，一个新的结构还没有被存放在Protein DataBank.Methods：我们已经解决了RAC 18，一个保护性的抗蓖麻毒素单克隆抗体的Fab片段的晶体结构，以1.9埃的分辨率。我们还使用公开可用的Ab建模工具免疫球蛋白结构预测（PIGS）、RosettaAntibody和Web抗体建模（WAM）对RAC 18的Fv结构进行了建模。模型结构进行能量最小化。我们比较结果的晶体结构的基础上的均方根偏差（RMSD），模板建模得分（TM得分），Z-得分，和MolProbity analysis.Findings：晶体结构显示了一个口袋，主要由AA残基形成的每个重链互补决定区（CDR）。晶体结构与建模工具预测的结构之间存在差异，特别是在CDR中。预测模型之间也存在差异，尽管差异很小，并且在实验误差范围内。没有一个建模程序明显优于其他的上级。在某些情况下，选择结构的基础上，只有序列同源性结晶抗体产生RMSDs可比的models.Conclusions：分子建模程序准确地预测抗体可变结构域的RAC 18的大部分区域的结构。高变CDR被证明是最难建模的，特别是H链CDR 3。由于CDR 3最常参与与抗原的接触，因此在使用模型鉴定抗体和抗原之间的潜在接触时必须考虑该缺陷。由于这项研究只代表一个单一的情况下，结果不能概括。相反，它们突出了建模程序的实用性和局限性。
Background: Many antibody crystal structures have been solved. Structural modeling programs have been developed that utilize this information to predict 3-D structures of an antibody based upon its sequence. Because of the problem of self-reference, the accuracy and utility of these predictions can only be tested when a new structure has not yet been deposited in the Protein Data Bank.Methods: We have solved the crystal structure of the Fab fragment of RAC18, a protective anti-ricin mAb, to 1.9 angstrom resolution. We have also modeled the Fv structure of RAC18 using publicly available Ab modeling tools Prediction of Immunoglobulin Structures (PIGS), RosettaAntibody, and Web Antibody Modeling (WAM). The model structures underwent energy minimization. We compared results to the crystal structure on the basis of root-mean-square deviation (RMSD), template modeling score (TM-score), Z-score, and MolProbity analysis.Findings: The crystal structure showed a pocket formed mainly by AA residues in each of the heavy chain complementarity determining regions (CDRs). There were differences between the crystal structure and structures predicted by the modeling tools, particularly in the CDRs. There were also differences among the predicted models, although the differences were small and within experimental error. No one modeling program was clearly superior to the others. In some cases, choosing structures based only on sequence homology to the crystallized Ab yielded RMSDs comparable to the models.Conclusions: Molecular modeling programs accurately predict the structure of most regions of antibody variable domains of RAC18. The hypervariable CDRs proved most difficult to model, particularly H chain CDR3. Because CDR3 is most often involved in contact with antigen, this defect must be considered when using models to identify potential contacts between antibody and antigen. Because this study represents only a single case, the results cannot be generalized. Rather they highlight the utility and limitations of modeling programs.