Analysis and modeling of the variable region of camelid single-domain antibodies.
Analysis and modeling of the variable region of camelid single-domain antibodies.
复制标题
DOI：
10.4049/jimmunol.1100116
复制
发表时间：
2011-06-01
期刊：
影响因子：
--
通讯作者：
Gray JJ
中科院分区：
文献类型：
--
作者：
Sircar A;Sanni KA;Shi J;Gray JJ
骆驼科动物有一种特殊类型的抗体，称为重链抗体（HCAb），缺乏经典的抗体轻链。相对于经典抗体，骆驼HCAb（cAbs）具有相当的免疫原性、抗原识别多样性和结合亲和力、更高的稳定性和溶解性以及更好的可制造性，使其成为替代治疗支架的有希望的候选者。合理改造cAb以改善治疗功能需要了解cAb与经典抗体之间的序列和结构特征的差异。在此，将27个cAb可变区（VHH）的氨基酸序列与54个经典抗体的相应区域进行比对以检测氨基酸差异，使得能够自动鉴定cAb VHH互补决定区（CDR）。CDR分析表明，H1经常（有时H2）采用不同的构象不能分类的既定的规范规则。此外，虽然cAb H3比经典的H3环长得多，但它通常含有共同的结构基序，有时还含有与H1连接的二硫键。利用这些观察结果，我们创建了基于Monte Carlo的cAb VHH结构建模工具，其中CDR H1和H2环显示出与天然抗体的中位均方根偏差（rmsd）分别为3.1和1.5 μ g。该方案产生了8-12、14-16和16-24个残基的H3环，相对于天然的中值rmsd分别为5.7、4.5和6.8 bp。预测循环的巨大偏差凸显了对此类长循环进行建模的挑战。cAb VHH同源性模型可以提供对相互作用机制的结构见解，以使得能够开发用于治疗和生物技术用途的新型抗体。
Camelids have a special type of antibodies, known as heavy chain antibodies (HCAbs), that are devoid of classical antibody light chains. Relative to classical antibodies, camelid HCAbs (cAbs) have comparable immunogenicity, antigen recognition diversity and binding affinities, higher stability and solubility, and better manufacturability, making them promising candidates for alternate therapeutic scaffolds. Rational engineering of cAbs to improve therapeutic function requires knowledge of the differences of sequence and structural features between cAbs and classical antibodies. Here, amino acid sequences of 27 cAb variable regions (VHH) were aligned with the respective regions of 54 classical antibodies to detect amino acid differences, enabling automatic identification of cAb VHH complementarity determining regions (CDRs). CDR analysis revealed that the H1 often (and sometimes the H2) adopts diverse conformations not classifiable by established canonical rules. Also, while the cAb H3 is much longer than classical H3 loops, it often contains common structural motifs and sometimes a disulfide bond to the H1. Leveraging these observations, we created a Monte Carlo based cAb VHH structural modeling tool, where the CDR H1 and H2 loops exhibited a median root-mean-square-deviation (rmsd) to native of 3.1 and 1.5 Å respectively. The protocol generated 8-12, 14-16 and 16-24 residue H3 loops with a median rmsd to native of 5.7, 4.5 and 6.8 Å respectively. The large deviation of the predicted loops underscores the challenge in modeling such long loops. cAb VHH homology models can provide structural insights into interaction mechanisms to enable development of novel antibodies for therapeutic and biotechnological use.
登录
查看更多内容
影响因子：
4.8
作者：
De Genest, E;Silence, K;Muyldermans, S
通讯作者：
Muyldermans, S
影响因子：
2.9
作者：
Fitch, CA;Whitten, ST;García-Moreno, B
通讯作者：
García-Moreno, B
影响因子：
5.6
作者：
AlLazikani, B;Lesk, AM;Chothia, C
通讯作者：
Chothia, C
影响因子：
4.8
作者：
Desmyter, A;Spinelli, S;Cambillau, C
通讯作者：
Cambillau, C
影响因子：
3.6
作者：
Abhinandan, K. R.;Martin, Andrew C. R.
通讯作者：
Martin, Andrew C. R.