Decanniere K, Desmyter A, Lauwereys M, Ghahroudi M A, Muyldermans S, Wyns L
Laboratorium voor Ultrastructuur, Vlaams Interuniversitair Instituut voor Biotechnologie, Vrije Universiteit Brussel, Paardenstraat 65, B-1640 St. Genesius-Rode, Belgium.
Structure. 1999 Apr 15;7(4):361-70. doi: 10.1016/s0969-2126(99)80049-5.
Camelid serum contains a large fraction of functional heavy-chain antibodies - homodimers of heavy chains without light chains. The variable domains of these heavy-chain antibodies (VHH) have a long complementarity determining region 3 (CDR3) loop that compensates for the absence of the antigen-binding loops of the variable light chains (VL). In the case of the VHH fragment cAb-Lys3, part of the 24 amino acid long CDR3 loop protrudes from the antigen-binding surface and inserts into the active-site cleft of its antigen, rendering cAb-Lys3 a competitive enzyme inhibitor.
A dromedary VHH with specificity for bovine RNase A, cAb-RN05, has a short CDR3 loop of 12 amino acids and is not a competitive enzyme inhibitor. The structure of the cAb-RN05-RNase A complex has been solved at 2.8 A. The VHH scaffold architecture is close to that of a human VH (variable heavy chain). The structure of the antigen-binding hypervariable 1 loop (H1) of both cAb-RN05 and cAb-Lys3 differ from the known canonical structures; in addition these H1 loops resemble each other. The CDR3 provides an antigen-binding surface and shields the face of the domain that interacts with VL in conventional antibodies.
VHHs adopt the common immunoglobulin fold of variable domains, but the antigen-binding loops deviate from the predicted canonical structure. We define a new canonical structure for the H1 loop of immunoglobulins, with cAb-RN05 and cAb-Lys3 as reference structures. This new loop structure might also occur in human or mouse VH domains. Surprisingly, only two loops are involved in antigen recognition; the CDR2 does not participate. Nevertheless, the antigen binding occurs with nanomolar affinities because of a preferential usage of mainchain atoms for antigen interaction.
骆驼科动物血清中含有很大一部分功能性重链抗体——即没有轻链的重链同型二聚体。这些重链抗体（VHH）的可变结构域具有一个长互补决定区3（CDR3）环，可弥补可变轻链（VL）抗原结合环的缺失。就VHH片段cAb-Lys3而言，24个氨基酸长的CDR3环的一部分从抗原结合表面突出并插入其抗原的活性位点裂隙中，使cAb-Lys3成为一种竞争性酶抑制剂。
对牛核糖核酸酶A具有特异性的单峰驼VHH，即cAb-RN05，具有一个12个氨基酸的短CDR3环，不是竞争性酶抑制剂。已解析出cAb-RN05-核糖核酸酶A复合物的结构，分辨率为2.8 Å。VHH支架结构与人类可变重链（VH）的结构相近。cAb-RN05和cAb-Lys3的抗原结合高变1环（H1）的结构均不同于已知的典型结构；此外，这些H1环彼此相似。CDR3提供一个抗原结合表面，并遮蔽了在传统抗体中与VL相互作用的结构域表面。
VHH采用可变结构域常见的免疫球蛋白折叠，但抗原结合环偏离预测的典型结构。我们以cAb-RN05和cAb-Lys3作为参考结构，定义了免疫球蛋白H1环的一种新的典型结构。这种新的环结构也可能出现在人类或小鼠的VH结构域中。令人惊讶的是，只有两个环参与抗原识别；CDR2不参与。然而，由于优先使用主链原子进行抗原相互作用，抗原结合以纳摩尔亲和力发生。
