Teaching an old scaffold new tricks: monobodies constructed using alternative surfaces of the FN3 scaffold.
Teaching an old scaffold new tricks: monobodies constructed using alternative surfaces of the FN3 scaffold.
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DOI：
10.1016/j.jmb.2011.12.019
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发表时间：
2012-01-13
影响因子：
5.6
通讯作者：
Koide, Shohei
中科院分区：
文献类型：
--
作者：
Koide, Akiko;Wojcik, John;Gilbreth, Ryan N.;Hoey, Robert J.;Koide, Shohei
纤连蛋白 III 型结构域 (FN3) 已成为最广泛使用的用于生成新结合蛋白的非抗体支架之一。由于其与免疫球蛋白结构域的结构同源性，迄今为止设计的 FN3 组合文库主要集中于将氨基酸多样性引入相当于抗体互补决定区的三个环中。在这里，我们报告了一个 FN3 文库，它利用替代位置来呈现氨基酸多样性。我们改变了β-折叠和表面环上的位置，共同形成凹面。新的文库产生了多种靶蛋白的结合蛋白（称为“单体”），通常与原始的环聚焦文库具有相似的功效。从新文库生成的单体与其靶标复合物 Abl SH2 结构域的晶体结构表明，按照我们设计的预期，单体的凹面与靶标的凸面结合，界面面积是已发表的单体-靶标复合物结构中最大的之一。这种相互作用模式不同于单域抗体和抗体模拟物的常见结合模式，在单域抗体和抗体模拟物中，识别环识别靶标中的裂口。总之，这项工作说明了利用单个免疫球蛋白样支架的不同表面来生成具有不同特征的结合蛋白。
The fibronectin type III domain (FN3) has become one of the most widely used non-antibody scaffolds for generating new binding proteins. Because of its structural homology to the immunoglobulin domain, combinatorial libraries of FN3 designed to date have primarily focused on introducing amino acid diversity into three loops that are equivalent to antibody complementarity-determining regions. Here, we report an FN3 library that utilizes alternative positions for presenting amino acid diversity. We diversified positions on a β-sheet and surface loops that together form a concave surface. The new library produced binding proteins (termed “monobodies”) to multiple target proteins, generally with similar efficacy as the original, loop-focused library. The crystal structure of a monobody generated from the new library in complex with its target, the Abl SH2 domain, revealed that a concave surface of the monobody, as intended in our design, bound to a convex surface of the target with the interface area being among the largest of published structures of monobody-target complexes. This mode of interaction differs from a common binding mode for single-domain antibodies and antibody mimics in which recognition loops recognize clefts in targets. Together, this work illustrates the utilization of different surfaces of a single immunoglobulin-like scaffold to generate binding proteins with distinct characteristics.
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DOI：
10.1107/s0907444904019158
发表时间：
2004-12-01
影响因子：
2.2
作者：
Emsley, P;Cowtan, K
通讯作者：
Cowtan, K
影响因子：
5.6
作者：
Gilbreth, Ryan N.;Esaki, Kaori;Koide, Shohei
通讯作者：
Koide, Shohei
影响因子：
5.6
作者：
DICKINSON, CD;VEERAPANDIAN, B;ELY, KR
通讯作者：
ELY, KR
DOI：
10.1107/s0907444998003254
发表时间：
1998-09-01
期刊：
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY
影响因子：
--
作者：
Brunger, AT;Adams, PD;Warren, GL
通讯作者：
Warren, GL
影响因子：
5.6
作者：
Hackel, Benjamin J.;Kapila, Atul;Wittrup, K. Dane
通讯作者：
Wittrup, K. Dane