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为Fcabs中的环延伸创建稳定的茎区——结合酵母表面展示、计算机辅助环重建和分子动力学模拟的见解

Creating stable stem regions for loop elongation in Fcabs - insights from combining yeast surface display, in silico loop reconstruction and molecular dynamics simulations.

作者信息

Hasenhindl Christoph, Lai Balder, Delgado Javier, Traxlmayr Michael W, Stadlmayr Gerhard, Rüker Florian, Serrano Luis, Oostenbrink Chris, Obinger Christian

机构信息

Christian Doppler Laboratory for Antibody Engineering, Vienna Institute of BioTechnology, BOKU - University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria; Department of Chemistry, Vienna Institute of BioTechnology, BOKU - University of Natural Resources and Life Sciences, Muthgasse 18, A-1190 Vienna, Austria.

Institute of Molecular Modeling and Simulation, Department of Material Sciences and Process Engineering, BOKU - University of Natural Resources and Life Sciences, A-1190 Vienna, Austria.

出版信息

Biochim Biophys Acta. 2014 Sep;1844(9):1530-40. doi: 10.1016/j.bbapap.2014.04.020. Epub 2014 May 2.

Abstract

Fcabs (Fc antigen binding) are crystallizable fragments of IgG where the C-terminal structural loops of the CH3 domain are engineered for antigen binding. For the design of libraries it is beneficial to know positions that will permit loop elongation to increase the potential interaction surface with antigen. However, the insertion of additional loop residues might impair the immunoglobulin fold. In the present work we have probed whether stabilizing mutations flanking the randomized and elongated loop region improve the quality of Fcab libraries. In detail, 13 libraries were constructed having the C-terminal part of the EF loop randomized and carrying additional residues (1, 2, 3, 5 or 10, respectively) in the absence and presence of two flanking mutations. The latter have been demonstrated to increase the thermal stability of the CH3 domain of the respective solubly expressed proteins. Assessment of the stability of the libraries expressed on the surface of yeast cells by flow cytometry demonstrated that loop elongation was considerably better tolerated in the stabilized libraries. By using in silico loop reconstruction and mimicking randomization together with MD simulations the underlying molecular dynamics were investigated. In the presence of stabilizing stem residues the backbone flexibility of the engineered EF loop as well as the fluctuation between its accessible conformations were decreased. In addition the CD loop (but not the AB loop) and most of the framework regions were rigidified. The obtained data are discussed with respect to the design of Fcabs and available data on the relation between flexibility and affinity of CDR loops in Ig-like molecules.

摘要

Fc抗原结合片段(Fcabs)是IgG的可结晶片段,其中CH3结构域的C端结构环经过工程改造用于抗原结合。对于文库设计而言,了解哪些位置能够允许环延长以增加与抗原的潜在相互作用表面是有益的。然而,额外环残基的插入可能会损害免疫球蛋白折叠。在本研究中,我们探究了随机化和延长环区域两侧的稳定化突变是否能提高Fcabs文库的质量。具体而言,构建了13个文库,其EF环的C端部分是随机化的,并且在不存在和存在两个侧翼突变的情况下分别携带额外的残基(分别为1、2、3、5或10个)。后者已被证明可提高相应可溶性表达蛋白CH3结构域的热稳定性。通过流式细胞术评估酵母细胞表面表达的文库的稳定性表明,在稳定化文库中环延长的耐受性明显更好。通过使用计算机环重建和模拟随机化以及分子动力学模拟研究了潜在的分子动力学。在存在稳定化主干残基的情况下,工程化EF环的主链柔韧性及其可及构象之间的波动减小。此外,CD环(而非AB环)和大多数框架区域都变得更加刚性。结合Fcabs的设计以及关于Ig样分子中CDR环柔韧性与亲和力之间关系的现有数据对所得数据进行了讨论。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/d18a/4118681/b415dda82059/fx1.jpg

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