Enshell-Seijffers David, Denisov Dmitri, Groisman Bella, Smelyanski Larisa, Meyuhas Ronit, Gross Gideon, Denisova Galina, Gershoni Jonathan M
Department of Cell Research and Immunology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.
J Mol Biol. 2003 Nov 14;334(1):87-101. doi: 10.1016/j.jmb.2003.09.002.
A method for the discovery of the structure of conformational discontinuous epitopes of monoclonal antibodies (mAbs) is described. The mAb is used to select specific phages from combinatorial phage-display peptide libraries that in turn are used as an epitope-defining database that is applied via a novel computer algorithm to analyze the crystalline structure of the original antigen. The algorithm is based on the following: (1) Most contacts between a mAb and an antigen are through side-chain atoms of the residues. (2) In the three-dimensional structure of a protein, amino acid residues remote in linear sequence can juxtapose to one another through folding. (3) Tandem amino acid residues of the selected phage-displayed peptides can represent pairs of juxtaposed amino acid residues of the antigen. (4) Contact residues of the epitope are accessible to the antigen surface. (5) The most frequent tandem pairs of amino acid residues in the selected phage-displayed peptides can reflect pairs of juxtaposed amino acid residues of the epitope. Application of the algorithm enabled prediction of epitopes. On the basis of these predictions, segments of an antigen were used to reconstitute an antigenic epitope mimetic that was recognized by its original mAb.
本文描述了一种发现单克隆抗体（mAb）构象不连续表位结构的方法。该单克隆抗体用于从组合噬菌体展示肽库中筛选特定噬菌体，这些噬菌体进而用作表位定义数据库，通过一种新颖的计算机算法应用于分析原始抗原的晶体结构。该算法基于以下几点：（1）单克隆抗体与抗原之间的大多数接触是通过残基的侧链原子进行的。（2）在蛋白质的三维结构中，线性序列中相距较远的氨基酸残基可通过折叠相互并列。（3）所选噬菌体展示肽的串联氨基酸残基可代表抗原并列的氨基酸残基对。（4）表位的接触残基可暴露于抗原表面。（5）所选噬菌体展示肽中最常见的串联氨基酸残基对可反映表位并列的氨基酸残基对。该算法的应用能够预测表位。基于这些预测，利用抗原片段重构了一种抗原表位模拟物，该模拟物可被其原始单克隆抗体识别。
