Characterization of the human Ig heavy chain antigen binding complementarity determining region 3 using a newly developed software algorithm, JOINSOLVER
Characterization of the human Ig heavy chain antigen binding complementarity determining region 3 using a newly developed software algorithm, JOINSOLVER
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DOI：
10.4049/jimmunol.172.11.6790
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发表时间：
2004-06-01
影响因子：
4.4
通讯作者：
Lipsky, PE
中科院分区：
文献类型：
--
作者：
Souto-Carneiro, MM;Longo, NS;Lipsky, PE
我们用新开发的程序JOINSOLVER分析了77个非生产性和574个生产性人类V（H）DJ（H）重排。在生产性库中，H链互补决定区3（CDR 3（H））比非生产性库（53.8 +/-1.9个核苷酸）明显短（46.7 +/-0.5个核苷酸），因为倾向于选择具有较低TdT活性和较短D片段的重排。使用Monte Carlo模拟建立的标准，可以在71.4%的非生产性重排和64.4%的生产性重排中鉴定出D片段，平均值分别为17.6 +/- 0.7和14.6 +/- 0.2个保留的种系核苷酸。27个D片段中有8个在非生产性库中的使用频率高于预期，而3个D片段被正向选择，3个被负向选择，表明分子机制和选择都偏向于D片段的使用。D片段阅读框（RF）在非生产性库中的使用没有偏倚，而在生产性库中注意到编码终止密码子的RF的负选择和经常编码亲水性氨基酸的RF 2的正选择。除了丝氨酸，没有一致的选择或亲水性氨基酸的表达。在非生产性组中观察到5' D片段与3' J（H）片段配对的偏好，而在生产性组中没有观察到，而V-H片段的使用是随机的。利用倒D片段、家系片段、15号染色体D片段和多个D片段进行重排的情况很少。使用JOINSOLVER对人CDR 3（H）进行的分析提供了有关影响V-H链这一重要Ag结合区的全面信息。
We analyzed 77 nonproductive and 574 productive human V(H)DJ(H) rearrangements with a newly developed program, JOINSOLVER. In the productive repertoire, the H chain complementarity determining region 3 (CDR3(H)) was significantly shorter (46.7 +/- 0.5 nucleotides) than in the nonproductive repertoire (53.8 +/- 1.9 nucleotides) because of the tendency to select rearrangements with less TdT activity and shorter D segments. Using criteria established by Monte Carlo simulations, D segments could be identified in 71.4% of nonproductive and 64.4% of productive rearrangements, with a mean of 17.6 +/- 0.7 and 14.6 +/- 0.2 retained germline nucleotides, respectively. Eight of 27 D segments were used more frequently than expected in the nonproductive repertoire, whereas 3 D segments were positively selected and 3 were negatively selected, indicating that both molecular mechanisms and selection biased the D segment usage. There was no bias for D segment reading frame (RF) use in the nonproductive repertoire, whereas negative selection of the RFs encoding stop codons and positive selection of RF2 that frequently encodes hydrophilic amino acids were noted in the productive repertoire. Except for serine, there was no consistent selection or expression of hydrophilic amino acids. A bias toward the pairing of 5' D segments with 3' J(H) segments was observed in the nonproductive but not the productive repertoire, whereas V-H usage was random. Rearrangements using inverted D segments, DIR family segments, chromosome 15 D segments and multiple D segments were found infrequently. Analysis of the human CDR3(H) with JOINSOLVER has provided comprehensive information on the influences that shape this important Ag binding region of V-H chains.