基于机器学习Rosetta的全人源化Spastin重组抗体的设计和验证

目的:基于机器学习软件Rosetta实现人源化Spastin重组抗体的设计、体外制备及验证。方法:使用Rosetta设计出针对人Spastin蛋白抗原表位的全人源化抗体,获得其抗体Fab段轻链及重链可变区的氨基酸序列,优化密码子后转化为核苷酸序列得到轻、重链的全长cDNA;随后将全人源化抗Spastin的轻、重链序列分别构建于重组表达载体;在293FT真核表达体系中表达并纯化该抗体;使用Western blot方法鉴定该抗体识别人Spastin重组蛋白信号的能力;通过Rosetta建模模拟抗体与抗原的结合及构象。结果:成功构建了全人源化Spastin重组抗体;该Spastin重组抗体能够在真核系统成功表达;构建的重组抗体轻、重链能够形成完整抗体,且能够特异性识别出人Spastin蛋白信号。结论:借助Rosetta软件成功设计了一种能够特异识别Spastin的重组全人源化抗体。

语言模型辅助人工智能抗体设计与优化的研究热点和进展分析

目的分析语言模型辅助人工智能抗体设计与优化研究领域的研究热点及进展,为抗体开发领域研究人员提供参考依据。方法通过CiteSpace软件对Web of Science、Pubmed和Scopus数据库中收集到的抗体设计与优化研究领域中3个重要研究任务(抗体预训练语言模型构建、抗体序列生成、抗体三维结构预测)的文献进行总体研究热点分析,并对各研究任务下的重要研究进展进行梳理总结,分析具体研究工作的异同点和当前研究面临的问题。结果2019年(10篇文献)至2023年(89篇文献),3个研究任务的研究规模和研究热度不断攀升。总体研究热点聚焦于通过语言模型辅助设计或优化得到人源化、亲和力高以及特异性强的抗体。在各研究任务中,模型架构多样性、训练数据一致性以及训练策略差异性反映了研究方法的特点。同时,当前研究仍然面临着抗原数据稀疏、计算算力限制以及干湿实验结合不足等问题。结论语言模型辅助人工智能抗体设计与优化的相关研究正在逐步兴起,目前已经取得了一定的成果,但研究者仍需解决模型对抗原抗体相互作用信息忽略和实验验证与模拟计算结合缺乏的问题,深化研究内容并扩展实际应用场景。

设计抗体研究进展

单克隆抗体虽已为临床实验室提供了大量试剂,但其特异性和亲合力还不能准确地满足临床需要,加之它们能引起球蛋白反应和血清病,大大限制了在病人中的应用。根据特殊需要用基因工程制造设计抗体解决了这些问题。设计抗体包括嵌合抗体、人化抗体、免疫粘连素、单链抗原结合蛋白、重链可变区蛋白和超变区多肽。该领域的研究进展十分迅速,可以相信,不入的将来设计抗体可望成为临床的主要资源。

Design of steel box girder for Taizhou Yangtze River Highway Bridge

Taizhou Yangtze River Highway Bridge is the first three-pylon two-span suspension bridge in China. The main girder adopts flat steamline steel closed box girder which has well wind-resistant capability and is technically mature besides beautiful appearance. Straight web plates of the steel box girder in longitudinal direction are proposed in order to ensure the integrity of the steel box girder, and to keep the stress of the steel box girder continuous in the middle pylon, as well as to reduce the gradient of the middle pylon columns. The cross section of the box girder has one box with three cells. Solid-web diaphragm plate with good integrity and high torsional stiffness is adopted. The lifting lugs are utilized in the anchors of suspender cable. In this paper, selection of the cross section of the steel box girder, the general structure design, local structure design and main structure calculation results of Taizhou Yangtze River Bridge are introduced emphatically.

毒素DON单链抗体的同源建模及与DON结合的分子模拟研究

通过同源模建及分子力学构建并优化了呕吐毒素DON单链抗体的三维结构,结合Procheck和verify_3D方法评估得到合理的抗体模型.利用分子对接方法研究了单链抗体与其抗原DON的识别及相互作用.结果表明,毒素结合到抗体轻链上,通过轻重链的交界区残基与重链结合,与残基Pro107之间存在氢键作用.采用分子动力学模拟和MM/GBSA方法计算了毒素DON与抗体之间的结合自由能,计算结果与实验值相吻合,体系疏水相互作用是维持复合物稳定结构的主要驱动力.动力学模拟氢键分析和能量分解结果共同表明,残基Pro107参与稳定氢键的形成并贡献很强的范德华作用,是毒素结合抗体最关键的残基.本研究为该毒素抗体的结构设计提供了重要的线索和理论依据,对毒素类分子新型抗体的研究和开发具有理论指导价值.

An extended HLA multilayer federation integration architecture for multidisciplinary collaborative simulation

The development of complex products is essentially concerned with multidisciplinary knowledge. Running on Internet, integration based on muhilayer federation architecture and dynamic reuse of simulation resources are the major difficulties for complex product collaborative design and simulation. Since the traditional Run-Time Infrastructure （RTI） is not good at supporting these new requirements, an extended high level architecture （HLA） multilayer federation integration architecture （MLFIA）, based on the resource management federation （RMF） and its supporting environment based Service-oriented architecture （SOA） and HLA （SOHLA） are proposed, The idea and realization of two key technologies, the dynamic creation of simulation federation based on RMF, TH RTI, an extensible HLA runtime infrastructure （RTI）, used at Internet are emphasized. Finally, an industry case about multiple unit （MU） is given.

10E8-like neutralizing antibodies against HIV-1 induced using a precisely designed conformational peptide as a vaccine prime

Recent studies have demonstrated that the membrane-proximal external region （MPER） of human immunodeficiency virus 1 （HIV-1） glycoprotein 41 contains a series of epitopes for human monoclonal antibodies, including 2F5, Zl3el, 4El0, and 10E8, which were isolated from HIV-l-infected individuals and show broad neutralizing activities. This suggests that MPER is a good target for the development of effective HIV-1 vaccines. However, many studies have shown that it is difficult to induce antibodies with similar broad neutralizing activities using MPER-based peptide antigens. Here, we report that 10E8-1ike neu- tralizing antibodies with effective anti-HIV-1 activity were readily induced using a precisely designed conformational immu- nogenic peptide containing the 10E8-specific epitope. This immunogenic peptide （designated T10HE） contains a 15-mer MPER-derived 10E8-specific epitope fused to T-helper-cell epitopes from tetanus toxin （tt）, which showed a significantly sta- bilized a-helix structure after a series of modifications, including substitution with an （S）-c^-（2＇-pentenyl） alanine containing an olefin-bearing tether and ruthenium-catalyzed olefin metathesis, compared with the unmodified T10E peptide. The stabilized （x-helix structure of T10HE did not affect its capacity to bind the 10E8 antibody, as evaluated with an enzyme linked immuno- sorbent assay （ELISA） and surface plasmon resonance binding assay （SPR assay）. The efficacies of the T10HE and T10E epitope vaccines were evaluated after a standard vaccination procedure in which the experimental mice were primed with ei- ther the T10HE or T10E immunogen and boosted with HIV-1 JRFL pseudoviruses. Higher titers of 10E8-1ike antibodies were induced by T10HE than that by T10E. More importantly, the antibodies induced by T10HE showed enhanced antiviral potency against HIV-1 strains with both X4 and R5 tropism and a greater degree of broad neutralizing activity than the antibodies in- duced by T10E. These results indicate that a 10E8-epitope-based structure-specific peptide immunogen can elicit neutralizing antibodies when used as a vaccine prime.