协助设计融合蛋白的开源硅学工作流程

IF 2.6 4区 生物学 Q2 BIOLOGY Computational Biology and Chemistry Pub Date : 2024-09-10 DOI:10.1016/j.compbiolchem.2024.108209
C.J. Lalaurie , C. Zhang , S.M. Liu , K.A. Bunting , P.A. Dalby
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引用次数: 0

摘要

融合蛋白有可能成为靶向治疗的新标准。通过将定制的靶向分子(如 VHH 结构域)与蛋白质的活性部分相结合,可以实现高特异性的有效载荷传递,而这些蛋白质具有的特殊活性并非天然针对目标细胞。相反,新型药物产品可以利用天然蛋白质的高度特异性靶向特性,并将其与定制的有效载荷相结合。在设计此类产品时,最终构建物很少有已知的结构,因此很难评估可能最终影响治疗效果的分子行为。考虑到表达构建体、优化纯化程序、获得足够数量的生物物理特征以及在体外进行结构研究所需的时间和成本,在湿实验室工作之前进行硅学研究大有裨益。然而,在设计新型融合蛋白时需要考虑很多方面,因此不忽略某些因素至关重要。在这项工作中,我们提出了一套用户友好的开源方法,可用于仅从序列筛选候选融合蛋白。我们将肉毒杆菌毒素 A(BoNT/A)的轻链和易位结构域与一个选定的 VHH 结构域融合(在此称为 LC-HN-VHH),作为设计、建模和模拟融合蛋白一般方法的案例研究。它在硅学中的表现与最初的体外研究结果有很好的相关性,SEC HPLC 显示溶液中有多种蛋白质状态,而且随着时间的推移,蛋白质会在这些状态之间发生动态变化,而不会丢失物质。
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An open source in silico workflow to assist in the design of fusion proteins

Fusion proteins have the potential to become the new norm for targeted therapeutic treatments. Highly specific payload delivery can be achieved by combining custom targeting moieties, such as VHH domains, with active parts of proteins that have a particular activity not naturally targeted to the intended cells. Conversely, novel drug products may make use of the highly specific targeting properties of naturally occurring proteins and combine them with custom payloads. When designing such a product, there is rarely a known structure for the final construct which makes it difficult to assess molecular behaviour that may ultimately impact therapeutic outcome. Considering the time and cost of expressing a construct, optimising the purification procedure, obtaining sufficient quantities for biophysical characterisation, and performing structural studies in vitro, there is an enormous benefit to conduct in silico studies ahead of wet lab work.

By following a repeatable, streamlined, and fast workflow of molecular dynamics assessment, it is possible to eliminate low-performing candidates from costly experimental work. There are, however, many aspects to consider when designing a novel fusion protein and it is crucial not to overlook some elements. In this work, we suggest a set of user-friendly, open-source methods which can be used to screen fusion protein candidates from the sequence alone. We used the light chain and translocation domain of botulinum toxin A (BoNT/A) fused with a selected VHH domain, termed here LC-HN-VHH, as a case study for a general approach to designing, modelling, and simulating fusion proteins. Its behaviour in silico correlated well with initial in vitro work, with SEC HPLC showing multiple protein states in solution and a dynamic protein shifting between these states over time without loss of material.

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来源期刊
Computational Biology and Chemistry
Computational Biology and Chemistry 生物-计算机:跨学科应用
CiteScore
6.10
自引率
3.20%
发文量
142
审稿时长
24 days
期刊介绍: Computational Biology and Chemistry publishes original research papers and review articles in all areas of computational life sciences. High quality research contributions with a major computational component in the areas of nucleic acid and protein sequence research, molecular evolution, molecular genetics (functional genomics and proteomics), theory and practice of either biology-specific or chemical-biology-specific modeling, and structural biology of nucleic acids and proteins are particularly welcome. Exceptionally high quality research work in bioinformatics, systems biology, ecology, computational pharmacology, metabolism, biomedical engineering, epidemiology, and statistical genetics will also be considered. Given their inherent uncertainty, protein modeling and molecular docking studies should be thoroughly validated. In the absence of experimental results for validation, the use of molecular dynamics simulations along with detailed free energy calculations, for example, should be used as complementary techniques to support the major conclusions. Submissions of premature modeling exercises without additional biological insights will not be considered. Review articles will generally be commissioned by the editors and should not be submitted to the journal without explicit invitation. However prospective authors are welcome to send a brief (one to three pages) synopsis, which will be evaluated by the editors.
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