结构基因组学:过去、现在和未来

Andrzej Joachimiak
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引用次数: 0

摘要

20 世纪 90 年代,基因组学序列信息呈指数级增长,导致我们对生物系统的认识存在巨大的知识差距。当时是这样,现在依然如此,序列信息对基因组编码的功能知之甚少。结构基因组学(SG)领域的出现就是为了填补这些空白。结构基因组学计划的任务是促进代表新蛋白质家族的蛋白质的快速从头结构测定,为基因组提供有意义的结构覆盖。要推进制备数千种蛋白质及其结构和功能表征的技术,面临着巨大的挑战。SG 计划迅速解决了这些障碍和缺陷,提高了效率和可重复性,并为蛋白质的制备和结构确定建立了高度集成、成本低廉的管道。由 SG 联合体开发的实验方法的改进使分子和结构生物学取得了快速进展,提高了结构质量,并极大地促进了生物和生物医学研究,为新的结构和功能空间提供了洞察力。实验性三维模型通过蛋白质数据库结构库迅速公布于众,促进了该家族其他成员的结构测定,并有助于了解其分子和生化功能。光源和专用的大分子晶体学光束线、先进的软件和计算资源为 SG 的成功做出了贡献,并扩大了生物学界确定蛋白质结构的能力。结构生物学研究必将经历一场重大变革。这些进步促成了数千种蛋白质结构的确定,其中大部分来自独特的蛋白质家族,并扩大了迅速扩展的蛋白质宇宙的结构覆盖范围。这些结构为 AlphaFold/RozeTTAFold 人工智能算法做出了贡献,使其能够准确预测数百万个蛋白质的结构。原则上,美国国立卫生研究院蛋白质结构计划提出的最初目标已经实现,即通过实验或计算向社会提供所有蛋白质的结构。在
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Structural genomics: past, present and future
The exponential growth of genomics sequence information in the 1990s led to significant knowledge gaps in our understanding of biological systems. It was true then, and it is still true now that the sequence information bore little insights about the functions encoded in the genomes. The fi eld of Structural Genomics (SG) arose to address these gaps. The mission of SG programs was to facilitate rapid de novo structure determination for proteins representing new protein families to provide meaningful structural coverage of the genomes. There were significant challenges to advance technologies for the prepara tion of thousands of proteins and for their structural and functional characterization. The SG programs quickly addressed barriers, and deficiencies, improved effectiveness, and reproducibility, and created highly integrated and cost - effective pipelines for p rotein production and structure determination. The improvements in experimental methods developed by the SG consortia resulted in fast progress in molecular and structural biology, enhanced structure quality, and significantly benefitted biological and biomedical research, providing insights into novel structural and functional space. The experimental three - dimensional models were promptly made public through the Protein Data Bank structure repository, facilitating the structure determination of other m embers of the family, and helping to understand their molecular and biochemical functions. The light sources and dedicated macromolecular crystallography beamlines, advanced software, and computing resources have contributed to SG success and expanded biology community competence in determining protein structures. Structural biology research was set to undergo a major transformation. The advancements resulted in the determination of thousands of protein structures, mostly from unique protein families, and increased structural coverage of the rapidly expanding protein universe. These structures contributed to AlphaFold/RozeTTAFold AI algorithms allowing accurate structure prediction of millions of proteins. In principle, the original goal propo sed by the National Institutes of Health Protein Structure Initiative, that structures of all proteins should be available to the community experimentally or computationally, has been accomplished. At
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