Shenzhen Key Laboratory of Marine Bioresources and Ecology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518055, China.
Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen 518055, China.
Molecules. 2020 Jul 24;25(15):3366. doi: 10.3390/molecules25153366.
Trace metals are inorganic elements that are required for all organisms in very low quantities. They serve as cofactors and activators of metalloproteins involved in a variety of key cellular processes. While substantial effort has been made in experimental characterization of metalloproteins and their functions, the application of bioinformatics in the research of metalloproteins and metalloproteomes is still limited. In the last few years, computational prediction and comparative genomics of metalloprotein genes have arisen, which provide significant insights into their distribution, function, and evolution in nature. This review aims to offer an overview of recent advances in bioinformatic analysis of metalloproteins, mainly focusing on metalloprotein prediction and the use of different metals across the tree of life. We describe current computational approaches for the identification of metalloprotein genes and metal-binding sites/patterns in proteins, and then introduce a set of related databases. Furthermore, we discuss the latest research progress in comparative genomics of several important metals in both prokaryotes and eukaryotes, which demonstrates divergent and dynamic evolutionary patterns of different metalloprotein families and metalloproteomes. Overall, bioinformatic studies of metalloproteins provide a foundation for systematic understanding of trace metal utilization in all three domains of life.
痕量金属是所有生物体都需要的无机元素，但其需求量非常低。它们作为金属蛋白的辅助因子和激活剂，参与多种关键细胞过程。尽管在金属蛋白及其功能的实验表征方面已经做了大量工作，但生物信息学在金属蛋白和金属蛋白组学研究中的应用仍然有限。在过去几年中，金属蛋白基因的计算预测和比较基因组学已经出现，这为它们在自然界中的分布、功能和进化提供了重要的见解。本文旨在概述金属蛋白生物信息学分析的最新进展，主要集中在金属蛋白预测和不同金属在生命之树上的应用。我们描述了当前用于识别金属蛋白基因和蛋白质中金属结合位点/模式的计算方法，然后介绍了一组相关的数据库。此外，我们还讨论了原核生物和真核生物中几种重要金属的比较基因组学的最新研究进展，这些进展表明不同金属蛋白家族和金属蛋白组具有不同的进化模式。总的来说，金属蛋白的生物信息学研究为系统理解生命三界中痕量金属的利用提供了基础。
