Bioinformatics of Metalloproteins and Metalloproteomes.

Yan Zhang,Junge Zheng

doi:10.3390/molecules25153366

Yan Zhang, Junge Zheng

Open Access

https://doi.org/10.3390/molecules25153366

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Abstract

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.

Highlights

Biological trace metals refer to those metals which are only needed in small quantities but are essential for normal development, survival, and reproduction of all living organisms [1,2]
This review focuses on current computational approaches used for metalloprotein gene prediction as well as relevant tools and resources
With the exponential increase in the number of completely sequenced genomes, there is an urgent need to develop bioinformatic algorithms allowing the prediction of new metalloprotein genes or even the search for entire sets of metalloproteins

Summary

Introduction

Biological trace metals refer to those metals which are only needed in small quantities but are essential for normal development, survival, and reproduction of all living organisms [1,2]. These micronutrients include iron (Fe), zinc (Zn), copper (Cu), manganese (Mn), molybdenum (Mo), tungsten (W), nickel (Ni), cobalt (Co), chromium (Cr), vanadium (V), and several other elements, which play vital roles in a wide variety of biological and chemical events. Some metals act as critical cofactors or as important structural components for different enzymes, whereas others can accept or donate electrons in various redox reactions, or regulate biological processes by facilitating the binding of molecules to corresponding receptors [3,4]. Fe and Zn are indispensable for all or almost all living organisms [7,8]

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