Amino Acid Composition in Various Types of Nucleic Acid-Binding Proteins.

Martin Bartas,Simona Guziurová,Petr Pečinka,Jiří Červeň,Kristyna Slychko

doi:10.3390/ijms22020922

Martin Bartas, Simona Guziurová + Show 3 more

Open Access

https://doi.org/10.3390/ijms22020922

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Abstract

Nucleic acid-binding proteins are traditionally divided into two categories: With the ability to bind DNA or RNA. In the light of new knowledge, such categorizing should be overcome because a large proportion of proteins can bind both DNA and RNA. Another even more important features of nucleic acid-binding proteins are so-called sequence or structure specificities. Proteins able to bind nucleic acids in a sequence-specific manner usually contain one or more of the well-defined structural motifs (zinc-fingers, leucine zipper, helix-turn-helix, or helix-loop-helix). In contrast, many proteins do not recognize nucleic acid sequence but rather local DNA or RNA structures (G-quadruplexes, i-motifs, triplexes, cruciforms, left-handed DNA/RNA form, and others). Finally, there are also proteins recognizing both sequence and local structural properties of nucleic acids (e.g., famous tumor suppressor p53). In this mini-review, we aim to summarize current knowledge about the amino acid composition of various types of nucleic acid-binding proteins with a special focus on significant enrichment and/or depletion in each category.

Highlights

Interactions between proteins and nucleic acids (DNA and RNA) are central to all aspects of maintaining and accessing genetic information
These DNA/RNA structures have important biological functions [37,38,39,40,41,42] and contribute to many human diseases [43,44,45,46]. It became more and more evident, that proteins preferentially interacting with these structures share distinct amino acid features/fingerprints [47,48]. This mini-review aims to focus on the amino acid composition of various types of DNA and RNA-binding proteins and to compare the amino acid composition of proteins that prefer binding to different noncanonical forms of nucleic acids
Inspiration can be found in the following review papers/databases focused on specific properties of proteins binding to G-quadruplexes [19,52,53,54], cruciforms [55], and Z-DNA/Z-RNA [56]

Summary

Introduction

Interactions between proteins and nucleic acids (DNA and RNA) are central to all aspects of maintaining and accessing genetic information. Noncanonical nucleic acid structures are DNA and RNA structures different from their basic form, i.e., double-stranded right-handed DNA or single-stranded RNA, and are often formed by simple nucleotide repeats [25,26,27,28] They are represented mainly by Gquadruplexes [29], i-motifs [30], triplexes [31], R-loops [32], slipped hairpins [33], DNA cruciforms [34], RNA hairpins [35], and Z-DNA [36]. These DNA/RNA structures have important biological functions [37,38,39,40,41,42] and contribute to many human diseases [43,44,45,46] It became more and more evident, that proteins preferentially interacting with these structures share distinct amino acid features/fingerprints [47,48]. This mini-review aims to focus on the amino acid composition of various types of DNA and RNA-binding proteins and to compare the amino acid composition of proteins that prefer binding to different noncanonical forms of nucleic acids

Amino Acid Composition of Nucleic Acid-Binding Proteins

History

Methods to Inspect the Amino Acid Composition of Proteins

Findings