<scp>RNA</scp>‐protein interactions in an unstructured context

Žagrović, Bojan; Bartonek, Lukas; Polyansky, Anton A.

doi:10.1002/1873-3468.13116

Cited by 57 publications

(75 citation statements)

References 112 publications

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“…In a comprehensive bioinformatics study carried out by Xie et al, a positive correlation between the functional annotation of the SwissProt database and the predicted intrinsic disorder has been found. Generally, IDPs/IDRs are enriched in proteins involved in signaling and regulatory functions, including transcription regulation, cell cycle, mRNA processing, scaffolding, and apoptosis . Consequently, dysregulation of IDPs/IDRs are associated with a variety of human diseases .…”

Section: Introductionmentioning

confidence: 99%

“…Generally, IDPs/IDRs are enriched in proteins involved in signaling and regulatory functions, including transcription regulation, cell cycle, mRNA processing, scaffolding, and apoptosis. 6,14,15,[18][19][20][21][22][23][24][25][26][27][28][29][30][31] Consequently, dysregulation of IDPs/IDRs are associated with a variety of human diseases. [32][33][34][35][36][37][38][39][40][41][42][43][44] Most recently, many IDPs/IDRs are found to be able to undergo liquid-liquid phase separation (LLPS), which is related to the assembling of membraneless organelles in vivo.…”

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confidence: 99%

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Features of molecular recognition of intrinsically disordered proteins via coupled folding and binding

et al. 2019

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The sequence–structure–function paradigm of proteins has been revolutionized by the discovery of intrinsically disordered proteins (IDPs) or intrinsically disordered regions (IDRs). In contrast to traditional ordered proteins, IDPs/IDRs are unstructured under physiological conditions. The absence of well‐defined three‐dimensional structures in the free state of IDPs/IDRs is fundamental to their function. Folding upon binding is an important mode of molecular recognition for IDPs/IDRs. While great efforts have been devoted to investigating the complex structures and binding kinetics and affinities, our knowledge on the binding mechanisms of IDPs/IDRs remains very limited. Here, we review recent advances on the binding mechanisms of IDPs/IDRs. The structures and kinetic parameters of IDPs/IDRs can vary greatly, and the binding mechanisms can be highly dependent on the structural properties of IDPs/IDRs. IDPs/IDRs can employ various combinations of conformational selection and induced fit in a binding process, which can be templated by the target and/or encoded by the IDP/IDR. Further studies should provide deeper insights into the molecular recognition of IDPs/IDRs and enable the rational design of IDP/IDR binding mechanisms in the future.

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Section: Introductionmentioning

confidence: 99%

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confidence: 99%

Features of molecular recognition of intrinsically disordered proteins via coupled folding and binding

et al. 2019

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“…There is some evidence for direct codon (RNA loop)‐to‐amino acid interactions. This would indicate a pre‐tRNA origin of a preliminary genetic code functioning as an emerging network of RNA–amino acid interactions …”

Section: Rna Populations and Their Historical Backgroundmentioning

confidence: 99%

“…This would indicate a pre-tRNA origin of a preliminary genetic code functioning as an emerging network of RNA-amino acid interactions. [16][17][18] Ribosomes are ribonucleoprotein complexes responsible for protein synthesis in all forms of life. They polymerize polypeptide chains templated by the nucleotide sequences in messenger RNA and mediated by transfer RNAs.…”

Section: Rna Populations and Their Historical Backgroundmentioning

confidence: 99%

That is life: communicating RNA networks from viruses and cells in continuous interaction

Villarreal

Witzany²

2019

Annals of the New York Academy of Sciences

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All the conserved detailed results of evolution stored in DNA must be read, transcribed, and translated via an RNA‐mediated process. This is required for the development and growth of each individual cell. Thus, all known living organisms fundamentally depend on these RNA‐mediated processes. In most cases, they are interconnected with other RNAs and their associated protein complexes and function in a strictly coordinated hierarchy of temporal and spatial steps (i.e., an RNA network). Clearly, all cellular life as we know it could not function without these key agents of DNA replication, namely rRNA, tRNA, and mRNA. Thus, any definition of life that lacks RNA functions and their networks misses an essential requirement for RNA agents that inherently regulate and coordinate (communicate to) cells, tissues, organs, and organisms. The precellular evolution of RNAs occurred at the core of the emergence of cellular life and the question remained of how both precellular and cellular levels are interconnected historically and functionally. RNA networks and RNA communication can interconnect these levels. With the reemergence of virology in evolution, it became clear that communicating viruses and subviral infectious genetic parasites are bridging these two levels by invading, integrating, coadapting, exapting, and recombining constituent parts in host genomes for cellular requirements in gene regulation and coordination aims. Therefore, a 21st century understanding of life is of an inherently social process based on communicating RNA networks, in which viruses and cells continuously interact.

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“…RNA‐protein interactions are discussed by Zagrovic et al . , Albihlal and Gerber and Gallagher and Ramos . These articles focus respectively, on computational work of the universal genetic code and the binding specificity of nucleobases and amino acids; on recent proteomic approaches that revealed many “unconventional” RNA‐binding proteins lacking characteristic RNA‐binding domains (e.g.…”

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confidence: 99%