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Nucleic Acids Research
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Nucleic Acids Research
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Nucleic Acids Research
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Constrained peptides mimic a viral suppressor of RNA silencing

Authors: Arne Kuepper; Niall M McLoughlin; Saskia Neubacher; Alejandro Yeste-Vázquez; Estel Collado Camps; Chandran Nithin; Sunandan Mukherjee; +5 Authors

Constrained peptides mimic a viral suppressor of RNA silencing

Abstract

Abstract The design of high-affinity, RNA-binding ligands has proven very challenging. This is due to the unique structural properties of RNA, often characterized by polar surfaces and high flexibility. In addition, the frequent lack of well-defined binding pockets complicates the development of small molecule binders. This has triggered the search for alternative scaffolds of intermediate size. Among these, peptide-derived molecules represent appealing entities as they can mimic structural features also present in RNA-binding proteins. However, the application of peptidic RNA-targeting ligands is hampered by a lack of design principles and their inherently low bio-stability. Here, the structure-based design of constrained α-helical peptides derived from the viral suppressor of RNA silencing, TAV2b, is described. We observe that the introduction of two inter-side chain crosslinks provides peptides with increased α-helicity and protease stability. One of these modified peptides (B3) shows high affinity for double-stranded RNA structures including a palindromic siRNA as well as microRNA-21 and its precursor pre-miR-21. Notably, B3 binding to pre-miR-21 inhibits Dicer processing in a biochemical assay. As a further characteristic this peptide also exhibits cellular entry. Our findings show that constrained peptides can efficiently mimic RNA-binding proteins rendering them potentially useful for the design of bioactive RNA-targeting ligands.

Country
Netherlands
Keywords

Cell Membrane Permeability, Radboudumc 19: Nanomedicine RIMLS: Radboud Institute for Molecular Life Sciences, Molecular Mimicry, Medizin, Radboud University Medical Center, RNA-Binding Proteins, Cucumovirus, MicroRNAs, Viral Proteins, Radboudumc 14: Tumours of the digestive tract RIMLS: Radboud Institute for Molecular Life Sciences, Chemical Biology and Nucleic Acid Chemistry, RNA Precursors, Humans, RNA Interference, Endopeptidase K, RNA, Small Interfering, K562 Cells, Peptides, RNA, Double-Stranded

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    selected citations
    These citations are derived from selected sources.
    This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
    18
    popularity
    This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
    Top 10%
    influence
    This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
    Average
    impulse
    This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
    Top 10%
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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
18
Top 10%
Average
Top 10%
Green
gold