RNA‐protein interactions in an unstructured context

B Zagrovic, L Bartonek, AA Polyansky - FEBS letters, 2018 - Wiley Online Library
Despite their importance, our understanding of noncovalent RNA–protein interactions is
incomplete. This especially concerns the binding between RNA and unstructured protein …

Hepatitis C virus translation inhibitors targeting the internal ribosomal entry site: Miniperspective

SM Dibrov, J Parsons, M Carnevali… - Journal of medicinal …, 2014 - ACS Publications
The internal ribosome entry site (IRES) in the 5′ untranslated region (UTR) of the hepatitis
C virus (HCV) genome initiates translation of the viral polyprotein precursor. The unique …

Improved computational target site prediction for pentatricopeptide repeat RNA editing factors

M Takenaka, A Zehrmann, A Brennicke, K Graichen - PloS one, 2013 - journals.plos.org
Pentatricopeptide repeat (PPR) proteins with an E domain have been identified as specific
factors for C to U RNA editing in plant organelles. These PPR proteins bind to a unique …

Assessing the performance of MM/PBSA and MM/GBSA methods. 8. Predicting binding free energies and poses of protein–RNA complexes

F Chen, H Sun, J Wang, F Zhu, H Liu, Z Wang, T Lei… - Rna, 2018 - rnajournal.cshlp.org
Molecular docking provides a computationally efficient way to predict the atomic structural
details of protein–RNA interactions (PRI), but accurate prediction of the three-dimensional …

Melanoma RBPome identification reveals PDIA6 as an unconventional RNA-binding protein involved in metastasis

N Mestre-Farras, S Guerrero, N Bley… - Nucleic Acids …, 2022 - academic.oup.com
RNA-binding proteins (RBPs) have been relatively overlooked in cancer research despite
their contribution to virtually every cancer hallmark. Here, we use RNA interactome capture …

Structure of a hepatitis C virus RNA domain in complex with a translation inhibitor reveals a binding mode reminiscent of riboswitches

SM Dibrov, K Ding, ND Brunn… - Proceedings of the …, 2012 - National Acad Sciences
The internal ribosome entry site (IRES) in the hepatitis C virus (HCV) RNA genome is
essential for the initiation of viral protein synthesis. IRES domains adopt well-defined folds …

Cas5d processes pre-crRNA and is a member of a larger family of CRISPR RNA endonucleases

EL Garside, MJ Schellenberg, EM Gesner, JB Bonanno… - Rna, 2012 - rnajournal.cshlp.org
Small RNAs derived from clustered, regularly interspaced, short palindromic repeat
(CRISPR) loci in bacteria and archaea are involved in an adaptable and heritable gene …

Quantifying sequence and structural features of protein–RNA interactions

S Li, K Yamashita, KM Amada… - Nucleic acids …, 2014 - academic.oup.com
Increasing awareness of the importance of protein–RNA interactions has motivated many
approaches to predict residue-level RNA binding sites in proteins based on sequence or …

Structure‐and interaction‐based design of anti‐SARS‐CoV‐2 aptamers

V Mironov, IA Shchugoreva… - … A European Journal, 2022 - Wiley Online Library
Aptamer selection against novel infections is a complicated and time‐consuming approach.
Synergy can be achieved by using computational methods together with experimental …

Mutations of NANOS1, a human homologue of the Drosophila morphogen, are associated with a lack of germ cells in testes or severe oligo-astheno-teratozoospermia

K Kusz-Zamelczyk, M Sajek, A Spik, R Glazar… - Journal of Medical …, 2013 - jmg.bmj.com
Background The Nanos gene is a key translational regulator of specific mRNAs involved in
Drosophila germ cell development. Disruption of mammalian homologues, Nanos2 or …