Frontiers and challenges of computing ncRNAs biogenesis, function and modulation

S Rinaldi, E Moroni, R Rozza… - Journal of Chemical …, 2024 - ACS Publications
Non-coding RNAs (ncRNAs), generated from nonprotein coding DNA sequences, constitute
98–99% of the human genome. Non-coding RNAs encompass diverse functional classes …

[HTML][HTML] Ensemble Docking as a Tool for the Rational Design of Peptidomimetic Staphylococcus aureus Sortase A Inhibitors

DA Shulga, KV Kudryavtsev - International Journal of Molecular Sciences, 2024 - mdpi.com
Sortase A (SrtA) of Staphylococcus aureus has long been shown to be a relevant molecular
target for antibacterial development. Moreover, the designed SrtA inhibitors act via the …

Dissecting the protein dynamics coupled ligand binding with kinetic models and single-molecule FRET

S Wu, W Zhang, W Li, W Huang, Q Kong, Z Chen… - Biochemistry, 2022 - ACS Publications
Protein–ligand interactions are crucial to many biological processes. Ligand binding and
dissociation are the basic steps that allow proteins to function. Protein conformational …

The dynamics of t1 adenosine binding on human Argonaute 2: Understanding recognition with conformational selection

S Rinaldi, G Colombo, A Paladino - Protein Science, 2022 - Wiley Online Library
The control of expression in genetic regulation is a fundamental process for cell life. In RNA‐
mediated silencing, human Argonaute‐2 protein (hAgo2) uses sequence information …

[HTML][HTML] Exploring phosphorene-protein interactions: An integrated computational and spectroscopic investigation

S Rinaldi, AM Grigoras, M Caporali, M Serrano-Ruiz… - FlatChem, 2024 - Elsevier
Among 2D materials, exfoliated black phosphorus (or phosphorene) shows great promise
for applications in biological domains. However, despite its performances, little is known …

Structural model for recruitment of RIT1 to the LZTR1 E3 ligase: evidences from an integrated computational approach

A Paladino, F D'Angelo, TMR Noviello… - Journal of chemical …, 2021 - ACS Publications
Leucine-zipper transcription regulator 1 (LZTR1) is a highly mutated tumor suppressor gene,
involved in the pathogenesis of several cancer types and developmental disorders. In …

Comparative structural insights and functional analysis for the distinct unbound states of Human AGO proteins

P Kakoulidis, E Theotoki, V Pantazopoulou, I Vlachos… - 2024 - researchsquare.com
The four human Argonaute (AGO) proteins, essential in RNA interference and gene
regulation, exhibit high sequence and structural similarity, yet differ functionally. Our …

[PDF][PDF] Structural basis of miRNA processing in mammals

D ZAPLETAL - is.muni.cz
Dicer is an RNase III endoribonuclease that produces small RNAs in microRNA (miRNA)
and RNA interference (RNAi) pathway in eukaryotes. In mammals, the highly conserved …