Using machine‐learning‐driven approaches to boost hot‐spot's knowledge

N Rosário‐Ferreira, AMJJ Bonvin… - Wiley Interdisciplinary …, 2022 - Wiley Online Library
Understanding protein–protein interactions (PPIs) is fundamental to describe and to
characterize the formation of biomolecular assemblies, and to establish the energetic …

Pab1 acetylation at K131 decreases stress granule formation in Saccharomyces cerevisiae

S Sivananthan, JT Gosse, S Huard, K Baetz - Journal of Biological …, 2023 - ASBMB
Under environmental stress, such as glucose deprivation, cells form stress granules—the
accumulation of cytoplasmic aggregates of repressed translational initiation complexes …

The RBS1 domain of Gemin5 is intrinsically unstructured and interacts with RNA through conserved Arg and aromatic residues

A Embarc-Buh, R Francisco-Velilla, S Camero… - RNA biology, 2021 - Taylor & Francis
Gemin5 is a multifaceted RNA-binding protein that comprises distinct structural domains,
including a WD40 and TPR-like for which the X-ray structure is known. In addition, the …

Exploring the Nature of Hydrogen Bonding between RNA and Proteins: A Comprehensive Analysis of RNA: Protein Complexes

D Kagra, R Jangra, P Sharma - ChemPhysChem, 2022 - Wiley Online Library
A nonredundant dataset of∼ 300 high (up to 2.5 Å) resolution X‐ray structures of RNA:
protein complexes were analyzed for hydrogen bonds between amino‐acid residues and …

Fluorescent tetrazolylpyrene unnatural nucleoside in sensing BSA protein

SS Bag, H Gogoi, S Roy, MK Pradhan… - Journal of Photochemistry …, 2025 - Elsevier
A spectroscopic investigation of the interaction of a fluorescent unnatural tetrazolylpyrene
nucleoside (TPy B Do) with model protein BSA is presented herein. The probe nucleoside …

Influence of the number, nature and position of methyl posttranscriptional modifications on nucleobase stacking in RNA

D Kagra, AS Mahmi, NVS Kumar… - …, 2021 - Wiley Online Library
DFT calculations are employed to quantify the influence of the presence, number, nature,
and position of posttranscriptional methylation on stacking strength of RNA bases. We carry …

Alignment of major-groove hydrogen bond arrays uncovers shared information between different DNA sequences that bind the same protein

J Sedhom, J Kinser, LA Solomon - NAR Genomics and …, 2022 - academic.oup.com
Protein–DNA binding is of a great interest due to its importance in many biological
processes. Previous studies have presented many factors responsible for the recognition …

Variable temperature FTIR spectra of polycrystalline purine nucleobases and estimating strengths of individual hydrogen bonds

M Rozenberg, R Fausto, I Reva - … Acta Part A: Molecular and Biomolecular …, 2021 - Elsevier
In the first part of this work, we report the FTIR spectra of pure NH and isotopically
substituted ND (10–15% D and 80–90% D) polycrystalline hypoxanthine, xanthine, adenine …

Can modified DNA base pairs with chalcogen bonding expand the genetic alphabet? A combined quantum chemical and molecular dynamics simulation study

KD Sharma, P Kathuria, SD Wetmore… - Physical Chemistry …, 2020 - pubs.rsc.org
A comprehensive (DFT and MD) computational study is presented with the goal to design
and analyze model chalcogen-bonded modified nucleobase pairs that replace one (ie, AXY …

An ultra-red fluorescent biosensor for highly sensitive and rapid detection of biliverdin

X Zhu, S Feng, Z Jiang, H Zhang, Y Wang, H Yang… - Analytica Chimica …, 2021 - Elsevier
The important role of BV in clinical diagnostics of liver-related diseases has been
established in veterinary medicine. However, the sensitivity and selectivity of the current BV …