Recent advances of nucleic acid-based cancer biomarkers and biosensors

J Zhao, K Xia, P He, G Wei, X Zhou, X Zhang - Coordination Chemistry …, 2023 - Elsevier
Nucleic acid-based cancer biomarkers (NABCBs) have emerged as a notable and
continuously captivating research focal point within the domain of oncology. As a result …

The Wako-Saitô-Muñoz-Eaton model for predicting protein folding and dynamics

K Ooka, R Liu, M Arai - Molecules, 2022 - mdpi.com
Despite the recent advances in the prediction of protein structures by deep neutral networks,
the elucidation of protein-folding mechanisms remains challenging. A promising theory for …

Functional regulation of an intrinsically disordered protein via a conformationally excited state

K Madhurima, B Nandi, S Munshi, AN Naganathan… - Science …, 2023 - science.org
A longstanding goal in the field of intrinsically disordered proteins (IDPs) is to characterize
their structural heterogeneity and pinpoint the role of this heterogeneity in IDP function …

HybridDBRpred: improved sequence-based prediction of DNA-binding amino acids using annotations from structured complexes and disordered proteins

J Zhang, S Basu, L Kurgan - Nucleic Acids Research, 2024 - academic.oup.com
Current predictors of DNA-binding residues (DBRs) from protein sequences belong to two
distinct groups, those trained on binding annotations extracted from structured protein-DNA …

Post-translational modification analysis of Saccharomyces cerevisiae histone methylation enzymes reveals phosphorylation sites of regulatory potential

RJ Separovich, MWM Wong, TR Chapman… - Journal of Biological …, 2021 - ASBMB
Histone methylation is central to the regulation of eukaryotic transcription. In Saccharomyces
cerevisiae, it is controlled by a system of four methyltransferases (Set1p, Set2p, Set5p, and …

[HTML][HTML] Thermodynamics and folding landscapes of large proteins from a statistical mechanical model

S Gopi, A Aranganathan, AN Naganathan - Current Research in Structural …, 2019 - Elsevier
Statistical mechanical models that afford an intermediate resolution between macroscopic
chemical models and all-atom simulations have been successful in capturing folding …

Twenty years of advances in prediction of nucleic acid-binding residues in protein sequences

S Basu, J Yu, D Kihara, L Kurgan - Briefings in Bioinformatics, 2025 - academic.oup.com
Computational prediction of nucleic acid-binding residues in protein sequences is an active
field of research, with over 80 methods that were released in the past 2 decades. We identify …

[HTML][HTML] A hierarchy of coupling free energies underlie the thermodynamic and functional architecture of protein structures

AN Naganathan, A Kannan - Current Research in Structural Biology, 2021 - Elsevier
Protein sequences and structures evolve by satisfying varied physical and biochemical
constraints. This multi-level selection is enabled not just by the patterning of amino acids on …

Phase separation and disorder-to-order transition of human brain expressed X-linked 3 (hBEX3) in the presence of small fragments of tRNA

MJ do Amaral, TS Araujo, NC Díaz, F Accornero… - Journal of molecular …, 2020 - Elsevier
Abstract Brain Expressed X-linked (BEX) protein family consists of five members in humans
and is highly expressed during neuronal development. They are known to participate in cell …

Insights into the Role of Side-Chain Team Work in nDsbDOx/Red Proteins: Mechanism of Substrate Binding

AG Nair, P Anjukandi - The Journal of Physical Chemistry B, 2024 - ACS Publications
N-terminal disulfide bond oxidoreductase (nDsbDOx/Red) proteins display divergent
substrate binding mechanisms depending on the conformational changes to the Phe70 cap …