Microscopic insight to specificity of metal ion cofactor in DNA cleavage by restriction endonuclease EcoRV

SC Mandal, L Maganti, M Mondal, J Chakrabarti - Biopolymers, 2020 - Wiley Online Library
Restriction endonucleases protect bacterial cells against bacteriophage infection by
cleaving the incoming foreign DNA into fragments. In presence of Mg2+ ions, EcoRV is able …

The effect of phosphorylation on the conformational dynamics and allostery of the association of death-associated protein kinase with calmodulin

X Li, C Hou, M Yang, B Luo, N Mao… - Journal of …, 2024 - Taylor & Francis
Protein phosphorylation plays an important role in the signal transduction and is capable of
regulation of cell activity. The death-associated protein kinase 1 (DAPK1), as a Ser/Thr …

Molecular dynamics simulations suggest novel allosteric modes in the Hsp70 chaperone protein

FK Mahto, A Bhattacharya… - Journal of Biomolecular …, 2025 - Taylor & Francis
The Hsp70 chaperone protein system is an essential component of the protein folding and
homeostasis machinery in E. Coli. Hsp70 is a three domain, 70 kDa protein which functions …

Correlated dipolar and dihedral fluctuations in a protein

AG Moulick, J Chakrabarti - Chemical Physics Letters, 2022 - Elsevier
Dihedral fluctuations are not directly amenable due to the limitation of the experimental
probe. NMR experiments probe dipolar fluctuations given in terms of cross-correlated …

Allostery in Orai1 binding to calmodulin revealed from conformational thermodynamics

L Maganti, S Dutta, M Ghosh… - Journal of Biomolecular …, 2019 - Taylor & Francis
Here, we study microscopic mechanism of complex formation between Ca2+-bound
calmodulin (holoCaM) and Orai1 that regulates Ca2+-dependent inactivation process in …

Uncovering allostery and regulation in SORCIN through molecular dynamics simulations

V Saravanan, I Ahammed, A Bhattacharya… - Journal of …, 2024 - Taylor & Francis
Soluble resistance-related calcium-binding protein or Sorcin is an allosteric, calcium-binding
Penta-EF hand (PEF) family protein implicated in multi-drug resistant cancers. Sorcin is …

In-silico studies on conformational stability of flagellin–receptor complexes

S Dutta, M Ghosh, J Chakrabarti - Journal of Biomolecular …, 2020 - Taylor & Francis
Flagellin is a protein, responsible for virulent activities of bacteria. The host cell surface
receptor protein TLR5 is known to interact with flagellin in order to activate immune …

Kinetic coherence underlies the dynamics of disordered proteins

A Tenenbaum - RSC advances, 2021 - pubs.rsc.org
The dynamics of two proteins of similar size, the globular lysozyme and the intrinsically
disordered Huntingtin interacting protein, has been simulated in three states resembling a …

Correlation between protein bond vector and dihedral fluctuations

AG Moulick, J Chakrabarti - AIP Conference Proceedings, 2020 - pubs.aip.org
Coordination between residues of protein is essential for various biophysical phenomena.
The coordination can be best understood in terms of correlation between dihedral angles of …