Publications by authors named "Diksha Parwana"
Article Synopsis
- RNA research is expanding, but understanding its structural dynamics and interactions with small molecules remains limited, especially when compared to protein studies.
- This study focuses on addressing the weak CH···O interactions in RNA, which are significant yet often overlooked in force field development, particularly in widely used Amber RNA force fields.
- By adjusting the CH···O repulsion in these force fields, the study found that RNA simulations became more stable, resulting in improved accuracy in modeling RNA structures during molecular dynamics simulations.
The Structural Role of N170 in Substrate-Assisted Deacylation in KPC-2 β-Lactamase.
Angew Chem Int Ed Engl
March 2024
The amino acid substitutions in Klebsiella pneumoniae carbapenemase 2 (KPC-2) that have arisen in the clinic are observed to lead to the development of resistance to ceftazidime-avibactam, a preferred treatment for KPC bearing Gram-negative bacteria. Specific substitutions in the omega loop (R164-D179) result in changes in the structure and function of the enzyme, leading to alterations in substrate specificity, decreased stability, and more recently observed, increased resistance to ceftazidime/avibactam. Using accelerated rare-event sampling well-tempered metadynamics simulations, we explored in detail the structural role of R164 and D179 variants that are described to confer ceftazidime/avibactam resistance.
View Article and Find Full Text PDFCellular membranes are highly crowded environments for biomolecular reactions and signaling. Yet, most in vitro experiments probing protein interaction with lipids employ naked bilayer membranes. Such systems lack the complexities of crowding by membrane-embedded proteins and glycans and exclude the associated volume effects encountered on cellular membrane surfaces.
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