Biology subjects

Razzokov, J.

Publications and source records attributed to Razzokov, J..

2 recordsLinked to original sources

bioRxiv2025

Selective Transport of Plasma-Derived Reactive Species through the Plant Aquaporin Channels: A Molecular Dynamics Study

The selective permeability of reactive oxygen and nitrogen species (RONS), generated by cold atmospheric plasma (CAP), through plant aquaporins was investigated to identify plasma-derived species capable of intracellular delivery. Using atomistic molecular dynamics and enhanced sampling methods, we quantified the free energy profiles of eight RONS (HNO3, HO2, cis-HNO2, trans-HNO2, N2O4, NO, NO2, and O3) across the PIP2;1 aquaporin channel embedded in a lipid bilayer. Hydrophobic species such as NO and O3 exhibited minimal energy barriers (~1-2 kJ{middle dot}mol-1) facilitating rapid permeation, while polar and bulky molecules like HNO3 and N2O4 encounter substantial energy barriers (>15 kJ{middle dot}mol-1), particularly near the selective region (also known as the ar/R constriction), which acts like a filter to control what can pass through the aquaporin. These results reveal that RONS permeability is governed by molecular size, polarity, and hydrogen bonding capacity. This mechanistic insight enables rational selection of CAP-generated species for enhancing plant uptake efficiency, with implications for sustainable plasma-based agricultural technologies.

biochemistry↗

bioRxiv2025

Enhancing Immune Cell Activation through Cold Atmospheric Plasma: Disruption of PD-1/PD-L1/PD-L2 Immune Checkpoints via Molecular Dynamics

The PD-1/PD-L1/PD-L2 immune checkpoint plays a critical role in regulating immune responses, and its dysfunction is implicated in immune evasion by cancer cells. Cold atmospheric plasma (CAP) has emerged as a promising cancer therapeutic modality with the potential to modulate immune checkpoints. This study employs molecular dynamics (MD) simulations to investigate the impact of CAP-induced oxidation on the interactions between PD-1 and its ligands, PD-L1 and PD-L2. We simulated the PD-1/PD-L1 and PD-1/PD-L2 complexes under different oxidation levels. Key residues within the interaction site of the ligands are modified using Vienna PTM 2.0 online server. Umbrella sampling and other MD analyses revealed that increasing oxidation levels leads to weaken the binding affinity between PD-1 and both PD-L1 and PD-L2. These findings suggest that CAP may offer a novel strategy for enhancing anti-tumor immunity. This computational study provides valuable insights into the molecular mechanisms underlying CAPs effects on immune regulation and highlights its potential for cancer immunotherapy.

immunology↗