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Reactive molecular dynamics simulations investigating ROS-mediated HIV damage from outer gp120 protein to internal
Cunjia Pan1, Qiaoyue Chen1, Danfeng Liu1
1Xinjiang Laboratory of Phase Transitions and Microstructures in Condensed Matter Physics, College of Physical Science and Technology, Yili Normal University Yining 835000 China suyi2046@sina.com.
Abstract:
Molecular dynamics (MD) with the ReaxFF force field is used to study the structural damage to HIV capsid protein and gp120 protein mediated by reactive oxygen species (ROS). Our results show that with an increase in ROS concentration, the structures of the HIV capsid protein and gp120 protein are more severely damaged, including dehydrogenation, increase in oxygen-containing groups, helix shortening or destruction, and peptide bond breaking. In particular, we noticed that extraction of H atoms from N atoms by ROS was significantly higher than that from C atoms. There was no significant difference in the effect of ROS on dehydrogenation and shortening or breaking of the helices. In contrast, the impact of O on the increase in oxygen-containing groups and the fracture of peptide bonds in the gp120 protein is more significant than that of O3, and the effect of O3 is greater than that of ˙OH. In addition, the degree of structural damage of the gp120 protein was greater than that of the capsid protein. These detailed findings deepen our understanding of the role of ROS in regulating the structure and function of the HIV capsid protein and gp120 protein and provide valuable insights for plasma therapy for acquired immune deficiency syndrome (AIDS).
Insights
Reactive oxygen species (ROS) cause significant structural damage to HIV capsid and gp120 proteins. Higher ROS concentrations lead to more severe damage, impacting protein function and offering insights for acquired immune deficiency syndrome (AIDS) plasma therapy.
Area of Science:
- Biochemistry
- Computational Biology
- Materials Science
Background:
- Human immunodeficiency virus (HIV) poses a global health challenge.
- Understanding HIV protein structure and function is crucial for developing effective treatments.
- Reactive oxygen species (ROS) are implicated in cellular damage, but their specific effects on HIV proteins are not fully elucidated.
Purpose of the Study:
- To investigate the structural damage to HIV capsid and gp120 proteins induced by ROS using molecular dynamics simulations.
- To elucidate the mechanisms of ROS-mediated protein damage, including dehydrogenation, oxidation, and peptide bond cleavage.
- To compare the relative impacts of different ROS species (O, O3, ˙OH) on HIV protein structures.
Main Methods:
- Utilized molecular dynamics (MD) simulations with the ReaxFF force field.
- Simulated the interaction of various reactive oxygen species (ROS) with HIV capsid and gp120 proteins.
- Analyzed structural changes including dehydrogenation, oxygenation, helix integrity, and peptide bond breaking.
Main Results:
- Increased ROS concentration correlated with more severe structural damage to both HIV capsid and gp120 proteins.
- ROS preferentially extracted hydrogen atoms from nitrogen compared to carbon atoms.
- The gp120 protein exhibited greater structural damage than the capsid protein.
- Specific ROS species had differential effects: O was more impactful than O3 and ˙OH on oxygenation and peptide bond fracture in gp120.
Conclusions:
- ROS significantly damages the structure and likely function of HIV capsid and gp120 proteins.
- Findings provide detailed insights into ROS-mediated HIV protein degradation mechanisms.
- Results offer valuable perspectives for the development of plasma-based therapies for acquired immune deficiency syndrome (AIDS).
