Studying the ssDNA loaded adeno-associated virus aggregation using coarse-grained molecular dynamics simulations

Area of Science:

• Biophysics
• Computational Biology
• Structural Biology

Background:

• Adeno-associated virus (AAV) capsids are crucial for gene therapy vectors.
• Understanding AAV capsid aggregation and stability is vital for optimizing vector design and function.
• Previous studies lacked detailed mechanistic insights into AAV capsid aggregation in aqueous environments.

Purpose of the Study:

• To investigate the driving forces and mechanisms of adeno-associated viral (AAV) capsid aggregation.
• To explore the influence of single-strand DNA (ssDNA) and temperature on AAV capsid stability.
• To develop and validate a computational model for studying AAV capsid behavior.

Main Methods:

• Coarse-grained molecular dynamics (CG-MD) simulations were employed to model AAV capsid aggregation.
• Simulations were conducted with and without ssDNA under various process temperatures.
• The CG-MD model was validated against experimental and prior simulation data.

Main Results:

• AAV capsid aggregation involves complex interactions between hydrophobic, polar, and charged residues.
• Two primary aggregation mechanisms were identified: fivefold face-to-face and edge-to-edge contacts.
• Single-strand DNA (ssDNA) destabilizes protein subunits, enhances charged residue interactions, and promotes non-reversible aggregation.
• Elevated temperatures lead to capsid instability, ssDNA expansion, reduced hydrogen bonds, and increased protein conformational deviations.

Conclusions:

• The study elucidates the intricate mechanisms of AAV capsid aggregation and the critical role of ssDNA.
• Computational modeling provides valuable insights into AAV capsid instability under varying conditions.
• Findings contribute to a deeper understanding of AAV capsid behavior for improved gene therapy applications.