Insight into dynamics of APOBEC3G protein in complexes with DNA assessed by high speed AFM

Area of Science:

• Structural biology
• Virology
• Biochemistry

Background:

• APOBEC3G (A3G) is a key antiviral protein that restricts HIV replication.
• A3G functions by deaminating cytosine to uracil in the viral DNA during reverse transcription.
• Previous structural data for A3G was limited, hindering understanding of its DNA interaction and deaminase activity.

Purpose of the Study:

• To elucidate the structure and dynamics of APOBEC3G (A3G) in complex with single-stranded DNA (ssDNA).
• To understand the molecular mechanisms of A3G's interaction with ssDNA and its role in HIV restriction.
• To visualize A3G's structural dynamics using advanced microscopy techniques.

Main Methods:

• Utilized time-lapse High-Speed Atomic Force Microscopy (HS-AFM) to directly visualize A3G structure and dynamics.
• Applied computational modeling to generate a full-length A3G monomer structure.
• Quantitatively analyzed A3G structures in the presence and absence of ssDNA substrate.

Main Results:

• Demonstrated that A3G exhibits a highly dynamic structure, fluctuating between compact globular and extended dumbbell forms.
• Observed a significant increase in A3G dumbbell structures upon binding to ssDNA.
• Indicated that ssDNA binding stabilizes the dumbbell conformation of A3G.

Conclusions:

• Proposed a model for A3G-ssDNA interaction involving both globular and dumbbell structures.
• Suggested that the stabilized dumbbell structure plays a critical role in A3G's antiviral function.
• Provided novel structural insights into the mechanism of HIV restriction by A3G.