RNA-protein interactions in some small plant viruses

Area of Science:

• Structural biology
• Virology
• Biochemistry

Background:

• The three-dimensional structure of Southern bean mosaic virus (SBMV) was determined using electron density maps.
• Previous studies on Satellite tobacco necrosis virus (STNV) and Alfalfa mosaic virus (AMV) protein provided comparative insights.

Purpose of the Study:

• To elucidate the precise structure of SBMV protein subunits (A, B, and C).
• To understand the interaction between SBMV coat protein and its RNA genome.
• To investigate the mechanism of SBMV self-assembly.

Main Methods:

• Refined electron density map analysis of the complete SBMV virus.
• Comparative structural analysis with STNV and AMV protein structures.
• Investigation of SBMV self-assembly factors including protein sequence, pH, and ions.

Main Results:

• The interior surface of the SBMV coat protein exhibits a pattern of basic residues crucial for RNA binding.
• This basic residue arrangement accurately docks a 9 base pair double-helical A-RNA structure, interacting with phosphates and minor grooves.
• A two-state model for SBMV self-assembly was proposed, involving 'relaxed' dimers forming 10-mer caps that nucleate capsid assembly.

Conclusions:

• The specific arrangement of basic residues on the SBMV coat protein is key to organizing the viral RNA.
• The self-assembly of SBMV is a dynamic process influenced by protein structure, ionic conditions, and RNA presence.
• The findings expand the theoretical framework for viral protein self-assembly, as proposed by Caspar and Klug.