HIV-1 immature virion network and icosahedral capsids self-assembly with patchy spheres

Abstract

The self-assembling process of a simple 3D molecular model that reproduces the hexagonal lattice that HIV-1 has in its immature stage is presented. The system is made of two overlapped repulsive spheres as a building block, both spheres are decorated with attractive patches simulating the main HIV-1 Gag interactions. If the overlapped spheres have the same diameter size, a flat lattice is assembled, while a curvature is induced in the resulting lattice when different diameters are used. Thus, the importance of this model lies on the fact that only by changing the overlapped spheres diameters it is possible to form icosahedral capsids according to the Kaspar and Klug model, known as T = 1, T = 3 and T = 4 without the use of any scaffold, such as the surface of a sphere. Only one molecular species is used to assemble hexagons and pentagons. WCA potential is used for repulsive particles and LJ for the attractive ones. Only two kinds of patches are needed to form a capsid. Two patches to form pairs, which form hexagons and pentagons, and the one that forms triplets, which connects the polygons together. These interactions are based on previous reports of the HIV-1 Gag protein.

GRAPHICAL ABSTRACT

Keywords:

• Viral capsids
• self-assembly
• simple models
• 3D MD simulations

Acknowledgments

We are greatful to Robijn Bruinsma for inspiring this work.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Additional information

Funding

Thanks to the Super Computer Center of UAM-Iztapalapa for allowing plenty of computing time and Consejo Nacional de Ciencia y Tecnología (CONACyT) [project number CB2016-285502] ‘Efecto de la Quiralidad, Polaridad y Anisotropia en el auto-ensamblaje molecular en dos dimensiones’.