Curvature Concentrations on the HIV-1 Capsid

Abstract

It is known that the retrovirus capsids possess a fullerene-like structure. These caged polyhedral arrangements are built entirely from hexagons and exactly 12 pentagons according to the Euler theorem. Viral capsids are composed of capsid proteins, which create the hexagon and pentagon shapes by groups of six (hexamer) and five (pentamer) proteins. Different distributions of these 12 pentamers result in icosahedral, tubular, or conical shaped capsids. These pentamer clusters introduce declination and hence curvature on the capsids. This paper provides explicit and quantitative characterization of curvature on virus capsids. The concept of curvature concentration is also introduced. For the HIV (5,7)-cone, it is shown that the curvature concentration at the narrow end is about at least four times higher than that at the broad end. Our modeling results about curvature concentrations on HIV-1 capsids echo the results in the literature that the pentamers are in the regions with the highest stress, although the connection between the two approaches (curvature concentration and stress) is to be explored. This also leads to a conjecture that "HIV-1 capsid narrow end may close last during maturation but open first during entry into a host cell".

A DNA-origami nuclear pore mimic reveals nuclear entry mechanisms of HIV-1 capsid

“…The observed dominant tip-binding mode of capsid cones to NUP153 NuPODs prompted us to investigate whether NUP153 has a curvature preference for binding. The cone-shaped capsid has a "flat" surface on its sides and highly curved tip regions (Liu et al, 2015) ( Figure 4A). It is well established that the CA tube is a good mimic of the flat side of the capsid (Zhao et al, 2011).…”

Critical mechanistic features of HIV-1 viral capsid assembly

“…Alternatively, the transition of CA-SP1 mutants with cleavage defects into mature cores supports the displacive model ( 49 ). Recent in vitro experiments and phenomenological computer simulations indicate a sequential combination of both displacive and disassembly/reassembly pathways during capsid maturation ( 51 ) where the growth of nucleated CA proceeds through initial formation of the broad capsid followed by capsid closure at the narrow end ( 52 , 53 ). Our simulations explore the basis of IP6-mediated capsid growth and closure, which is relevant for both the sequential displacive and disassembly/reassembly pathways and CA assembly under in vitro conditions.…”

Mathematical determination of the HIV-1 matrix shell structure and its impact on the biology of HIV-1

“…HIV-1 capsids are built from ~216 hexamer and 12 pentamer units of CA [16]. Introduction of pentamer units into the geometry of the HIV-1 capsid allows for the necessary curvature required to enclose the core [17]. In their manuscript Liu et .…”