Despite tremendous efforts, the exact structure of SARS-CoV-2 and related betacoronaviruses remains elusive. SARS-CoV-2 envelope is a key structural component of the virion that encapsulates viral RNA. It is composed of three structural proteins, spike, membrane (M), and envelope, which interact with each other and with the lipids acquired from the host membranes. Here, we developed and applied an integrative multi-scale computational approach to model the envelope structure of SARS-CoV-2 with near atomistic detail, focusing on studying the dynamic nature and molecular interactions of its most abundant, but largely understudied, M protein. The molecular dynamics simulations allowed us to test the envelope stability under different configurations and revealed that the M dimers agglomerated into large, filament-like, macromolecular assemblies with distinct molecular patterns. These results are in good agreement with current experimental data, demonstrating a generic and versatile approach to model the structure of a virus de novo.
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Many origin of life theories argue that molecular self-organization explains the spontaneous emergence of structural and dynamical constraints. However, the preservation of these constraints over time is not well-explained because ofthe self-undermining and self-limiting nature of these same processes. A process called autogenesis has been proposed in which a synergetic coupling between self-organized processes preserves the constraints thereby accumulated. Thispaper presents a computer simulation of this process (the AutogenicAutomaton) and compares its behavior to the same self-organizing processes when uncoupled. We demonstrate that this coupling produces a second-order constraint that can both resist dissipation and become replicated in new substrates over time.
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