Reciprocal Nucleopeptides as the Ancestral Darwinian Self-Replicator.

Even the simplest organisms are too complex to have spontaneously arisen fully formed, yet precursors to first life must have emerged ab initio from their environment. A watershed event was the appearance of the first entity capable of evolution: the Initial Darwinian Ancestor. Here, we suggest that nucleopeptide reciprocal replicators could have carried out this important role and contend that this is the simplest way to explain extant replication systems in a mathematically consistent way. We propose short nucleic acid templates on which amino-acylated adapters assembled. Spatial localization drives peptide ligation from activated precursors to generate phosphodiester-bond-catalytic peptides. Comprising autocatalytic protein and nucleic acid sequences, this dynamical system links and unifies several previous hypotheses and provides a plausible model for the emergence of DNA and the operational code.

Group theory of icosahedral virus capsid vibrations: a top-down approach.

We explore the use of a top-down approach to analyse the dynamics of icosahedral virus capsids and complement the information obtained from bottom-up studies of viral vibrations available in the literature. A normal mode analysis based on protein association energies is used to study the frequency spectrum, in which we reveal a universal plateau of low-frequency modes shared by a large class of Caspar-Klug capsids. These modes break icosahedral symmetry and are potentially relevant to the genome release mechanism. We comment on the role of viral tiling theory in such dynamical considerations.

Twenty-four near-instabilities of Caspar-Klug viruses.

Group theoretical arguments combined with normal mode analysis techniques are applied to a coarse-grained approximation of icosahedral viral capsids which incorporates areas of variable flexibility. This highlights a remarkable structure of the low-frequency spectrum in this approximation, namely, the existence of a plateau of 24 near zero modes with universal group theory content.