Scrapie, ribosomal proteins and biological information

Aminoacyl-tRNA synthetase urzymes optimized by deep learning behave as a quasispecies

Protein design plays a key role in our efforts to work out how genetic coding began. That effort entails urzymes. Urzymes are small, conserved excerpts from full-length aminoacyl-tRNA synthetases that remain active. Urzymes require design to connect disjoint pieces and repair naked nonpolar patches created by removing large domains. Rosetta allowed us to create the first urzymes, but those urzymes were only sparingly soluble. We could measure activity, but it was hard to concentrate those samples to levels required for structural biology. Here, we used the deep learning algorithms ProteinMPNN and AlphaFold2 to redesign a set of optimized LeuAC urzymes derived from leucyl-tRNA synthetase. We select a balanced, representative subset of eight variants for testing using principal component analysis. Most tested variants are much more soluble than the original LeuAC. They also span a range of catalytic proficiency and amino acid specificity. The data enable detailed statistical analyses of the sources of both solubility and specificity. In that way, we show how to begin to unwrap the elements of protein chemistry that were hidden within the neural networks. Deep learning networks have thus helped us surmount several vexing obstacles to further investigations into the nature of ancestral proteins. Finally, we discuss how the eight variants might resemble a sample drawn from a population similar to one subject to natural selection.

Origins of Genetic Coding: Self-Guided Molecular Self-Organisation

The origin of genetic coding is characterised as an event of cosmic significance in which quantum mechanical causation was transcended by constructive computation. Computational causation entered the physico-chemical processes of the pre-biotic world by the incidental satisfaction of a condition of reflexivity between polymer sequence information and system elements able to facilitate their own production through translation of that information. This event, which has previously been modelled in the dynamics of Gene-Replication-Translation systems, is properly described as a process of self-guided self-organisation. The spontaneous emergence of a primordial genetic code between two-letter alphabets of nucleotide triplets and amino acids is easily possible, starting with random peptide synthesis that is RNA-sequence-dependent. The evident self-organising mechanism is the simultaneous quasi-species bifurcation of the populations of information-carrying genes and enzymes with aminoacyl-tRNA synthetase-like activities. This mechanism allowed the code to evolve very rapidly to the ~20 amino acid limit apparent for the reflexive differentiation of amino acid properties using protein catalysts. The self-organisation of semantics in this domain of physical chemistry conferred on emergent molecular biology exquisite computational control over the nanoscopic events needed for its self-construction.

A Hilly path through the thermodynamics and statistical mechanics of protein solutions

The opus of Don Winzor in the fields of physical and analytical biochemistry is a major component of that certain antipodean approach to this broad area of research that blossomed in the second half of the twentieth century. The need to formulate problems in terms of thermodynamic nonideality posed the challenge of describing a clear route from molecular interactions to the parameters that biochemists routinely measure. Mapping out this route required delving into the statistical mechanics of solutions of macromolecules, and at every turn mathematically complex, rigorous, general results that had previously been derived previously, often by Terrell Hill, came to the fore. Central to this work were the definition of the "thermodynamic activity", the pivotal position of the polynomial expansion of the osmotic pressure in terms of molar concentration and the relationship of virial coefficients to details of the forces between limited-size groups of interacting molecules. All of this was richly exploited in the task of taking account of excluded volume and electrostatic interactions, especially in the use of sedimentation equilibrium to determine values of constants for molecular association reactions. Such an approach has proved relevant to the study of molecular interactions generally, even those between the main macromolecular solute and components of the solvent, by using techniques such as exclusion and affinity chromatography as well as light scattering.

Harnessing our very life

The Aristotelian ideas of nature (physis) and technology (techné) are taken as a starting point for understanding what it would mean for technology to be truly living. Heidegger's critique of the conflation of scientific and technological thinking in the current era is accepted as demonstrating that humanity does not have a deep enough appreciation of the nature of life to harness its essence safely. Could the vision of harnessing life be realized, which we strongly doubt, living technology would give selected humans transforming powers that could be expected to exacerbate, rather than solve, current global problems. The source of human purposefulness, and hence of both technology and ethics, is identified in nature's emergent capability to instantiate informational representations in material forms. Ethics that are properly grounded in an appreciation of intrinsic value, especially that of life, demand that proposals to give humanity the capabilities of living technology address the social, political, economic, and environmental problems inherent in its development and potential deployment. Before any development is embarked on, steps must be taken to avoid living technology, whatever the term eventually designates, becoming available for destructive or antisocial purposes such as those that might devastate humanity or irrevocably damage the natural world.

The clinical neurology and epidemiology of Creutzfeldt-Jakob disease, with special reference to iatrogenic cases

The clinical characteristics of Creutzfeldt-Jakob disease (CJD) in a newly analysed group of 223 cases transmitted to primates at the NIH are compared to a recent large series of neuropathologically verified cases in France, and the limited conclusions from worldwide epidemiological studies are briefly summarized. Discussion then focuses on iatrogenic CJD, with special attention to the interplay of clinical, laboratory and epidemiological features of the current outbreak of CJD in hypopituitary dwarfs treated with growth hormone extracted from pools of human pituitary glands.

Prion diseases and the frame-shifting hypothesis

A group of neurological diseases, which includes scrapie, bovine spongiform encephalopathy and Creutzfeldt-Jakob disease, is caused by prion agents which appear to be comprised solely of an abnormal variant of a cellular protein, PrP. Infectious agents which contain no genetic material pose a conundrum for molecular biologists. Theoretical analysis of the gene encoding PrP has suggested a possible mechanism of replication for this proteinaceous infectious agent. The putative mechanism involves frame-shifting during translation of the PrP gene. The normal and abnormal forms of PrP are predicted to have different amino acid sequences.

Induced frameshifting mechanism of replication for an information-carrying scrapie prion

A specific mistranslation mechanism for the replication of an infectious protein is described. The feedback mechanism requires the infectious agent to induce concerted frameshifts during the translation of a cellular gene. Each module of the tandem repeat region of the gene encoding the prion protein (PrP) associated with scrapie infectivity contains multiple sites of potential ribosomal frameshifting. It is proposed that some aberrant variants of PrP containing frameshifted peptides within the octapeptide repeat region of the protein backbone are able to replicate and cause scrapie by interfering with the translation and simultaneous translocation of nascent PrP molecules into the lumen of the endoplasmic reticulum. The model provides a plausible explanation for the behaviour of host-adapted scrapie strains as well as the aetiology of scrapie-like diseases. The hypothesis that a mistranslated PrP is the scrapie agent can also explain discrepancies between the published amino acid sequence of PrP and the sequence deduced from the gene.