Experimental Test of L- and D-Amino Acid Binding to L- and D-Codons Suggests that Homochirality and Codon Directionality Emerged with the Genetic Code

Biophysical Interactions Underpin the Emergence of Information in the Genetic Code

The genetic code conceals a 'code within the codons', which hints at biophysical interactions between amino acids and their cognate nucleotides. Yet, research over decades has failed to corroborate systematic biophysical interactions across the code. Using molecular dynamics simulations and NMR, we have analysed interactions between the 20 standard proteinogenic amino acids and 4 RNA mononucleotides in 3 charge states. Our simulations show that 50% of amino acids bind best with their anticodonic middle base in the -1 charge state common to the backbone of RNA, while 95% of amino acids interact most strongly with at least 1 of their codonic or anticodonic bases. Preference for the cognate anticodonic middle base was greater than 99% of randomised assignments. We verify a selection of our results using NMR, and highlight challenges with both techniques for interrogating large numbers of weak interactions. Finally, we extend our simulations to a range of amino acids and dinucleotides, and corroborate similar preferences for cognate nucleotides. Despite some discrepancies between the predicted patterns and those observed in biology, the existence of weak stereochemical interactions means that random RNA sequences could template non-random peptides. This offers a compelling explanation for the emergence of genetic information in biology.

Antisense Peptide Technology for Diagnostic Tests and Bioengineering Research

Antisense peptide technology (APT) is based on a useful heuristic algorithm for rational peptide design. It was deduced from empirical observations that peptides consisting of complementary (sense and antisense) amino acids interact with higher probability and affinity than the randomly selected ones. This phenomenon is closely related to the structure of the standard genetic code table, and at the same time, is unrelated to the direction of its codon sequence translation. The concept of complementary peptide interaction is discussed, and its possible applications to diagnostic tests and bioengineering research are summarized. Problems and difficulties that may arise using APT are discussed, and possible solutions are proposed. The methodology was tested on the example of SARS-CoV-2. It is shown that the CABS-dock server accurately predicts the binding of antisense peptides to the SARS-CoV-2 receptor binding domain without requiring predefinition of the binding site. It is concluded that the benefits of APT outweigh the costs of random peptide screening and could lead to considerable savings in time and resources, especially if combined with other computational and immunochemical methods.

Protein Homochirality May Be Derived from Primitive Peptide Synthesis by RNA

Homochirality is a feature of life, but its origin is still disputed. Recent theories indicate that the origin of homochirality coincided with that of the RNA world, but proteins have not yet been incorporated into the story. Ribosome is considered a living fossil that survived the RNA world and records the oldest interaction between RNA and proteins. Inspired by several ribosome-related findings, we propose a hypothesis as follows: the substrate chirality preference of some primitive peptide synthesis ribozymes can mediate the chirality transmission from RNA to protein. In return, the chiral preference of protective peptide-RNA interaction can bring these ribozymes an evolutionary advantage and facilitate the expansion of enantiomeric excess in peptides. Monte Carlo simulation results show that this system's chemistry model is plausible. This model can be further tested through investigation of the chirality preference for the interactions between d/l-ribose-composed rRNA homologs and l/d-amino acid-composed peptides.

First arrived, first served: competition between codons for codon-amino acid stereochemical interactions determined early genetic code assignments

Stereochemical nucleotide-amino acid interactions, in the form of noncovalent nucleotide-amino acid interactions, potentially produced the genetic code's codon-amino acid assignments. Empirical estimates of single nucleotide-amino acid affinities on surfaces and in solution are used to test whether trinucleotide-amino acid affinities determined genetic code assignments pending the principle "first arrived, first served": presumed early amino acids have greater codon-amino acid affinities than ulterior ones. Here, these single nucleotide affinities are used to approximate all 64 × 20 trinucleotide-amino acid affinities. Analyses show that (1) on surfaces, genetic code codon-amino acid assignments tend to match high affinities for the amino acids that integrated earliest the genetic code (according to Wong's metabolic coevolution hypothesis between nucleotides and amino acids) and (2) in solution, the same principle holds for the anticodon-amino acid assignments. Affinity analyses match best genetic code assignments when assuming that trinucleotides competed for amino acids, rather than amino acids for trinucleotides. Codon-amino acid affinities stick better to genetic code assignments than anticodon-amino acid affinities. Presumably, two independent coding systems, on surfaces and in solution, converged, and formed the current translation system. Proto-translation on surfaces by direct codon-amino acid interactions without tRNA-like adaptors coadapted with a system emerging in solution by proto-tRNA anticodon-amino acid interactions. These systems assigned identical or similar cognates to codons on surfaces and to anticodons in solution. Results indicate that a prebiotic metabolism predated genetic code self-organization.

Chirality in a quaternionic representation of the genetic code

A quaternionic representation of the genetic code, previously reported by the authors (BioSystems 141 (10-19), 2016), is updated in order to incorporate chirality of nucleotide bases and amino acids. The original representation associates with each nucleotide base a prime integer quaternion of norm 7 and involves a function that assigns to each codon, represented by three of these quaternions, another integer quaternion (amino acid type quaternion). The assignation is such that the essentials of the standard genetic code (particularly its degeneration) are preserved. To show the advantages of such a quaternionic representation we have designed an algorithm to go from the primary to the tertiary structure of the protein. The algorithm uses, besides of the type quaternions, a second kind of quaternions with real components that we additionally associate with the amino acids according to their order along the proteins (order quaternions). In this context, we incorporate chirality in our representation by observing that the set of eight integer quaternions of norm 7 can be partitioned into a pair of subsets of cardinality four each with their elements mutually conjugate and by putting them into correspondence one to one with the two sets of enantiomers (D and L) of the four nucleotide bases adenine, cytosine, guanine and uracil, respectively. We then propose two diagrams in order to describe the hypothetical evolution of the genetic codes corresponding to both of the chiral systems of affinities: D-nucleotide bases/L-amino acids and L-nucleotide bases/D-amino acids at reading frames 5'→3' and 3'→5', respectively. Guided by these diagrams we define functions that in each case assign to the triplets of D- (L-) bases a L- (D-) amino acid type integer quaternion. Specifically, the integer quaternion associated with a given D-amino acid is the conjugate of that one corresponding to the enantiomer L. The chiral type quaternions obtained for the amino acids are used, together with a common set of order quaternions, to describe the folding of the two classes, L and D, of homochiral proteins.

A modular hierarchy-based theory of the chemical origins of life based on molecular complementarity

Albert Szent-Gyorgyi once defined discovery as seeing what everyone else sees and thinking what no one else thinks. I often find that phenomena that are obvious to other people are not obvious to me. Molecular complementarity is one of these phenomena: while rare among any random set of compounds, it is ubiquitous in living systems. Because every molecule in a living system binds more or less specifically to several others, we now speak of "interactomes". What explains the ubiquity of molecular complementarity in living systems? What might such an explanation reveal about the chemical origins of life and the principles that have governed its evolution? Beyond this, what might complementarity tell us about the optimization of integrated systems in general? My research combines theoretical and experimental approaches to molecular complementarity relating to evolution from prebiotic chemical systems to superorganismal interactions. Experimentally, I have characterized complementarity involving specific binding between small molecules and explored how these small-molecule modules have been incorporated into macromolecular systems such as receptors and transporters. Several general principles have emerged from this research. Molecules that bind to each other almost always alter each other's physiological effects; and conversely, molecules that have antagonistic or synergistic physiological effects almost always bind to each other. This principle suggests a chemical link between biological structure and function. Secondly, modern biological systems contain an embedded molecular paleontology based on complementarity that can reveal their chemical origins. This molecular paleontology is often manifested through modules involving small, molecularly complementary subunits that are built into modern macromolecular structures such as receptors and transporters. A third principle is that complementary modules are conserved and repurposed at every stage of evolution. Molecular complementarity plays critical roles in the evolution of chemical systems and resolves a significant number of outstanding problems in the emergence of complex systems. All physical and mathematical models of organization within complex systems rely upon nonrandom linkage between components. Molecular complementarity provides a naturally occurring nonrandom linker. More importantly, the formation of hierarchically organized stable modules vastly improves the probability of achieving self-organization, and molecular complementarity provides a mechanism by which hierarchically organized stable modules can form. Finally, modularity based on molecular complementarity produces a means for storing and replicating information. Linear replicating molecules such as DNA or RNA are not required to transmit information from one generation of compounds to the next: compositional replication is as ubiquitous in living systems as genetic replication and is equally important to its functions. Chemical systems composed of complementary modules mediate this compositional replication and gave rise to linear replication schemes. In sum, I propose that molecular complementarity is ubiquitous in living systems because it provides the physicochemical basis for modular, hierarchical ordering and replication necessary for the evolution of the chemical systems upon which life is based. I conjecture that complementarity more generally is an essential agent that mediates evolution at every level of organization.