The Graph, Geometry and Symmetries of the Genetic Code with Hamming Metric

Lenstra, Reijer

doi:10.3390/sym7031211

Cited by 4 publications

(2 citation statements)

References 65 publications

(179 reference statements)

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“…At the same time, three amino acids may turn out to be an information codon in DNA or RHA, e.g., AAA, AGA, and GGG are codons [49]. Therefore, considering triplets of amino acids as carriers of some topological symmetry may be a useful marker in the study of peptides, at least in the QSPR/QSAR aspects [49].…”

Section: Discussionmentioning

confidence: 99%

Quantitative Structure–Activity Relationship Models for the Angiotensin-Converting Enzyme Inhibitory Activities of Short-Chain Peptides of Goat Milk Using Quasi-SMILES

Toropova,

Toropov,

Roncaglioni

et al. 2024

Macromol

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The inhibitory activity of peptides on angiotensin-converting enzyme (ACE) is a measure of their antihypertensive potential. Quantitative structure–activity relationship (QSAR) models obtained based on the analysis of sequences of amino acids are suggested. The average determination coefficient for the active training sets is 0.36 ± 0.07. The average determination coefficient for validation sets is 0.79 ± 0.02. The paradoxical situation is caused by applying the vector of ideality of correlation, which improves the statistical quality of a model for the calibration and validation sets but is detrimental to the statistical quality of models for the training sets.

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Section: Discussionmentioning

confidence: 99%

Quantitative Structure–Activity Relationship Models for the Angiotensin-Converting Enzyme Inhibitory Activities of Short-Chain Peptides of Goat Milk Using Quasi-SMILES

Toropova,

Toropov,

Roncaglioni

et al. 2024

Macromol

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“…But this demonstrates the evolutionary opportunity available for amino acids like valine and aspartic acid. A thorough mathematical framework for a gradual, symmetry-breaking pathway to get from a restricted code to the present-day genetic code can be found in [ 21 , 22 ]. It is important to realize that as soon as tRNA genes had come into existence, a process of coevolution between the tRNA genes and the mRNA genes started.…”

Section: The Origin Of the Feedback Loopmentioning

confidence: 99%

On the Origin of Sequence

Gulik

2015

Life

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Three aspects which make planet Earth special, and which must be taken in consideration with respect to the emergence of peptides, are the mineralogical composition, the Moon which is in the same size class, and the triple environment consisting of ocean, atmosphere, and continent. GlyGly is a remarkable peptide because it stimulates peptide bond formation in the Salt-Induced Peptide Formation reaction. The role glycine and aspartic acid play in the active site of RNA polymerase is remarkable too. GlyGly might have been the original product of coded peptide synthesis because of its importance in stimulating the production of oligopeptides with a high aspartic acid content, which protected small RNA molecules by binding Mg2+ ions. The feedback loop, which is closed by having RNA molecules producing GlyGly, is proposed as the essential element fundamental to life. Having this system running, longer sequences could evolve, gradually solving the problem of error catastrophe. The basic structure of the standard genetic code (8 fourfold degenerate codon boxes and 8 split codon boxes) is an example of the way information concerning the emergence of life is frozen in the biological constitution of organisms: the structure of the code contains historical information.

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The Standard Genetic Code can Evolve from a Two-Letter GC Code Without Information Loss or Costly Reassignments

Frank

Froese

2018

Orig Life Evol Biosph

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It is widely agreed that the standard genetic code must have been preceded by a simpler code that encoded fewer amino acids. How this simpler code could have expanded into the standard genetic code is not well understood because most changes to the code are costly. Taking inspiration from the recently synthesized six-letter code, we propose a novel hypothesis: the initial genetic code consisted of only two letters, G and C, and then expanded the number of available codons via the introduction of an additional pair of letters, A and U. Various lines of evidence, including the relative prebiotic abundance of the earliest assigned amino acids, the balance of their hydrophobicity, and the higher GC content in genome coding regions, indicate that the original two nucleotides were indeed G and C. This process of code expansion probably started with the third base, continued with the second base, and ended up as the standard genetic code when the second pair of letters was introduced into the first base. The proposed process is consistent with the available empirical evidence, and it uniquely avoids the problem of costly code changes by positing instead that the code expanded its capacity via the creation of new codons with extra letters.

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The Graph, Geometry and Symmetries of the Genetic Code with Hamming Metric

Cited by 4 publications

References 65 publications

Quantitative Structure–Activity Relationship Models for the Angiotensin-Converting Enzyme Inhibitory Activities of Short-Chain Peptides of Goat Milk Using Quasi-SMILES

Quantitative Structure–Activity Relationship Models for the Angiotensin-Converting Enzyme Inhibitory Activities of Short-Chain Peptides of Goat Milk Using Quasi-SMILES

On the Origin of Sequence

The Standard Genetic Code can Evolve from a Two-Letter GC Code Without Information Loss or Costly Reassignments

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