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

Root‐Bernstein, Robert

doi:10.3390/sym2021180

Cited by 9 publications

(10 citation statements)

References 62 publications

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“…This way preference of L-amino acids by D-bases triplets has been demonstrated [8][9][10][11][12][13][14][15][16]. Moreover, the non-biological affinity of D-amino acids by L-codons is also observed [8,16,17]. Besides, the hypothesis of coevolution of homochirality with the genetic code, makes a number of additional predictions such as the possibility that each codon can encode at least two different amino acids (according with the reading direction: 5´→ 3´or 3´→ 5´) so the eventual existence of more than a single code becomes possible [16].…”

Section: Introductionmentioning

confidence: 83%

“…First we take into account that Miller-Urey like experiments on the synthesis of organic molecules in a primordial environment [32,33] show the formation of amino acids in racemic mixtures. Also, as we have already mentioned, by studying the affinity of amino acids with small RNA-oligonucleotides the preference of D-and L-bases triplets by L-and D-amino acids, respectively, has been observed [16], so we assume that from the beginnings, the two chirality systems (D-bases/L-amino acids) and (L-bases/D-amino acids) evolve independent one of the other. Moreover, as we describe next, the proposed evolution diagrams for the two systems are very similar since we assume that the changes in the corresponding genetic codes are basically independent of the chirality.…”

Section: Chiral Diagrams For the Evolution Of The Genetic Codementioning

confidence: 99%

“…Moreover, the non-biological affinity of D-amino acids by L-codons is also observed [8,16,17]. Besides, the hypothesis of coevolution of homochirality with the genetic code, makes a number of additional predictions such as the possibility that each codon can encode at least two different amino acids (according with the reading direction: 5´→ 3´or 3´→ 5´) so the eventual existence of more than a single code becomes possible [16]. We must mention, however, that, despite the possibility of existence of ancestral L-ribonucleic sites for D-amino acids, there is also experimental evidence of the impossibility of incorporating D-amino acids in protein structures in present biosynthetic pathways.…”

Section: Introductionmentioning

confidence: 99%

“…The goal is that this early affinity between triplets of nucleotide bases and amino acids can at present be studied in standard laboratories by simply synthesizing small RNA-oligonucleotides [7]. This way preference of L-amino acids by D-bases triplets has been demonstrated [8][9][10][11][12][13][14][15][16]. Moreover, the non-biological affinity of D-amino acids by L-codons is also observed [8,16,17].…”

Section: Introductionmentioning

confidence: 99%

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Chirality in a quaternionic representation of the genetic code

2016

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A quaternionic representation of the genetic code, previously reported by the authors, is updated in order to incorporate chirality of nucleotide bases and amino acids. The original representation assigns to each nucleotide base a prime integer quaternion of norm 7 and involves a function that associates with each codon, represented by three of these quaternions, another integer quaternion (amino acid type quaternion) in such a way that the essentials of the standard genetic code (particulaty its degeneration) are preserved. To show the advantages of such a quaternionic representation we have, in turn, associated with each amino acid of a given protein, besides of the type quaternion, another real one according to its order along the protein (order quaternion) and have designed an algorithm to go from the primary to the tertiary structure of the protein by using type and 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 conjugates and by putting they in correspondence one to one with the two sets of enantiomers (D and L) of the four nucleotide bases adenine, cytosine, guanine and uracil, respectively. Thus, guided by two diagrams -specifically proposed to describe the hypothetical evolution of the genetic codes corresponding to both of the chiral systems of affinities: D-nucleotide bases/Lamino acids and L-nucleotide bases/D-amino acids at reading frames 5´→ 3´and 3´→ 5´, respectively-we define functions that in each case assign a L-(D-) amino acid type integer quaternion to the triplets of D-(L-) bases. The assignation is such that for a given D-amino acid, the associated integer quaternion 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.

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Section: Introductionmentioning

confidence: 83%

Section: Chiral Diagrams For the Evolution Of The Genetic Codementioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Chirality in a quaternionic representation of the genetic code

2016

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“…Amino acid isomerization may also be an important factor in modifying protein or peptide structure, interaction, and receptor binding properties [16,19,33,[38][39][40].…”

Section: Difficulties In the Estimation Of Structure-function Relationships Between Specific Ligand-acceptor (Receptor) Pairsmentioning

confidence: 99%

Antisense Peptide Technology for Diagnostic Tests and Bioengineering Research

Štambuk

Konjevoda

Pavan

2021

IJMS

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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.

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

Seligmann

2020

Sci Nat

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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

Cited by 9 publications

References 62 publications

Chirality in a quaternionic representation of the genetic code

Chirality in a quaternionic representation of the genetic code

Antisense Peptide Technology for Diagnostic Tests and Bioengineering Research

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

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