Determining amino acid scores of the genetic code table: Complementarity, structure, function and evolution

Štambuk, Nikola; Konjevoda, Paško

doi:10.1016/j.biosystems.2019.104026

Cited by 16 publications

(17 citation statements)

References 71 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…APT is based on a heuristic algorithm for rational peptide design of the interacting ligand-receptor (acceptor) sequences specified by the complementary codons (Tables 1 and 2, Figure 1) . Heuristic methods reduce solution space by focusing on results based on the reduced set of criteria-in this case, complementarity rules defined by the standard genetic code (SGC) table [19,24].…”

Section: Antisense Peptide Technology (Apt)mentioning

confidence: 99%

“…Four main problems of sense and antisense peptide applications in immunochemistry are comparable to the reasons for the lack of success of the synthetic peptide vaccines [25], while the fifth topic addressed is related to the application of antisense/complementary sequences in bioengineering [18][19][20]24]:…”

Section: Antisense Peptide Technology (Apt)mentioning

confidence: 99%

“…The clustering of amino acid pairs, according to interaction preference, is defined by the complementary U ↔ A and C ↔ G bases of the second codon base. The second codon base, according to Woese, specifies the physicochemical properties of the amino acids [24,34]. Therefore, it is not surprising that diverse amino acid properties-like hydrophobicity, hydrophilicity, lipophilicity, and molecular descriptors of contact potential (Miyazawa-Jernigan), hydrophobic moment, and intrinsic disorder-follow the identical sense and antisense complementarity clustering scheme that is associated with molecular interaction at the peptide level (≥4 aa) [7][8][9][10][11][12][13][14][15][16][17][18][19][20][21][22][23][24].…”

Section: Amino Acid Bias In Characterizing Ligand-acceptor (Receptor) Interactionsmentioning

confidence: 99%

“…The second codon base, according to Woese, specifies the physicochemical properties of the amino acids [24,34]. Therefore, it is not surprising that diverse amino acid properties-like hydrophobicity, hydrophilicity, lipophilicity, and molecular descriptors of contact potential (Miyazawa-Jernigan), hydrophobic moment, and intrinsic disorder-follow the identical sense and antisense complementarity clustering scheme that is associated with molecular interaction at the peptide level (≥4 aa) [7][8][9][10][11][12][13][14][15][16][17][18][19][20][21][22][23][24]. In a recent article, Štambuk et al [19] emphasized that "the natural genetic coding algorithm for sense and antisense peptide interactions combines elements of amino acid physico-chemical properties, stereochemical interactions, and bidirectional transcription".…”

Section: Amino Acid Bias In Characterizing Ligand-acceptor (Receptor) Interactionsmentioning

confidence: 99%

See 3 more Smart Citations

Antisense Peptide Technology for Diagnostic Tests and Bioengineering Research

Štambuk

Konjevoda

Pavan

2021

IJMS

Self Cite

View full text Add to dashboard Cite

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.

show abstract

Section: Antisense Peptide Technology (Apt)mentioning

confidence: 99%

Section: Antisense Peptide Technology (Apt)mentioning

confidence: 99%

Section: Amino Acid Bias In Characterizing Ligand-acceptor (Receptor) Interactionsmentioning

confidence: 99%

Section: Amino Acid Bias In Characterizing Ligand-acceptor (Receptor) Interactionsmentioning

confidence: 99%

See 2 more Smart Citations

Antisense Peptide Technology for Diagnostic Tests and Bioengineering Research

Štambuk

Konjevoda

Pavan

2021

IJMS

Self Cite

View full text Add to dashboard Cite

show abstract

“…Previous studies have indicated that the second base of mRNA codons determines the hydrophobicity of the encoded amino acids: The majority codons for hydrophilic amino acids have A in the second position; the majority codons for hydrophobic amino acids have U in the second position (Chiusano et al, 2000;Copley, Smith, & Morowitz, 2005;Lehmann & Libchaber, 2008;Rogers, 2019;Stambuk & Konjevoda, 2019). Seven hydrophilic amino acids, glutamine (Gln…”

Section: Previous Studies On the Association Between Mrna Codons And mentioning

confidence: 99%

The Eight Trigrams of the I Ching Provide a New Avenue for Characterizing the Association between mRNA Codons and the Hydrophobicity of the Encoded Amino Acids

Wang¹

2020

OJPP

View full text Add to dashboard Cite

The standard genetic code is nearly universal, and relates the sequence of a translated messenger RNA (mRNA) to the sequence of amino acids in the resultant protein. Previous studies have related the second position of the mRNA codon to the hydrophobicity of the encoded amino acid. The research aim of this study was to investigate any other relationships that might exist. The author explored the association between both the first and the second positions of the mRNA codon with the hydrophobicity of the encoded amino acid based on their characterization according to the eight trigrams of the I Ching. The author found that most hydrophilic amino acids are associated with mRNA codons whose first two bases are in the middle four trigrams and form intermediate or weak hydrogen bonds with tRNA anticodons, whereas most hydrophobic amino acids are associated with mRNA codons located at the Yang end (i.e., the first two bases of the codon are strong followed by strong) or the Yin end (i.e., the first two bases of the codon are weak followed by weak). The eight trigrams provide a new avenue for characterizing the association between mRNA codons and the hydrophobicity of the encoded amino acids.

show abstract

The New World of Codes

Barbieri

2024

Biosemiotics

View full text Add to dashboard Cite

Determining amino acid scores of the genetic code table: Complementarity, structure, function and evolution

Cited by 16 publications

References 71 publications

Antisense Peptide Technology for Diagnostic Tests and Bioengineering Research

Antisense Peptide Technology for Diagnostic Tests and Bioengineering Research

The Eight Trigrams of the I Ching Provide a New Avenue for Characterizing the Association between mRNA Codons and the Hydrophobicity of the Encoded Amino Acids

The New World of Codes

Contact Info

Product

Resources

About