The genetic code revisited

Pohlmeyer, Roland

doi:10.1016/j.jtbi.2008.04.028

Cited by 9 publications

(7 citation statements)

References 3 publications

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“…Although changes in codon position 2 are generally believed to be more important for protein structure and function than changes in codon position 1 (Berleant et al, 2009;Pohlmeyer, 2008), our results challenge this general assumption. In this context, it is important to note that in previous studies in which the physicochemical properties of amino acids like size, hydropathy and charge were considered, charged amino acids were usually classified by simply having a charged side chain or not.…”

Section: Resultscontrasting

confidence: 52%

Global importance of RNA secondary structures in protein-coding sequences

Fricke

Gerst²,

Ibrahim

et al. 2018

Bioinformatics

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We show that the nucleotide distribution within codons is biased in all taxa of life on a global scale. Thereby, RNA secondary structures that require base-pairing between the position 1 of a codon with the position 1 of an opposing codon (here named RNA secondary structure class c1) are under-represented. We conclude that this bias may result from the co-evolution of codon sequence and mRNA secondary structure, suggesting that RNA secondary structures are generally important in protein coding regions of mRNAs. The above result also implies that codon position 2 has a smaller influence on the amino acid choice than codon position 1.

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Section: Resultscontrasting

confidence: 52%

Global importance of RNA secondary structures in protein-coding sequences

Fricke

Gerst²,

Ibrahim

et al. 2018

Bioinformatics

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“…By regrouping the nucleotides of the codons within a circular genetic code, in the non-conventional order 2–1–3, starting at the center (clockwise: C , G , A , U ), Pohlmeyer (2008) was able to bind the six codons for Ser into one cluster, the six codons for Arg into another cluster, the six codons for Leu into another cluster, and the three stop codons into another cluster, as well as the acidic amino acids with their respective amides surrounding them in one macro-cluster. Every codon having U at its center was also macro-clustered in the fourth quadrant.…”

Section: Discussionmentioning

confidence: 99%

The rules of variation: Amino acid exchange according to the rotating circular genetic code

Castro-Chavez

2010

Journal of Theoretical Biology

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General guidelines for the molecular basis of functional variation are presented while focused on the rotating circular genetic code and allowable exchanges that make it resistant to genetic diseases under normal conditions. The rules of variation, bioinformatics aids for preventive medicine, are: (1) same position in the four quadrants for hydrophobic codons, (2) same or contiguous position in two quadrants for synonymous or related codons, and (3) same quadrant for equivalent codons. To preserve protein function, amino acid exchange according to the first rule takes into account the positional homology of essential hydrophobic amino acids with every codon with a central uracil in the four quadrants, the second rule includes codons for identical, acidic, or their amidic amino acids present in two quadrants, and the third rule, the smaller, aromatic, stop codons, and basic amino acids, each in proximity within a 90 degree angle. I also define codifying genes and palindromati, CTCGTGCCGAATTCGGCACGAG.

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“…More revealing representations have been achieved using the 6-dimensional hypercube (Jiménez-Montaño et al 1996;Sánchez et al 2005) of the 64 codons of the SGC. Additionally, circular representations of the SGC have been proposed (Pohlmeyer 2008;Davis 1999Davis , 2009. A 3-dimensional algebraic model was used for the first time by Sánchez et al (2006) using a structure of a Lie algebra over the Galois Field GF(4).…”

Section: Introductionmentioning

confidence: 99%

Genetic Hotels for the Standard Genetic Code: Evolutionary Analysis Based upon Novel Three-Dimensional Algebraic Models

2010

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Herein, we rigorously develop novel 3-dimensional algebraic models called Genetic Hotels of the Standard Genetic Code (SGC). We start by considering the primeval RNA genetic code which consists of the 16 codons of type RNY (purine-any base-pyrimidine). Using simple algebraic operations, we show how the RNA code could have evolved toward the current SGC via two different intermediate evolutionary stages called Extended RNA code type I and II. By rotations or translations of the subset RNY, we arrive at the SGC via the former (type I) or via the latter (type II), respectively. Biologically, the Extended RNA code type I, consists of all codons of the type RNY plus codons obtained by considering the RNA code but in the second (NYR type) and third (YRN type) reading frames. The Extended RNA code type II, comprises all codons of the type RNY plus codons that arise from transversions of the RNA code in the first (YNY type) and third (RNR) nucleotide bases. Since the dimensions of remarkable subsets of the Genetic Hotels are not necessarily integer numbers, we also introduce the concept of algebraic fractal dimension. A general decoding function which maps each codon to its corresponding amino acid or the stop signals is also derived. The Phenotypic Hotel of amino acids is also illustrated. The proposed evolutionary paths are discussed in terms of the existing theories of the evolution of the SGC. The adoption of 3-dimensional models of the Genetic and Phenotypic Hotels will facilitate the understanding of the biological properties of the SGC.

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The genetic code revisited

Cited by 9 publications

References 3 publications

Global importance of RNA secondary structures in protein-coding sequences

Global importance of RNA secondary structures in protein-coding sequences

The rules of variation: Amino acid exchange according to the rotating circular genetic code

Genetic Hotels for the Standard Genetic Code: Evolutionary Analysis Based upon Novel Three-Dimensional Algebraic Models

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