Subscribe to the gold package and get unlimited access to Shamra Academy
Register a new userThe ancient Operational Code is embedded in the amino acid substitution matrix and aaRS phylogenies
96
0
0.0
(
0
)
Ask ChatGPT about the research
No Arabic abstract
The underlying structure of the canonical amino acid substitution matrix (aaSM) is examined by considering stepwise improvements in the differential recognition of amino acids according to their chemical properties during the branching history of the two aminoacyl-tRNA synthetase (aaRS) superfamilies. The evolutionary expansion of the genetic code is described by a simple parameterization of the aaSM, in which (i) the number of distinguishable amino acid types, (ii) the matrix dimension, and (iii) the number of parameters, each increases by one for each bifurcation in an aaRS phylogeny. Parameterized matrices corresponding to trees in which the size of an amino acid sidechain is the only discernible property behind its categorization as a substrate, exclusively for a Class I or II aaRS, provide a significantly better fit to empirically determined aaSM than trees with random bifurcation patterns. A second split between polar and nonpolar amino acids in each Class effects a vastly greater further improvement. The earliest Class-separated epochs in the phylogenies of the aaRS reflect these enzymes capability to distinguish tRNAs through the recognition of acceptor stem identity elements via the minor (Class I) and major (Class II) helical grooves, which is how the ancient Operational Code functioned. The advent of tRNA recognition using the anticodon loop supports the evolution of the optimal map of amino acid chemistry found in the later Genetic Code, an essentially digital categorization, in which polarity is the major functional property, compensating for the unrefined, haphazard differentiation of amino acids achieved by the Operational Code.
rate research
Read More
A molecular dynamics calculation of the amino acid polar requirement is presented and used to score the canonical genetic code. Monte Carlo simulation shows that this computational polar requirement has been optimized by the canonical genetic code more than any previously-known measure. These results strongly support the idea that the genetic code evolved from a communal state of life prior to the root of the modern ribosomal tree of life.
The twenty protein coding amino acids are found in proteomes with different relative abundances. The most abundant amino acid, leucine, is nearly an order of magnitude more prevalent than the least abundant amino acid, cysteine. Amino acid metabolic costs differ similarly, constraining their incorporation into proteins. On the other hand, sequence diversity is necessary for protein folding, function and evolution. Here we present a simple model for a cost-diversity trade-off postulating that natural proteomes minimize amino acid metabolic flux while maximizing sequence entropy. The model explains the relative abundances of amino acids across a diverse set of proteomes. We found that the data is remarkably well explained when the cost function accounts for amino acid chemical decay. More than one hundred proteomes reach comparable solutions to the trade-off by different combinations of cost and diversity. Quantifying the interplay between proteome size and entropy shows that proteomes can get optimally large and diverse.
In this work it is shown that 20 canonical amino acids (AAs) within genetic code appear to be a whole system with strict AAs positions; more exactly, with AAs ordinal number in three variants; first variant 00-19, second 00-21 and third 00-20. The ordinal number follows from the positions of belonging codons, i.e. their digrams (or doublets). The reading itself is a reading in quaternary numbering system if four bases possess the values within a specific logical square: A = 0, C = 1, G = 2, U = 3. By this, all splittings, distinctions and classifications of AAs appear to be in accordance to atom and nucleon number balance as well as to the other physico-chemical properties, such as hydrophobicity and polarity.
This note represents the further progress in understanding the determination of the genetic code by Golden mean (Rakocevic, 1998). Three classes of amino acids that follow from this determination (the 7 golden amino acids, 7 of their complements, and 6 non-complements) are observed now together with two further possible splittings into 4 x 5 and 5 x 4 amino acids.
The correlations of primary and secondary structures were analyzed using proteins with known structure from Protein Data Bank. The correlation values of amino acid type and the eight secondary structure types at distant position were calculated for distances between -25 and 25. Shapes of the diagrams indicate that amino acids polarity and capability for hydrogen bonding have influence on the secondary structure at some distances. Clear preference of most of the amino acids towards certain secondary structure type classifies amino acids into four groups: alpha-helix admirers, strand admirers, turn and bend admirers and the others. Group four consists of His and Cis, the amino acids that do not show clear preference for any secondary structure. Amino acids from a group have similar physicochemical properties, and the same structural characteristics. The results suggest that amino acid preference for secondary structure type is based on the structural characteristics at Cb and Cg atoms of amino acid. alpha-helix admirers do not have polar heteroatoms on Cb and Cg atoms, nor branching or aromatic group on Cb atom. Amino acids that have aromatic groups or branching on Cb atom are strand admirers. Turn and bend admirers have polar heteroatom on Cb or Cg atoms or do not have Cb atom at all. Our results indicate that polarity and capability for hydrogen bonding have influence on the secondary structure at some distance, and that amino acid preference for secondary structure is caused by structural properties at Cb or Cg atoms.
Log in to be able to interact and post comments
comments
Fetching comments
Sign in to be able to follow your search criteria
