scholarly journals System-directed pairing of protein amino acids. Part I

2021 ◽  
Author(s):  
Miloje M. Rakočević
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Genetic Code ◽  
Chemical Reactions ◽  
Review Paper ◽  
Point Of View ◽  
Second Phase ◽  
Protein Amino Acids ◽  
The Moment ◽  
Current Science

The idea of this review paper is as follows. If it can be shown (and it can!) that the pairing of protein amino acids is system-directed (determined), then the hypothesis of a prebiotically determined genetic code (Rakočević, 2004a) gets its full meaning. The hypothesis is supported by the fact that all these pairings come to the fore primarily through classes and subclasses of amino acid molecules. What is, however, unexpected and even unbelievable from the point of view of current science is the fact that the quantities, i.e. number of atoms (in a direct or indirect relation to the number of nucleons), in these classes and subclasses, are determined by Gauss’ number 51 (51 = 3 x 17), or Gauss’ sequence: 51 ± 10, 51 ± 20, 51 ± 30, 51 ± 40 and 51 ± 50; also by Dürer’s number 34 (34 = 2 x 17), even more either by its double value, 68; or by Dürer’s sequences: 34 ± 10, 34 ± 5 and 68 ± 10, 68 ± 5. Since the hypothesis refers to constituents – amino acids and nucleotides – it follows that in terms of the type and number of constituents, it makes no sense to talk about evolution of GC, but only about its generating. [Generated, not degenerated code!] It makes sense to talk about the evolution of the genetic code only from the "moment" when the resulting peptide and nucleotide chains enter into chemical reactions and interactions; although even then it can be said that this is just a second phase of GC generation.

scholarly journals The Alanine World Model for the Development of the Amino Acid Repertoire in Protein Biosynthesis

2019 ◽  
Vol 20 (21) ◽  
pp. 5507 ◽  
Author(s):  
Vladimir Kubyshkin ◽  
Nediljko Budisa
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Genetic Code ◽  
Rna World ◽  
Protein Biosynthesis ◽  
Second Phase ◽  
Nucleotide Biosynthesis ◽  
The Core ◽  
Protein World ◽  
Α Helix

A central question in the evolution of the modern translation machinery is the origin and chemical ethology of the amino acids prescribed by the genetic code. The RNA World hypothesis postulates that templated protein synthesis has emerged in the transition from RNA to the Protein World. The sequence of these events and principles behind the acquisition of amino acids to this process remain elusive. Here we describe a model for this process by following the scheme previously proposed by Hartman and Smith, which suggests gradual expansion of the coding space as GC–GCA–GCAU genetic code. We point out a correlation of this scheme with the hierarchy of the protein folding. The model follows the sequence of steps in the process of the amino acid recruitment and fits well with the co-evolution and coenzyme handle theories. While the starting set (GC-phase) was responsible for the nucleotide biosynthesis processes, in the second phase alanine-based amino acids (GCA-phase) were recruited from the core metabolism, thereby providing a standard secondary structure, the α-helix. In the final phase (GCAU-phase), the amino acids were appended to the already existing architecture, enabling tertiary fold and membrane interactions. The whole scheme indicates strongly that the choice for the alanine core was done at the GCA-phase, while glycine and proline remained rudiments from the GC-phase. We suggest that the Protein World should rather be considered the Alanine World, as it predominantly relies on the alanine as the core chemical scaffold.

scholarly journals Genetic code: Chemical Distinctions of Protein Amino Acids

2017 ◽  
Author(s):  
Miloje M. Rakocevic
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Genetic Code ◽  
Standard Genetic Code ◽  
Atom Number ◽  
Canonical Bases ◽  
Ordinal Numbers ◽  
Intelligent Structures ◽  
Protein Amino Acids

In the work it is shown that 20 protein amino acids ("the canonical amino acids" within the genetic code) appear to be a whole and very symmetrical system, in many ways, all based on strict chemical distinctions from the aspect of their similarity, complexity, stereochemical and diversity types. By this, all distinctions are accompanied by specific arithmetical and algebraic regularities, including the existence of amino acid ordinal numbers from 1 to 20. The classification of amino acids into two decades (1-10 and 11-20) appears to be in a strict correspondence with the atom number balances. From the presented "ideal" and "intelligent" structures and arrangements follow the conclusions that the genetic code was complete even in prebiotic conditions (as a set of 20 canonical amino acids and the set of 2+2 pyrimidine / purine canonical bases, respectively); and the notion "evolution" of the genetic code can only mean the degree of freedom of standard genetic code, i.e. the possible exceptions and deviations from the standard genetic code. [This is the second version with minimal interventions in the text. In addition, one passage was added in front of the second star, with quoting of T. Jukes. Added is Remark 4 and a more adequate shading in the Table inside Box 2.]

scholarly journals Genetic code: Chemical Distinctions of Protein Amino Acids

2017 ◽  
Author(s):  
Miloje M. Rakočević
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Genetic Code ◽  
Standard Genetic Code ◽  
Atom Number ◽  
Canonical Bases ◽  
Ordinal Numbers ◽  
Intelligent Structures ◽  
Protein Amino Acids

In the work it is shown that 20 protein amino acids ("the canonical amino acids" within the genetic code) appear to be a whole and very symmetrical system, in many ways, all based on strict chemical distinctions from the aspect of their similarity, complexity, stereochemical and diversity types. By this, all distinctions are accompanied by specific arithmetical and algebraic regularities, including the existence of amino acid ordinal numbers from 1 to 20. The classification of amino acids into two decades (1-10 and 11-20) appears to be in a strict correspondence with the atom number balances. From the presented "ideal" and "intelligent" structures and arrangements follow the conclusions that the genetic code was complete even in prebiotic conditions (as a set of 20 canonical amino acids and the set of 2+2 pyrimidine / purine canonical bases, respectively); and the "evolution" of the genetic code can only mean the degree of freedom of standard genetic code, i.e. the possible exceptions and deviations from the standard genetic code.

scholarly journals Transferability of N-terminal mutations of pyrrolysyl-tRNA synthetase in one species to that in another species on unnatural amino acid incorporation efficiency

Amino Acids ◽  
2020 ◽  
Author(s):  
Thomas L. Williams ◽  
Debra J. Iskandar ◽  
Alexander R. Nödling ◽  
Yurong Tan ◽  
Louis Y. P. Luk ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Genetic Code ◽  
Unnatural Amino Acids ◽  
Trna Synthetase ◽  
Unnatural Amino Acid ◽  
Amino Acid Incorporation ◽  
Acid Incorporation ◽  
Genetic Code Expansion ◽  
Incorporation Efficiency

AbstractGenetic code expansion is a powerful technique for site-specific incorporation of an unnatural amino acid into a protein of interest. This technique relies on an orthogonal aminoacyl-tRNA synthetase/tRNA pair and has enabled incorporation of over 100 different unnatural amino acids into ribosomally synthesized proteins in cells. Pyrrolysyl-tRNA synthetase (PylRS) and its cognate tRNA from Methanosarcina species are arguably the most widely used orthogonal pair. Here, we investigated whether beneficial effect in unnatural amino acid incorporation caused by N-terminal mutations in PylRS of one species is transferable to PylRS of another species. It was shown that conserved mutations on the N-terminal domain of MmPylRS improved the unnatural amino acid incorporation efficiency up to five folds. As MbPylRS shares high sequence identity to MmPylRS, and the two homologs are often used interchangeably, we examined incorporation of five unnatural amino acids by four MbPylRS variants at two temperatures. Our results indicate that the beneficial N-terminal mutations in MmPylRS did not improve unnatural amino acid incorporation efficiency by MbPylRS. Knowledge from this work contributes to our understanding of PylRS homologs which are needed to improve the technique of genetic code expansion in the future.

scholarly journals BIOSYNTHESIS IN ISOLATED ACETABULARIA CHLOROPLASTS

1972 ◽  
Vol 54 (2) ◽  
pp. 279-294 ◽  
Author(s):  
David C. Shephard ◽  
Wendy B. Levin
Keyword(s):  
Amino Acids ◽  
Protein Synthesis ◽  
Amino Acid ◽  
Technical Problems ◽  
Hydrolyzed Protein ◽  
Protein Amino Acids ◽  
Amino Acid Labeling ◽  
Labeling Pattern

The ability of chloroplasts isolated from Acetabulana mediterranea to synthesize the protein amino acids has been investigated. When this chloroplast isolate was presented with 14CO2 for periods of 6–8 hr, tracer was found in essentially all amino acid species of their hydrolyzed protein Phenylalanine labeling was not detected, probably due to technical problems, and hydroxyproline labeling was not tested for The incorporation of 14CO2 into the amino acids is driven by light and, as indicated by the amount of radioactivity lost during ninhydrin decarboxylation on the chromatograms, the amino acids appear to be uniformly labeled. The amino acid labeling pattern of the isolate is similar to that found in plastids labeled with 14CO2 in vivo. The chloroplast isolate did not utilize detectable amounts of externally supplied amino acids in light or, with added adenosine triphosphate (ATP), in darkness. It is concluded that these chloroplasts are a tight cytoplasmic compartment that is independent in supplying the amino acids used for its own protein synthesis. These results are discussed in terms of the role of contaminants in the observed synthesis, the "normalcy" of Acetabularia chloroplasts, the synthetic pathways for amino acids in plastids, and the implications of these observations for cell compartmentation and chloroplast autonomy.

Inter-annual and seasonal dynamics of amino acid, mineral and vitamin composition of silver belly Leiognathus splendens

2014 ◽  
Vol 95 (4) ◽  
pp. 817-828 ◽  
Author(s):  
Kajal Chakraborty ◽  
Deepu Joseph
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Protein Content ◽  
West Coast ◽  
Sensor Data ◽  
The South ◽  
Post Monsoon ◽  
South West ◽  
South West Coast ◽  
Protein Amino Acids

Silver bellies, Leiognathus splendens were studied for their spatial (south-west and south-east coasts of India), annual (2008–2011) and seasonal (pre-monsoon, monsoon and post-monsoon) variations of protein, amino acids, vitamins and minerals. The monthly mean Sea Viewing Wide Field-of-view Sensor data for the period from January 2008 to December 2011 were taken into account to indicate the distribution of the photosynthetic pigment chlorophyll-a to test the hypothesis that surface productivity might be related to nutritional biochemistry of this species. The four year average total protein content and chlorophyll-a showed good correlation during monsoon on the south-west coast and monsoon/post-monsoon on the south-east coast, suggesting that the protein content is prejudiced by the chlorophyll-a concentration. Amino acid scores observed monsoon maxima along the south-west and south-east coasts. Significant seasonal variations in vitamin content were observed at the study locations with high content of vitamins D3, E, K1 and C on the south-west coast. Na content was maximal during pre-monsoon on the south-west coast, while post-monsoon maxima of Ca and K content were observed. The Fe, Mn and Zn were abundant in the samples collected from the south-west coast. The concentration of Se exhibited maximum values post-monsoon along the south-west and south-east coasts. The present study demonstrated L. splendens as a valuable source of the protein, amino acids, minerals and vitamins, showing that this low-value species is a good source of well balanced proteins with high biological value to be qualified as a preferred healthy food for human consumption.

Chemically Selective Reactions in Confined Spaces in Hybrid Aerogels

2005 ◽  
Vol 899 ◽  
Author(s):  
Xipeng Liu ◽  
Chunhua Yao ◽  
William M Risen
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Metal Ions ◽  
Chemical Reactions ◽  
Reaction Products ◽  
Spatial Confinement ◽  
Confined Spaces ◽  
Hybrid Silica ◽  
Hybrid Aerogels ◽  
Chemically Selective

AbstractBy employing novel hybrid silica/functional polymer aerogels, control of the course of chemical reactions between reactants confined inside of the aerogels with reactants whose access to the confinement domain is controlled by diffusion has been explored. Thus, monolithic silica/biopolymer hybrid aerogels have been synthesized with coordinated metal ions that can react with amino acids, such as L-cysteine, that are provided externally in a surrounding solution. Metal ions, such as Au(III), that can react in solution with the amino acid to produce one set of products under a given set of stoichiometric or concentration conditions, and a different set of products under a second set of conditions, were selected for incorporation into the aerogel. It was discovered that the course of the reaction can be changed by spatial confinement of the reaction domain in the aerogel. For example, in the case of Au(III) and L-cysteine, the Au(III) ions are confined in nanoscale domains, and when they are reacted with the amino acid, the nature of the reaction products is controlled by diffusion of the L-cysteine into the domains. Exploration of these and related phenomena will be presented.

THE PROTEOLYTIC ACTIVITY OF INSULIN

1967 ◽  
Vol 45 (9) ◽  
pp. 1329-1333
Author(s):  
Michel Page ◽  
Claude Godin
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Proteolytic Activity ◽  
Protein Amino Acids

The action of insulin on hemoglobin at pH 7.5 was studied. Four different methods were used to determine the degree of proteolysis. After mixtures of hemoglobin and insulin were incubated for 2 hours, very little amino acid or peptide material was liberated from the proteins. As many amino acids are liberated from hemoglobin when it is incubated alone under the same conditions. It is concluded that autolysis is responsible for the observed increases in non-protein amino acids and that insulin has no proteolytic activity under the conditions used in this study.

The Oocytes of the Goby Pomatoschistus minutus. III. Determination of Amino Acid Component

1980 ◽  
Vol 35 (11-12) ◽  
pp. 1094-1095
Author(s):  
Rüdiger Riehl
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Glutamic Acid ◽  
Acid Content ◽  
Amino Acid Content ◽  
Acid Component ◽  
Pomatoschistus Minutus ◽  
Protein Amino Acids ◽  
Amino Acid Component

Abstract The oocytes of the marine goby Pomatoschistus minutus were analyzed for their amino acid content. Most of the amino acids exist as protein, only a little part is free or peptide-bound. Among the protein-bound amino acids, high levels of glutamic acid, proline, alanine, aspartic acid, valine and leucine were detected. These represent more than 60% of the protein amino acids. Among the free acids, glutamic acid, serine and alanine, are dominant. There are no certain proofs of the occurrence of peptide pools in the oocytes of Pomatoschistus minutus.

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