scholarly journals Evolution as a Guide to Designing xeno Amino Acid Alphabets

2021 ◽  
Vol 22 (6) ◽  
pp. 2787
Author(s):  
Christopher Mayer-Bacon ◽  
Neyiasuo Agboha ◽  
Mickey Muscalli ◽  
Stephen Freeland
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Theoretical Research ◽  
Empirical Science ◽  
Scoring Functions ◽  
Special Issue ◽  
Standard Genetic Code ◽  
Protein Structure Analysis ◽  
Standard Amino Acid ◽  
Amino Acid Alphabet

Here, we summarize a line of remarkably simple, theoretical research to better understand the chemical logic by which life’s standard alphabet of 20 genetically encoded amino acids evolved. The connection to the theme of this Special Issue, “Protein Structure Analysis and Prediction with Statistical Scoring Functions”, emerges from the ways in which current bioinformatics currently lacks empirical science when it comes to xenoproteins composed largely or entirely of amino acids from beyond the standard genetic code. Our intent is to present new perspectives on existing data from two different frontiers in order to suggest fresh ways in which their findings complement one another. These frontiers are origins/astrobiology research into the emergence of the standard amino acid alphabet, and empirical xenoprotein synthesis.

scholarly journals Did Amino Acid Side Chain Reactivity Dictate the Composition and Timing of Aminoacyl-tRNA Synthetase Evolution?

Genes ◽  
2021 ◽  
Vol 12 (3) ◽  
pp. 409
Author(s):  
Tamara L. Hendrickson ◽  
Whitney N. Wood ◽  
Udumbara M. Rathnayake
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Genetic Code ◽  
Chemical Reactivity ◽  
Trna Synthetase ◽  
Amino Acid Side Chain ◽  
Standard Genetic Code ◽  
Last Universal Common Ancestor ◽  
Trna Synthetases ◽  
Universal Common Ancestor

The twenty amino acids in the standard genetic code were fixed prior to the last universal common ancestor (LUCA). Factors that guided this selection included establishment of pathways for their metabolic synthesis and the concomitant fixation of substrate specificities in the emerging aminoacyl-tRNA synthetases (aaRSs). In this conceptual paper, we propose that the chemical reactivity of some amino acid side chains (e.g., lysine, cysteine, homocysteine, ornithine, homoserine, and selenocysteine) delayed or prohibited the emergence of the corresponding aaRSs and helped define the amino acids in the standard genetic code. We also consider the possibility that amino acid chemistry delayed the emergence of the glutaminyl- and asparaginyl-tRNA synthetases, neither of which are ubiquitous in extant organisms. We argue that fundamental chemical principles played critical roles in fixation of some aspects of the genetic code pre- and post-LUCA.

scholarly journals Amino Acid Nutrition and Metabolism in Health and Disease

Nutrients ◽  
2019 ◽  
Vol 11 (11) ◽  
pp. 2623
Author(s):  
Rose
Keyword(s):  
Amino Acids ◽  
Clinical Trials ◽  
Amino Acid ◽  
Animal Models ◽  
Original Research ◽  
Special Issue ◽  
Health And Disease ◽  
Fundamental Research ◽  
Critical Nutrients

Here an overview of the special issue “Amino acid nutrition and metabolism in health and disease” is given. In addition to several comprehensive and timely reviews, this issue had some original research contributions on fundamental research in animal models as well as human clinical trials exploring how the critical nutrients amino acids affect various traits.

scholarly journals The Mutational Robustness of the Genetic Code and Codon Usage in Environmental Context: A Non-Extremophilic Preference?

Life ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 773
Author(s):  
Ádám Radványi ◽  
Ádám Kun
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Physicochemical Properties ◽  
Genetic Code ◽  
Computational Models ◽  
Environmental Data ◽  
Standard Genetic Code ◽  
Mutational Robustness ◽  
Domains Of Life ◽  
History Of

The genetic code was evolved, to some extent, to minimize the effects of mutations. The effects of mutations depend on the amino acid repertoire, the structure of the genetic code and frequencies of amino acids in proteomes. The amino acid compositions of proteins and corresponding codon usages are still under selection, which allows us to ask what kind of environment the standard genetic code is adapted to. Using simple computational models and comprehensive datasets comprising genomic and environmental data from all three domains of Life, we estimate the expected severity of non-synonymous genomic mutations in proteins, measured by the change in amino acid physicochemical properties. We show that the fidelity in these physicochemical properties is expected to deteriorate with extremophilic codon usages, especially in thermophiles. These findings suggest that the genetic code performs better under non-extremophilic conditions, which not only explains the low substitution rates encountered in halophiles and thermophiles but the revealed relationship between the genetic code and habitat allows us to ponder on earlier phases in the history of Life.

scholarly journals The Combinatorial Fusion Cascade to Generate the Standard Genetic Code

Life ◽  
2021 ◽  
Vol 11 (9) ◽  
pp. 975
Author(s):  
Alexander Nesterov-Mueller ◽  
Roman Popov
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Genetic Code ◽  
Temporal Order ◽  
Prebiotic Chemistry ◽  
Standard Genetic Code ◽  
The Road ◽  
Novel Technology ◽  
Three Stages ◽  
Combinatorial Fusion

Combinatorial fusion cascade was proposed as a transition stage between prebiotic chemistry and early forms of life. The combinatorial fusion cascade consists of three stages: eight initial complimentary pairs of amino acids, four protocodes, and the standard genetic code. The initial complimentary pairs and the protocodes are divided into dominant and recessive entities. The transitions between these stages obey the same combinatorial fusion rules for all amino acids. The combinatorial fusion cascade mathematically describes the codon assignments in the standard genetic code. It explains the availability of amino acids with the even and odd numbers of codons, the appearance of stop codons, inclusion of novel canonical amino acids, exceptional high numbers of codons for amino acids arginine, leucine, and serine, and the temporal order of amino acid inclusion into the genetic code. The temporal order of amino acids within the cascade is congruent with the consensus temporal order previously derived from the similarities between the available hypotheses. The control over the combinatorial fusion cascades would open the road for a novel technology to develop artificial microorganisms.

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 On the Importance of Asymmetry in the Phenotypic Expression of the Genetic Code upon the Molecular Evolution of Proteins

Symmetry ◽  
2020 ◽  
Vol 12 (6) ◽  
pp. 997
Author(s):  
Marco V. José ◽  
Gabriel S. Zamudio
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Genetic Code ◽  
Phenotypic Expression ◽  
Standard Genetic Code ◽  
Specific Amino Acid ◽  
Trna Synthetases ◽  
Probability Of Occurrence ◽  
Genetic Codes ◽  
Evolution Of Proteins

The standard genetic code (SGC) is a mapping between the 64 possible arrangements of the four RNA nucleotides (C, A, U, G) into triplets or codons, where 61 codons are assigned to a specific amino acid and the other three are stop codons for terminating protein synthesis. Aminoacyl-tRNA synthetases (aaRSs) are responsible for implementing the SGC by specifically amino-acylating only its cognate transfer RNA (tRNA), thereby linking an amino acid with its corresponding anticodon triplets. tRNAs molecules bind each codon with its anticodon. To understand the meaning of symmetrical/asymmetrical properties of the SGC, we designed synthetic genetic codes with known symmetries and with the same degeneracy of the SGC. We determined their impact on the substitution rates for each amino acid under a neutral model of protein evolution. We prove that the phenotypic graphs of the SGC for codons and anticodons for all the possible arrangements of nucleotides are asymmetric and the amino acids do not form orbits. In the symmetrical synthetic codes, the amino acids are grouped according to their codonicity, this is the number of triplets encoding a given amino acid. Both the SGC and symmetrical synthetic codes exhibit a probability of occurrence of the amino acids proportional to their degeneracy. Unlike the SGC, the synthetic codes display a constant probability of occurrence of the amino acid according to their codonicity. The asymmetry of the phenotypic graphs of codons and anticodons of the SGC, has important implications on the evolutionary processes of proteins.

Characterization and Prediction of Presynaptic and Postsynaptic Neurotoxin by Reduced Amino Acid and Biological Property.

2020 ◽  
Vol 15 ◽  
Author(s):  
Yiyin Cao ◽  
Chunlu Yu ◽  
Shenghui Huang ◽  
Shiyuan Wang ◽  
Yongchun Zuo ◽  
...  
Keyword(s):  
Amino Acids ◽  
Support Vector Machine ◽  
Amino Acid ◽  
Biological Properties ◽  
Statistical Test ◽  
Support Vector ◽  
Reduced Amino Acid Alphabet ◽  
The Difference ◽  
Amino Acid Alphabet

Background: Presynaptic and postsynaptic neurotoxins are two important neurotoxins. Due to the important role of presynaptic and postsynaptic neurotoxins in pharmacology and neuroscience, identification of them becomes very important in biology. Method: In this study, the statistical test and F-score were used to calculate the difference between amino acids and biological properties. The support vector machine was used to predict the presynaptic and postsynaptic neurotoxins by using the reduced amino acid alphabet types. Results: By using the reduced amino acid alphabet as the input parameters of support vector machine, the overall accuracy of our classifier had increased to 91.07%, which was the highest overall accuracy in this study. When compared with the other published methods, better predictive results were obtained by our classifier. Conclusion: In summary, we analyzed the differences between two neurotoxins in amino acids and biological properties, and constructed a classifier that could predict these two neurotoxins by using the reduced amino acid alphabet.

scholarly journals Predicting the Types of J-Proteins Using Clustered Amino Acids

2014 ◽  
Vol 2014 ◽  
pp. 1-8 ◽  
Author(s):  
Pengmian Feng ◽  
Hao Lin ◽  
Wei Chen ◽  
Yongchun Zuo
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Support Vector ◽  
Type I ◽  
Practical Applications ◽  
Type Iv ◽  
Proposed Model ◽  
J Proteins ◽  
Amino Acid Alphabet ◽  
Online Web

J-proteins are molecular chaperones and present in a wide variety of organisms from prokaryote to eukaryote. Based on their domain organizations, J-proteins can be classified into 4 types, that is, Type I, Type II, Type III, and Type IV. Different types of J-proteins play distinct roles in influencing cancer properties and cell death. Thus, reliably annotating the types of J-proteins is essential to better understand their molecular functions. In the present work, a support vector machine based method was developed to identify the types of J-proteins using the tripeptide composition of reduced amino acid alphabet. In the jackknife cross-validation, the maximum overall accuracy of 94% was achieved on a stringent benchmark dataset. We also analyzed the amino acid compositions by using analysis of variance and found the distinct distributions of amino acids in each family of the J-proteins. To enhance the value of the practical applications of the proposed model, an online web server was developed and can be freely accessed.

Constructing a Syntheses Table of the Standard Amino Acid Based on the PAM250 Matrix

2011 ◽  
Vol 335-336 ◽  
pp. 1279-1284
Author(s):  
Xiao Hong Shi ◽  
Xiang Hong Wang
Keyword(s):  
Amino Acids ◽  
Molecular Weight ◽  
Amino Acid ◽  
Physicochemical Properties ◽  
Side Chain ◽  
Side Chains ◽  
Chemical Structures ◽  
Naturally Occurring ◽  
Standard Amino Acid ◽  
Similar Amino Acid

It is well known that there are some similarities among various naturally occurring amino acids. The standard amino acids have been grouped by their general properties and the chemical structures of their side chains. In this paper we divided the molecular weight of amino acid into two parts: backbone molecular weight Mband side chain molecular weight Ms. We naturally grouped the amino acids into two sets according to the rate of Ms/ Mb. We developed a method to construct a syntheses table to reflect the relevant physicochemical properties based on the PAM250 matrix and successfully established an elegant table of the twenty amino acids. Our work proved that PAM250 matrix could be used not only in finding reasonable alignments but also in grouping similar amino acid.

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