A Mathematical Formula Predicts the Third Base Wobble in Codons

2017 ◽  
Author(s):  
Brenda K. Krkosska Bayles
Keyword(s):  
Amino Acids ◽  
Mathematical Logic ◽  
Protein Synthesis ◽  
Reading Process ◽  
Specific Question ◽  
Complete Understanding ◽  
Mathematical Formula ◽  
The Third ◽  
Wobble Hypothesis ◽  
Do So

The 64 codons of the genetic code determine which amino acids are linked into a sequence to produce protein synthesis. Some of the codons specify the same amino acid by using only the first two letters of their codon triplet to do so, thus rendering their 3rd base irrelevant. Crick called this the wobble hypothesis, and a more complete understanding of the reading process could someday lead to a drug that can repair a misreading or to the creation of synthetic ribosomes capable of healthy protein synthesis. A step towards this goal is to apply mathematical logic to the 64 codons so that experimental results can be reproduced and to answer the specific question, how can the nucleotides in the three base positions be interpreted using mathematical code? Here it is shown that a mathematical formula derived from fluid mechanics predicts which codons in the dictionary will encode using their 3rd bases and which ones will not.

scholarly journals Differential inhibition of the initiation of DNA replication in stringent and relaxed strains ofEscherichia coli

1988 ◽  
Vol 51 (3) ◽  
pp. 173-177 ◽  
Author(s):  
Elena C. Guzman ◽  
Francisco J. Carrillo ◽  
Alfonso Jimenez-Sanchez
Keyword(s):  
Amino Acids ◽  
Protein Synthesis ◽  
Dna Replication ◽  
Ofescherichia Coli ◽  
Differential Inhibition ◽  
E Coli ◽  
Pbr322 Dna ◽  
Initiation Of Dna Replication ◽  
Do So

SummaryStarvation for isoleucine inhibits chromosome, minichromosome and pBR322 DNA replication in a stringent strain ofE. coli, but does not do so in a relaxed mutant. Starvation for other amino acids inhibits either chromosome and minichromosome replication in both strains. From these results we conclude thatoriCand pBR322 replication are stringently regulated and that isoleucine seems not to be essential for the protein synthesis required at the initiation oforiCreplication. Deprivation of isoleucine in a Rel−strain gives rise to amplification of minichromosome and pBR322 with a better yield of the latter plasmid than that following treatment with chloramphenicol.

Homochirality as the Signature of Extra-Terrestrial Life

1997 ◽  
Vol 161 ◽  
pp. 505-510
Author(s):  
Alexandra J. MacDermott ◽  
Laurence D. Barron ◽  
Andrè Brack ◽  
Thomas Buhse ◽  
John R. Cronin ◽  
...  
Keyword(s):  
Amino Acids ◽  
Protein Synthesis ◽  
Optical Rotation ◽  
Physical Origin ◽  
Natural Choice ◽  
Rosetta Mission ◽  
Terrestrial Life ◽  
Subsurface Layers ◽  
Solar System Bodies ◽  
Origin Of Homochirality

AbstractThe most characteristic hallmark of life is its homochirality: all biomolecules are usually of one hand, e.g. on Earth life uses only L-amino acids for protein synthesis and not their D mirror images. We therefore suggest that a search for extra-terrestrial life can be approached as a Search for Extra- Terrestrial Homochirality (SETH). The natural choice for a SETH instrument is optical rotation, and we describe a novel miniaturized space polarimeter, called the SETH Cigar, which could be used to detect optical rotation as the homochiral signature of life on other planets. Moving parts are avoided by replacing the normal rotating polarizer by multiple fixed polarizers at different angles as in the eye of the bee. We believe that homochirality may be found in the subsurface layers on Mars as a relic of extinct life, and on other solar system bodies as a sign of advanced pre-biotic chemistry. We discuss the chiral GC-MS planned for the Roland lander of the Rosetta mission to a comet and conclude with theories of the physical origin of homochirality.

Increased Protein Synthesis by Human Platelets during Phagocytosis of Latex Particles in Vitro

1976 ◽  
Vol 35 (02) ◽  
pp. 350-357 ◽  
Author(s):  
Hana Bessler ◽  
Galila Agam ◽  
Meir Djaldetti
Keyword(s):  
Protein Synthesis ◽  
Fold Increase ◽  
Human Platelets ◽  
Polystyrene Latex ◽  
Latex Particles ◽  
The Third ◽  
Platelet Protein ◽  
Dose Dependent ◽  
Phagocytotic Activity

SummaryA three-fold increase of protein synthesis by human platelets during in vitro phagocytosis of polystyrene latex particles was detected. During the first two hours of incubation, the percentage of phagocytizing platelets and the number of latex particles per platelet increased; by the end of the third hour, the first parameter remained stable, while the number of latex particles per cell had decreased.Vincristine (20 μg/ml of cell suspension) inhibited platelet protein synthesis. This effect was both time- and dose-dependent. The drug also caused a decrease in the number of phagocytizing cells, as well as in their phagocytotic activity.

scholarly journals A political ontology for Europe: Roberto Esposito’s instituent paradigm

2021 ◽  
Author(s):  
Rita Fulco
Keyword(s):  
Political Theology ◽  
Political Crisis ◽  
Recent Proposal ◽  
Political Ontology ◽  
The Third ◽  
European Crisis ◽  
Do So

AbstractThe aim of my article is to relate Roberto Esposito’s reflections on Europe to his more recent proposal of instituent thought. I will try to do so by focusing on three theoretical cornerstones of Esposito’s thought: the first concerns the evidence of a link between Europe, philosophy and politics. The second is deconstructive: it highlights the inadequacy of the answers of the most important contemporary ontological-political paradigms to the European crisis, as well as the impossibility of interpreting this crisis through theoretical-political categories such as sovereignty. The third relates more directly to the proposal of a new political ontology, which Esposito defines as instituent thought. Esposito’s discussion of political theology is the central theoretical nucleus of this study. This discussion will focus, in particular, on the category of negation, from which any political ontology that is based on pure affirmativeness or absolute negation is criticized. In his opinion, philosophical theories developed on the basis of these assumptions have proved to be incomplete or ineffective in relation to the current European and global philosophical and political crisis. Esposito therefore perceives the urgent need to propose a line of thought that is neither negatively destituent (post-Heideggerian), nor affirmatively constituent (post-Deleuzian, post-Spinozian), but instituent (neo-Machiavellian), capable of thinking about order through conflict (the affirmative through the negative). Provided that we do not think of the institution statically–in a conservative sense–but dynamically, as constant instituting in which conflict can become an instrument of a politics increasingly inspired by justice.

scholarly journals Destruxin A Interacts with Aminoacyl tRNA Synthases in Bombyx mori

2021 ◽  
Vol 7 (8) ◽  
pp. 593
Author(s):  
Jingjing Wang ◽  
Alexander Berestetskiy ◽  
Qiongbo Hu
Keyword(s):  
Amino Acids ◽  
Protein Synthesis ◽  
Bombyx Mori ◽  
Metarhizium Anisopliae ◽  
Free Amino ◽  
Molecular Target ◽  
Trna Synthetases ◽  
Interaction Mode ◽  
Aminoacyl Trna Synthetases ◽  
Wide Range

Destruxin A (DA), a hexa-cyclodepsipeptidic mycotoxin produced by the entomopathogenic fungus Metarhizium anisopliae, exhibits insecticidal activities in a wide range of pests and is known as an innate immunity inhibitor. However, its mechanism of action requires further investigation. In this research, the interactions of DA with the six aminoacyl tRNA synthetases (ARSs) of Bombyx mori, BmAlaRS, BmCysRS, BmMetRS, BmValRS, BmIleRS, and BmGluProRS, were analyzed. The six ARSs were expressed and purified. The BLI (biolayer interferometry) results indicated that DA binds these ARSs with the affinity indices (KD) of 10−4 to 10−5 M. The molecular docking suggested a similar interaction mode of DA with ARSs, whereby DA settled into a pocket through hydrogen bonds with Asn, Arg, His, Lys, and Tyr of ARSs. Furthermore, DA treatments decreased the contents of soluble protein and free amino acids in Bm12 cells, which suggested that DA impedes protein synthesis. Lastly, the ARSs in Bm12 cells were all downregulated by DA stress. This study sheds light on exploring and answering the molecular target of DA against target insects.

scholarly journals 146 Prematurity Blunts the Protein Synthetic Response of Skeletal Muscle to Insulin and Amino Acids

2020 ◽  
Vol 98 (Supplement_4) ◽  
pp. 118-119
Author(s):  
Teresa A Davis ◽  
Marko Rudar ◽  
Jane Naberhuis ◽  
Agus Suryawan ◽  
Marta Fiorotto
Keyword(s):  
Skeletal Muscle ◽  
Amino Acids ◽  
Protein Synthesis ◽  
Amino Acid ◽  
Body Weight Gain ◽  
Human Infant ◽  
Long Term Effects ◽  
Plasma Insulin Concentration ◽  
Akt Phosphorylation ◽  
Relative Body Weight

Abstract Livestock animals are important dual-purpose models that benefit both agricultural and biomedical research. The neonatal pig is an appropriate model for the human infant to assess long-term effects of early life nutrition on growth and metabolic outcomes. Previously we have demonstrated that prematurity blunts the feeding-induced stimulation of translation initiation and protein synthesis in skeletal muscle of neonatal pigs. The objective of this study was to determine whether reduced sensitivity to insulin and/or amino acids drives this blunted response. Pigs were delivered by caesarean section at preterm (PT, 103 d gestation) or at term (T, 112 d gestation) and fed parenterally for 4 d. On day 4, pigs were subject to euinsulinemic-euaminoacidemic-euglycemic (FAST), hyperinsulinemic-euaminoacidemic-euglycemic (INS), or euinsulinemic-hyperaminoacidemic-euglycemic (AA) clamps for 120 min, yielding six treatments: PT-FAST (n = 7), PT-INS (n = 9), PT-AA (n = 9), T-FAST (n = 8), T-INS (n = 9), and T-AA (n = 9). A flooding dose of L-[4-3H]Phe was injected into pigs 30 min before euthanasia. Birth weight and relative body weight gain were lower in PT than T pigs (P < 0.001). Plasma insulin concentration was increased from ~3 to ~100 µU/mL in INS compared to FAST and AA pigs (P < 0.001); plasma BCAA concentration was increased from ~250 to ~1,000 µmol/L in AA compared to FAST and INS pigs (P < 0.001). Despite achieving similar insulin and amino acid levels, longissimus dorsi AKT phosphorylation, mechanistic target of rapamycin (mTOR)·Rheb abundance, mTOR activation, and protein synthesis were lower in PT-INS than T-INS pigs (Table 1). Although amino-acid induced dissociation of Sestrin2 from GATOR2 was not affected by prematurity, mTOR·RagA abundance, mTOR·RagC abundance, mTOR activation, and protein synthesis were lower in PT-AA than T-AA pigs. The impaired capacity of premature skeletal muscle to respond to insulin or amino acids and promote protein synthesis likely contributes to reduced lean mass accretion. Research was supported by NIH and USDA.

scholarly journals Effect of long-term refeeding on protein metabolism in patients with cirrhosis of the liver

1997 ◽  
Vol 77 (2) ◽  
pp. 197-212 ◽  
Author(s):  
Jens Kondrup ◽  
Klaus Nielsen ◽  
Anders Juul
Keyword(s):  
Amino Acids ◽  
Protein Synthesis ◽  
Protein Degradation ◽  
Protein Metabolism ◽  
Cirrhosis Of The Liver ◽  
N Balance ◽  
Whole Body ◽  
Protein Requirement ◽  
Protein Utilization ◽  
Igf I

Patients with cirrhosis of the liver require an increased amount of protein to achieve N balance. However, the utilization of protein with increased protein intake, i.e. the slope from regression analysis of N balance v. intake, is highly efficient (Nielsen et al. 1995). In the present study, protein requirement and protein utilization were investigated further by measuring protein synthesis and degradation. In two separate studies, five or six patients with cirrhosis of the liver were refed on a balanced diet for an average of 2 or 4 weeks. Protein and energy intakes were doubled in both studies. Initial and final whole-body protein metabolism was measured in the fed state by primed continous [15N]glycine infusion. Refeeding caused a statistically significant increase of about 30% in protein synthesis in both studies while protein degradation was only slightly affected. The increase in protein synthesis was associated with significant increases in plasma concentrations of total amino acids (25%), leucine (58%), isoleucine (82%), valine (72%), proline (48%) and triiodothyronine (27%) while insulin, growth hormone, insulin-like growth factor (IGF)-I and IGF-binding protein-3 were not changed significantly. The results indicate that the efficient protein utilization is due to increased protein synthesis, rather than decreased protein degradation, and suggest that increases in plasma amino acids may be responsible for the increased protein synthesis. A comparison of the patients who had a normal protein requirement with the patients who had an increased protein requirement suggests that the increased protein requirement is due to a primary increase in protein degradation. It is speculated that this is due to low levels of IGF-I secondary to impaired liver function, since initial plasma concentration of IGF-I was about 25% of control values and remained low during refeeding.

scholarly journals Exercise, Amino Acids, and Aging in the Control of Human Muscle Protein Synthesis

2011 ◽  
Vol 43 (12) ◽  
pp. 2249-2258 ◽  
Author(s):  
DILLON K. WALKER ◽  
JARED M. DICKINSON ◽  
KYLE L. TIMMERMAN ◽  
MICAH J. DRUMMOND ◽  
PAUL T. REIDY ◽  
...  
Keyword(s):  
Amino Acids ◽  
Protein Synthesis ◽  
Muscle Protein ◽  
Muscle Protein Synthesis ◽  
Human Muscle

Manipulation of rumen fermentation in sheep by increasing the rate of flow of water from the rumen

1975 ◽  
Vol 85 (1) ◽  
pp. 93-101 ◽  
Author(s):  
D. G. Harrison ◽  
D. E. Beever ◽  
D. J. Thomson ◽  
D. F. Osbourn
Keyword(s):  
Amino Acids ◽  
Protein Synthesis ◽  
Dilution Rate ◽  
Volatile Fatty Acids ◽  
Artificial Saliva ◽  
Microbial Protein ◽  
Microbial Protein Synthesis ◽  
Glucose Polymer ◽  
Carbohydrate Digestion ◽  
Total Amino Acids

SUMMARYThe effects of an altered rumen dilution rate (D) upon the molar proportions of volatile fatty acids (VFA) in rumen liquor, VFA production rate, microbial protein synthesis and carbohydrate digestion within the rumen were studied using adult wether sheep.Dilution rate and VFA proportions were unaltered by the infusion of up to 121 water/day into the rumen of sheep fed dried grass and concentrate (9:1). There was a small but significant (P< 0·05) increase in the rumen volume when the infusion rate was increased from 8 to 12 1/day.The intraruminal infusion of artificial saliva (41/day), or artificial saliva containing 4% or 8% w/v polyethylene glycol (PEG) caused a significant increase in D with an associated decline in the molar proportion of propionate (Pr) in the rumen liquor. A similar effect was obtained with the intraruminal infusion of 2·5% w/v sodium bicarbonate. The overall regression of Pr on D was highly significant: Pr = 32·5–82·1D;r= –0·99, P < 0·001.A diet of flaked maize: dried grass (6:4) was offered to three sheep each fitted with a rumen cannula and with a re-entrant cannula at the proximal duodenum. The intraruminal infusion (4 1/day) of artificial saliva containing 4% w/v PEG caused a significant (P< 0·01) increase in D and a significant (P< 0·01) depression in Pr in two animals. The dilution rate and Pr in the third animal were virtually unaltered by infusion. The regression of Pr on D for the three animals was highly significant: Pr = 34·8–136·8D; r = –0·98, P < 0·001. Each increase in D was associated with an increased flow of α-linked glucose polymer, total amino acids and total microbial amino acids into the small intestine and with an increased efficiency of microbial protein synthesis within the rumen.

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