scholarly journals Modular Organization of Residue-Level Contacts Shapes the Selection Pressure on Individual Amino Acid Sites of Ribosomal Proteins

2017 ◽  
Vol 9 (4) ◽  
pp. 916-931
Author(s):  
Saurav Mallik ◽  
Sudip Kundu
Keyword(s):  
Amino Acid ◽  
Ribosomal Proteins ◽  
Selection Pressure ◽  
Acid Sites ◽  
Residue Level ◽  
Modular Organization ◽  
Individual Amino Acid

scholarly journals Smoothed Bootstrap Aggregation for Assessing Selection Pressure at Amino Acid Sites

2016 ◽  
Vol 33 (11) ◽  
pp. 2976-2989 ◽  
Author(s):  
Joseph Mingrone ◽  
Edward Susko ◽  
Joseph Bielawski
Keyword(s):  
Amino Acid ◽  
Selection Pressure ◽  
Acid Sites ◽  
Smoothed Bootstrap ◽  
Bootstrap Aggregation

scholarly journals Amino-Acid Co-Variation in HIV-1 Gag Subtype C: HLA-Mediated Selection Pressure and Compensatory Dynamics

PLoS ONE ◽  
2010 ◽  
Vol 5 (9) ◽  
pp. e12463 ◽  
Author(s):  
Morgane Rolland ◽  
Jonathan M. Carlson ◽  
Siriphan Manocheewa ◽  
J. Victor Swain ◽  
Erinn Lanxon-Cookson ◽  
...  
Keyword(s):  
Amino Acid ◽  
Selection Pressure ◽  
Subtype C ◽  
Hiv 1

scholarly journals Disclosing the Nutritional Quality Diversity of Portuguese Common Beans—The Missing Link for Their Effective Use in Protein Quality Breeding Programs

Agronomy ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 221
Author(s):  
Elsa Mecha ◽  
Sofia Natalello ◽  
Bruna Carbas ◽  
Andreia Bento da Silva ◽  
Susana T. Leitão ◽  
...  
Keyword(s):  
Heat Stress ◽  
Amino Acid ◽  
Nutritional Quality ◽  
Dietary Habits ◽  
Protein Quality ◽  
Trypsin Inhibitor Activity ◽  
Environment Interaction ◽  
Individual Amino Acid ◽  
Common Beans ◽  
Breeding Programs

The common bean (Phaseolus vulgaris L.) represents a sustainable and affordable source of protein, namely, to populations with vegetarian dietary habits. Despite the national germplasm genetic diversity, little is known about the Portuguese accessions’ nutritional and protein quality, leading to their underuse in breeding programs. To fill this gap, a representative collection (106 accessions) was cropped under two contrasting environments (traditional versus heat stress) and evaluated in terms of nutritional quality by near-infrared spectroscopy. Protein quality was assessed, under the stressful environment, considering the individual amino acid contents and the activity of trypsin inhibitors through mass spectrometry (LC-MS/MS) and spectrophotometry, respectively. On top of strong genotypic control, the nutritional composition (protein, fat, fiber, moisture and ash) was also highly influenced by the environment and by genotype × environment interaction, with a clear nutritional quality ranking change for the accessions in heat stress conditions. Classified into three clusters, the accessions from the cluster with the highest individual amino acid and protein contents also showed higher trypsin inhibitor activity (TIA). Since different levels of TIA had no translation into contrasting protein digestibility, breeders focusing on common beans’ protein quality improvement, especially under challenging warming climate conditions, may take advantage of this group of accessions.

scholarly journals Codon-Substitution Models for Heterogeneous Selection Pressure at Amino Acid Sites

Genetics ◽  
2000 ◽  
Vol 155 (1) ◽  
pp. 431-449 ◽  
Author(s):  
Ziheng Yang ◽  
Rasmus Nielsen ◽  
Nick Goldman ◽  
Anne-Mette Krabbe Pedersen
Keyword(s):  
Amino Acid ◽  
Positive Selection ◽  
Selective Pressure ◽  
Acid Sites ◽  
Data Sets ◽  
Protein Coding ◽  
Important Indicator ◽  
Diversifying Selection ◽  
Codon Substitution ◽  
Neutral Mutations

AbstractComparison of relative fixation rates of synonymous (silent) and nonsynonymous (amino acid-altering) mutations provides a means for understanding the mechanisms of molecular sequence evolution. The nonsynonymous/synonymous rate ratio (ω = dN/dS) is an important indicator of selective pressure at the protein level, with ω = 1 meaning neutral mutations, ω < 1 purifying selection, and ω > 1 diversifying positive selection. Amino acid sites in a protein are expected to be under different selective pressures and have different underlying ω ratios. We develop models that account for heterogeneous ω ratios among amino acid sites and apply them to phylogenetic analyses of protein-coding DNA sequences. These models are useful for testing for adaptive molecular evolution and identifying amino acid sites under diversifying selection. Ten data sets of genes from nuclear, mitochondrial, and viral genomes are analyzed to estimate the distributions of ω among sites. In all data sets analyzed, the selective pressure indicated by the ω ratio is found to be highly heterogeneous among sites. Previously unsuspected Darwinian selection is detected in several genes in which the average ω ratio across sites is <1, but in which some sites are clearly under diversifying selection with ω > 1. Genes undergoing positive selection include the β-globin gene from vertebrates, mitochondrial protein-coding genes from hominoids, the hemagglutinin (HA) gene from human influenza virus A, and HIV-1 env, vif, and pol genes. Tests for the presence of positively selected sites and their subsequent identification appear quite robust to the specific distributional form assumed for ω and can be achieved using any of several models we implement. However, we encountered difficulties in estimating the precise distribution of ω among sites from real data sets.

Changes in the mixed function oxidase enzymes as a result of individual amino acid deficiencies

1977 ◽  
Vol 26 (7) ◽  
pp. 667-670 ◽  
Author(s):  
C.Richard Truex ◽  
Lena Brattsten ◽  
Willard J. Visek
Keyword(s):  
Amino Acid ◽  
Mixed Function Oxidase ◽  
Individual Amino Acid

An intergenic G-rich region in Leishmania tarentolae kinetoplast maxicircle DNA is a pan-edited cryptogene encoding ribosomal protein S12

1992 ◽  
Vol 12 (1) ◽  
pp. 56-67
Author(s):  
D A Maslov ◽  
N R Sturm ◽  
B M Niner ◽  
E S Gruszynski ◽  
M Peris ◽  
...  
Keyword(s):  
Amino Acid ◽  
Ribosomal Protein ◽  
Ribosomal Proteins ◽  
Sequence Similarity ◽  
Rich Region ◽  
Leishmania Tarentolae ◽  
Significant Sequence Similarity ◽  
The Family ◽  
Intergenic Regions ◽  
Ribosomal Protein S12

Six short G-rich intergenic regions in the maxicircle of Leishmania tarentolae are conserved in location and polarity in two other kinetoplastid species. We show here that G-rich region 6 (G6) represents a pan-edited cryptogene which contains at least two domains edited independently in a 3'-to-5' manner connected by short unedited regions. In the completely edited RNA, 117 uridines are added at 49 sites and 32 uridines are deleted at 13 sites, creating a translated 85-amino-acid polypeptide. Similar polypeptides are probably encoded by pan-edited G6 transcripts in two other species. The G6 polypeptide has significant sequence similarity to the family of S12 ribosomal proteins. A minicircle-encoded gRNA overlaps 12 editing sites in G6 mRNA, and chimeric gRNA/mRNA molecules were shown to exist, in agreement with the transesterification model for editing.

scholarly journals Regulation of AE2-mediated Cl− Transport by Intracellular or by Extracellular pH Requires Highly Conserved Amino Acid Residues of the AE2 NH2-terminal Cytoplasmic Domain

2002 ◽  
Vol 120 (5) ◽  
pp. 707-722 ◽  
Author(s):  
A.K. Stewart ◽  
M.N. Chernova ◽  
B.E. Shmukler ◽  
S. Wilhelm ◽  
S.L. Alper
Keyword(s):  
Amino Acid ◽  
Anion Exchange ◽  
Cytoplasmic Domain ◽  
Weak Acid ◽  
Extracellular Ph ◽  
Individual Amino Acid ◽  
Amino Acid Residues ◽  
General Importance ◽  
Alanine Scan ◽  
Intracellular Alkalinization

We reported recently that regulation by intracellular pH (pHi) of the murine Cl−/HCO3− exchanger AE2 requires amino acid residues 310–347 of the polypeptide's NH2-terminal cytoplasmic domain. We have now identified individual amino acid residues within this region whose integrity is required for regulation of AE2 by pH. 36Cl− efflux from AE2-expressing Xenopus oocytes was monitored during variation of extracellular pH (pHo) with unclamped or clamped pHi, or during variation of pHi at constant pHo. Wild-type AE2–mediated 36Cl− efflux was profoundly inhibited by acid pHo, with a value of pHo(50) = 6.87 ± 0.05, and was stimulated up to 10-fold by the intracellular alkalinization produced by bath removal of the preequilibrated weak acid, butyrate. Systematic hexa-alanine [(A)6]bloc substitutions between aa 312–347 identified the greatest acid shift in pHo(50) value, ∼0.8 pH units in the mutant (A)6342–347, but only a modest acid-shift in the mutant (A)6336–341. Two of the six (A)6 mutants retained normal pHi sensitivity of 36Cl− efflux, whereas the (A)6 mutants 318–323, 336–341, and 342–347 were not stimulated by intracellular alkalinization. We further evaluated the highly conserved region between aa 336–347 by alanine scan and other mutagenesis of single residues. Significant changes in AE2 sensitivity to pHo and to pHi were found independently and in concert. The E346A mutation acid-shifted the pHo(50) value to the same extent whether pHi was unclamped or held constant during variation of pHo. Alanine substitution of the corresponding glutamate residues in the cytoplasmic domains of related AE anion exchanger polypeptides confirmed the general importance of these residues in regulation of anion exchange by pH. Conserved, individual amino acid residues of the AE2 cytoplasmic domain contribute to independent regulation of anion exchange activity by pHo as well as pHi.

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