scholarly journals Oxidant-Mediated Protein Amino Acid Conversion

Antioxidants ◽  
2019 ◽  
Vol 8 (2) ◽  
pp. 50 ◽  
Author(s):  
Yuichiro Suzuki
Keyword(s):  
Protein Structure ◽  
Amino Acid ◽  
Biological System ◽  
Redox Regulation ◽  
Amino Acid Sequences ◽  
Biological Oxidation ◽  
Oxidation Reactions ◽  
Protein Amino Acid ◽  
Peroxiredoxin 6 ◽  
Protein Molecules

Biological oxidation plays important roles in the pathogenesis of various diseases and aging. Carbonylation is one mode of protein oxidation. It has been reported that amino acids that are susceptible to carbonylation are arginine (Arg), proline (Pro), lysine, and threonine residues. The carbonylation product of both Arg and Pro residues is glutamyl semialdehyde. While chemically the oxidation reactions of neither Pro to glutamyl semialdehyde nor Arg to glutamyl semialdehyde are reversible, experimental results from our laboratory suggest that the biological system may drive the reduction of glutamyl semialdehyde to Pro in the protein structure. Further, glutamyl semialdehyde can be oxidized to become glutamic acid (Glu). Therefore, I hypothesize that biological oxidation post-translationally converts Arg to Pro, Arg to Glu, and Pro to Glu within the protein structure. Our mass spectrometry experiments provided evidence that, in human cells, 5–10% of peroxiredoxin 6 protein molecules have Pro-45 replaced by Glu. This concept of protein amino acid conversion challenges the dogma that amino acid sequences are strictly defined by nucleic acid sequences. I propose that, in the biological system, amino acid replacements can occur post-translationally through redox regulation, and protein molecules with non-DNA coding sequences confer functions.

scholarly journals Alignment of Amino Acid and DNA Sequences of Human Proline-rich Proteins

1993 ◽  
Vol 4 (3) ◽  
pp. 287-292 ◽  
Author(s):  
D.L. Kauffman ◽  
P.J. Keller ◽  
A. Bennick ◽  
M. Blum
Keyword(s):  
Amino Acid ◽  
Dna Sequences ◽  
Sequence Data ◽  
Gel Filtration ◽  
Exchange Chromatography ◽  
Amino Acid Sequences ◽  
Secreted Proteins ◽  
Dna Encoding ◽  
Protein Amino Acid ◽  
Primary Gene

Human proline-rich proteins (PRPs) constitute a complex family of salivary proteins that are encoded by a small number of genes. The primary gene product is cleaved by proteases, thereby giving rise to about 20 secreted proteins. To determine the genes for the secreted PRPs, therefore, it is necessary to obtain sequences of both the secreted proteins and the DNA encoding these proteins. We have sequenced most PRPs from one donor (D.K.) and aligned the protein sequences with available DNA sequences from unrelated individuals. Partial sequence data have now been obtained for an additional PRP from D.K. named II-1. This protein was purified from parotid saliva by gel filtration and ion-exchange chromatography. Peptides were obtained by cleavage with trypsin, clostripain, and N-bromosuccinimide, followed by column chromatography. The peptides were sequenced on a gas-phase protein sequenator. Overlapping peptide sequences were obtained for most of II-1 and aligned with translated DNA sequences. The best fit was obtained with clones containing sequences for the allele PRB4" (Lyons et al., 1988). However, there was not complete identity of the protein amino acid sequence and the DNA-derived sequences, indicating that II-1 is not encoded by PRB4". Other PRPs isolated from D.K. also fail to conform to any DNA structure so far reported. This shows the need to obtain amino acid sequences and corresponding DNA sequences from the same person to assign genes for the PRPs and to determine the location of the postribosomal cleavage points in the primary translation product.

scholarly journals iSulfoTyr-PseAAC: Identify Tyrosine Sulfation Sites by Incorporating Statistical Moments via Chou’s 5-steps Rule and Pseudo Components

2019 ◽  
Vol 20 (4) ◽  
pp. 306-320 ◽  
Author(s):  
Omar Barukab ◽  
Yaser Daanial Khan ◽  
Sher Afzal Khan ◽  
Kuo-Chen Chou
Keyword(s):  
Amino Acid ◽  
Computational Model ◽  
Amino Acid Sequences ◽  
Site Directed Mutagenesis ◽  
Statistical Moments ◽  
Amino Acid Residues ◽  
Tyrosine Sulfation ◽  
Protein Amino Acid ◽  
Jackknife Test ◽  
Self Consistency

Background: The amino acid residues, in protein, undergo post-translation modification (PTM) during protein synthesis, a process of chemical and physical change in an amino acid that in turn alters behavioral properties of proteins. Tyrosine sulfation is a ubiquitous posttranslational modification which is known to be associated with regulation of various biological functions and pathological processes. Thus its identification is necessary to understand its mechanism. Experimental determination through site-directed mutagenesis and high throughput mass spectrometry is a costly and time taking process, thus, the reliable computational model is required for identification of sulfotyrosine sites. Methodology: In this paper, we present a computational model for the prediction of the sulfotyrosine sites named iSulfoTyr-PseAAC in which feature vectors are constructed using statistical moments of protein amino acid sequences and various position/composition relative features. These features are incorporated into PseAAC. The model is validated by jackknife, cross-validation, self-consistency and independent testing. Results: Accuracy determined through validation was 93.93% for jackknife test, 95.16% for crossvalidation, 94.3% for self-consistency and 94.3% for independent testing. Conclusion: The proposed model has better performance as compared to the existing predictors, however, the accuracy can be improved further, in future, due to increasing number of sulfotyrosine sites in proteins.

scholarly journals Intergenic ORFs as elementary structural modules of de novo gene birth and protein evolution

2021 ◽  
Author(s):  
Chris Papadopoulos ◽  
Isabelle Callebaut ◽  
Jean-Christophe Gelly ◽  
Isabelle Hatin ◽  
Olivier Namy ◽  
...  
Keyword(s):  
Protein Structure ◽  
Amino Acid ◽  
De Novo ◽  
Protein Structures ◽  
Structural Diversity ◽  
Building Blocks ◽  
Amino Acid Sequences ◽  
Novel Genes ◽  
Noncoding Sequences ◽  
De Novo Gene

The noncoding genome plays an important role in de novo gene birth and in the emergence of genetic novelty. Nevertheless, how noncoding sequences' properties could promote the birth of novel genes and shape the evolution and the structural diversity of proteins remains unclear. Therefore, by combining different bioinformatic approaches, we characterized the fold potential diversity of the amino acid sequences encoded by all intergenic ORFs (Open Reading Frames) of S. cerevisiae with the aim of (i) exploring whether the large structural diversity observed in proteomes is already present in noncoding sequences, and (ii) estimating the potential of the noncoding genome to produce novel protein bricks that can either give rise to novel genes or be integrated into pre-existing proteins, thus participating in protein structure diversity and evolution. We showed that amino acid sequences encoded by most yeast intergenic ORFs contain the elementary building blocks of protein structures. Moreover, they encompass the large structural diversity of canonical proteins with strikingly the majority predicted as foldable. Then, we investigated the early stages of de novo gene birth by identifying intergenic ORFs with a strong translation signal in ribosome profiling experiments and by reconstructing the ancestral sequences of 70 yeast de novo genes. This enabled us to highlight sequence and structural factors determining de novo gene emergence. Finally, we showed a strong correlation between the fold potential of de novo proteins and the one of their ancestral amino acid sequences, reflecting the relationship between the noncoding genome and the protein structure universe.

scholarly journals Novel mutations of the SRF gene in Chinese sporadic conotruncal heart defect patients

2020 ◽  
Author(s):  
Xu Mengmeng ◽  
Xu Yuejuan ◽  
Chen Sun ◽  
Lu Yanan ◽  
Li Fen ◽  
...  
Keyword(s):  
Amino Acid ◽  
Heart Development ◽  
Heart Defects ◽  
Amino Acid Sequences ◽  
Luciferase Reporter ◽  
Novel Mutations ◽  
Protein Amino Acid ◽  
Cross Sectional ◽  
Congenital Heart Malformations ◽  
Conotruncal Heart Defect

Abstract Background: Conotruncal heart defects (CTDs) are a group of congenital heart malformations that cause anomalies of cardiac outflow tracts. In the past few decades, many genes related to CTDs have been reported. Serum response factor (SRF) is a ubiquitous nuclear protein that acts as transcription factor, and SRF was found to be a critical factor in heart development and to be strongly expressed in the myocardium of the developing mouse and chicken hearts. The targeted inactivation of SRF during heart development leads to embryonic lethality and myocardial defects in mice. Results: To illustrate the relationship between SRF and human heart defects, we screened SRF mutations in 527 CTD patients, a cross sectional study. Two novel mutations (Mut1: c.821A>G p.G274D, the adenine(A) was mutated to guanine(G) at position 821 of the SRF gene coding sequences (CDS), lead to the Glycine(G) mutated to Asparticacid(D) at position 274 of the SRF protein amino acid sequences; Mut2: c.880G>T p.G294C, the guanine(G) was mutated to thymine (T) at position 880 of the SRF CDS, lead to the Glycine(G) mutated to Cysteine (C) at position 294 of the SRF protein amino acid sequences.) of SRF (NM_003131.2) were identified. Western blotting and real-time PCR showed that there were no obvious differences between the protein expression and mRNA transcription of mutants and wild-type SRF. A dual luciferase reporter assay showed that both SRF mutants (G274D and G294C) impaired SRF transcriptional activity at the SRF promoter and atrial natriuretic factor (ANF) promoter (p<0.05), additionally, the mutants displayed reduced synergism with GATA4. Conclusion: These results suggest that SRF-p.G274D and SRF-p.G294C may have potential pathogenic effects.

scholarly journals Dye Decoloring Peroxidase Structure, Catalytic Properties and Applications: Current Advancement and Futurity

Catalysts ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 955
Author(s):  
Lingxia Xu ◽  
Jianzhong Sun ◽  
Majjid A. Qaria ◽  
Lu Gao ◽  
Daochen Zhu
Keyword(s):  
Protein Structure ◽  
Amino Acid ◽  
High Efficiency ◽  
Chemical Properties ◽  
Catalytic Efficiency ◽  
Industrial Applications ◽  
Research Strategy ◽  
Amino Acid Sequences ◽  
Alkali Resistance ◽  
Wide Range

Dye decoloring peroxidases (DyPs) were named after their high efficiency to decolorize and degrade a wide range of dyes. DyPs are a type of heme peroxidase and are quite different from known heme peroxidases in terms of amino acid sequences, protein structure, catalytic residues, and physical and chemical properties. DyPs oxidize polycyclic dyes and phenolic compounds. Thus they find high application potentials in dealing with environmental problems. The structure and catalytic characteristics of DyPs of different families from the amino acid sequence, protein structure, and enzymatic properties, and analyzes the high-efficiency degradation ability of some DyPs in dye and lignin degradation, which vary greatly among DyPs classes. In addition, application prospects of DyPs in biomedicine and other fields are also discussed briefly. At the same time, the research strategy based on genetic engineering and synthetic biology in improving the stability and catalytic activity of DyPs are summarized along with the important industrial applications of DyPs and associated challenges. Moreover, according to the current research findings, bringing DyPs to the industrial level may require improving the catalytic efficiency of DyP, increasing production, and enhancing alkali resistance and toxicity.

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