scholarly journals In-silico analysis of Salmonella typhimurium and E.coli Methionyl tRNA synthetase at primary, secondary, tertiary level with protein disorder and functional association of differences

2016 ◽  
Author(s):  
Prabhakar B. Ghorpade ◽  
Pooja Kadu ◽  
Amit Pandey ◽  
Yogesh Banger ◽  
Bhaskar Sharma
Keyword(s):  
Amino Acid ◽  
Salmonella Typhimurium ◽  
Tertiary Structure ◽  
3D Structure ◽  
In Silico Analysis ◽  
Trna Synthetase ◽  
Amino Acid Sequences ◽  
Functional Protein ◽  
Functional Differences ◽  
Methionyl Trna Synthetase

AbstractThe identification changes in amino acid for same protein in closely related species are necessary in order to identify its effect at various structural and functional levels. Salmonella typhimurium and E.coli Methionyl tRNA synthetase taken in current study as these bacteria are closely related to each other and have fewer differences in amino acid sequences for MetG. This study helps to identify various structural and functional differences at primary, secondary and tertiary levels, with functional differences by Docking study with Methionine. Study involves analysis of differences based on observation of differences in modeled 3D protein for sequences available at NCBI and its comparison with Known 3D structure. As sequences difference are in functional protein from non-mutant species, the differences are analysed in context of Primary, secondary, tertiary structure differences, Disorder differences, and docking differences.

In-silico Analysis of Evolution of Plant Polyamine Oxidases

2021 ◽  
Vol 16 (8) ◽  
pp. 11-21
Author(s):  
H.P. Pratheek ◽  
N. Manikanta ◽  
K.S. Shashidhara ◽  
M.S.P. Kanavi
Keyword(s):  
Amino Acid ◽  
Glutamic Acid ◽  
3D Structure ◽  
In Silico Analysis ◽  
Amino Acid Sequences ◽  
Soluble Form ◽  
Multiple Sequence ◽  
Clade B ◽  
Clade C ◽  
Key Terms

Amino oxidase enzymes have attractive role in programmed cell death. Full length amino acid sequences of 46 polyamino oxidases (PAO) and 8 diamino oxidases (DAO) were retrieved from major sequence repositories. Sequences were obtained using combination of queries based on key terms and BLASTp searches. The PAOs belong to 21 and DAOs belong to 5 families. Multiple sequence alignment of amino-acid sequences identified the conserved residues to be Glycine, Glutamic acid, Alanine, Arginine, Tryptophan, Proline, Valine, Leucine, Phenylalanine, Tyrosine and Lysine. Glycine is most conserved followed by glutamic acid and proline. The phylogenetic analysis revealed the three main nodes/clades A, B and C. Clade C containing highest number of PAO species was followed by clade B. Clade A mostly contains tree species PAOs. Similar trend has been observed for DAOs. PAO and DAO genes of plants including Arabidopsis thaliana, Brachipodium, Glycin max, Oryza sativa present on different chromosomes. Comparative modelling was done to build 3D structure of the PAO and DAO from A. thaliana. In the Ramachandran plot, more than 90% residues were in most allowed regions. DAOs are mostly located in lysosomes and vacuoles in the cell and are in soluble form. PAOs located in cytoplasm and peroxisomes are in soluble form.

Functional Replacement of Hamster Lysyl-tRNA Synthetase by the Yeast Enzyme Requires Cognate Amino Acid Sequences for Proper tRNA Recognition†

Biochemistry ◽  
1996 ◽  
Vol 35 (48) ◽  
pp. 15322-15331 ◽  
Author(s):  
Fabrice Agou ◽  
Sophie Quevillon ◽  
Pierre Kerjan ◽  
Marie-Thérèse Latreille ◽  
Marc Mirande
Keyword(s):  
Amino Acid ◽  
Trna Synthetase ◽  
Amino Acid Sequences ◽  
Trna Recognition ◽  
Functional Replacement

scholarly journals In-silicoprediction and modeling of theEntamoeba histolyticaproteins: Serine-richEntamoeba histolyticaprotein and 29 kDa Cysteine-rich protease

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3160 ◽  
Author(s):  
Kumar Manochitra ◽  
Subhash Chandra Parija
Keyword(s):  
Amino Acid ◽  
Structure Prediction ◽  
Tertiary Structure ◽  
Protein Structures ◽  
Amino Acid Sequences ◽  
Treatment Modalities ◽  
Bioinformatic Tools ◽  
Complex Protein ◽  
A Cell ◽  
Quaternary Structures

BackgroundAmoebiasis is the third most common parasitic cause of morbidity and mortality, particularly in countries with poor hygienic settings. There exists an ambiguity in the diagnosis of amoebiasis, and hence there arises a necessity for a better diagnostic approach. Serine-richEntamoeba histolyticaprotein (SREHP), peroxiredoxin and Gal/GalNAc lectin are pivotal inE. histolyticavirulence and are extensively studied as diagnostic and vaccine targets. For elucidating the cellular function of these proteins, details regarding their respective quaternary structures are essential. However, studies in this aspect are scant. Hence, this study was carried out to predict the structure of these target proteins and characterize them structurally as well as functionally using appropriatein-silicomethods.MethodsThe amino acid sequences of the proteins were retrieved from National Centre for Biotechnology Information database and aligned using ClustalW. Bioinformatic tools were employed in the secondary structure and tertiary structure prediction. The predicted structure was validated, and final refinement was carried out.ResultsThe protein structures predicted by i-TASSER were found to be more accurate than Phyre2 based on the validation using SAVES server. The prediction suggests SREHP to be an extracellular protein, peroxiredoxin a peripheral membrane protein while Gal/GalNAc lectin was found to be a cell-wall protein. Signal peptides were found in the amino-acid sequences of SREHP and Gal/GalNAc lectin, whereas they were not present in the peroxiredoxin sequence. Gal/GalNAc lectin showed better antigenicity than the other two proteins studied. All the three proteins exhibited similarity in their structures and were mostly composed of loops.DiscussionThe structures of SREHP and peroxiredoxin were predicted successfully, while the structure of Gal/GalNAc lectin could not be predicted as it was a complex protein composed of sub-units. Also, this protein showed less similarity with the available structural homologs. The quaternary structures of SREHP and peroxiredoxin predicted from this study would provide better structural and functional insights into these proteins and may aid in development of newer diagnostic assays or enhancement of the available treatment modalities.

How methionyl-tRNA synthetase creates its amino acid recognition pocket upon l-methionine binding

2001 ◽  
Vol 306 (4) ◽  
pp. 863-876 ◽  
Author(s):  
Laurence Serre ◽  
Grégory Verdon ◽  
Thomas Choinowski ◽  
Nadège Hervouet ◽  
Jean-Loup Risler ◽  
...  
Keyword(s):  
Amino Acid ◽  
Trna Synthetase ◽  
Methionyl Trna Synthetase ◽  
Amino Acid Recognition

scholarly journals Use of β3-methionine as an amino acid substrate of Escherichia coli methionyl-tRNA synthetase

2020 ◽  
Vol 209 (2) ◽  
pp. 107435 ◽  
Author(s):  
Giuliano Nigro ◽  
Sophie Bourcier ◽  
Christine Lazennec-Schurdevin ◽  
Emmanuelle Schmitt ◽  
Philippe Marlière ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Amino Acid ◽  
Trna Synthetase ◽  
Methionyl Trna Synthetase ◽  
Acid Substrate ◽  
Amino Acid Substrate

scholarly journals Amino Acids Sequence Based in Silico Analysis of RuBisCO (Ribulose-1,5 Bisphosphate Carboxylase Oxygenase) Proteins in Some Carthamus L. ssp.

2017 ◽  
Vol 9 (2) ◽  
pp. 204-208 ◽  
Author(s):  
Emre SEVİNDİK
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Average Length ◽  
3D Structure ◽  
Three Dimensional ◽  
In Silico Analysis ◽  
Bisphosphate Carboxylase ◽  
Molecular Weights ◽  
Acid Ratio ◽  
Important Enzyme

RuBisCO is an important enzyme for plants to photosynthesize and balance carbon dioxide in the atmosphere. This study aimed to perform sequence, physicochemical, phylogenetic and 3D (three-dimensional) comparative analyses of RuBisCO proteins in the Carthamus ssp. using various bioinformatics tools. The sequence lengths of the RuBisCO proteins were between 166 and 477 amino acids, with an average length of 411.8 amino acids. Their molecular weights (Mw) ranged from 18711.47 to 52843.09 Da; the most acidic and basic protein sequences were detected in C. tinctorius (pI = 5.99) and in C. tenuis (pI = 6.92), respectively. The extinction coefficients of RuBisCO proteins at 280 nm ranged from 17,670 to 69,830 M-1 cm-1, the instability index (II) values for RuBisCO proteins ranged from 33.31 to 39.39, while the GRAVY values of RuBisCO proteins ranged from -0.313 to -0.250. The most abundant amino acid in the RuBisCO protein was Gly (9.7%), while the least amino acid ratio was Trp (1.6 %). The putative phosphorylation sites of RuBisCO proteins were determined by NetPhos 2.0. Phylogenetic analysis revealed that RuBisCO proteins formed two main clades. A RAMPAGE analysis revealed that 96.3%-97.6% of residues were located in the favoured region of RuBisCO proteins. To predict the three dimensional (3D) structure of the RuBisCO proteins PyMOL was used. The results of the current study provide insights into fundamental characteristic of RuBisCO proteins in Carthamus ssp.

scholarly journals Identification of potential amino acid residues supporting anticodon recognition in yeast methionyl-tRNA synthetase

FEBS Letters ◽  
1991 ◽  
Vol 289 (2) ◽  
pp. 217-220 ◽  
Author(s):  
Laurence Despons ◽  
Philippe Walter ◽  
Bruno Senger ◽  
Jean-Pierre Ebel ◽  
Franco Fasiolo
Keyword(s):  
Amino Acid ◽  
Trna Synthetase ◽  
Amino Acid Residues ◽  
Methionyl Trna Synthetase

scholarly journals Analysis of a nucleotide-binding site of 5-lipoxygenase by affinity labelling: binding characteristics and amino acid sequences

2000 ◽  
Vol 351 (3) ◽  
pp. 697-707 ◽  
Author(s):  
Ying-Yi ZHANG ◽  
Tove HAMMARBERG ◽  
Olof RADMARK ◽  
Bengt SAMUELSSON ◽  
Carol F. NG ◽  
...  
Keyword(s):  
Amino Acid ◽  
Binding Site ◽  
Tertiary Structure ◽  
Nucleotide Binding ◽  
Peptide Sequencing ◽  
Amino Acid Sequences ◽  
Nucleotide Binding Site ◽  
Atp Binding ◽  
Binding Characteristics ◽  
Atp Binding Site

5-Lipoxygenase (5LO) catalyses the first two steps in the biosynthesis of leukotrienes, which are inflammatory mediators derived from arachidonic acid. 5LO activity is stimulated by ATP; however, a consensus ATP-binding site or nucleotide-binding site has not been found in its protein sequence. In the present study, affinity and photoaffinity labelling of 5LO with 5′-p-fluorosulphonylbenzoyladenosine (FSBA) and 2-azido-ATP showed that 5LO bound to the ATP analogues quantitatively and specifically and that the incorporation of either analogue inhibited ATP stimulation of 5LO activity. The stoichiometry of the labelling was 1.4mol of FSBA/mol of 5LO (of which ATP competed with 1mol/mol) or 0.94mol of 2-azido-ATP/mol of 5LO (of which ATP competed with 0.77mol/mol). Labelling with FSBA prevented further labelling with 2-azido-ATP, indicating that the same binding site was occupied by both analogues. Other nucleotides (ADP, AMP, GTP, CTP and UTP) also competed with 2-azido-ATP labelling, suggesting that the site was a general nucleotide-binding site rather than a strict ATP-binding site. Ca2+, which also stimulates 5LO activity, had no effect on the labelling of the nucleotide-binding site. Digestion with trypsin and peptide sequencing showed that two fragments of 5LO were labelled by 2-azido-ATP. These fragments correspond to residues 73–83 (KYWLNDDWYLK, in single-letter amino acid code) and 193–209 (FMHMFQSSWNDFADFEK) in the 5LO sequence. Trp-75 and Trp-201 in these peptides were modified by the labelling, suggesting that they were immediately adjacent to the C-2 position of the adenine ring of ATP. Given the stoichiometry of the labelling, the two peptide sequences of 5LO were probably near each other in the enzyme's tertiary structure, composing or surrounding the ATP-binding site of 5LO.

scholarly journals In silico analysis of virulence associated genes in genomes of Escherichia coli strains causing colibacillosis in poultry

2017 ◽  
Vol 61 (4) ◽  
pp. 421-426 ◽  
Author(s):  
Joanna Kołsut ◽  
Paulina Borówka ◽  
Błażej Marciniak ◽  
Ewelina Wójcik ◽  
Arkadiusz Wojtasik ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Amino Acid ◽  
Virulence Factors ◽  
De Novo ◽  
Protein Sequences ◽  
In Silico Analysis ◽  
Amino Acid Sequences ◽  
Common Disease ◽  
Bacterial Genomes ◽  
E Coli

AbstractIntroduction: Colibacillosis – the most common disease of poultry, is caused mainly by avian pathogenic Escherichia coli (APEC). However, thus far, no pattern to the molecular basis of the pathogenicity of these bacteria has been established beyond dispute. In this study, genomes of APEC were investigated to ascribe importance and explore the distribution of 16 genes recognised as their virulence factors.Material and Methods: A total of 14 pathogenic for poultry E. coli strains were isolated, and their DNA was sequenced, assembled de novo, and annotated. Amino acid sequences from these bacteria and an additional 16 freely available APEC amino acid sequences were analysed with the DIFFIND tool to define their virulence factors.Results: The DIFFIND tool enabled quick, reliable, and convenient assessment of the differences between compared amino acid sequences from bacterial genomes. The presence of 16 protein sequences indicated as pathogenicity factors in poultry resulted in the generation of a heatmap which categorises genomes in terms of the existence and similarity of the analysed protein sequences.Conclusion: The proposed method of detection of virulence factors using the capabilities of the DIFFIND tool may be useful in the analysis of similarities of E. coli and other sequences deriving from bacteria. Phylogenetic analysis resulted in reliable segregation of 30 APEC strains into five main clusters containing various virulence associated genes (VAGs).

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