Physico-chemical characterization and topological analysis of pathogenesis-related proteins from Arabidopsis thaliana and Oryza sativa using in-silico approaches

Kaur, Amritpreet; Pati, Pratap Kumar; Pati, Aparna Maitra; Nagpal, Avinash Kaur

doi:10.1371/journal.pone.0239836

Cited by 37 publications

(25 citation statements)

References 62 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…More experiments are needed to uncover the relationship between McHB7 and Rubisco. D7KSJ9 is known to play an important role in response to stimulus and regulation [50]. Its protein level is two times higher in OE plants than in the WT before salt stress.…”

Section: Discussionmentioning

confidence: 99%

Proteomics of Homeobox7 Enhanced Salt Tolerance in Mesembryanthemum crystallinum

Zhang

Tan

Zhu

et al. 2021

IJMS

View full text Add to dashboard Cite

Mesembryanthemum crystallinum (common ice plant) is a halophyte species that has adapted to extreme conditions. In this study, we cloned a McHB7 transcription factor gene from the ice plant. The expression of McHB7 was significantly induced by 500 mM NaCl and it reached the peak under salt treatment for 7 days. The McHB7 protein was targeted to the nucleus. McHB7-overexpressing in ice plant leaves through Agrobacterium-mediated transformation led to 25 times more McHB7 transcripts than the non-transformed wild type (WT). After 500 mM NaCl treatment for 7 days, the activities of superoxide dismutase (SOD) and peroxidase (POD) and water content of the transgenic plants were higher than the WT, while malondialdehyde (MDA) was decreased in the transgenic plants. A total of 1082 and 1072 proteins were profiled by proteomics under control and salt treatment, respectively, with 22 and 11 proteins uniquely identified under control and salt stress, respectively. Among the 11 proteins, 7 were increased and 4 were decreased after salt treatment. Most of the proteins whose expression increased in the McHB7 overexpression (OE) ice plants under high salinity were involved in transport regulation, catalytic activities, biosynthesis of secondary metabolites, and response to stimulus. The results demonstrate that the McHB7 transcription factor plays a positive role in improving plant salt tolerance.

show abstract

Section: Discussionmentioning

confidence: 99%

Proteomics of Homeobox7 Enhanced Salt Tolerance in Mesembryanthemum crystallinum

Zhang

Tan

Zhu

et al. 2021

IJMS

View full text Add to dashboard Cite

show abstract

“…The instability index indicates protein stability under both in vivo and in vitro conditions, and values of more than 40 indicate unstable proteins [22]. The aliphatic index (AI) refers to the volume occupied by aliphatic side chains, and with the instability index, AI is another parameter to define the stability of the proteins [23]. All the parameters were calculated using Protparam Expasy available at https://web.expasy.org/protparam/ (assessed on 6 July 2021) [24] and PEPTIDE 2 tools (https://www.peptide2.com/) assessed on 6 July 2021.…”

Section: Protein Indices Calculationmentioning

confidence: 99%

Genes Common in Primary Immunodeficiencies and Cancer Display Overrepresentation of Codon CTG and Dominant Role of Selection Pressure in Shaping Codon Usage

Khandia

Alqahtani

2021

Biomedicines

View full text Add to dashboard Cite

Primary immunodeficiencies (PIDs) are disorders of the immune system that involve faulty cellular, humoral, or both cellular and humoral functions. PIDs are present at the crossroad between infections, immune dysregulation, and cancers. A panel encompassing 42 genes involved in both PIDs and cancer has been investigated for the genes’ compositional properties, codon usage patterns, various forces affecting codon choice, protein properties, and gene expression profiles. In the present study, the codon choice of genes was found to be dependent upon the richness of the nucleotide; the viz AT nucleotide rich genome preferred AT ending codons. The dinucleotide TpA adversely affected protein expression, while CpG did not. The CTG codon was the most overrepresented codon in 80.95% of genes. Analysis of various protein properties, including GRAVY, AROMA, isoelectric point, aliphatic index, hydrophobicity, instability index, and numbers of acidic, basic, and neutral amino acid residues revealed that the hydrophobicity index, instability index, and numbers of acidic and basic amino acid residues are the factors affecting gene expression. Based on neutrality analysis, parity analysis, ENc-GC3 analysis, and regression analysis of nucleotides present at the first and third positions of the codon, it was determined that selection pressure, mutation pressure, and compositional constraints all participated in shaping codon usage. The study will help determine the various evolutionary forces acting on genes common to both PIDs and cancer. Codon usage analysis might be helpful in the future to augment both diseases simultaneously. The research also indicates a peculiar pattern adapted by a set of genes involved in any disease.

show abstract

“…A high aliphatic index value of more than 50 indicates that the protein is temperature stable. In general, the aliphatic index is closely attributed to the protein or peptide’s thermostability (Kaur et al 2020). In this study, the modelled protein Cytochrome c oxidase subunit 2 of Cyprinus carpio and Cytochrome c oxidase subunit 1 of Tubifex tubifex exhibited the aliphatic index value of 110.61 and 113.31, which indicates that the predicted proteins are highly thermostable.…”

Section: Resultsmentioning

confidence: 99%

Homology Modelling, In Silico Prediction And Characterization Of Cytochrome c oxidase In Cyprinus carpio And Tubifex tubifex And Molecular Docking Studies Between The Modelled Protein And Three Commonly Used Surfactants Sodium Dodecyl Sulphate, Cetylpyridinium Chloride And Sodium Laureth Sulphate

Bhattacharya

Daoud

Chatterjee

et al. 2021

Preprint

View full text Add to dashboard Cite

The purpose of this work is to evaluate the homology modeling, in silico prediction, and characterisation of Cytochrome c oxidase from Cyprinus carpio and Tubifex tubifex, as well as molecular docking experiments between the modelled protein and three frequently used surfactants. Using the template crystal structure of bovine heart Cytochrome c oxidase, homology modeling of Cytochrome c oxidase (Subunit 2) of Cyprinus carpio (Accession # P24985) and Cytochrome c oxidase (Subunit 1) of Tubifex tubifex (Accession # Q7YAA6) was conducted. The model structure was improved further with 3Drefine, and the final 3D structure was verified with PROCHEK and ERRATA. The physiochemical, as well as the stereochemical parameters of the modelled protein, were evaluated using various tools like ExPASy’s ProtParam, Hydropathy Analysis and EMBOSS pepwheel. The projected model was then docked with toxic ligands, Sodium dodecyl sulfate (SDS), Cetylpyridinium chloride (CPC), and Sodium laureth sulfate (SLES), whose 3D structures were obtained from the Uniprot database. CPC interacted best with Cytochrome c oxidase subunit 2 of Cyprinus carpio and Cytochrome c oxidase subunit 1 of Tubifex tubifex, according to our findings. Furthermore, in the case of all surfactants, hydrophobic interactions with the active site amino acid residues of the modelled protein were observed to be more common than hydrogen bonds and salt bridges. Molecular simulation studies exhibited that the surfactants alter the structural flexibility of the predicted proteins. Hence it may be inferred that the surfactants might alter the structure and dynamics of Cytochrome c oxidase of both worm and fish.

show abstract

Physico-chemical characterization and topological analysis of pathogenesis-related proteins from Arabidopsis thaliana and Oryza sativa using in-silico approaches

Cited by 37 publications

References 62 publications

Proteomics of Homeobox7 Enhanced Salt Tolerance in Mesembryanthemum crystallinum

Proteomics of Homeobox7 Enhanced Salt Tolerance in Mesembryanthemum crystallinum

Genes Common in Primary Immunodeficiencies and Cancer Display Overrepresentation of Codon CTG and Dominant Role of Selection Pressure in Shaping Codon Usage

Homology Modelling, In Silico Prediction And Characterization Of Cytochrome c oxidase In Cyprinus carpio And Tubifex tubifex And Molecular Docking Studies Between The Modelled Protein And Three Commonly Used Surfactants Sodium Dodecyl Sulphate, Cetylpyridinium Chloride And Sodium Laureth Sulphate

Contact Info

Product

Resources

About