In silico Analysis of Human Endothelial Cell-specific Molecule 1 and Interleukin-6 Genetic Variants Involved in Coronary Artery Disease
Background: Recent epidemiological studies have highlighted the connection between endothelial cell-specific molecule (ESM-1) and interleukin-6 (IL-6) with coronary artery disease. This study aims to assess the influence of nonsynonymous single-nucleotide polymorphisms (nsSNPs) in ESM-1 and IL-6 on...
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| Format: | Article |
| Language: | English |
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Wolters Kluwer Medknow Publications
2024-12-01
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| Series: | Biomedical and Biotechnology Research Journal |
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| Online Access: | https://journals.lww.com/10.4103/bbrj.bbrj_258_24 |
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| author | Vineet Kulkarni Sukanya Shetty Roopa Bhandary Yanglem Mary |
| author_facet | Vineet Kulkarni Sukanya Shetty Roopa Bhandary Yanglem Mary |
| author_sort | Vineet Kulkarni |
| collection | DOAJ |
| description | Background:
Recent epidemiological studies have highlighted the connection between endothelial cell-specific molecule (ESM-1) and interleukin-6 (IL-6) with coronary artery disease. This study aims to assess the influence of nonsynonymous single-nucleotide polymorphisms (nsSNPs) in ESM-1 and IL-6 on protein expression through computational methods.
Methods:
A total of 141 SNPs in the ESM-1 gene and 22 SNPs in the IL-6 gene were retrieved from the dbSNP database. The pathogenicity of the SNPs was evaluated using SIFT and PolyPhen-2. The functional impact of the SNPs was analyzed using Functional Analysis through Hidden Markov Models, Combined Annotation Dependent Depletion, Protein Analysis through Evolutionary Relationships, PredictSNP, Multivariate Analysis of Protein Polymorphism, Screening for Nonacceptable Polymorphisms, Predictor of human Deleterious Single-nucleotide Polymorphisms, and SNP functional annotation. The MUpro and I-Mutant web tools were used to predict protein stability, and the Group-based Prediction System (GPS)-MSP tool was used for posttranslational modification analysis. SOPMA was utilized to determine the proteins’ secondary structure.
Results:
SIFT analysis identified 57 intolerant and 65 tolerant SNPs in ESM-1. CADD results indicated that several ESM-1 SNPs were pathogenic, while the majority were nonpathogenic. For IL-6, a small number of SNPs were identified as pathogenic, with the majority being nonpathogenic. The MUpro tool suggested that some ESM-1 SNPs enhanced stability, while the majority decreased protein stability. For IL-6, only a few SNPs increased protein stability, while the majority decreased it.
Conclusion:
In silico analysis of both ESM-1 and IL-6 SNPs suggests an impact on protein regulation. Further in vitro studies are necessary to validate these findings and their potential role in the pathogenesis of coronary artery disease. |
| format | Article |
| id | doaj-art-e923b497bb6b462a941f40306d1f65d9 |
| institution | DOAJ |
| issn | 2588-9834 2588-9842 |
| language | English |
| publishDate | 2024-12-01 |
| publisher | Wolters Kluwer Medknow Publications |
| record_format | Article |
| series | Biomedical and Biotechnology Research Journal |
| spelling | doaj-art-e923b497bb6b462a941f40306d1f65d92025-08-20T02:44:52ZengWolters Kluwer Medknow PublicationsBiomedical and Biotechnology Research Journal2588-98342588-98422024-12-018442242710.4103/bbrj.bbrj_258_24In silico Analysis of Human Endothelial Cell-specific Molecule 1 and Interleukin-6 Genetic Variants Involved in Coronary Artery DiseaseVineet KulkarniSukanya ShettyRoopa BhandaryYanglem MaryBackground: Recent epidemiological studies have highlighted the connection between endothelial cell-specific molecule (ESM-1) and interleukin-6 (IL-6) with coronary artery disease. This study aims to assess the influence of nonsynonymous single-nucleotide polymorphisms (nsSNPs) in ESM-1 and IL-6 on protein expression through computational methods. Methods: A total of 141 SNPs in the ESM-1 gene and 22 SNPs in the IL-6 gene were retrieved from the dbSNP database. The pathogenicity of the SNPs was evaluated using SIFT and PolyPhen-2. The functional impact of the SNPs was analyzed using Functional Analysis through Hidden Markov Models, Combined Annotation Dependent Depletion, Protein Analysis through Evolutionary Relationships, PredictSNP, Multivariate Analysis of Protein Polymorphism, Screening for Nonacceptable Polymorphisms, Predictor of human Deleterious Single-nucleotide Polymorphisms, and SNP functional annotation. The MUpro and I-Mutant web tools were used to predict protein stability, and the Group-based Prediction System (GPS)-MSP tool was used for posttranslational modification analysis. SOPMA was utilized to determine the proteins’ secondary structure. Results: SIFT analysis identified 57 intolerant and 65 tolerant SNPs in ESM-1. CADD results indicated that several ESM-1 SNPs were pathogenic, while the majority were nonpathogenic. For IL-6, a small number of SNPs were identified as pathogenic, with the majority being nonpathogenic. The MUpro tool suggested that some ESM-1 SNPs enhanced stability, while the majority decreased protein stability. For IL-6, only a few SNPs increased protein stability, while the majority decreased it. Conclusion: In silico analysis of both ESM-1 and IL-6 SNPs suggests an impact on protein regulation. Further in vitro studies are necessary to validate these findings and their potential role in the pathogenesis of coronary artery disease.https://journals.lww.com/10.4103/bbrj.bbrj_258_24endocan-1interleukin-6single-nucleotide polymorphism |
| spellingShingle | Vineet Kulkarni Sukanya Shetty Roopa Bhandary Yanglem Mary In silico Analysis of Human Endothelial Cell-specific Molecule 1 and Interleukin-6 Genetic Variants Involved in Coronary Artery Disease Biomedical and Biotechnology Research Journal endocan-1 interleukin-6 single-nucleotide polymorphism |
| title | In silico Analysis of Human Endothelial Cell-specific Molecule 1 and Interleukin-6 Genetic Variants Involved in Coronary Artery Disease |
| title_full | In silico Analysis of Human Endothelial Cell-specific Molecule 1 and Interleukin-6 Genetic Variants Involved in Coronary Artery Disease |
| title_fullStr | In silico Analysis of Human Endothelial Cell-specific Molecule 1 and Interleukin-6 Genetic Variants Involved in Coronary Artery Disease |
| title_full_unstemmed | In silico Analysis of Human Endothelial Cell-specific Molecule 1 and Interleukin-6 Genetic Variants Involved in Coronary Artery Disease |
| title_short | In silico Analysis of Human Endothelial Cell-specific Molecule 1 and Interleukin-6 Genetic Variants Involved in Coronary Artery Disease |
| title_sort | in silico analysis of human endothelial cell specific molecule 1 and interleukin 6 genetic variants involved in coronary artery disease |
| topic | endocan-1 interleukin-6 single-nucleotide polymorphism |
| url | https://journals.lww.com/10.4103/bbrj.bbrj_258_24 |
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