Prediction of single nucleotide polymorphisms (SNPs) in apolipoprotein E gene and their possible associations with a deleterious effect on the structure and functional properties: an in silico approach

Saeed, Noor Al-Huda Ali A.H.; Hamzah, Israa Hussein; Ali, Alaa Naseer Mohammed; Abuderman, Abdulwahab

doi:10.1007/s13721-018-0178-9

Cited by 3 publications

(1 citation statement)

References 22 publications

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“…44 Analysis of the prediction score (which ranges from 100 strong neutral predictions to +100 strong effect prediction) suggests that it is somewhat correlated with the severity of the effect (https://rostlab.org/services/snap/). 45 Stability Analysis of Mutant Type and Wild Type CTLA-4 Protein I-Mutant 3.0 was used to predict changes in protein stability caused by single-site aa changes in the protein structure or sequence. It predicts the reliability index (RI) of the results, which ranges from 0 to 10, with 10 being the most reliable.…”

Section: Dovepressmentioning

confidence: 99%

Association of Cytotoxic T-Lymphocyte Antigen-4 Gene Polymorphism with Type 1 Diabetes Mellitus: In silico Analysis of Biological Features of CTLA-4 Protein on Ethiopian Population

Ebrahim¹,

Teklu²,

Tajebe³

et al. 2022

DMSO

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Background: T1DM is a chronic organ-specific T-cell-mediated autoimmune disease characterized by the selective destruction of βcells in the islets of Langerhans, resulting in insulin deficiency and hyperglycemia. Genes for cytotoxic T lymphocyte-associated antigen 4 have been hypothesized as possible contender genes for T1DM vulnerability. However, it has not been studied in the Ethiopian population yet. Objective: The aim of the study was to investigate CTLA-4 exon 1 was linked to A49G polymorphism with T1DM and its biological features of CTLA-4 among T1DM patients, in Ethiopia. Methods: A case-control study was done from December 2019 to March 2020 on 210 study participants (105 T1DM patients and 105 healthy controls). Polymerase Chain Reaction amplification with forward and reverse primers was followed by restriction fragment length polymorphism and gel electrophoresis to determine gene polymorphism. Bioinformatics data of SNP was retrieved from National Centers for Biotechnology Information databases. The chi-square test and logistic regression were used. Statistical significance was defined as a P-value of less than 0.05. Results:The CTLA-4 (+A49G) gene polymorphism was observed on 56 (26.7%) study participants, 39 (18.57%) of T1DM patients, and 17 (0.08%) were controls. In T1DM and controls, the frequency of the A allele was 73.3% and 89.5%, while the G allele was 26.7% and 10.5%, respectively. The G allele was found to be associated with T1DM (OR=3.1; 95% CI, 1.82 −5.32; P=0.001). Statistical analysis revealed an association between the likelihood of T1DM and GG genotype of the CTLA-4 (+A49G) gene polymorphism (OR=3.11; 95% CI, 1.37-10.90; P=0.01). Further in silico analyzed the SNP to assess its biological features. Conclusion:The study showed as CTLA-4 (+A49G) gene polymorphism is linked with T1DM in the Ethiopian population.

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Section: Dovepressmentioning

confidence: 99%

Association of Cytotoxic T-Lymphocyte Antigen-4 Gene Polymorphism with Type 1 Diabetes Mellitus: In silico Analysis of Biological Features of CTLA-4 Protein on Ethiopian Population

Ebrahim¹,

Teklu²,

Tajebe³

et al. 2022

DMSO

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Biyoinformatik araçlar aracılığıyla insan APOE (Apolipoprotein E) genindeki yanlış anlamlı SNV'lerin değerlendirilmesi

Karasakal

Oktay

Kaman

2023

Balıkesir Üniversitesi Fen Bilimleri Enstitüsü Dergisi

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Apolipoprotein E (APOE) is one of the main proteins responsible for cholesterol transport. It has three major isoforms, APOE2, APOE3, and APOE4. The purpose of this study is to investigate the possible effects of single nucleotide variations (SNVs) in the APOE gene, which cause amino acid substitution, on the function, structure and stabilization of the APOE protein using bioinformatics/s tools. SNVs and protein sequence information were obtained from NCBI and UniProt databases. Bioinformatical analysis was performed using a series of tools such as SIFT, PolyPhen-2, SNPs&GO, Mutation Assessor, PROVEAN, SNAP2, I-Mutant-3, MUPro, and Project HOPE. As a result, 321 missense SNVs were analyzed and rs7412 (R176C), rs769455 (R163C), rs11542029 (R50C), rs121918393 (R154S), rs121918394 (K164Q), rs200703101 (R154P), rs387906567 (R160C), rs11542040 (P102T), rs11542041 (R132S) and rs41382345 (E139V) were predicted to be deleterious/disease related after functional analysis and pathological effect analysis via all of the bioinformatics/s tools. According to the protein stabilization results, it was determined that all SNVs decreased protein stabilization with the MUPro software tool, and two SNVs (rs121918394, rs41382345) increased protein stabilization with the I-Mutant-3 software tool. The models of protein and amino acid properties were obtained via Project HOPE for all high-risk SNVs. We hope our analysis will be valuable for further proteomic, genomic, and clinical research.

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The Risk of Genetic Polymorphisms in the Immune Genes on the Developed of Respiratory Allergic Diseases

Hamzah

Saeed

Ali

2022

RJPT

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Allergic diseases are intricate and improvement includes both natural and hereditary components. besides classic Tcell-originated T helper form-2 cytokine comparable to IL4; IL5; IL13. Tissues created cytokine akin to thymic-stromal-lymphopoietin. IL25 as well as IL33 at the moment is famous the main contribution of allergies irritation. IL33 generated via quite a lot of tissue living cells and generally enhances allergic infection using its results in hematopoietic-cells varieties. Ecological and endogenously triggered which induce IL33 cell released could also correlated to contamination, irritation and tissues harm. Current review brief an extensive variety for certified IL33 efficiency in human-cellular-mediatory in irritation like good as genetically marker when IL33 contributed with sickness. At last, IL33 attached with IL1/RL1 was engaged with asthma. previous information shows in some investigation that contribution by IL33-IL1RL1 gene with asthma was biologically conceivable, IL33 on asthma patients can influence expressing levels for IL33 serum. Moreover, rs16924159/G-A variation is related in IL33 level of respiratory hypersensitive diseases patients.

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Prediction of single nucleotide polymorphisms (SNPs) in apolipoprotein E gene and their possible associations with a deleterious effect on the structure and functional properties: an in silico approach

Cited by 3 publications

References 22 publications

Association of Cytotoxic T-Lymphocyte Antigen-4 Gene Polymorphism with Type 1 Diabetes Mellitus: In silico Analysis of Biological Features of CTLA-4 Protein on Ethiopian Population

Association of Cytotoxic T-Lymphocyte Antigen-4 Gene Polymorphism with Type 1 Diabetes Mellitus: In silico Analysis of Biological Features of CTLA-4 Protein on Ethiopian Population

Biyoinformatik araçlar aracılığıyla insan APOE (Apolipoprotein E) genindeki yanlış anlamlı SNV'lerin değerlendirilmesi

The Risk of Genetic Polymorphisms in the Immune Genes on the Developed of Respiratory Allergic Diseases

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