In-silico analysis of deleterious missense SNPs of human TYR gene associated with oculocutaneous albinism type 1 (OCA1)

Mahmood, Malik Siddique; Irshad, Saba; Butt, Tehreem Aqdas; Batool, Hina; Batool, Sana; Ashraf, Naeem Mahmood

doi:10.1016/j.mgene.2020.100674

Cited by 5 publications

(6 citation statements)

References 35 publications

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“…This divergence might be because of the distortion in the secondary conformation and folding of the protein. 15,44 The same results were also confirmed by the MD simulation analysis (Figure 5). Hence, these findings suggest a significant decrease in the stability of the LHPP protein by L22P mutant, which might contribute to the pathogenesis of HCC by inducing tumorigeneses.…”

Section: Discussionsupporting

confidence: 80%

“…14 The in silico approaches offer significant advantages over the experimental methods in terms of speed, reliability, convenience, and cost. 15…”

Section: Introductionmentioning

confidence: 99%

“…14 The in silico approaches offer significant advantages over the experimental methods in terms of speed, reliability, convenience, and cost. 15 This study is designed for the computational screening of the missense SNVs from the LHPP gene, regulating the structure, function, and stability of its protein. Furthermore, the impact of pathogenic mutations on the structure of the protein is evaluated via geometrical simulations.…”

Section: Introductionmentioning

confidence: 99%

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Screening of Pathogenic Missense Single Nucleotide Variants From LHPP Gene Associated With the Hepatocellular Carcinoma: An In silico Approach

Mahmood

Afzal

Batool

et al. 2022

Bioinform Biol Insights

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LHPP gene encodes a phospholysine phosphohistidine inorganic pyrophosphate phosphatase, which functions as a tumor-suppressor protein. The tumor suppression by this protein has been confirmed in various cancers, including hepatocellular carcinoma (HCC). LHPP downregulation promotes cell growth and proliferation by modulating the PI3K/AKT signaling pathway. This study identifies potentially deleterious missense single nucleotide variants (SNVs) associated with the LHPP gene using multiple computational tools based on different algorithms. A total of 4 destabilizing mutants are identified as L22P, I212T, G227R, and G236R, from the conserved region of the phosphatase. The 3-dimensional (3D) modeling and structural comparison of variants with the native protein reveals significant structural and conformational variations after mutations, suggesting disruption in the function of phospholysine phosphohistidine inorganic pyrophosphate phosphatase. The identified mutations might, therefore, participate in the cause of HCC.

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Section: Discussionsupporting

confidence: 80%

“…14 The in silico approaches offer significant advantages over the experimental methods in terms of speed, reliability, convenience, and cost. 15…”

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Screening of Pathogenic Missense Single Nucleotide Variants From LHPP Gene Associated With the Hepatocellular Carcinoma: An In silico Approach

Mahmood

Afzal

Batool

et al. 2022

Bioinform Biol Insights

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“…7 a–c). After structural modelling, Verify 3D, ERRAT, and PROCHECK from SAVES server were used for the model validations (Mahmood et al 2020 ). The verify3D evaluates these models by determining the compatibility of models with amino acid sequences and assigned the structural scores for the alpha, beta, loop, polar, and non-polar to these sequences.…”

Section: Resultsmentioning

confidence: 99%

Analysis of Putative Epitope Candidates of Mycobacterium tuberculosis Against Pakistani Human Leukocyte Antigen Background: An Immunoinformatic Study for the Development of Future Vaccine

Mahmood

Bin-T-Abid

Irshad

et al. 2020

Int J Pept Res Ther

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Tuberculosis (TB), a chronic disease caused by Mycobacterium tuberculosis (Mtb), is a global health issue across the world. Pakistan ranks fifth among the countries, which are facing, a significantly great number of mortalities and morbidities due to TB. Unfortunately, all previously reported treatments are not successful for the eradication of TB. Here in this study, we report an emerging treatment option for this disease. We have applied immunoinformatics to predict highly conserved B and T-cell epitopes from Mtb, showing significant binding affinities to the frequent HLA alleles in the Pakistani population. A total of ten highly referenced and experimentally validated epitopes were selected from the Immune Epitope Database (IEDB), followed by their conservancy analysis using weblogos. The consensus sequences and variants derived from these sequences were examined, for their binding affinities, with prevalent HLA alleles of Pakistan. Moreover, the antigenic and allergenic natures of these peptides were also evaluated via Vaxijen and AllerTOP, respectively. Consequently, all potentially allergenic and non-antigenic, peptide fragments, were excluded from the analysis. Among all putative epitopes, three CD8 + T-cell epitopes were selected, as ideal vaccine candidates and, population coverage analysis revealed that the combination of these three peptides was covering, 67.28% Pakistani Asian and 57.15% mixed Pakistani populations. Likewise, eleven linear and six conformational or discontinuous B-cell epitopes were also marked as potential vaccine candidates based on their prediction score, non-allergenic nature, and antigenic properties. These epitopes, however, need the final validation via wet-lab studies. After their approval, these epitopes would be effective candidates for the future designing of epitope-based vaccines against Mtb infections in Pakistan.

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“…Bioinformatic studies have been used to examine functional and structural genomics (genetics, [ 551,552 ] gene expression of tyrosinase‐induced melanogenesis, [ 553 ] albinism‐associated single nucleotide polymorphisms reported in oculocutaneous albinism, [ 554–557 ] identification of potential inhibitors against Rab38 and melanoma cancer [ 558 ] ), proteomics (protein conformations and interactions (e.g., melanin‐concentrating hormone; [ 559–564 ] melanin‐concentrating hormone receptors [ 563,565–567 ] and their antagonists; [ 563,566,568–570 ] structure–function relationships of tyrosinase mutants, [ 571–574 ] substances that inhibit tyrosinase activity; [ 550,575–599 ] the role of melanocortin 1 Receptor (MC1R) in skin tanning with potential to resolve pigmentary disorders, [ 600 ] physiology, [ 601–605 ] and pathology. [ 94,606–608 ] Such studies can offer insight into intermolecular interactions with melanins, [ 609–611 ] drug pharmacokinetics, [ 94,612–614 ] and antibody targeting for anticancer treatments.…”

Section: Analysis Of Melaninsmentioning

confidence: 99%

Melanins as Sustainable Resources for Advanced Biotechnological Applications

et al. 2020

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Melanins are a class of biopolymers that are widespread in nature and have diverse origins, chemical compositions, and functions. Their chemical, electrical, optical, and paramagnetic properties offer opportunities for applications in materials science, particularly for medical and technical uses. This review focuses on the application of analytical techniques to study melanins in multidisciplinary contexts with a view to their use as sustainable resources for advanced biotechnological applications, and how these may facilitate the achievement of the United Nations Sustainable Development Goals.

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In-silico analysis of deleterious missense SNPs of human TYR gene associated with oculocutaneous albinism type 1 (OCA1)

Cited by 5 publications

References 35 publications

Screening of Pathogenic Missense Single Nucleotide Variants From LHPP Gene Associated With the Hepatocellular Carcinoma: An In silico Approach

Screening of Pathogenic Missense Single Nucleotide Variants From LHPP Gene Associated With the Hepatocellular Carcinoma: An In silico Approach

Analysis of Putative Epitope Candidates of Mycobacterium tuberculosis Against Pakistani Human Leukocyte Antigen Background: An Immunoinformatic Study for the Development of Future Vaccine

Melanins as Sustainable Resources for Advanced Biotechnological Applications

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