Insilico Analysis Reveal Three novel nsSNPs May effect on GM2A protein Leading to AB variant of GM2 gangliosidosis

ABSTRACTBackgroundAB variant of GM2 gangliosidosis caused as a result of mutations in GM2 activator gene (GM2A) which is regarded as neurodegenerative disorder. This study aimed to predict the possible damaging SNPs of this gene and their impact on the protein using different bioinformatics tools.MethodsSNPs retrieved from the NCBI database were analyzed using several bioinformatics tools. The different tools collectively predicted the effect of single nucleotide substitution on both structure and function of GM2 activator.ResultsThree novel mutations were found to be highly damaging to the structure and function of the GM2A gene.ConclusionFour SNPs were found to be highly damaging SNPs that affect function, structure and stability of GM2A protein, which they are: C99Y, C112F, C138S and C138R, three of them are novel SNPs (C99Y, C112F and C138S). Also 46 SNPs were predicted to affect miRNAs binding sites on 3’UTR leading to abnormal expression of the resulting protein. These SNPs should be considered as important candidates in causing AB variant of GM2 gangliosidosis and may help in diagnosis and genetic screening of the disease.

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Thirty two novel nsSNPs May effect on HEXA protein Leading to Tay-Sachs disease (TSD) Using a Computational Approach

10.1101/762518 ◽

2019 ◽

Author(s):

Tebyan A. Abdelhameed ◽

Mohamed Mustafa Osman Fadul ◽

Dina Nasereldin Abdelrahman Mohamed ◽

Amal Mohamed Mudawi ◽

Sayaf Kamal Khalifa Fadul Allah ◽

...

Keyword(s):

Nucleotide Substitution ◽

Neurodegenerative Disorder ◽

Structure And Function ◽

Single Nucleotide Substitution ◽

Single Nucleotide ◽

Bioinformatics Tools ◽

Tay Sachs Disease ◽

Hexosaminidase A ◽

And Function

ABSTRACTBackgroundGenetic polymorphisms in the HEXA gene are associated with a neurodegenerative disorder called Tay-Sachs disease (TSD) (GM2 gangliosidosis type 1). This study aimed to predict the possible pathogenic SNPs of this gene and their impact on the protein using different bioinformatics tools.MethodsSNPs retrieved from the NCBI database were analyzed using several bioinformatics tools. The different algorithms collectively predicted the effect of single nucleotide substitution on both structure and function of the hexosaminidase A protein.ResultsFifty nine mutations were found to be highly damaging to the structure and function of the HEXA gene protein.ConclusionAccording to this study, thirty two novel nsSNP in HEXA are predicted to have possible role in Tay-Saches Disease using different bioinformatics tools. Our findings could help in genetic study and diagnosis of Tay-Saches Disease.

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Thirty five novel nsSNPs may effect on ADAMTS13 protein leading to Thrombotic thrombocytopenic purpura (TTP) using bioinformatics approach

10.1101/759787 ◽

2019 ◽

Author(s):

Tebyan A. Abdelhameed ◽

Arwa I. Ahmed ◽

Mujahed I. Mustafa ◽

Amel N. Eltayeb ◽

Fatima A. Abdelrhman ◽

...

Keyword(s):

Thrombotic Thrombocytopenic Purpura ◽

Nucleotide Substitution ◽

Structure And Function ◽

Biomedical Data ◽

Single Nucleotide Substitution ◽

Single Nucleotide ◽

Thrombocytopenic Purpura ◽

Bioinformatics Tools ◽

Life Threatening ◽

And Function

ABSTRACTBackgroundGenetic polymorphisms in the ADAMTS13 gene are associated with thrombotic thrombocytopenic purpura or TTP, a life-threatening microangiopathic disorder. This study aims to predict the possible pathogenic SNPs of this gene and their impact on the protein structure and function using insilico methods.MethodsSNPs retrieved from the NCBI database were analyzed using several bioinformatics tools. The different algorithms applied collectively to predictthe effect of single nucleotide substitution on both structure and function of the ADAMTS13 protein.ResultsFifty one mutations were found to be highly damaging to the structure and function of the protein. Of those, thirty five were novel nsSNPs not previously reported in the literature.ConclusionAccording to our analysis we found thirty five nsSNPs effects on ADAMTS13 protein leading to thrombotic thrombocytopenic purpura using computational approach. Bioinformatics tools are vital in prediction analysis, making use of increasingly voluminous biomedical data thereby providing markers for screening or for genetic mapping studies.

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Comprehensive Analysis of HEXB Protein Reveal Forty Two Novel nsSNPs That May Lead to Sandhoff disease (SD) Using Bioinformatics

10.1101/853077 ◽

2019 ◽

Author(s):

Tebyan A. Abdelhameed ◽

Mosab M. Gasmelseed ◽

Mujahed I. Mustafa ◽

Dina N. Abdelrahman ◽

Fatima A. Abdelrhman ◽

...

Keyword(s):

Neurodegenerative Disorder ◽

Sandhoff Disease ◽

Structure And Function ◽

Beta Subunit ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Bioinformatics Tools ◽

Hexosaminidase A ◽

And Function ◽

Hexb Gene

ABSTRACTBackgroundSingle Nucleotide Polymorphisms (SNPs) in the HEXB gene are associated with a neurodegenerative disorder called Sandhoff disease (SD) (GM2 gangliosidosis-O variant). This study aimed to predict the possible pathogenic SNPs of this gene and their impact on the protein using different bioinformatics tools.MethodsSNPs retrieved from the NCBI database were analyzed using several bioinformatics tools. The different algorithms collectively predicted the effect of single nucleotide substitution on both structure and function of beta subunit beta subunit of both hexosaminidase A and hexosaminidase B proteins.ResultsForty nine mutations were found to be extremely damaging to the structure and function of the HEXB gene protein.ConclusionAccording to this study, forty two novel nsSNP in HEXB are predicted to have possible role in Sandhoff disease using different bioinformatics tools, beside two SNPs found to have effect on miRNAs binding site affecting expression of HEXB gene. Our findings may assist in genetic study and diagnosis of Sandhoff disease.

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Novel deleterious nsSNPs within MEFV gene that could be used as Diagnostic Markers to Predict Hereditary Familial Mediterranean Fever: Using bioinformatics analysis

10.1101/424796 ◽

2018 ◽

Author(s):

Mujahed I. Mustafa ◽

Tebyan A Abdelhameed ◽

Fatima A. Abdelrhman ◽

Soada Ahmed Osman ◽

Mohamed A. Hassan

Keyword(s):

Familial Mediterranean Fever ◽

In Silico ◽

Mediterranean Basin ◽

Mefv Gene ◽

Structure And Function ◽

Diagnostic Markers ◽

Novel Mutations ◽

Bioinformatics Tools ◽

Mediterranean Fever ◽

And Function

AbstractBackgroundFamilial Mediterranean Fever (FMF) is the most common auto inflammatory disease (AID) affecting mainly the ethnic groups originating from Mediterranean basin, we aimed to identify the pathogenic SNPs in MEFV by computational analysis software.MethodsWe carried out in silico prediction of structural effect of each SNP using different bioinformatics tools to predict substitution influence on protein structure and function.Result23 novel mutations out of 857 nsSNPs that are found to be deleterious effect on the MEFV structure and function.ConclusionThis is the first in silico analysis in MEFV gene to prioritize SNPs for further genetic mapping studies. After using multiple bioinformatics tools to compare and rely on the results predicted, we found 23 novel mutations that may cause FMF disease and it could be used as diagnostic markers for Mediterranean basin populations.

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Novel Deleterious nsSNPs within MEFV Gene that Could Be Used as Diagnostic Markers to Predict Hereditary Familial Mediterranean Fever: Using Bioinformatics Analysis

Advances in Bioinformatics ◽

10.1155/2019/1651587 ◽

2019 ◽

Vol 2019 ◽

pp. 1-13

Author(s):

Mujahed I. Mustafa ◽

Tebyan A. Abdelhameed ◽

Fatima A. Abdelrhman ◽

Soada A. Osman ◽

Mohamed A. Hassan

Keyword(s):

Familial Mediterranean Fever ◽

In Silico ◽

Mediterranean Basin ◽

Mefv Gene ◽

Structure And Function ◽

Diagnostic Markers ◽

Novel Mutations ◽

Bioinformatics Tools ◽

Mediterranean Fever ◽

And Function

Background. Familial Mediterranean Fever (FMF) is the most common autoinflammatory disease (AID) affecting mainly the ethnic groups originating from Mediterranean basin. We aimed to identify the pathogenic SNPs in MEFV by computational analysis software. Methods. We carried out in silico prediction of structural effect of each SNP using different bioinformatics tools to predict substitution influence on protein structure and function. Result. 23 novel mutations out of 857 nsSNPs are found to have deleterious effect on the MEFV structure and function. Conclusion. This is the first in silico analysis of MEFV gene to prioritize SNPs for further genetic mapping studies. After using multiple bioinformatics tools to compare and rely on the results predicted, we found 23 novel mutations that may cause FMF disease and it could be used as diagnostic markers for Mediterranean basin populations.

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In silicoanalysis of coding SNPs and 3′-UTR associated miRNAs inDCAF17gene that may affect the regulation and pathogenesis of Woodhouse-Sakati Syndrome

10.1101/601310 ◽

2019 ◽

Author(s):

Abdelrahman H. Abdelmoneim ◽

Asia M. Elrashied ◽

Alaa I. Mohammed ◽

Sara A. Mirghani ◽

Rania E. Osman ◽

...

Keyword(s):

Diabetes Mellitus ◽

Protein Structure ◽

In Silico Analysis ◽

Structure And Function ◽

Novel Mutations ◽

Inherited Disorders ◽

Bioinformatics Tools ◽

Extrapyramidal Signs ◽

And Function ◽

Silico Analysis

AbstractBackgroundWoodhouse-Sakati Syndrome refers to a group of inherited disorders characterized by alopecia, hypogonadism, diabetes mellitus, hypothyroidism and progressive extrapyramidal signs. The aim of this study is to identify the pathogenic SNPs in theDCAF17gene with their related mciroRNAs and their effect on the structure and function of the protein.Material and MethodsWe used different bioinformatics tools to predict the effect of each SNP on the structure and function of the protein. After that we defined the miRNAs founded in the 3′-UTR region on theDCAF17gene and studied the annotations relative to it.ResultsTen deleterious SNPs out of 339 were found to have a damaging effect on the protein structure and function, with one significant micoRNA in the 3′-UTR region.ConclusionThis was the first in silico analysis ofDCAF17gene, in which 10 novel mutations were found using different bioinformatics tools that could be used as a diagnostic markers for Woodhouse-Sakati syndrome, with one relevant microRNA that can regulate the function of the protein.

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In silico analysis ofIDH3Agene revealed Novel mutations associated with Retinitis Pigmentosa

10.1101/554196 ◽

2019 ◽

Author(s):

Thwayba A. Mahmoud ◽

Abdelrahman H. Abdelmoneim ◽

Naseem S. Murshed ◽

Zainab O. Mohammed ◽

Dina T. Ahmed ◽

...

Keyword(s):

Retinitis Pigmentosa ◽

In Silico ◽

In Silico Analysis ◽

Photoreceptor Cells ◽

Structure And Function ◽

Novel Mutations ◽

Inherited Disorders ◽

Bioinformatics Tools ◽

And Function ◽

Silico Analysis

AbstractBackgroundRetinitis Pigmentosa (RP) refers to a group of inherited disorders characterized by the death of photoreceptor cells leading to blindness. The aim of this study is to identify the pathogenic SNPs in the IDH3A gene and their effect on the structure and function of the protein.Methodwe used different bioinformatics tools to predict the effect of each SNP on the structure and function of the protein.Result20 deleterious SNPs out of 178 were found to have a damaging effect on the protein structure and function.Conclusionthis is the first in silico analysis of IDH3A gene and 20 novel mutations were found using different bioinformatics tools, and they could be used as diagnostic markers for Retinitis Pigmentosa.

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Bioinformatics Tools and Genomic Resources Available in Understanding the Structure and Function of Gossypium

Bioinformatics - Updated Features and Applications ◽

10.5772/64325 ◽

2016 ◽

Cited By ~ 1

Author(s):

Venkateswara R. Sripathi ◽

Ramesh Buyyarapu ◽

Siva P. Kumpatla ◽

Abreeotta J. Williams ◽

Seloame T. Nyaku ◽

...

Keyword(s):

Structure And Function ◽

Genomic Resources ◽

Bioinformatics Tools ◽

And Function

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Catalytic and Noncatalytic Nucleotide Binding Sites of F1-ATPases: Probes of Location, Structure and Function by Use of 2-N3-ATP

Molecular Structure, Function, and Assembly of the ATP Synthases ◽

10.1007/978-1-4613-0593-4_22 ◽

1989 ◽

pp. 219-228

Author(s):

John G. Wise ◽

Zhixiong Xue ◽

Chad G. Miller ◽

Brian J. Hicke ◽

Karen J. Guerrero ◽

...

Keyword(s):

Binding Sites ◽

Nucleotide Binding ◽

Structure And Function ◽

Nucleotide Binding Sites ◽

And Function

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The Significance of Calcium in Photosynthesis

International Journal of Molecular Sciences ◽

10.3390/ijms20061353 ◽

2019 ◽

Vol 20 (6) ◽

pp. 1353 ◽

Cited By ~ 7

Author(s):

Quan Wang ◽

Sha Yang ◽

Shubo Wan ◽

Xinguo Li

Keyword(s):

Signal Transduction ◽

Binding Sites ◽

Current Knowledge ◽

Structure And Function ◽

Biochemical Reactions ◽

Chloroplast Proteins ◽

Secondary Messenger ◽

And Function ◽

The Relationship ◽

Physiological And Biochemical

As a secondary messenger, calcium participates in various physiological and biochemical reactions in plants. Photosynthesis is the most extensive biosynthesis process on Earth. To date, researchers have found that some chloroplast proteins have Ca2+-binding sites, and the structure and function of some of these proteins have been discussed in detail. Although the roles of Ca2+ signal transduction related to photosynthesis have been discussed, the relationship between calcium and photosynthesis is seldom systematically summarized. In this review, we provide an overview of current knowledge of calcium’s role in photosynthesis.

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