Investigating the function of single nucleotide polymorphisms in the CTSB gene: a computational approach

Nitin Chitranshi, Amit K. Tiwari, Pallavi Somvanshi, Pushpendra K. Tripathi, Prahlad K. Seth

Research output: Contribution to journalReview articleResearchpeer-review

Abstract

Aim: Recent genome-wide association studies have revealed large numbers of single nucleotide polymorphisms (SNPs) related to Alzheimer's disease. Here, we have investigated the gene CTSB, which plays a crucial role in encoding CTSB, a lysosomal cysteine proteinase protein. CTSB is also involved in the proteolytic processing of amyloid precursor protein (APP), which is believed to be a causative factor in Alzheimer's disease. Materials & methods: Several bioinformatics algorithms such as, Sorting Intolerant from Tolerant (SIFT), Polymorphism Phenotyping (PolyPhen) and CUPSAT could identify the synonymous SNPs and nonsynonymous SNPs (nsSNPs), which are predicted to be deleterious and nondeleterious, respectively. Similar tools were used to predict the impact of single amino acid substitutions on CTSB protein activity. The FASTSNP server and UTRscan were used to predict the influence on splicing regulations. The stability and solvent-accessible surface area of modeled mutated proteins were analyzed using PBEQ solver and NetASA view. Furthermore, the DSP program was used to determine the secondary structures of the modeled protein. Results: A total of 999 SNPs in CTSB were retrieved from the SNP database; 55 nsSNPs, 35 synonymous SNPs, 165 mRNA were found in the 3́untranslated region SNPs, 12 SNPs were found in the 5́untranslated region in addition to 732 intronic SNPs. Potential functions of SNPs in the CTSB gene were identified using different web servers. For example, SIFT, PolyPhen and CUPSAT servers predicted ten nsSNPs to be intolerant, three nsSNPs to be damaging and eight nsSNPs to have the potential to destabilize protein structure. The FASTSNP server predicted 12 SNPs to influence splicing regulation, whereas two SNPs could predict a risk in the range of 3-4 (medium to high). Furthermore, mutant proteins were modeled and the total energy values were compared with the native CTSB protein. It was observed that on the surface of the protein, a mutation from threonine to serine at position 235 (rs17573) caused the greatest impact on stability. Conclusion: The genome-wide association studies database has already found rs7003814 of the CTSB gene reported against Alzheimer's disease. Our study demonstrates the presence of other deleterious nsSNPs, which may play a crucial role in predicting Alzheimer's disease risk.

LanguageEnglish
Pages469-483
Number of pages15
JournalFuture Neurology
Volume8
Issue number4
DOIs
Publication statusPublished - Jul 2013
Externally publishedYes

Fingerprint

Single Nucleotide Polymorphism
Genes
Alzheimer Disease
Genome-Wide Association Study
Proteins
Databases
Secondary Protein Structure
Cysteine Proteases
Amyloid beta-Protein Precursor
Mutant Proteins
Threonine
Amino Acid Substitution
Computational Biology
Serine
Membrane Proteins

Keywords

  • Alzheimer
  • CTSB
  • CTSB gene
  • SNP

Cite this

Chitranshi, Nitin ; Tiwari, Amit K. ; Somvanshi, Pallavi ; Tripathi, Pushpendra K. ; Seth, Prahlad K. / Investigating the function of single nucleotide polymorphisms in the CTSB gene : a computational approach. In: Future Neurology. 2013 ; Vol. 8, No. 4. pp. 469-483.
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abstract = "Aim: Recent genome-wide association studies have revealed large numbers of single nucleotide polymorphisms (SNPs) related to Alzheimer's disease. Here, we have investigated the gene CTSB, which plays a crucial role in encoding CTSB, a lysosomal cysteine proteinase protein. CTSB is also involved in the proteolytic processing of amyloid precursor protein (APP), which is believed to be a causative factor in Alzheimer's disease. Materials & methods: Several bioinformatics algorithms such as, Sorting Intolerant from Tolerant (SIFT), Polymorphism Phenotyping (PolyPhen) and CUPSAT could identify the synonymous SNPs and nonsynonymous SNPs (nsSNPs), which are predicted to be deleterious and nondeleterious, respectively. Similar tools were used to predict the impact of single amino acid substitutions on CTSB protein activity. The FASTSNP server and UTRscan were used to predict the influence on splicing regulations. The stability and solvent-accessible surface area of modeled mutated proteins were analyzed using PBEQ solver and NetASA view. Furthermore, the DSP program was used to determine the secondary structures of the modeled protein. Results: A total of 999 SNPs in CTSB were retrieved from the SNP database; 55 nsSNPs, 35 synonymous SNPs, 165 mRNA were found in the 3́untranslated region SNPs, 12 SNPs were found in the 5́untranslated region in addition to 732 intronic SNPs. Potential functions of SNPs in the CTSB gene were identified using different web servers. For example, SIFT, PolyPhen and CUPSAT servers predicted ten nsSNPs to be intolerant, three nsSNPs to be damaging and eight nsSNPs to have the potential to destabilize protein structure. The FASTSNP server predicted 12 SNPs to influence splicing regulation, whereas two SNPs could predict a risk in the range of 3-4 (medium to high). Furthermore, mutant proteins were modeled and the total energy values were compared with the native CTSB protein. It was observed that on the surface of the protein, a mutation from threonine to serine at position 235 (rs17573) caused the greatest impact on stability. Conclusion: The genome-wide association studies database has already found rs7003814 of the CTSB gene reported against Alzheimer's disease. Our study demonstrates the presence of other deleterious nsSNPs, which may play a crucial role in predicting Alzheimer's disease risk.",
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Investigating the function of single nucleotide polymorphisms in the CTSB gene : a computational approach. / Chitranshi, Nitin; Tiwari, Amit K.; Somvanshi, Pallavi; Tripathi, Pushpendra K.; Seth, Prahlad K.

In: Future Neurology, Vol. 8, No. 4, 07.2013, p. 469-483.

Research output: Contribution to journalReview articleResearchpeer-review

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