LinkedIn

 آمار

تعداد نشریات20
تعداد شماره‌ها1,089
تعداد مقالات9,995
تعداد مشاهده مقاله26,449,124
تعداد دریافت فایل اصل مقاله7,287,675
Zarenezhad, M, Dehghani, S M, Ejtehadi, F, Fattahi, M R, Mortazavi, M, Tabei, S M B. (1398). Molecular Modelling and Evaluation of Hidden Information in ABCB11 Gene Mutations. سامانه مدیریت نشریات علمی, 9(3), 303-316. doi: 10.31661/jbpe.v9i3Jun.680
M Zarenezhad; S M Dehghani; F Ejtehadi; M R Fattahi; M Mortazavi; S M B Tabei. "Molecular Modelling and Evaluation of Hidden Information in ABCB11 Gene Mutations". سامانه مدیریت نشریات علمی, 9, 3, 1398, 303-316. doi: 10.31661/jbpe.v9i3Jun.680
Zarenezhad, M, Dehghani, S M, Ejtehadi, F, Fattahi, M R, Mortazavi, M, Tabei, S M B. (1398). 'Molecular Modelling and Evaluation of Hidden Information in ABCB11 Gene Mutations', سامانه مدیریت نشریات علمی, 9(3), pp. 303-316. doi: 10.31661/jbpe.v9i3Jun.680
Zarenezhad, M, Dehghani, S M, Ejtehadi, F, Fattahi, M R, Mortazavi, M, Tabei, S M B. Molecular Modelling and Evaluation of Hidden Information in ABCB11 Gene Mutations. سامانه مدیریت نشریات علمی, 1398; 9(3): 303-316. doi: 10.31661/jbpe.v9i3Jun.680

Molecular Modelling and Evaluation of Hidden Information in ABCB11 Gene Mutations

Journal of Biomedical Physics and Engineering
مقاله 7، دوره 9، شماره 3، مرداد و شهریور 2019، صفحه 303-316    اصل مقاله (911.02 K)
نوع مقاله: Original Article
شناسه دیجیتال (DOI): 10.31661/jbpe.v9i3Jun.680
نویسندگان
M Zarenezhad1، 2؛ S M Dehghani* 3؛ F Ejtehadi3؛ M R Fattahi3؛ M Mortazavi4؛ S M B Tabei5
1MD, PhD, Gastroenterohepatology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
2MD, PhD, legal medicine research center, legal medicine organization, Tehran , iran
3MD, Gastroenterohepatology Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
4PhD, Department of Biotechnology, Institute of Science and High Technology and Environmental Science, Graduate University of Advanced Technology, Kerman, Iran
5MD, Genetic Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
چکیده
Background: Cholestatic disorders are divided in the extra and intra-hepatic that created due to the severe liver diseases. ABCB11 encodes the bile salt export pump and this gene is mutated in several forms of intrahepatic cholestasis. So far, some molecular features of this gene was studies.
Objective: Using a developed web server, we identified high number of rare codons in this gene, and four cases were related to BSEP-deficient patients which can be used for drug design.
Material and Methods: By in-silico modelling of ABCB11, some of rare codons in different locations of ATP8b1 gene were identified and evaluated. Using several web servers a number of mutations that converted non-rare codons to rare codon in these patients were identified.
Results: Some of these rare Codons were located at special positions by mutation of which, the new side chains do not seem suitable for protein structure and function. Furthermore, this mutation changed the protein folding rate that may have a critical role in proper folding. Thus, primary change of these codons contributes to BSEP deficiency.
Conclusion: This work is a comprehensive analysis of rare codons of ABCB11 and assessment of a number of these rare codon in protein levels. Rare codons evaluation can enhance our understanding of ABCB11 structural protein of ABCB11, and help us to develop mutation-specific therapies in design of new drugs.
کلیدواژه‌ها
ABCB11؛ Bioinformatics Analysis؛ Rare Codon؛ Mutation
مراجع
  1. Byrne JA, Strautnieks SS, Ihrke G, Pagani F, Knisely AS, Linton KJ, et al. Missense mutations and single nucleotide polymorphisms in ABCB11 impair bile salt export pump processing and function or disrupt pre-messenger RNA splicing. Hepatology. 2009;49:553-67. doi.org/10.1002/hep.22683. PubMed PMID: 19101985.
  2. Jacquemin E. Progressive familial intrahepatic cholestasis. Clinics and research in hepatology and gastroenterology. 2012;36:S26-S35. doi.org/10.1016/S2210-7401(12)70018-9.
  3. Sira AM, Sira MM. Progressive familial intrahepatic cholestasis: INTECH Open Access Publisher; 2013.
  4. Reichel C, Meier-Abt PJ. Cholestatic liver diseases. Ther Umsch. 1997;54:639-44. PubMed PMID: 9454366.
  5. Engelmann G, Wenning D, Herebian D, Sander O, Droge C, Kluge S, et al. Two Case Reports of Successful Treatment of Cholestasis With Steroids in Patients With PFIC-2. Pediatrics. 2015;135:e1326-32. doi.org/10.1542/peds.2014-2376. PubMed PMID: 25847799.
  6. Fathy M, Kamal M, Al-Sharkawy M, Al-Karaksy H, Hassan N. Molecular characterization of exons 6, 8 and 9 of ABCB4 gene in children with Progressive Familial Intrahepatic Cholestasis type 3. Biomarkers. 2016;21:573-7. doi.org/10.3109/1354750X.2016.1166264. PubMed PMID: 27075526.
  7. Carlton VE, Knisely AS, Freimer NB. Mapping of a locus for progressive familial intrahepatic cholestasis (Byler disease) to 18q21-q22, the benign recurrent intrahepatic cholestasis region. Hum Mol Genet. 1995;4:1049-53. doi.org/10.1093/hmg/4.6.1049. PubMed PMID: 7655458.
  8. Dröge C, Kluge S, Häussinger D, Kubitz R, Keitel V. Sequencing of ATP8B1, ABCB11 and ABCB4 revealed 135 genetic variants in 374 unrelated patients with suspected intrahepatic cholestasis. Zeitschrift für Gastroenterologie. 2015;53:A3_27.
  9. Kane JF. Effects of rare codon clusters on high-level expression of heterologous proteins in Escherichia coli. Curr Opin Biotechnol. 1995;6:494-500. doi.org/10.1016/0958-1669(95)80082-4. PubMed PMID: 7579660.
  10. Chartier M, Gaudreault F, Najmanovich R. Large-scale analysis of conserved rare codon clusters suggests an involvement in co-translational molecular recognition events. Bioinformatics. 2012;28:1438-45. doi.org/10.1093/bioinformatics/bts149. PubMed PMID: 22467916. PubMed PMCID: 3465090.
  11. Giovannoni I, Callea F, Bellacchio E, Torre G, De Ville De Goyet J, Francalanci P. Genetics and Molecular Modeling of New Mutations of Familial Intrahepatic Cholestasis in a Single Italian Center. PLoS One. 2015;10:e0145021. doi.org/10.1371/journal.pone.0145021. PubMed PMID: 26678486. PubMed PMCID: 4683058.
  12. Zhang Y. I-TASSER server for protein 3D structure prediction. BMC Bioinformatics. 2008;9:40. doi.org/10.1186/1471-2105-9-40. PubMed PMID: 18215316. PubMed PMCID: 2245901.
  13. Thanaraj TA, Argos P. Protein secondary structural types are differentially coded on messenger RNA. Protein Sci. 1996;5:1973-83. doi.org/10.1002/pro.5560051003. PubMed PMID: 8897597. PubMed PMCID: 2143259.
  14. Theodosiou A, Promponas VJ. LaTcOm: a web server for visualizing rare codon clusters in coding sequences. Bioinformatics. 2012;28:591-2. doi.org/10.1093/bioinformatics/btr706. PubMed PMID: 22199385.
  15. Daniel E, Onwukwe GU, Wierenga RK, Quaggin SE, Vainio SJ, Krause M. ATGme: Open-source web application for rare codon identification and custom DNA sequence optimization. BMC Bioinformatics. 2015;16:303. doi.org/10.1186/s12859-015-0743-5. PubMed PMID: 26391121. PubMed PMCID: 4578782.
  16. Wu S, Zhang Y. LOMETS: a local meta-threading-server for protein structure prediction. Nucleic Acids Res. 2007;35:3375-82. doi.org/10.1093/nar/gkm251.
  17. DeLano WL. The PyMOL molecular graphics system. San Carlos: PyMOL; 2002.
  18. Kaplan W, Littlejohn TG. Swiss-PDB Viewer (Deep View). Brief Bioinform. 2001;2:195-7. doi.org/10.1093/bib/2.2.195. PubMed PMID: 11465736.
  19. Tina K, Bhadra R, Srinivasan N. PIC: Protein Interactions Calculator. Nucleic Acids Res. 2007;W473–6.
  20. Vriend G. WHAT IF: a molecular modeling and drug design program. J Mol Graph. 1990;8:52-6, 29. PubMed PMID: 2268628.
  21. Gruber A, Durham A, Huynh C, del Portillo H. Bioinformatics in tropical disease research: a practical and case-study approach. Bethesda (MD): National Library of Medicine (US), NCBI; 2008.
  22. Gasteiger E, Hoogland C, Gattiker A, Duvaud Se, Wilkins MR, Appel RD, et al. Protein identification and analysis tools on the ExPASy server: Springer; 2005.
  23. Sonnhammer EL, Eddy SR, Durbin R. Pfam: a comprehensive database of protein domain families based on seed alignments. Proteins. 1997;28:405-20. doi.org/10.1002/(SICI)1097-0134(199707)28:33.0.CO;2-L. PubMed PMID: 9223186.
  24. Dong H, Nilsson L, Kurland CG. Co-variation of tRNA abundance and codon usage in Escherichia coli at different growth rates. J Mol Biol. 1996;260:649-63. doi.org/10.1006/jmbi.1996.0428. PubMed PMID: 8709146.
  25. Pauli-Magnus C, Lang T, Meier Y, Zodan-Marin T, Jung D, Breymann C, et al. Sequence analysis of bile salt export pump (ABCB11) and multidrug resistance p-glycoprotein 3 (ABCB4, MDR3) in patients with intrahepatic cholestasis of pregnancy. Pharmacogenetics. 2004;14:91-102. doi.org/10.1097/00008571-200402000-00003. PubMed PMID: 15077010.
  26. Noe J, Kullak-Ublick GA, Jochum W, Stieger B, Kerb R, Haberl M, et al. Impaired expression and function of the bile salt export pump due to three novel ABCB11 mutations in intrahepatic cholestasis. J Hepatol. 2005;43:536-43. doi.org/10.1016/j.jhep.2005.05.020. PubMed PMID: 16039748.
  27. Strautnieks SS, Byrne JA, Pawlikowska L, Cebecauerova D, Rayner A, Dutton L, et al. Severe bile salt export pump deficiency: 82 different ABCB11 mutations in 109 families. Gastroenterology. 2008;134:1203-14. doi.org/10.1053/j.gastro.2008.01.038. PubMed PMID: 18395098.
  28. Jansen PL, Strautnieks SS, Jacquemin E, Hadchouel M, Sokal EM, Hooiveld GJ, et al. Hepatocanalicular bile salt export pump deficiency in patients with progressive familial intrahepatic cholestasis. Gastroenterology. 1999;117:1370-9. doi.org/10.1016/S0016-5085(99)70287-8. PubMed PMID: 10579978.
  29. Pauli-Magnus C, Kerb R, Fattinger K, Lang T, Anwald B, Kullak-Ublick GA, et al. BSEP and MDR3 haplotype structure in healthy Caucasians, primary biliary cirrhosis and primary sclerosing cholangitis. Hepatology. 2004;39:779-91. doi.org/10.1002/hep.20159. PubMed PMID: 14999697.
  30. van Mil SW, van der Woerd WL, van der Brugge G, Sturm E, Jansen PL, Bull LN, et al. Benign recurrent intrahepatic cholestasis type 2 is caused by mutations in ABCB11. Gastroenterology. 2004;127:379-84. doi.org/10.1053/j.gastro.2004.04.065. PubMed PMID: 15300568.
  31. Strautnieks SS, Bull LN, Knisely AS, Kocoshis SA, Dahl N, Arnell H, et al. A gene encoding a liver-specific ABC transporter is mutated in progressive familial intrahepatic cholestasis. Nat Genet. 1998;20:233-8. doi.org/10.1038/3034. PubMed PMID: 9806540.
  32. Erlinger S, Arias IM, Dhumeaux D. Inherited disorders of bilirubin transport and conjugation: new insights into molecular mechanisms and consequences. Gastroenterology. 2014;146:1625-38. doi.org/10.1053/j.gastro.2014.03.047. PubMed PMID: 24704527.
  33. Nicolaou M, Andress EJ, Zolnerciks JK, Dixon PH, Williamson C, Linton KJ. Canalicular ABC transporters and liver disease. J Pathol. 2012;226:300-15. doi.org/10.1002/path.3019. PubMed PMID: 21984474.
  34. Bina S, Shenavar F, Khodadad M, Haghshenas MR, Mortazavi M, Fattahi MR, et al. Impact of RGD Peptide Tethering to IL24/mda-7 (Melanoma Differentiation Associated Gene-7) on Apoptosis Induction in Hepatocellular Carcinoma Cells. Asian Pac J Cancer Prev. 2015;16:6073-80. doi.org/10.7314/APJCP.2015.16.14.6073. PubMed PMID: 26320498.
  35. Fattahi M, Malekpour A, Mortazavi M, Safarpour A, Naseri N. The characteristics of rare codon clusters in the genome and proteins of hepatitis C virus; a bioinformatics look. Middle East J Dig Dis. 2014;6:214-27. PubMed PMID: 25349685. PubMed PMCID: 4208930.
  36. Mortazavi M, Hosseinkhani S. Surface charge modification increases firefly luciferase rigidity without alteration in bioluminescence spectra. Enzyme Microb Technol. 2017;96:47-59. doi.org/10.1016/j.enzmictec.2016.09.014. PubMed PMID: 27871385.
  37. Mortazavi M, Hosseinkhani S. Design of thermostable luciferases through arginine saturation in solvent-exposed loops. Protein Eng Des Sel. 2011;24:893-903. doi.org/10.1093/protein/gzr051. PubMed PMID: 22068960.
  38. Mortazavi M, Zarenezhad M, Alavian SM, Gholamzadeh S, Malekpour A, Ghorbani M, et al. Bioinformatic Analysis of Codon Usage and Phylogenetic Relationships in Different Genotypes of the Hepatitis C Virus. Hepat Mon. 2016;16:e39196. doi.org/10.5812/hepatmon.39196. PubMed PMID: 27882066. PubMed PMCID: 5111459.
  39. Mortazavi M, Zarenezhad M, Gholamzadeh S, Alavian SM, Ghorbani M, Dehghani R, et al. Bioinformatic Identification of Rare Codon Clusters (RCCs) in HBV Genome and Evaluation of RCCs in Proteins Structure of Hepatitis B Virus. Hepat Mon. 2016;16:e39909 . doi.org/10.5812/hepatmon.39909. PubMed PMID: 27882067. PubMed PMCID: 5116127.
آمار
تعداد مشاهده مقاله: 653
تعداد دریافت فایل اصل مقاله: 350


سامانه مدیریت نشریات علمی. قدرت گرفته از سیناوب