Genomics & Informatics

Korea Genome Organization (한국유전체학회)
권호 표지
DOI QR코드

DOI QR Code

In Silico Study of Human Gap Junction Beta-2 Protein by Homology Modeling

  • Shehzadi, Abida (Bioinformatics Wing, Center of Excellence in Molecular Biology, University of the Punjab) ;
  • Masood, Khalid (Bioinformatics Wing, Center of Excellence in Molecular Biology, University of the Punjab)
  • Accepted : 2010.06.13
  • Published : 2010.06.30
Download PDF
⟨ Previous Next ⟩

Abstract

Asp66his, Asp54Lys, and Asp50Asn are mutations in connexin 26 that are observed in the clinic and give rise to autosomal dominant syndromes. They are the result of point mutations in the human gap junction ${\beta}-2$ gene. In order to investigate the structural mechanism of Bart-Pumphrey Syndrome, Keratitis-Ichthyosis-Deafness Syndrome, and Vohwinkel Syndrome, homology modeling was carried out. Asp66 has direct contact with Asn62 by two hydrogen bonds in the wild-type protein, and in Asp66His, the biggest change observed is a tremendous energy increase caused by hydrogen bond breakage to Asn62. Shifts in the side chain and new hydrogen bond formation are observed for Lys54 compared to the wild-type protein (Asn54) and result in closer contact to Val84. Asp50Asn causes a significant decrease in bond energy, and residual charge reversal repels the ion and metabolites and, hence, inhibits their transportation. Such perturbations are likely to be a factor contributing to abnormal functioning of ion channels, resulting cell death and disease.

Keywords

References

  1. Abe, S., Usami, S., Shinkawa, H., Kelley, M.P., and Kimberling, J.W. (2000). Prevalent connexin 26 gene (GJB2) mutations in Japanese. J. Med. Genet . 37, 41-43. https://doi.org/10.1136/jmg.37.1.41
  2. Bairoch, A., and Apweiler, R. (1997). The SWISS-PROT protein sequence data bank and its supplement TrEMBL. Nucl. Acids Res . 25, 31-36. https://doi.org/10.1093/nar/25.1.31
  3. Bart, R.S., and Pumphrey, R.E. (1967). Knuckle pads, Leukonychia & Deafness. A Dominantly Inherited Syndrome. N. Engl. J. Med. 276, 202-207. https://doi.org/10.1056/NEJM196701262760403
  4. Bitner-Glindzicz, M. (2002). Hereditary deafness and phenotyping in humans. Br. Med. Bull. 63, 73-94. https://doi.org/10.1093/bmb/63.1.73
  5. Castillo, J.F., Rodriguez-Ballesteros, M., A'lvarez, A., Hutchin, T., Leonardi, E., Oliveira, A.C., Azaiez, H., Brownstein, Z., Avenarius, R.M., Marlin, S., Pandya, A., Shahin, H., Siemering, R.K., Weil, D., Wuyts, W., Aguirre, A.L., Martin,Y., Moreno-Pelayo, A.M., Villamar, M., Avraham, B.K., Dahl, M.H., Kanaan, M., Nance, E.W., Petit, C., Smith, H.J.R., Camp, V.G., Sartorato, L.E., Murgia, A., Moreno, F., and Castillo, I. (2005). A novel deletion involving the connexin-30 gene, del (GJB6-d13s1854), found in trans with mutations in the GJB2 gene (connexin-26) in subjects with DFNB1 non-syndromic hearing impairment. J. Med. Genet . 42, 588-594. https://doi.org/10.1136/jmg.2004.028324
  6. Denoyelle, F., Lina-Granade, G., Plauchu, H., Bruzzone, R., Chaib, H., Levi-Acobas, F., Weil, D., and Petit, C. (1998). Connexin 26 gene linked to a dominant deafness. Nature 393, 319-320. https://doi.org/10.1038/30639
  7. Eyken, V.E., Camp, V.G., and Laer, V.L. (2007). The Complexity of age-related hearing impairment: contributing environmental and genetic factors. Audiol. Neurotol. 12, 345-358. https://doi.org/10.1159/000106478
  8. Forge, A., Becker, D., Casalotti, S., Edwards, J., Marziano, N., and Nickel, R. (2002). Connexins and gap junctions in the inner ear. Audiol. Neurootol. 7, 141-145. https://doi.org/10.1159/000058299
  9. Karaguler, G.N., Sessions, B.R., Moreton, M. K., Clarke, R. A., and Holbrook, J.J. (2004). Estimating the energetic contribution of hydrogen bonding to the stability of Candida methylica formate dehydrogenase by using double mutant cycle. Biotechnol. Lett. 26, 1137-1140. https://doi.org/10.1023/B:BILE.0000035485.43826.03
  10. Kelsell, D.P., Dunlop, J., Stevens, H.P., Lench, N., Liang, J.N., Parry, G., Mueller, R.F., and Leigh, I.M. (1997). Connexin 26 mutations in hereditary non-syndromic sensorineural deafness. Nature 387, 80-83. https://doi.org/10.1038/387080a0
  11. Laer, V.L., Coucke, P., Mueller, F.R., Caethoven, G., Flothmann, K., Prasad, D.S., Chamberlin, P.G., Houseman, M., Taylor, R.G., Heyning, V.M.C., Fransen, E., Rowland, J., Cucci, A.R., Smith, H.J.R., and Camp, V.G. (2001). A common founder for the 35delG GJB2 gene mutation in connexin 26 hearing impairment. J. Med. Genet. 38, 515-518. https://doi.org/10.1136/jmg.38.8.515
  12. Lattig, M.C., Gelvez, N., Plaza, S.L., Tamayo, G., Uribe, J.I., Salvatierra, I., Bernal, J.E., and Tamayo, M.L. (2008). Deafness on the island of Providencia - Colombia: different etiology, different genetic counseling. Genet. Couns . 19, 403-412.
  13. Lautermann, J., ten Cate, W.J., Altenhoff, P., Grummer, R., Traub, O., Frank, H., Jahnke, K., and Winterhager, E. (1998). Expression of the gap-junction connexins 26 and 30 in the rat cochlea. Cell Tissue Res . 294, 415-420. https://doi.org/10.1007/s004410051192
  14. Mahasneh, A.A., and Battah, R.M. (2006). Prevalence of connexin 26 mutations in patients from jordan with non syndromic hearing loss. Int. J. Hum. Genet. 6, 119-124. https://doi.org/10.1080/09723757.2006.11885951
  15. Maestrini, E., Korge, P.B., Ocana-Sierra, J., Calzolari, E., Cambiaghi, S., Scudder, M.P., Hovnanian, A., Monaco, P.A., and Munro, S.C. (1999). A missense mutation in connexin26, D66H, causes mutilating keratoderma with sensorineural deafness (Vohwinkel's syndrome) in three unrelated families. Hum. Mol. Genet. 8, 1237- 1243. https://doi.org/10.1093/hmg/8.7.1237
  16. Marziano, K.N., Casalotti, O.S., Partelli, E.A., Becker, L.D., and Forage, A. (2003). Mutations in the gene for connexin 26 (GJB2) that cause hearing loss have a dominant negative effect on connexin 30. Hum. Mole. Genet . 12, 805-812. https://doi.org/10.1093/hmg/ddg076
  17. Musil, L.S., and Goodenough, D.A. (1993). Multisubunit assembly of an integral plasma membrane channel protein, gap junction connexin43, occurs after exit from the ER. Cell 74, 1065-1077. https://doi.org/10.1016/0092-8674(93)90728-9
  18. Richard, G., Brown, N., Ishida-Yamamoto, A., and Krol, A. (2004). Expanding the phenotypic spectrum of Cx26 disorders: bart-pumphrey syndrome is caused by a novel missense mutation in GJB2. J. Invest. Dermatol . 123, 856- 863. https://doi.org/10.1111/j.0022-202X.2004.23470.x
  19. Saez, J.C., Branes. M.C., Corvalan, L.A., Eugenin, E.A., Gonzalez, H., Martinez, A.D., and Palisson, F. (2000). Gap junctions in cells of immune system: structure, regulation and possible functional roles. Braz. J. Med. Biol. Res . 33, 447-455. https://doi.org/10.1590/S0100-879X2000000400011
  20. Snoeckx, L.R., Hassan, M.D., Kamal, M.N., Bogaert, D.V.K., and Camp, V.G. (2005). Mutation analysis of the GJB2 (connexin 26) gene in egypt. J. Hum. Mut. 26, 60-61.
  21. Sosinsky, G. (1995). Mixing of connexins in gap junction membrane channels. Proc. Natl. Acad. Sci. 92, 9210-9214. https://doi.org/10.1073/pnas.92.20.9210
  22. Talley, K., Ng, C., Shoppell, M., Kundrotas, P., and Alexov, E. (2008). On the electrostatic component of protein-protein binding free energy PMC Biophysics 1:2 doi:10.1186/ 1757-5036-1-2. http://www.physmathcentral.com/1757-5036/1/2
  23. Tremblay, K., and Ross, B. (2007). Effects of age and age-related hearing loss on the brain. J. Commun. Disorders 40, 305-312. https://doi.org/10.1016/j.jcomdis.2007.03.008
  24. Williams, R.W., Chang, A., Juretic, D., and Loughran, S. (1987). Secondary structure predictions and medium range interactions. Biochim Biophys Acta. 916, 200-204. https://doi.org/10.1016/0167-4838(87)90109-9
  25. Xiang, Z. (2006). Advances in homology protein structure modeling. Curr. Protein Pept. Sci . 7, 217-227. https://doi.org/10.2174/138920306777452312
  26. Yotsumoto, S., Hashiguchi, T., Chen, X., Ohtake, N., Tomitaka, A., Akamatsu, H., Matsunaga, K., Shiraishi, S., Miura, H., Adachi, J., and Kanzaki, T. (2003). Novel mutations in GJB2 encoding connexin-26 in Japanese patients with keratitis-ichthyosis-deafness syndrome. Br. J. Dermatol . 148, 649-653. https://doi.org/10.1046/j.1365-2133.2003.05245.x
  27. Zelante, L., Gasparini, P., Estivill, X., Melchionda, S., D'Agruma, L., Govea, N., Mila, M., Monica, M.D., Lutfi, J., Shohat, M., Mansfield E., Delgrosso, K., Rappaport, E., Surrey, S., and Fortina, P. (1997). Connexin26 mutations associated with the most common form of non-syndromic neurosensory autosomal recessive deafness (DFNB1) in Mediterraneans. Hum. Mol. Genet. 6, 1605-1609. https://doi.org/10.1093/hmg/6.9.1605