A graph-theoretic model of single point mutations in the cystic fibrosis transmembrane conductance regulator

Authors

  • Samuel Kakraba University of Arkansas at Little Rock and the University of Arkansas Medical Sciences
  • Debra Knisley East Tennessee State University, Department of Mathematics and Statistics, Johnson City TN USA 37614

DOI:

https://doi.org/10.24297/jbt.v6i1.4013

Keywords:

Cystic fibrosis, graph theory, graph-theoretic model, mutation.

Abstract

Cystic fibrosis is one of the most prevalent inherited diseases. This disease is caused by a mutation in a membrane protein, the cystic fibrosis transmembrane conductance regulator (CFTR). CFTR is known to function as a chloride channel that regulates the viscosity of mucus that lines the ducts of a number of organs. The most prevalent mutation of CFTR is located in one of two nucleotide binding domains, namely, the nucleotide binding domain one (NBD1). However, some mutations in nucleotide binding domain two (NBD2) can equally cause cystic fibrosis. In this work, a graph-theoretic model is built for NBD2. Using this model for NBD2, we examine the consequences of single point mutations on NBD2. We collate the wildtype structure with eight of the most prevalent mutations and observe how the NBD2 is affected by each of these mutations.

 

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References

1. K. Roberts, P. Cushing, P. Boisguerin, D. Madden, and B. Donald, “Computational Design of a PDZ domain
peptide inhibitor that rescues CFTR activity,” PLOS Computational Biology, vol. 8, no. 4, Article ID e1002477,
2012.
2. A. Aleksandrov, P. Kota, L. Cui et al., “Allosteric modulation balances thermodynamic stability and restores
function of ΔF508 CFTR,” Journal of Molecular Biology, vol. 419, pp. 41–60, 2012.
3. A. W. R. Serohijos, T. Hegedus, A. A. Aleksandrov et al., “Phenylalanine-508 mediates a cytoplasmic-membrane
domain contact in the CFTR 3D structure crucial to assembly and channel function,”Proceedings of the National
Academy of Sciences of the United States of America, vol. 105, no. 9, pp. 3256–3261, 2008.
4. L. He, A. A. Aleksandrov, A. W. R. Serohijos et al., “Multiple membrane-cytoplasmic domain contacts in the cystic
fibrosis transmembrane conductance regulator (CFTR) mediate regulation of channel gating,”Journal of
Biological Chemistry, vol. 283, no. 39, pp. 26383–26390, 2008.
5. A. W. R. Serohijos, T. Hegedus, J. R. Riordan, and N. V. Dokholyan, “Diminished self-chaperoning activity of the
ΔF508 mutant of CFTR results in protein misfolding,” PLoS Computational Biology, vol. 4, no. 2, Article ID
e1000008, 2008.
6. D. J. Knisley, J.R. Knisley and A. C. Herron, “Graph-Theoretic Models of Mutations in the Nucleotide Binding
Domain 1 of the Cystic Fibrosis Transmembrane Conductance Regulator,” Computational Biology Journal, vol.
2013, Article ID 938169, 9 pages, 2013. doi:10.1155/2013/938169
7. J.M. Chen, C. Cutler, C. Jacques, G. Boeuf, E. Denamur, G. Lecointre, B. Mercier, G. Cramb, and C.
F´erec. , “A combined analysis of the cystic fibrosis transmembrane conductance regulator: Implications for
structure and disease models, . Molecular Biology and Evolution, 18(9):1771–1788, 2001.
8. D. Knisley and J Knisley, “Predicting protein-protein interactions using graph invariants and a neural network “
Computationa l Biology and Chemistry, 35(2):108 -– 113, 2011.
9. L. Osborne, R. Knight, G. Santis, and M. Hodson. “ A mutation in the second nucleotide binding fold of the cystic
fibrosis gene”, 48(PMC1682979), 1991/03/.
10. The Protein Data Bank, www.pdb.org (Crystal Structure of Human Nbd2 Complexed With N6- Phenylethyl-atp (Patp).
11. The Clinical Functional and Translation Website for Cystic Fibrosis, www.cftr2.org
12. 12. R: A language and environment for statistical computing, http://www.R-project.org/, Retrieved on
3/12/2015.
13. About cystic fibrosis. http://www.cff.org/AboutCF, Retrieved on 3/20/2015.
14. D. Rapino, I. Sabirzhanova, M. Lopes-Pacheco, R. Grover, W.B. Guggino, and L. Cebotaru, “Rescue of NBD2
mutants of N1303K and S1235R of CFTR by small-molecule correctors and transcomplementation” ,.PLOS ONE,
10(3):e0119796. doi: 10.1371/journal.pone.0119796. eCollection 2015.

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Published

2016-06-17

How to Cite

Kakraba, S., & Knisley, D. (2016). A graph-theoretic model of single point mutations in the cystic fibrosis transmembrane conductance regulator. JOURNAL OF ADVANCES IN BIOTECHNOLOGY, 6(1), 780–786. https://doi.org/10.24297/jbt.v6i1.4013

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