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Metabolic Brain Disease

, Volume 33, Issue 5, pp 1443–1457 | Cite as

Computational insights of K1444N substitution in GAP-related domain of NF1 gene associated with neurofibromatosis type 1 disease: a molecular modeling and dynamics approach

  • Ashish Kumar Agrahari
  • Meghana Muskan
  • C. George Priya Doss
  • R. Siva
  • Hatem Zayed
Original Article

Abstract

The NF1 gene encodes for neurofibromin protein, which is ubiquitously expressed, but most highly in the central nervous system. Non-synonymous SNPs (nsSNPs) in the NF1 gene were found to be associated with Neurofibromatosis Type 1 disease, which is characterized by the growth of tumors along nerves in the skin, brain, and other parts of the body. In this study, we used several in silico predictions tools to analyze 16 nsSNPs in the RAS-GAP domain of neurofibromin, the K1444N (K1423N) mutation was predicted as the most pathogenic. The comparative molecular dynamic simulation (MDS; 50 ns) between the wild type and the K1444N (K1423N) mutant suggested a significant change in the electrostatic potential. In addition, the RMSD, RMSF, Rg, hydrogen bonds, and PCA analysis confirmed the loss of flexibility and increase in compactness of the mutant protein. Further, SASA analysis revealed exchange between hydrophobic and hydrophilic residues from the core of the RAS-GAP domain to the surface of the mutant domain, consistent with the secondary structure analysis that showed significant alteration in the mutant protein conformation. Our data concludes that the K1444N (K1423N) mutant lead to increasing the rigidity and compactness of the protein. This study provides evidence of the benefits of the computational tools in predicting the pathogenicity of genetic mutations and suggests the application of MDS and different in silico prediction tools for variant assessment and classification in genetic clinics.

Keywords

NF1 RAS-GAP domain K1444N (K1423N) Homology modeling Molecular dynamics simulation Variant classification 

Notes

Acknowledgements

I would like to thank VIT management for providing the facility, seed money, and platform to carry out the research. No conflict of interest exists.

Supplementary material

11011_2018_251_MOESM1_ESM.docx (128 kb)
ESM 1 (DOCX 128 kb)
11011_2018_251_MOESM2_ESM.docx (83 kb)
Supplementary Fig. 1 Ramachandran plot of native model RAS-GAP domain of NF1 protein obtained by RAMPAGE server. (DOCX 83 kb)
11011_2018_251_MOESM3_ESM.docx (948 kb)
Supplementary Fig. 2 Conservational analysis of residues of RAS-GAP domain of NF1 protein using the ConSurf server. (DOCX 948 kb)
11011_2018_251_MOESM4_ESM.docx (99 kb)
Supplementary Fig. 3 RMSD plot of RAS-GAP domain of NF1 protein (a) first run (b) second run (c) third run of 50 ns of simulation. (DOCX 99 kb)
11011_2018_251_MOESM5_ESM.docx (15 kb)
Supplementary Fig. 4 Analysis of secondary structure element contribution in native and K1444N mutant. (DOCX 15 kb)
11011_2018_251_MOESM6_ESM.docx (1009 kb)
Supplementary Fig. 5 Illustration of an explicit change in secondary structure conformation in native (blue) and mutant K1444N mutant (green) RAS-GAP domain of NF1 protein (a) 0 ns (b) 40 ns (c) 50 ns. Color magenta and red are representing the residue region in between 60 and 68 of native and mutant respectively, color yellow and cyan are representing the residue region in between 110 and 120 of native and mutant respectively. (DOCX 1009 kb)

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Authors and Affiliations

  1. 1.Department of Integrative Biology, School of Biosciences and TechnologyVellore Institute of TechnologyVelloreIndia
  2. 2.Department of Biomedical Sciences, College of Health and SciencesQatar UniversityDohaQatar

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