1. Network topology of NaV1.7 mutations in sodium channel-related painful disorders
- Author
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Kapetis D, Sassone J, Yang Y, Galbardi B, Mn, Xenakis, Rl, Westra, Szklarczyk R, Lindsey P, Cg, Faber, Gerrits M, Is, Merkies, Sd, Dib-Hajj, Massimo Mantegazza, Sg, Waxman, Lauria G, Propane, Study Group, Promovendi MHN, Genetica & Celbiologie, RS: MHeNs - R3 - Neuroscience, DKE Scientific staff, RS: FSE MaCSBio, RS: FSE DACS BMI, MUMC+: DA KG Lab Centraal Lab (9), Klinische Genetica, RS: GROW - R4 - Reproductive and Perinatal Medicine, Complexe Genetica, RS: CARIM - R2.10 - Mitochondrial disease, MUMC+: MA Med Staf Spec Neurologie (9), RS: MHeNs - R1 - Cognitive Neuropsychiatry and Clinical Neuroscience, Klinische Neurowetenschappen, RS: FHML MaCSBio, Kapetis, D, Sassone, J, Yang, Y, Galbardi, B, Xenakis, Mn, Westra, Rl, Szklarczyk, R, Lindsey, P, Faber, Cg., Gerrits, M, Merkies, Isj, Sulayman, D, Mantegazza, M, Waxman, Sg, Lauria, G, and on behalf of thePROPANE Study Group
- Subjects
Models, Molecular ,0301 basic medicine ,MOLECULAR-DYNAMICS SIMULATIONS ,Protein Conformation ,SLOW-INACTIVATION ,TRANSFER-RNA SYNTHETASE ,Bioinformatics ,medicine.disease_cause ,Neuropathic pain ,0302 clinical medicine ,Protein structure ,Structural Biology ,Protein Interaction Mapping ,OF-FUNCTION MUTATIONS ,PRIMARY ERYTHERMALGIA ,Structural modeling ,Genetics ,Mutation ,Chemistry ,Sodium channel ,Applied Mathematics ,NAV1.7 Voltage-Gated Sodium Channel ,Computer Science Applications1707 Computer Vision and Pattern Recognition ,ELECTROPHYSIOLOGICAL PROPERTIES ,Computer Science Applications ,Modeling and Simulation ,Network analysis ,STRUCTURE PREDICTION ,RESPONSIVE ERYTHROMELALGIA ,Research Article ,Pain ,Mutagenesis (molecular biology technique) ,Single-nucleotide polymorphism ,Polymorphism, Single Nucleotide ,03 medical and health sciences ,Erythromelalgia ,Modelling and Simulation ,Paroxysmal extreme pain disorder ,medicine ,Journal Article ,Humans ,Molecular Biology ,NA(V)1.7 MUTATION ,Computational Biology ,Network analysi ,medicine.disease ,030104 developmental biology ,Mutagenesis ,NAV1 ,NEURON HYPEREXCITABILITY ,030217 neurology & neurosurgery - Abstract
Gain-of-function mutations in SCN9A gene that encodes the voltage-gated sodium channel NaV1.7 have been associated with a wide spectrum of painful syndromes in humans including inherited erythromelalgia, paroxysmal extreme pain disorder and small fibre neuropathy. These mutations change the biophysical properties of NaV1.7 channels leading to hyperexcitability of dorsal root ganglion nociceptors and pain symptoms. There is a need for better understanding of how gain-of-function mutations alter the atomic structure of Nav1.7. We used homology modeling to build an atomic model of NaV1.7 and a network-based theoretical approach, which can predict interatomic interactions and connectivity arrangements, to investigate how pain-related NaV1.7 mutations may alter specific interatomic bonds and cause connectivity rearrangement, compared to benign variants and polymorphisms. For each amino acid substitution, we calculated the topological parameters betweenness centrality (B ct ), degree (D), clustering coefficient (CC ct ), closeness (C ct ), and eccentricity (E ct ), and calculated their variation (Δ value = mutant value -WT value ). Pathogenic NaV1.7 mutations showed significantly higher variation of |ΔB ct | compared to benign variants and polymorphisms. Using the cut-off value ±0.26 calculated by receiver operating curve analysis, we found that ΔB ct correctly differentiated pathogenic NaV1.7 mutations from variants not causing biophysical abnormalities (nABN) and homologous SNPs (hSNPs) with 76% sensitivity and 83% specificity. Our in-silico analyses predict that pain-related pathogenic NaV1.7 mutations may affect the network topological properties of the protein and suggest |ΔB ct | value as a potential in-silico marker.
- Published
- 2017
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