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:: Volume 2, Issue 2 (Spring - 2014) ::
Shefaye Khatam 2014, 2(2): 21-30 Back to browse issues page
Modeling and Bioinformatics Investigations of Human Voltage-gated Sodium Ion Channels
Ali Jahanbazi Jahan Abad , Rahman Yolmeh , Fereshteh Parto , Abdorrahim Absalan *
Shefa Neuroscience Research Center, KhatamAlanbia Hospital, Tehran, Iran. , a.r.absalan@gmail.com
Abstract:   (3605 Views)

Introduction: Tertiary (3D) structure determination using X-ray diffraction crystallography is a time consuming method, needs special facilities and expert operators. 3D structure determination by bioinformatics software is worth in experimental research, especially for drug discovery purposes and evolutionary relationships. Using computational biology software and databases, we have determined probable 3D structure of human voltage-gated sodium ion channels (VGSCs) and their developmental associations. Materials and Methods: Amino acid sequences of VGSCs were obtained from Uniprot and used to predict their 3D structure using SWISS-MODEL server and by its definitive algorithm for protein basic local alignment search tool (BLAST)-(followed by visualization using Molegro Virtual Viewer software). Phylogenic tree was plotted using Mega 5 application for VGSCs sequences. VGSCs interactions were determined by String-db server. Results: According to the Neuron data-base, there are 9 types of human VGSCs named SCN1A-5A and SCN8A-11A. SWISS-MODEL software was just only able to predict some domains of VGSCs with high identity percentages. The identity percentages were variable for each VGSC and varied from 16.57% (SCN4A) to 100% (SCN2A, SCN5A). Blast results and drawing phylogenetic trees practice showed that animals, such as chimpanzee, gibbon, and gorilla have the most similar protein sequences. Conclusion: In most cases, modeling using SWISS-MODEL is not enough decisive for prediction of protein 3D structure. Thus, we propose that researchers use mentioned animals for experiments of VGSCs, characterized structures for bioinformatics and drug designing surveys. In this case, the results of animal trials could be generalized to human more precisely.

Keywords: Protein Structure, Tertiary, Computational Biology, Sodium Channels, Phylogeny
Full-Text [PDF 906 kb]   (1376 Downloads)    
Type of Study: Research --- Open Access, CC-BY-NC | Subject: Basic research in Neuroscience



DOI: 10.18869/acadpub.shefa.2.2.21


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Jahanbazi Jahan Abad A, Yolmeh R, Parto F, Absalan A. Modeling and Bioinformatics Investigations of Human Voltage-gated Sodium Ion Channels. Shefaye Khatam. 2014; 2 (2) :21-30
URL: http://shefayekhatam.ir/article-1-81-en.html
Volume 2, Issue 2 (Spring - 2014) Back to browse issues page
مجله علوم اعصاب شفای خاتم The Neuroscience Journal of Shefaye Khatam
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