3D structure of NT-3 Protein (Neurotropin 3) of Pigeon (Columba livia) using Server-Swiss Model

Tina Zarkiyani, I Made Budiarsa, Astija Astija, Mursito S Bialangi


The NT-3 protein plays an important role in the development and differentiation of neurons, and is unique in the neurotropin family, that it can bind to 3 Trk receptors, namely TrkC, TrkA and TrkB. This study aimed to analyze the characteristics and three-dimensional structure of NT-3 protein in Columba livia. The target protein was obtained from Uniprot server with the access code of PKK30025.1 using template 3buk.1A (PDB-ID) analyzed in-silico through homology method using SWISS-MODEL server. The results showed that the three-dimensional structure of the target NT-3 protein with a template formed a β-sheet and loop structure, which was composed of 304 amino acids, with the highest amino acid composition was serine at 8.88 mol polar, and the lowest amino acid was tryptophan at 1.32. moles which was relatively nonpolar. The analysis results of the structural quality revealed an identity value of 98.20%, QMEAN of 0.8, QMQE of 0.25, and the analysis on the Ramachandran plot presented an outlier value of 0.92%; the most favored region value was 94.5%, with good structural quality. The results of the 3-dimensional structure of the NT-3 Columba livia protein are expected to be useful for further research to determine the active side and interactions of proteins in carrying out their functions.


NT-3 Protein; 3-Dimensional Structure; Homology; In-silico; Columba livia

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Agung, M. B., I. M. Budiarsa., & I. N. Suwastika. (2016). Analisa In Silico Gen Kakao (Theobroma cacao L.) yang terlibat dalam Sistem KetahananTerhadap Hama dan Penyakit. Journal of Natural Science. Vol. 5 No. 2, 234-250.

Arjunan, S. N. V., S. Deris & R. M. Illias. (2001). Literature Survey Of Protein Secondary Structure Prediction. Jurnal Teknologi. 34 : 63-72.

Ayupov, R. & Akberova N. (2016). Prediction of the three-dimensional structure of theprotein SaHPF and analysis of its molecular dynamics. International Journal of Pharmacy and Technology. Vol.8 : 14548-14557.

Baker, D., & A. Sali. (2001). Protein structure prediction and structural genomics. Science. Vol .294 No. 5540, 93-96.

Balchin, D., M. Hayert-Hartl & F. U. Hartl. (2016). In Vivo Aspects of Protein Folding and Quality Control. Science. Vol.353

Biasini, M., S. Bienert., A. Waterhouse., K. Arnold., G. Studer., T. Schmidt., F. Kiefer., T. G. Cassarino., M. Bertoni., L. Bordoli & T. Schwede. (2014). SWISS-MODEL : Modelling Protein Tertiary and Quaternary Structure Using Evolutionary Information. Nucleic Acids Research.

Djuwita, I., V. Riyacumala., K. Mohamad.,W.E.Prasetyaningtyas., & Nurhidayat. (2012). Pertumbuhan dan sekresi protein hasil kultur primer sel sel serebrum anak tikus. J Veteriner. Vol. 13 No. 2, 125-135.

Ekins, S., J. Liebler., B.J. Neves., W. G. Lewis., M. Coffee., R. Bienstock., C. Southan & C. H. Andrade. (2016). Illustrating and homology modeling the proteins of the Zika virus. F1000Reasearch. 5 :275.

Gaffar, S., A. A. Masyhuri., Y. W. Hartati & Rustaman. (2016). Studi In Silico Single Chain Variable Fragment (SCFV) Selektif Terhadap Hormon Basic Natriuretic Peptide (BNP). Chimica et Natura Acta. Vol. 4 No. 2, 52-59.

Handayani, N. S. N., N. Husna., & I. Sanka. (2017). Α-globin Alteratin in α-thalassemia Disorder : Prediction and Interaction Defect. Pakistan Journal of Bilogical Sciences. Vol. 20 No. 7, 343-349.

Harti, A. S & Soebiyanto. (2017). Biokimia Kesehatan. Jakarta : CV.Trans Info Media.

Iriyanto, Koes. (2017). Biologi Molekuler. Bandung : Alfabeta.

Jackson, J.S., J.P.Golding., C. Chapon., W.A. Jones & K.K. Bhakpp. (2010). Homing of stem cells to sites of imflammatory brain injury after intracerebral and intravenous administration: a longitudinal imaging study. Stem Cells Research and Therapy 1:17.

Jhonsen, I.A., Y. Naito., A. M. Craig & H. Takahashi. (2015). Neurotrophin-3 Enhances the Synaptic Organizing Function of TrkC–Protein Tyrosine Phosphatase _ in Rat Hippocampal Neurons. The Journal of Neuroscience. 35 (36) : 12425-12431.

Kanfar, M.A., M.M. Abukhader., S. Alqtaishat & M.O. Taha (2013). Pharmacophore modeling, homology modeling, and in silico screening reveal mammalian target of rapamycin inhibitory activities for sotalol, glyburide, metipranolol, sulfamethizole, glipizide, and pioglitazone. Journal of molecular Graphics and Modelling. 39-49.

Khanikor, B., P. Parida., R.N.S. Yadav & D. Bora (2013). Comparative mode of action of some terpene compounds against octopamine receptor and acetyl cholinesterase of mosquito and human system by the help of homology modeling and Docking studies. Journal of Applied Pharmaceutical Science Vol. 3 (02),

Kiefer, F., K. Arnold., M. KU. Nzli., L. Bordoli & T. Schwede. (2008). The SWISS-MODEL Repository and Associated Resources. Nucleic Acids Research. 37: 387-392.

Kleywegt, G. J & T. A. Jones. (1996). Ramachandran Revisited. Structure. 4 : 1395-1400.

Lakhlili, W., G. Cheve., A. Yasri & A. Ibrahim. (2015). Determination and validation of mTOR kinase-domain 3D structure by homology modeling. Onco Targets and Therapy. 8 : 1923-1930.

Lee, A.L., W.O. Ogle., R.M. Sapolsky. (2002). Stress and depression in the central nervous system. Glia. Vol. 30 No. 2, 105-121.

Lukitaningsih, E., A. Wisnusaputra., & B. S. A. Sudarmanto. (2015). Skrining In silico Senyawa Aktif Bengkoang (Pachyrrhizus erosus) sebagai Antitirosinase pada Aspergilus oryzae (Studi Komputasional dengan Homologi Modeling dan Moleculer Docking). Traditional Mediciene Journal. Vol. 20 No.1, 7-15.

Maisonpierre, P. C., M. M. Le Beau., R.III. Espinosa., N. Y. Ip., L. Belluscio., S. M. de la Monte., S. Squinto., M. E. Furth., G. D. Yancopoulos. (1991). “Human and rat brain-derived neurotrophic factor and neurotrophin-3: gene structures, distributions, and chromosomal localizations”. Genomics. 10: 558-568.

Rajendran, S. C. K., B. Mason., & C. C. Udenigwe. (2016). Peptidomics of Peptic Digest of Selected Potato Tuber Proteins : Post-Translation Modifications and Limited Cleavage Specificity. Agricultural and Food Chemistry.

Reddy, A.R., TC. Venkateswarulu., D.J. Babu & M. Indira. (2015). Homology Modeling Studies of Human Genome Receptor Using Modeller, Swiss-Model Server and Esypred-3D Tools. International Journal of Pharmaceutical Sciences Review and Research. No.1 : 1-6.

Ryde’n, M., & C.F. Ibanez. (1996). “Binding of Neurotrophin-3 to p75LNGFR, TrkA, and TrkB Mediated by a Single Functional Epitope Distinct from That Recognized by TrkC”. The Journal of Biological Chemistry. Vol. 271 No. 10, 5623-5627.

Schwede, T., A. Sali., N. Eswar., M C. Peitsch. (2008). Protein Structure Modeling in Computational Structural Biology. Singapore: World Scientific Publishing.

Sugiyono. (2004). Kimia Pangan. Universitas Negeri Yogyakarta. Fakultas Teknik.

Suparman., H. Ahmad., & Z. Ahmad. (2016). Desain Primer PCR Secara In silico untuk Amplifikasi Gen COI pada Kupu-kupu Papilio Ulysses Linnaeus dari Pulau Bacan. Jurnal Pendidikan Matematika dan IPA. Vol. 7 No. 1, 14-24.

Tokheim, C., R. Bhattacharya., N. Niknafs., D.M. Gygax., R. Kim., M. Ryan., D.L. Masica & R. karchin (2016). Exom- Scale Discovery of Hotspot Mutation Ragion in Human Cancer Using 3D Protein Structure. American Association for Cancer Research. 76 (13), 3719-3731.

Waterhouse, A., M. Bertoni., S. Bienert., G. Studer., G. Tauriello., R. Gumienny., F. T. Heer., T.A.P. de Beer., C. Rempfer., L. Bordoli., R. Lepore & T. Schwede (2018). SWISS-MODEL : homology modeling of protein structures and complexes. Nucleic Acids Research. Vol. 46.

Wijaya, H. & F. Hasanah. (2016). “Prediksi Struktur Tiga Dimensi Protein Alergen Pangan Dengan Metode Homologi Menggunakan Program Swiss-Model”. Biopropal Industri. Vol 7 No. 2, 83-94.

DOI: http://dx.doi.org/10.26418/jpmipa.v12i2.39762


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