Analisis In-Silico Struktur Tiga Dimensi Reseptor Trk A dan Trk B Protein Neurotrophin 3 Pada Gallus gallus (Chicken)


  • Muhammad F. Rahman PS Pendidikan Biologi Universitas Tadulako
  • Amiruddin Kasim PS Pendidikan Biologi Universitas Tadulako
  • Muchlis L. Djirimu PS Pendidikan Biologi Universitas Tadulako
  • I. Made Budiarsa PS Pendidikan Biologi Universitas Tadulako



NT3 protein is expressed by Neurotrophin 3 (NTF-3) which plays a role in the process of differentiation, survival of peripheral and neuropathological of neurons. The information of structure and function of NT-3 proteins is still very limited, especially in Gallus gallus. This study aims to predict the three-dimensional structure of the Trk A and Trk B proteins in Gallus gallus. The target protein obtained from the UniProt server with access codes Q91009 (Trk A) and Q91987 (Trk B) using the 6kzc 1.A (PDB ID) template was analyzed in silico through a homology approach and describing the structural assessment using Chimera UCSF software. The analysis showed that the Trk A protein had a QMEAN value of -0.08, composed of 778 amino acids, mass 87334.30 Daltons, and Seq Identity 79.93%. Trk B had a QMEAN value of 0.16, consisting of 818 amino acids, mass 91732.05 Daltons, and Seq Identity 84.30%. 

Key words: NT3; homology; UCSF chimera; G. gallus


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Author Biographies

Muhammad F. Rahman, PS Pendidikan Biologi Universitas Tadulako

PS Pendidikan Biologi Universitas Tadulako

Amiruddin Kasim, PS Pendidikan Biologi Universitas Tadulako

PS Pendidikan Biologi Universitas Tadulako

Muchlis L. Djirimu, PS Pendidikan Biologi Universitas Tadulako

PS Pendidikan Biologi Universitas Tadulako

I. Made Budiarsa, PS Pendidikan Biologi Universitas Tadulako

PS Pendidikan Biologi Universitas Tadulako


Amelia, F. dan Iryani. 2012. Comparrative modelling protein vaksin NA BTB H5N1 menggunakan SWISS MODEL. Jurnal Sains dan Teknologi. 4(2): 165-169.

Ardiani, Y., Defrin, dan H. Yetti. 2019. Kajian pustaka: Kadar brain derived neurotrophic factor mempengaruhi berat badan lahir pada bayi. Jurnal Ilmiah Universitas Batanghari Jambi. 19(1): 152-155.

Baker, D., and A. Sali. 2001. Protein structure prediction and structural genomics. Science. 294:93-96.

Berman, H., K. Henrick, H. Nakamura, and J.L. Markley. 2006. The orldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data. Nucleic Acids Research. 35: 301–303.

Bosco, K.H., and R. Brasseur. 2005. The ramachandran plots of glycine and pre-proline. BMC Structural Biology. 5(14): 1-11.

Budiarsa, I. M., I.W.T. Artama, L. Sembiring, and J. Situmorang. 2010. Analisis filogenetik burung maleo (Macrocephalon maleo) berdasarkan sekuen intron satu gen rhodopsin (RDP1) nukleus. Biota. 15(2): 160−166.

Chao, M.V. 2003. Neurotrophins and their receptors: a convergence point for many signalling pathways. Neuroscience. 4: 299-309.

Gowder, S.M., J. Chatterjee, T. Chaudhuri, and K. Paul. 2014. Prediction and analysis of surface hydrophobic residue in tertiary structure of protein. The Scientific World Journal. Article ID 971258. 1-7.

Haddad, Y., V. Adam, and Z. Heger. 2017. Trk receptors and neurotrophin cross-interactions: new perspectives toward manipulating therapeutic side-effects. Frontiers in Molecular Neuroscience. 10: 1-7.

Hillisch, A., L.F. Pineda and R. Hilgenfeld. 2004. Utility of homology models in the drug discovery process. Drug Discovery Today. 171(2): 659-669.

Irfanuddin. 2018. Karakteristik biomolekuler mutasi amyloid precursor protein sebagai penyebab penyakit alzheimer yang dianalisis melalui media bioinformatika. Sriwijaya Journal of Medicine. 1(1): 61-73.

Jullien, J., V. Guili., L.F. Reichardt, and B.B. Rudkin. 2002. Molecular kinetics of nerve growth factor receptor trafficking and activation. The Journal of Biological Chemistry. 277(41): 38.700-38.708.

Lamballe, F., R. Klein, and M. Barbacid. 1991. Trk c, a new member of the trk family of tyrosine protein kinases, is a receptor for neurotrophin-3. Depertement of Moleculer Biology Bristol-Myers Squibb Pharmaceutical research Institute Princeton. 66: 967-979.

Lukitaningsih, E., A.A. Mustikawaty, and A. Sudarmanto. 2013. Homology modelling dan moleculer docking senyawa aktif dari bengkoang (Pachyrrhizus erosus) sebagai inhibitor tirosinase pada Homo sapiens. Jurnal Ilmu Kefarmasisan Indonesia. 11(2): 134-141.

Lovell, S.C., I.W. Davis, W.B. Arendall Ill, P.I.W. De Bakker, J.M. Word, M.G. Prisant, J.S. Richardson, and D.C. Richardson. 2003. Structure validation by calpha geometry: phi, psi and c beta deviation. Proteins: Structure, Function & Genetics. 50: 437-450.

Malau, N.D., and M. Sianturi. 2019. Analisa interaksi hidrofobik terhadap kestabilan termal enzim xilanase Aspergillus niger. Jurnal Edu Mat Sains. 3(2): 215-227.

Maisa, B. 2019. Penggunaan workflows dalam aplikasi bioinformatika geneious untuk menganalisis data genomik. Jurnal Kesehatan Andalas. 8 (Supplement 1): 47–50.

Maness, L.M., A.J Kastin., J.T Weber., W.A Banks., B.S Beckman, and J.E. Zadina. 1994. The neurotrophins and their receptors : structure, function, and neuropathology. Nenroscience and Biobehavioral Reviews. 18(1): 143-159.

Mawardi, A., and M.L. Simonapendi. 2016. Uji efektivitas metode isolasi DNA genom kopi arabika (Coffea arabica L.) asal kabupaten Jayawijaya. Jurnal Biologi Papua. 8(1): 7–12.

Nestler, E.J., S.E. Hyman, and R.C. Malenka. 2009. Molecular neuropharmacology: a foundation for clinical neuroscience 2nd edition. USA: McGraw-Hill.

Parikesit, A.A., and D. Anugrogo. 2018. Kajian prediksi 3-dimensi biomarker kanker payudara dari jalur ekspresi LINCRA–ROR/mir–145/ARF6. Jurnal Sains dan Teknologi. 2(1): 10-19.

Rekik, I., Z. Chaabenel, C. Douglas Grubb, N. Drira1, F. Cheour, and A. Elleuch. 2015. In silico characterization and molecular modeling of double-strand break repair protein MRE11 from Phoenix dactylifera v deglet nour. Theoretical Biology and Medical Modelling. 12: 23. doi: 10.1186/s12976-015-0013-2.

Sheu, S., E.W. Schlag, L. Heinrich, Selzle, and D.Y. Yang. 2009. Hydrogen bonds in membrane proteins. J. Phys. Chem. 113: 5318–5326.

Wijaya, H., dan F. Hasanah. 2016. Prediksi struktur tiga dimensi protein alergen pangan dengan metode homologi menggunakan program SWISS MODEL. Bioporpal Industri. 7(2): 83-94.

Wilkinson, G.A., I. Farinas., C. Backus, C.K. Yoshida, and L.F. Reichardt. 1996. Neurotrophin-3 is a survival factor in vivo for early mouse trigeminal neurons. The Journal of Neuroscience. 16(23): 7661–7669.

Windisch, J.M., R. Marksteiner, M.E. Lang, B. Auer, and R. Schneider. 1995. Brain-derived neurotrophic factor, neurotrophin-3 and neurotrophin-4 bind to a single leucine-rich motif of Trk B. Biochemistry. (34): 11256- 11263.

Zhang, D., L. Yao, and P. Bernd. 1994. Expression of Trk and neurotrophin mRNA in dorsal root and sympathetic ganglia of the quail during development. Journal of Neurobiology. 25(12): 1517-1532.

Zhou, X.F., and R.A. Rush. 1996. Funcional Roles of Neurotrophin3 in the Developing and Mature Sympathetic Nervous System. Moleculer Neurobiology. 133(3): 185-197.






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