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

https://doi.org/10.31957/jbp.1059

Authors

  • 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

Abstract

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

Downloads

Download data is not yet available.

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

References

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.

Downloads

Published

2020-09-30

Issue

Vol. 12 No. 2 (2020)

Section

Research Articles

License

1. Copyright Policy

Jurnal Biologi Papua is committed to promoting the dissemination, accessibility, and responsible reuse of scholarly research in biology and related disciplines.

Under this policy, authors retain copyright ownership of their published articles and grant Jurnal Biologi Papua the non-exclusive right of first publication.

Authors retain the right to use, distribute, reproduce, and share their scholarly work in accordance with the applicable publication license.

The journal acknowledges the intellectual contributions of authors and respects their moral rights, including the right to be properly identified as creators of their work.

2. Publication License

Articles published under this policy are distributed under the Creative Commons Attribution 4.0 International License (CC BY 4.0).

License URL: https://creativecommons.org/licenses/by/4.0/

Under this license, users are permitted to:

  1. Share: Copy and redistribute published articles in any medium or format.

  2. Adapt: Remix, transform, and build upon published materials for any purpose, including commercial purposes.

  3. Redistribute: Make articles available through repositories, websites, databases, and other scholarly platforms.

These permissions are subject to the Creative Commons Attribution 4.0 International License.

Users must provide appropriate credit to the original authors, include a link to the license, and indicate whether changes have been made.

Reuse must not imply endorsement by the authors or publisher.

3. Rights of Authors

Authors publishing in Jurnal Biologi Papua retain the following rights:

  1. Copyright ownership of their original scholarly work.

  2. The right to distribute and share their published articles.

  3. The right to deposit their articles in institutional or subject repositories.

  4. The right to reuse their work in subsequent scholarly publications, subject to appropriate acknowledgment and applicable ethical standards.

  5. The right to share their work for teaching, research, academic collaboration, and other lawful purposes.

Authors must acknowledge the original publication in Jurnal Biologi Papua when distributing or reusing the published version.

4. Rights of the Publisher

Authors grant Jurnal Biologi Papua the non-exclusive right to publish, disseminate, archive, and preserve accepted manuscripts.

The journal may reproduce and distribute the published version through its official website and authorized indexing, archiving, and scholarly dissemination services.

The publisher is responsible for maintaining the integrity of published content and accurately displaying copyright and licensing information.

5. Open Access Policy

Jurnal Biologi Papua supports immediate open access to scholarly research.

Articles published under this policy are freely accessible to readers without subscription requirements or access fees.

The journal encourages the responsible dissemination and reuse of published research to support scientific progress, academic collaboration, and the broader exchange of knowledge.

Published content may be accessed, downloaded, shared, and reused in accordance with the applicable Creative Commons license.

6. Third-Party Materials

Authors are responsible for ensuring that all materials included in their manuscripts comply with applicable copyright and intellectual property laws.

Permission must be obtained when required for the use of third-party figures, photographs, tables, illustrations, or other copyrighted materials.

Materials excluded from the article's Creative Commons license must be clearly identified with their applicable copyright and permission notices.

The journal's publication license does not override the rights of third-party copyright holders.

7. Repository and Self-Archiving Policy

Authors are permitted and encouraged to deposit and share their published articles through institutional repositories, academic repositories, and personal or institutional websites.

Authors must provide appropriate acknowledgment of the article's original publication in Jurnal Biologi Papua, including its citation information and DOI where available.

Repository deposits and subsequent distribution must comply with the license applicable to the relevant version of the article.

8. Licensing Information and Article Metadata

The applicable copyright holder and publication license should be clearly identified on each published article's webpage.

Where supported, licensing information should also be included in article metadata and the published PDF.

The journal is committed to maintaining accurate and consistent licensing information across its online publishing platform and scholarly indexing services.

9. Policy Application and Previously Published Articles

This policy applies to manuscripts accepted following its formal adoption by the journal and publisher.

Articles published before the adoption of this policy remain subject to the copyright arrangements and licenses applicable at the time of their publication, unless a valid change is authorized by the relevant rights holders.

The journal will not apply a new license retroactively without the necessary authorization.

10. Policy Commitment

Jurnal Biologi Papua is committed to transparent copyright arrangements, responsible open access publishing, and respect for intellectual property rights.

The journal will periodically review its copyright and licensing practices to maintain consistency with recognized standards of scholarly communication.

References

Creative Commons Attribution 4.0 International License: https://creativecommons.org/licenses/by/4.0/

Directory of Open Access Journals (DOAJ): https://doaj.org/apply/copyright-and-licensing/