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Volume : III, Issue : XI, December - 2013 Structure Prediction Of Neuronal Per- Arnt- Sim (b-hlh-pas) Protein- Npas4 Using Insightii And Modeller 9.11, A Homology Based Approach And A Comparative Study Of The Results. Akhil Jobby , Satish Chandra Verma And Gess Thoms Xavier Published By : Laxmi Book Publication Abstract : The neuronal pas domain protein 4 (npas4) is a neuronal activity dependant gene that has recently been identified as a transcription factor which regulates the transcription of genes that control inhibitory synapse development and synaptic plasticity. The role of npas4 is in learning and memory, however 3D structure of npas4 is unknown . The prediction of protein structure from purely sequenced data and improvement of homology modelling tools has benefited in modelling novel proteins. Hence, this approach was used to model the structure of unmodelled protein npas4. Here the protein structure was built manually, following each steps from alignment to loop modelling to refinement using insight II. Another homology modeling tool, Modeller 9.11 was used to compare the results from Insight II. It was concluded that model from Modeller 9.11 produced a better model when compared to Insight II due to the manual approach in Insight II when compared to automatic modelling in Modeller 9.11. Keywords : Article : Cite This Article : Akhil Jobby , Satish Chandra Verma And Gess Thoms Xavier, (2013). Structure Prediction Of Neuronal Per- Arnt- Sim (b-hlh-pas) Protein- Npas4 Using Insightii And Modeller 9.11, A Homology Based Approach And A Comparative Study Of The Results.. Indian Streams Research Journal, Vol. III, Issue. XI, http://oldisrj.lbp.world/UploadedData/3408.pdf References : - Insight, I. I. (1993). User Guide, version 2.3. 0. San Diego Biosym Technologies
- Insight, I. I. (2000). Accelrys Inc. San Diego, CA
- Ooe N., Saito K., Mikami N., Nakatuka I. and Kaneko H. (2004) Identification of a novel basic helix-loop-helix-PAS factor, NXF, reveals a Sim2 competitive, positive role in dendritic-cytoskeleton modulator Drebrin gene expression. Mol. Cell. Biol. 24(2), 608– 616.
- Ooe N., Motonaga K., Kobayashi K., Saito K. and Kaneko H. (2009) Functional characterization of basic helix-loophelix- PAS type transcription factor NXF in vivo: putative involvement in an ''on demand'' neuroprotection system. J. Biol. Chem. 284(2), 1057– 1063.
- Yun, J., Koike, H., Ibi, D., Toth, E., Mizoguchi, H., Nitta, A., ... & Yamada, K. (2010). Chronic restraint stress impairs neurogenesis and hippocampus-dependent fear memory in mice: possible involvement of a brain-specific transcription factor Npas4. Journal of neurochemistry, 114(6), 1840-1851. 2.
- Lin, Y., Bloodgood, B. L., Hauser, J. L., Lapan, A. D., Koon, A. C., Kim, T. K., ... & Greenberg, M. E. (2008). Activity-dependent regulation of inhibitory synapse development by Npas4. Nature, 455(7217), 1198-1204.
- K. Ramamoorthi, R. Fropf, G. M. Belfort, H. L. Fitzmaurice, R. M. McKinney, R. L. Neve, T. Otto, Y. Lin. Npas4 Regulates a Transcriptional Program in CA3 Required for Contextual Memory Formation. Science, 2011; 334 (6063): 1669
- N. Eswar, M. A. Marti-Renom, B. Webb, M. S. Madhusudhan, D. Eramian, M. Shen, U. Pieper, A. Sali. Comparative Protein Structure Modeling With MODELLER. Current Protocols in Bioinformatics, John Wiley & Sons, Inc., Supplement 15, 5.6.1-5.6.30, 2006
- M.A. Marti-Renom, A. Stuart, A. Fiser, R. Sánchez, F. Melo, A. Sali. Comparative protein structure modeling of genes and genomes. Annu. Rev. Biophys. Biomol. Struct. 29, 291-325, 2000.
- A. Sali & T.L. Blundell. Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol. 234, 779- 815, 1993
- Insight, I. I. (1993). User Guide, version 2.3. 0. San Diego Biosym Technologies
- Insight, I. I. (2000). Accelrys Inc. San Diego, CA
- Ooe N., Saito K., Mikami N., Nakatuka I. and Kaneko H. (2004) Identification of a novel basic helix-loop-helix-PAS factor, NXF, reveals a Sim2 competitive, positive role in dendritic-cytoskeleton modulator Drebrin gene expression. Mol. Cell. Biol. 24(2), 608– 616.
- Ooe N., Motonaga K., Kobayashi K., Saito K. and Kaneko H. (2009) Functional characterization of basic helix-loophelix- PAS type transcription factor NXF in vivo: putative involvement in an ''on demand'' neuroprotection system. J. Biol. Chem. 284(2), 1057– 1063.
- Yun, J., Koike, H., Ibi, D., Toth, E., Mizoguchi, H., Nitta, A., ... & Yamada, K. (2010). Chronic restraint stress impairs neurogenesis and hippocampus-dependent fear memory in mice: possible involvement of a brain-specific transcription factor Npas4. Journal of neurochemistry, 114(6), 1840-1851. 2.
- Lin, Y., Bloodgood, B. L., Hauser, J. L., Lapan, A. D., Koon, A. C., Kim, T. K., ... & Greenberg, M. E. (2008). Activity-dependent regulation of inhibitory synapse development by Npas4. Nature, 455(7217), 1198-1204.
- K. Ramamoorthi, R. Fropf, G. M. Belfort, H. L. Fitzmaurice, R. M. McKinney, R. L. Neve, T. Otto, Y. Lin. Npas4 Regulates a Transcriptional Program in CA3 Required for Contextual Memory Formation. Science, 2011; 334 (6063): 1669
- N. Eswar, M. A. Marti-Renom, B. Webb, M. S. Madhusudhan, D. Eramian, M. Shen, U. Pieper, A. Sali. Comparative Protein Structure Modeling With MODELLER. Current Protocols in Bioinformatics, John Wiley & Sons, Inc., Supplement 15, 5.6.1-5.6.30, 2006
- M.A. Marti-Renom, A. Stuart, A. Fiser, R. Sánchez, F. Melo, A. Sali. Comparative protein structure modeling of genes and genomes. Annu. Rev. Biophys. Biomol. Struct. 29, 291-325, 2000.
- A. Sali & T.L. Blundell. Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol. 234, 779- 815, 1993
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