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International Journal of Computational Bioinformatics and In Silico Modeling
2015: Volume-4 Issue-6
ISSN: 2320-0634

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ABSTRACT   REFERENCES  
International Journal of Computational Bioinformatics and In Silico Modeling 4(6) 2015: 753-760

Structural insight into the homology modeled human N-acetyl-alpha-neuraminidase 3 (NEU3): Part2



Katsuyoshi Kamiie1, Toshiro Noshita2, Yumi Kidachi1 and Hideaki Yamaguchi3*

1 Department of Pharmacy, Faculty of Pharmaceutical Sciences, Aomori University, 2-3-1 Kobata, Aomori 030-0943, Japan
2 Department of Life Sciences, Faculty of Life and Environmental Sciences, Prefectural University of Hiroshima, 562 Nanatsuka, Shobara 727-0023, Japan
3 Department of Applied Biological Chemistry, Faculty of Agriculture, Meijo University, 1-501 Shiogamaguchi, Tempaku, Nagoya 468-8502, Japan

* Corresponding Author

ABSTRACT

This is a sequel to the previous study on the structural insight into the homology modeled human N-acetyl-alpha-neuraminidase 3 (NEU3). Further analysis was performed with a software package the Molecular Operating Environment. A human NEU2 (PDB code: 1SNT) was selected as template for the 3D structure modeling of NEU3. The template NEU2 lacks the catalytically important Asp46 that is equivalent to Asp50 in NEU3. The superimposition and root mean square deviation analysis indicated that the modeled NEU3 showed significant 3D similarity to NEU2. However, the molecular electrostatic potential (MEP) map of the NEU3 model exhibited that the model was electrostatically different from the NEU2 model and also the NEU3 model constructed from 1VCU at the ligand-binding site (LBS). Further, docking simulations between the N-acetyl-2,3-dehydro-2-deoxyneuraminic acid (DANA)-NEU2 and DANA-NEU3 complexes revealed the dissimilarity of the ligand-receptor binding orientation between the NEU2 and 3 models. The different binding orientation between the DANA-NEU2 and DANA-NEU3 complexes reflected the different MEP maps at the LBSs between the NEU2 and 3 models. The docking simulation also revealed that DANA was unable to create interactions with the residues that are considered crucial to the DANA-NEU3 binding. These results indicate that missing a very important residue (Asp50) at the LBS can modify the interaction of NEU3 with ligands and possibly nullify its enzyme activity, although the 3D structure of the enzyme remains almost completely intact.

 


Copyright © 2015 | AIZEON publishers | All rights reserved

 

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Citation: Katsuyoshi Kamiie et al. (2015). Structural insight into the homology modeled human N-acetyl-alpha-neuraminidase 3 (NEU3): Part2. Int J Comput Bioinfo In Silico Model 4(6): 753-760

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