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Build mutant and build homology protein structure predictions for indonesian avian influenza neuraminidase

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Journal of Biophysical Chemistry 2012年第2期3卷 183-190页

作者： sigit jaya herlambang Rosari Saleh Departemen Fisika Fakultas MIPA Universitas Indonesia Depok Indonesia

Protein structure modeling using a homologous template is one of many routines that accompany the molecular dynamics simulation for biological material. There are currently two protocols of protein modeling available in Accelrys Discovery Studio 2.1, Build Mutants and Build Homology Modeling protocols. Both are template-based modeling, but with a different process. In this study, two different templates, 3CKZ and 274Y, have been used to see how much the differences will be made by those two protocols if the templates has significant percentage of identity. Evaluation of structure models has been performed using DOPE score, 3D-profile, and PROCHECK. The results indicated that Build Mutants Protocols produces more stable structures but has a low reliability values and low quality of stereochemistry when using a template that has a lower percentage of identity. The results also yield more stable, reliable, and higher percentage of residues in most favoured and additionally allowed region for the usage of Build Homology Modeling Protocol on both templates. These observations suggest that Build Homology Modeling protocol is recommended for protein modeling.

关键词： Protein Modeling Mutation Build Model Protocols

Molecular docking investigation for Indonesian H274Y mutant neuraminidase type 1 with neuraminidase inhibitors

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American Journal of Molecular Biology 2012年第1期2卷 49-59页

作者： sigit jaya herlambang Rosari Saleh Department of Physics Mathematics and Science Faculty University of Indonesia Depok Indonesia

The aim of this study is to get insight the interaction between Indonesian H274Y mutant neuraminidase with four inhibitors. Not only to seek preferable inhibitor to be used, but also to investigate the interaction occurred, especially hydrogen bonds formed. Hydrogen bonds analysis and its interaction energies calculation showed that zanamivir is the most preferable inhibitor with 13 hydrogen bonds formed and –439.96 kcal/mol. Laninamivir would be an alternative inhibitor since it has 10 hydrogen bonds and –307.19 kcal/mol. The investigation of ΔSAS showed almost all active site residues buried when interacted with inhibitors. Only a few residues have an increases ΔSAS. Lipinski rule analysis showed that zanamivir and laninamivir would be best taken by injection or inhalation.

关键词： Molecular Docking Neuraminidase Inhibitor Resistance

Indonesian avian influenza H274Y mutant neuraminidase homology models assessment

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Journal of Biophysical Chemistry 2011年第3期2卷 345-352页

作者： sigit jaya herlambang Rosari Saleh Departement of Physics Mathematics and Science Faculty University of Indonesia Depok Indonesia 16424

Five models of Indonesian H274Y mutant neuralminidase type 1 (N1) were generated from the template 3CKZ by homology modeling. The template has the best similarity percentage 97% with the model sequence. The models was evaluated to search the best model with DOPE, 3D-profiles and PROCHECK in a good rank. The results show model 3 as a potential model to be used in the simulation with the lowest DOPE score, highest verify-3D score and from Ramachandran plots we inferred that it also shared the 1st rank with model 4 based on the 99.4% of the residues found, without Glycine and Proline, at the most favoured and additionally allowed region of both model structures.

关键词： Neuraminidase Model Assessment Homology Model Mutant Avian Influenza

The Comparison of Substrate Stability in Neuraminidase Type 2 (N2) Active Site between A/Tokyo/3/67 and A/Pennsylvania/10218/84 with Heating Dynamics Simulation

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World Journal of Condensed Matter Physics 2011年第3期1卷 77-87页

作者： sigit jaya herlambang Rosari Saleh Departement of Physics Mathematics and Science Faculty University of Indonesia Depok Indonesia 16424

A molecular dynamics simulation of two neuraminidase-sialic acid (NA-SA) complexes show a difference of the level of stability between sialic acid and neuraminidases that originated from viruses A/Tokyo/3/67 (Structure A) dan A/Pennsylvania/10218/84 (Structure B). Analyses of sialic acid RMSD and the change of torsional angles suggest that the sialic acid in Structure A is much more twisted and able to be influenced more by the binding of the neuraminidase functional residues than Structure B. Moreover, analyses upon hydrogen bond occupancy and binding free energy of both complexes showed that Structure A had more stable hydrogen bonds and each complex’s binding free energy were calculated to be –1.37 kcal/mol and 17.97 kcal/mol for Structure A and Structure B, respectively, further suggesting stability more dominant in Structure A than Structure B. Overall, Structure A has a more stable enzyme-substrate than Structure B.

关键词： Neuraminidase Sialic Acid Bind Stability Functional Residues Avian Influenza