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Molecular Dynamics and In Silico Analysis of Oligomerization Surfaces of CYND Enzymes
Published: 01 February 2018 by MDPI AG in Proceedings of MOL2NET 2018, International Conference on Multidisciplinary Sciences, 4th edition in MOL2NET 2018, International Conference on Multidisciplinary Sciences, 4th edition
MDPI AG, 10.3390/mol2net-04-05126
Abstract:

Cyanide is a toxic compund widely used in mining. Naturally some bacterias are capable to degrade this molecules. CynD is a type of prokaryote enzyme able to degrade cyanide and its active form seems to be an oligomer. Several attempts to obtain structural models of CynD by crystallography has not success mainly due the insolubility of the oligomeric state of this protein. In this work we aimed to use in silico tools to identify the aminoacids implied in the oligomerization surfaces. These knowledge could lead us to rationally design CynD variants that are not able to form tights oligomers stabilizing other forms such as dimers or monomers that could be better in purification and crystallization assays. For this, we prepared structural models using SWISS-MODEL, PHYRE2, I-TASSER and ROBETTA. Then, we analyzed chemical parameters of the models using RAMPAGE, PDBsum and ModFold6. Next, we did dimer models using dockings in Hex. The monomer and dimer models were used to perform molecular dynamics simulation in order to determine flexible regions, important aminoacids stabilizing the dimeric interface and the stability of the dimer form. We obtain models with good chemical parameters to perform the dynamics simulation. These assays allow us to identify flexible regions that could be removed to stabilize the dimer or monomer in solution. Finally, the docking showed us which are the probable aminoacids stabilizing the dimer interface. Experimental data is now neccesary to confirm those hypotheses.

JANDHYLA, D.; Berman, M.;Meyeres, P.; Sewell, B.; Willson, R.; Benedik, M. cynD, the Cyanide Dihidratase from Bacillus pumilus: Gene Cloning and Structural Studies. Applied and Environmental Microbiology. Vol 69, No. 8. Aug. 2003. p 4794 – 4805

Crum, M. A. N., Park, J. M., Mulelu, A. E., Sewell, B. T., & Benedik, M. J. (2015). Probing C-terminal interactions of the Pseudomonas stutzeri cyanide-degrading CynD protein. Applied microbiology and biotechnology, 99(7), 3093-3102.

Keywords: biotechnology, crystallization, cyanide, Cynd, dimer, docking, dynamics simulation, Microbiology, molecular dynamics, purification

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