Question: in silico study of enzyme-dye interaction
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gravatar for Arindam Ghosh
4.1 years ago by
Arindam Ghosh280
India
Arindam Ghosh280 wrote:

An enzyme is responsible for degradation of a specific dye. Is it possible to use MD simulation to understand the mechanism.

ADD COMMENTlink modified 4.1 years ago by anp375170 • written 4.1 years ago by Arindam Ghosh280
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gravatar for anp375
4.1 years ago by
anp375170
anp375170 wrote:

How I would approach it: need to dock before, after, and the transition states. Make an electrostatic map of the contact areas before and after degradation. Then ask an organic chemist to figure out the transition states, or try to figure it out myself. Dock the transition states. But I don't really know this so I'm gonna come back to check this question.

ADD COMMENTlink modified 4.1 years ago • written 4.1 years ago by anp375170

how do i get the transition states?

ADD REPLYlink written 4.1 years ago by Arindam Ghosh280

I don't know what the dye, the enzyme, the products, or the docking states look like so I don't know how they are interacting - amino acid side chains in contact, which parts of them, what parts of the dye they are in contact with. So I can't answer your question. Even if I knew, I'm not an organic chemist so I won't know if I'm correct. Again, I don't actually know this stuff so you should check with someone else.

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4749658/pdf/pone.0148191.pdf http://www.pnas.org/content/105/26/9059.full.pdf http://www.sciencedirect.com/science/article/pii/S0168165606000800

ADD REPLYlink written 4.1 years ago by anp375170
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