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I want to know the protonation state of some pdb ligands. For example, on the ligand, I want to know if the nitrogen is in its tertiary or quaternary form. I have been looking on the structure page and on the validation report without success. I am thinking about deriving the protonation state from the ph information of the structure environment, in this case 7.2. But I am not sure if this make sense.

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  • $\begingroup$ There are a few different packages which can calculate protonation state of proteins and ligands. For example propka can do this. I'm not exactly familiar with the technique however so I can't make this an answer $\endgroup$ – Cody Aldaz Aug 23 '20 at 22:53
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In general, you have to decide the system pH for which you want to do the simulations, then, use a tool to protonate your system accordingly.

The choosing of the pH will depends on the type of system, applicability, physiology, etc. For example, you could simulate a protein in physiological conditions (pH 7.2) but also simulate the behavior of the same protein in a sensor that works at different pH. In this case, you have to protonate two times.

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    $\begingroup$ Can you please clarify what you mean by "sensor that works at different pH"? $\endgroup$ – BND Aug 24 '20 at 20:37
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    $\begingroup$ It is possible to work in the field of biosensors where a biomarker can be attached to the surface of the sensor. A biomarker can be a protein and the biosensor can work in an specific pH (the pH can affect its efficiency). So, in this case, if you want to simulate the interaction between protein and surface, you specify the working pH and protonate accordingly. $\endgroup$ – Camps Aug 25 '20 at 18:25

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