[AMBER] How to study the redox properties of a partially dried protein

From: Matthew Guberman-Pfeffer <matthew.guberman-pfeffer.uconn.edu>
Date: Fri, 9 Jul 2021 16:41:45 -0400

Dear Amber community,

I’m trying to design simulations to capture the change in redox properties upon drying a protein on an Au electrode. I have two questions:

First, my understanding is that the constant redox approach is parameterized against a fully water-solvated heme. Is it fair to think that I would need to limit my use of MD for structural insights on the drying process and turn to other methods for assessing changes in redox potentials? (As a footnote, constant redox potential simulations on the fully solvated structure give me very small energy differences (typically tens of meV) between the hemes, but some numerical simulations indicate that the experimental observation can be explained with much larger energy differences. My thought is that perhaps the binding site differences will be less screened in the absence of solvent.)

Second, I know of a procedure for de-solvating a protein (described in the SI of this publication <https://pubs.acs.org/doi/10.1021/acs.jpclett.0c02686>). What I don’t understand is why the authors switch from using a Berendsen to Nose-Hoover thermostat during their series of MD steps. If someone could kindly explain (or point me to a discussion) of why one would use different thermostats, I’d greatly appreciate the help.

More generally, if there is any advice about how to tackle the larger question of studying the impact of the drying process, it’s definitely welcomed.

Best regards,
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Received on Fri Jul 09 2021 - 14:00:02 PDT
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