From: Lizelle Lubbe (
Date: Wed Nov 08 2017 - 12:43:15 CST

Hi VMD users,

I have performed explicit solvent MD using AMBER on a glycosylated zinc metalloprotease and just came across the implicit ligand sampling method of mapping gas migration pathways in VMD.

The MD's aim was to investigate the role of glycans in protecting the active site from diffuse radical oxidation observed experimentally. I simulated two highly homologous proteins (90% active site identity) that differ greatly in glycan location and abundance. Experimentally, I see time-dependent oxidative inactivation of the enzyme in the presence of molecular oxygen, H2O2 and ascorbate. I still need to determine if the species responsible for inactivation is superoxide or hydroxide. The enzyme with the least glycans is the most susceptible to diffuse radical oxidation. The solvent accessibility will be mapped to these proteins and the glycan influence assessed in combination with mass spectrometry (similar to hydroxyl radical protein footprinting mass spectrometry).

I found the gas migration pathway mapping analyses very interesting and thought of applying it to my work.
I understand that it is an analysis for gas molecules but could the O2 gas pathway perhaps be used as an indication for the superoxide entry to the active site prior to enzyme inactivation?

The pathway won't be taken as the final result since further experimental work will involve mass spectrometric identification of the oxidation sites. If the sites superimpose onto the oxygen migration pathway it would serve as validation (to my understanding) and yield a more thorough mechanism than simply relating the solvent accessibility to oxidation sites as in radical footprinting mass spectrometry.

Could someone please comment on whether this type of analysis could be considered scientifically sound?

Kind regards

Lizelle Lubbe

PhD (Medical biochemistry) candidate
Department of Integrative Biomedical Sciences
University of Cape Town
Disclaimer - University of Cape Town This e-mail is subject to UCT policies and e-mail disclaimer published on our website at or obtainable from +27 21 650 9111. If this e-mail is not related to the business of UCT, it is sent by the sender in an individual capacity. Please report security incidents or abuse via