I'm homology-modeling the ubiquitin-bound form of a deubiquitinase for which only the apo form is available as a crystal structure, using a homolog that has a crystal structure with ubiquitin bound. I'm performing energy minimization on the model, but I'm wondering if there are any pitfalls in doing this.
Specifically, would this cause the model to not reflect the likely conformation of the ubiquitin-bound form, for whatever reason? And when I perform energy minimization, would it be advantageous to include ubiquitin (from the homolog's crystal structure) superposed in the active site?
In any cases energy minimization can relax your systems based on the used forcefield.
After homology modeling, application of geometry optimization for relaxation of the structure is a good idea; energy minimization will not lead a dramatic change in topology (backbone) of protein
If one intends to perform a molecular dynamics (MD) simulation of the complex, and if there are no obvious clashes in the structure, one can skip energy minimization for its purpose can be fulfilled by the initial stage of the equilibration MD simulation (see stage I in Table S4 in the linked document): a very short simulation (10,000 steps) at very low temperature (5 K; with strong coupling to an external bath: 0.1 fs) and with very short time-step ( 0.01 fs).
Data Supporting Information to 'Uniform Free-Energy Profiles of t...
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