Although we mostly join the backbone gaps in the protein before starting a MD Simulation, longer gaps (more than 10 residues) are sometimes difficult to join.
If we conduct MD Simulation without joining them, and the gaps are away from the binding site, will it make any difference in result?
How much residue gap is allowable?
If by "joining the gaps" you're referring to missing residues in your protein model, I would strongly suggest to model these residue segments. Leaving "gaps" in the protein can lead to unwanted effect with severe impact on the protein's dynamic (e.g. misfolding, disruption of inter-domain interactions, unrealistic solvent exposure).
To refine your model you may find experimental structures that include the missing segment, or you can use one of the many structural prediction methods available. The final model's precision will depend on the scope of your experiment and the knowledge available.
Sincerely,
Raphael
It’s okay if the gaps are far from the binding site, but larger gaps may lead to instability or artifact formation. Ideally, gaps should be less than 5 residues to avoid significant structural issues.
All of which can we easily done at mdsim360.com, a new platform that lets you run MD simulations entirely online without local installation.
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