Hi all!
Well, I have a protein (TubulinG) X-ray, however it lacks last 10-11 residues, which are probably exposured to the solvent (and it seems are flexible enough to be invisible for X-ray). The protein exists in two isoforms, which differ on a single amino acid (approximately -15 position from the end), however, some in-house biochemical experiments stated that this change is crucial for the degree of motility. The problem is that: I can't predict the exact initial location/conformation of this short C-termini and all standard MD simulations (gromacs) showed different, not similar, positions of the terminal region - it can be either flexible or pinned to the 'protein's body' during the MD. Before starting a production MD for subsequent analysis I should be somehow ensured that the initial conformation is reliable. i-Tasser is not a good way, because it doesn't guarantee nothing, except the total minimization state, and homology modelling is also impotent. One user suggested rosetta fragment method, but it is more useful for unresolved structures. That is why I want to start a preliminary MD to sample these C-terminal end (rebuild with any program like pymol, molsoft or swissmodel server) and I bet on these two approaches like replica exhange or simulated annealing (not sure in the last one). Does anybody know is it possible or even reasonable? where I can find a working tutorial to provide some changes or use it as it is? The additional question is about 'partial application' of the method to the fragment of the protein in Gromacs, to avoid time consuming calculations with parameters, which are applied to the whole system, which is not a priority, as the final goal is just a minimized protein with a more informed preparation alghorithm. Thank You in advance!!!
With rosetta, you would not do ab-initio refolding, but rather re-model only the missing residues: https://www.rosettacommons.org/docs/latest/application_documentation/design/rosettaremodel (look at option: Extension)
- Badges
- Science topic