There are missing residues in the crystal structure of my protein. One part of this missing residue region (30 residues length) has no template. When I modelled this protein in modeller by taking the same crystal structure as the template, this part of the structure modelled as a coil, whereas the same region has two beta sheets when I modelled by swiss-model server. Another missing region in the protein structure is alpha helix (from literature). But it was modelled as coil from both. I had run 10ns molecular dynamics simulation of this protein in gromacs. But I could not find any differences in the structure. Is there any other way like by giving restraints to that particular part of the protein? How far this would work out?
Hello,
When you use Modeller for missing residues modeling You can do it manually where beta sheets or alpha helix starts/finish. You can predict secoundary structure to check present those beta sheets or alpha helix in Your protein. You can also try use I-Tasser server to build Your structure.
To add to Tomasz's answer, if you know what the secondary structure of the missing region should be, then the methods mentioned can be used to force the secondary structure into a specific type. If you don't know what the secondary structure should be, you should expect to see variations in models produced. Tools like Modeller and Swiss-Model use what is known about existing protein structures (and their sequences, which influence structure) to predict secondary structure. 30 residues is a sizable gap. Predictions for secondary structure typically work better with smaller missing regions (e.g., 5-10 missing residues). Generating multiple models and running dynamics on these will help with sampling conformations. With enough sampling, you can see secondary structure changes (using DSSP analysis you can generate a graph of that too), and figure out which type of structure is the predominant one. Also, 10ns of production run may not be enough MD to see if the predicted secondary structure is truly stable. You may also need extended energy minimization prior to the production run to make sure the modeled region sits in an energetically favorable well.
Modeling is a process that takes quite a bit of try and try again. Good luck.
You need to consider what percentage of your total sequence is represented by 30 residues. Most likely it is a highly mobile and flexible loop or is an intrinsically disordered segment. A careful inspection of the sequence is useful to have clarity on these issues. The molecular dynamics is very useful to have structural details about your segments of 30 amino acids but, if the protein is quite large, 10 ns are certainly not sufficient. In addition, modeling and dynamics must be made in explicit water otherwise it will not make much sense. If the protein has a globular structure, topologically fixed in time, during the whole dynamics this part must always be organized, otherwise there is something wrong in the model.
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