Hello everyone,
I'm building an homology model of a nicotinic receptor, but there are missing residues in the intracellular domain (dotted line in figure) which lead to strange spaghetti like regions in the homology model. I intend to use the model for molecular docking and molecular dynamics, so I doubt I can just delete that region and leave the two helices unconnected, what can I do to fix it?
Depending on the modelling program, these are either natively unfolded regions, that in reality do not assume a fixed conformation, loops that even in the context of a protein crystal are too flexible to yield a meaningful diffraction in the crystal or regions that have no correspondence in the experimental structure because they had to be deleted from the construct to achieve crystallisations. Some of these may interact with other proteins or upon oligomerisation (the nicotinic acetylcholine receptor is a pentamer) and assume some folding in the complex, others represent flexible tethers.
Compare available template structures to see whether any alternative template yields additional information on some of these regions, and use appropriate prediction algorithms to identify natively unfolded regions. Shorter loops needed to keep your structure from falling apart during MD simulation you can model in using a loop modelling algorithm, very long unresolved loops you may want to replace with shorter modelled loops, long terminal unfolded regions you may want to remove before you do MD, as they would require a very large solvent box and due to their flexibility dominate some of the diagnostics in a non-informative manner. How exactly you treat these flexible regions also depends on the questions you want to address with your simulation.
Hi,
it also depends on the part of the model that you want to evaluate. If your only concern is the transmembrane part, you can maybe ignore them and, eventually, also shorten the longer intracellular helix. That would also decrease the number of atoms in your models and thus increase speed of MD simulations. In this particular case, the membrane will be important to keep all transmembrane helices in their location.
Deleting will cause the non-standard, unwanted, non-realistic changes and output to your exercise. Better to ignore as told by Prof. Annemarie and Prof. Ferreira.
Actually, the green image looks close to what alpha fold would give - modelling the unpredictable part as a very loose, highly solvated, quite extended coil, with a very low probability for this part of the model (see https://www.uniprot.org/uniprot/P43144 for an example . You have to accept that not every amino acid sequence assumes a compact folded structure, and intrinsically unfolded domains still can have functions. Many mammalian transmembrane proteins have long unfolded cytoplasmic tails, and these frequently are sites of post translational modification (Phosphorylation).
If the transmembrane domain falls apart or collapses in your simulation, you may have to include a micelle or membrane in the simulation. Alternatively, you may place some constraints to keep pieces in place - However, carefully document any such "cheats"!
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