MED27 and the Mediator complex (cropped)
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Description
Shown is MED27 and a cropped form of PDB:6W1S —the full complex is too resource intensive for some devices (e.g. mobiles).
- MED11 (head module, chain H) in moonstone
- MED14 (scaffold module, chain I) in muted green
- MED15 (tail module, chain J) in turquoise
- MED16 (tail module, chain K) in muted green
- MED17 (head module, chain L) in cyan
- MED20 (head module, chain O) in teal
- MED22 (head module, chain Q) in muted green
- MED27 (upper tail module, chain V) in lavender
- MED28 (upper tail module, chain W) in muted green
- MED29 (upper tail module, chain X) in lime
- MED30 (upper tail module, chain Y) in aero
MED27 along with MED28, MED29 and MED30 form the upper tail module.
Pathogenic variants
The residues with pathogenic variants in MED27 have a variety of effects are not simple destabilisation.
- V63G (wild type/mutant/overlay). V63 is a surface residue close to MED29. V63G destabilises the helix by virtue of a loss of several hydrophobic interactions, resulting in weaker London dispersion forces (predicted ∆∆G = +5.0 kcal/mol, difference in weighted r
6 -term of the Lenard-Jones potential (fa_atr): +5.5 kcal/mol). However, the MED27-MED29 interaction is not affected. This is the only pathogenic mutation found not in the C-terminal domain. - H179P (wild type/mutant/overlay). This beta-sheet residue in the C-terminal domain. Proline disrupts the binding to the other strand (backbone bonding to L191). Therefore, resulting in a large destabilisation (+18 kcal/mol).
- I230R (wild type/mutant/overlay). This hydrophobic C-terminal domain residue is part of a loop that features some phosphorylated residues (phosphorylated residues).
- S232F (wild type/mutant/overlay). This partially buried mutation in on a loop in the C-terminal domain is overall neutral in terms of stability, but is a phosphorylation site (phosphorylated).
- V242A (wild type/mutant/overlay). This hydrophobic C-terminal domain residue is buried and on a helix and when mutated to a smaller residue, result is a mostly neutral difference in Gibbs free energy of folding (∆∆G=+1.9 kcal/mol), but majorly it is next to a phosphorylated residue (phosphorylated T243).
- P259L (wild type/mutant/overlay). This C-terminal domain residue is at the end of a helix and is stabilising (∆∆G=-6.9 kcal/mol). This is primarily endowed by a more satisfied Ramachandran propensity term (-6.6 kcal/mol).However, it halves its dynamic flexibility (RMSD(residue) after that its 12 Å neighbour is neutrally thermodynamically drifted at 37°C).
- P280L (wild type/mutant/overlay). This C-terminal domain residue is part of a beta-turn (trans, i+1) in a disordered loop and is destabilizing (∆∆G=+7.5 kcal/mol). Primarily due to a variety of terms, such as worse backbone torsion (Ramachandran propensity term: +2.4 kcal/mol), but not solubility (-1.3 kcal/mol).
- G291S (wild type/mutant/overlay). This is a buried residue in the C-terminal domain. Despite seeming mild it is highly disruptive forcing nearby residues to shift in position. (Calculated ∆∆G is +17 kcal/mol, but may be excessive due to a 12 Å neighbour window being minimised).
- P293L (wild type/mutant/overlay). This C-terminal domain loop residue is buried. The mutation, despite being better at excluding water (-3. kcal/mol) has significant strain on the sidechain torsion (fa_dun term: +8.7 kcal/mol), making it destabilising (∆∆G=+8.7 kcal/mol).
Only one of the variants from gnomAD control set is found homozygously. Namely I203V (wild type/mutant/overlay) in the C-terminal domain. The stability of the MED27 protein is reduced by 3.7 kcal/mol, which a smaller effect that the destabilising pathogenic mutants in the C-terminal. Curiously, it mildly weakens the interface with MED17 by +1.3 kcal/mol, while none of the pathogenic variants do so. Two other variants found at a frequency greater than 5e-5 are in the C-terminal domain, namely P174A (slightly disrupts a beta-turn: +3 kcal/mol) and A150T (missing density). The other three >5e-5 frequency variants are A2V (missing density), I5V (mouse: is L5), S26F (destabilizing by +2 kcal/mol, but improves MED14 binding) and K36R (neutral).
Methods
Details and scripts in GitHub repo.
6W1S was energy minimised with restrained CA atoms with Pyrosetta using the LocalRelax mover (sampler). The model is mouse, but for MED27 only L5I, S6N, G8S, N55H, S220N, S235N differ, so it was not humanised.