von Willebrand factor A domain-containing protein 1
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Description
von Willebrand factor A domain-containing protein 1 (VWA1) is a protein composed of three domains.
- VWFA
- Fibronectin type-III 1
- Fibronectin type-III 2
The following missense mutations were found:
S74R
- wild type
- mutant
- phosphoserine
- overlay mutant
- overlay template
- ∆∆GS74R: +24 kcal/mol
- VWFA domain
This mutation is highly destabilising and is very likely to make the protein aggregate or result in protein degradation. The introduction of a buried phosphate on serine-74 means that it may be flexible or adopt an alternative conformation. However, the effect of the phosphate is much less than the mutation to an arginine. The model used diverges slightly in the core of the VWFA domain, but the mutation is so severe, any imprecisions in the model are neglible.
Y364N
- wild type
- mutant
- overlay mutant
- overlay template
- ∆∆GY364N: +10 kcal/mol
- Fibronectin type-III 2 domain
This mutation shrinks the core of the domain and is destabilising. The domain, being small is likely sensitive to such changes.
Truncations
- G25∗ truncates the protein at the export sequence, therefore all the model shown is missing.
- M155∗ (remainder/missing)
- R293∗ (remainder/missing)
- Q367∗ (remainder/missing)
Methods
The protein is not crystallised. However, there are crystallised homologues close enough that SwissModel has models of VWA1 .- The N-terminal VWFA domain (32–211) had been threaded against 1PT6 (32% identity).
- The two C-terminal Fibronectin type-III domains had been threaded against either 2GEE (23%) or 6GVK (21%).
As the 2GEE structure lacked a CCP4 map and the Y364 equivalent was a phenylanine, while in 6GVK it was a tyrosine, the latter model was chosen.
The models were energy minised with the electron density maps from the templates as a reference (cf. protocol)
with a decreasing density constrain each 5 cycles of 15, 10, 5, 1 on the ref2015 scorefunction and compared in parallel with a pose from 15 cycles of FastRelax to make sure the difference was not greater than 20 kcal/mol in favour of the unconstrained.
The mutations (including the patched residue SER:phosphorylated) were introduced and the 9Å neighbourhood was energy minimised with 15 cycles of FastRelax.
Trapped waters were removed for simplicity, had they been kept the VWFA domain wild type and phosphorylated would have had better scores, but not the the VWFA domain mutant.
The Fibronectin domain mutant might have had a slightly better score, by 1-2 kcal/mol, with a water placed in the location of the former ring hydroxyl of tyrosine if even possible.
Models were placed close to each other afterwards to avoid unneccessary issues in the visualisation —whether or how these domains interact is not known.
The templates that SwissModel used were likewise placed and renumbered for better comparison with the VWA1.