Models for crystallography have two purposes: refinement and
interpretation. Here these two purposes are in conflict. Neither case is
handled well by either trim or not trim scenario, but trimming results
in a deficit for refinement and not-trimming results in a deficit for
interpretation.
Our computational tools are not “fixed” in the same way that the
standard amino acids are “fixed” or your government’s bureaucracy
pathways are “fixed”. They are open for debate and for adjustments. This
is a fine example where it may be more productive to discuss the options
for making changes to the model itself or its representation, to better
account for awkward situations such as these. Otherwise we are left
figuring out the best imperfect way to use an imperfect tool (as all
tools are, to varying degrees!), which isn’t satisfying for enough
people, enough of the time.
I now appreciate the hypocrisy in the argument “do not trim, but also
don’t model disordered regions”, even though I’d be keen to avoid
trimming. This discussion has therefore softened my own viewpoint.
My refinement models (as implemented in Vagabond) do away with the
concept of B factors precisely for the anguish it causes here, and
refines a distribution of protein conformations which is sampled to
generate an ensemble. By describing the conformations through the
torsion angles that comprise the protein, modelling flexibility of a
disordered lysine is comparatively trivial, and indeed modelling all
possible conformations of a disordered loop becomes feasible. Lysines
end up looking like a frayed end of a rope. Each conformation can
produce its own solvent mask, which can be summed together to produce a
blurring of density that matches what you would expect to see in the
crystal.
In my experience this doesn’t drop the R factors as much as you’d
assume, because blurred out protein density does look very much like
solvent, but it vastly improves the interpretability of the model. This
also better models the boundary between the atoms you would trim and
those you’d leave untrimmed, by avoiding such a binary distinction. No
fear of trimming and pushing those errors unseen into the rest of the
structure. No fear of leaving atoms in with an inadequate B factor model
that cannot capture the nature of the disorder.
Vagabond is undergoing a heavy rewrite though, and is not yet ready for
human consumption. Its first iteration worked on
single-dataset-single-model refinement, which handled disordered side
chains well enough, with no need to decide to exclude atoms. The heart
of the issue lies in main chain flexibility, and this must be handled
correctly, for reasons of interpretability and elucidating the
biological impact. This model isn’t perfect either, and necessitates its
own compromises - but will provide another tool in the structural
biology arsenal.
—-
Dr Helen Ginn
Group leader, DESY
Hamburg Advanced Research Centre for Bioorganic Chemistry (HARBOR)
Luruper Chaussee 149
22607 Hamburg
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