2.3 | Crystal environment effect, T1160 and T1161
These targets, provided by Shunsuke Tagami, are two versions of a small
(48 residue) protein. T1160 has a putative ancestral sequence derived
from the protein family phylogenetic tree, and includes only seven amino
acid types instead of 20. There are two almost identical structures with
this sequence in the PDB (7DXZ and 7DYC), but the target structure is
different (GDT_TS of the experimental T1160 structure with respect to
7DXZ is only 61), probably because of change of crystallization
conditions (sulphate as opposed to malonate or malate for the two
earlier structures). T1161 has five mutations with respect to T1160 and
adopts a slightly different conformation (GDT_TS of 89 for T1161
against T1160), presumably because of the mutations. Both targets are
dimers. A few groups were successful with these targets (best monomer
GDT_TS of 90 for T1160 and 94 for T1161, and the dimer interface
accuracy of these models is also high (ICS of ~80).
However, the best performances are by different groups for the two
targets and the models ranked as likely most accurate (model 1) have
GDT_TS in the 70s. The highest GDT_TS values are, again, for groups
using enhanced sampling with AF2 methods. Thus, a reasonable explanation
for the high accuracy is that the conformations are not fully dependent
on the environment and so can be obtained with isolated dimers if enough
structure diversity is generated.