Primary Citation PubMed: 11851337
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The befores and afters of molecular replacement.
(2008) Acta Crystallogr D Biol Crystallogr 64
PubMed: 18094463 | PubMedCentral: PMC2394785 | DOI: 10.1107/S0907444907049736
I will discuss models 1irj (41% sequence identity) and 1mho (39% sequence identity).
Although the matched chains do not fit so well, the relative orientation of the monomers is closer than that for 1irj .
A post mortem comparison of these models with the S100 structure shows that the root-mean-square (r.m.s.) difference in C α positions of the monomers is 0.88 Å ( 1irj ) and 1.23 Å ( 1mho ), whilst for the 1irj dimer it is 2.64 Å and for the 1mho dimer it is 1.68 Å.
( b ) The pairwise alignment for one of the models, 1irj .
If searching with a monomer 1irj would prove the better model, but if searching with a dimer the 1mho example is better.
( c ) The overlap, based on one chain only, of the final S100 dimer model, 1e8a , onto the 1irj dimer.
Figure 6 The first maximum-likelihood weighted electron-density map for S100 from the 1irj solution after ten initial rounds of refinement.
The two chains of the S100 dimer are shown in green and blue and those of the 1irj dimer in yellow and tan.
Publication Year: 2008
Amyloid formation by the pro-inflammatory S100A8/A9 proteins in the ageing prostate.
(2009) PLoS One 4
PubMed: 19440546 | PubMedCentral: PMC2678268 | DOI: 10.1371/journal.pone.0005562
In the S100A8/A9 oligomeric complex (references for the structures: pdb 1xk4 for S100A8 and pdb 1irj for S100A9) the aggregation profiles ( Figure 3 ) and the scores of 0.18 and 0.32 for S100A8 and S1... 0A9, respectively, are significantly reduced, indicating that most of the aggregation-prone sequences are involved in the oligomeric interactions.
Protein aggregation propensity profiles Intrinsic aggregation propensity profiles of S100A8/A9 proteins were calculated as described previously  ,  by using the pdb files of 1xk4 for S100A8 and 1irj for S100A9 from the Protein Data Bank.
Publication Year: 2009
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