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Blood, Vol. 113, Issue 9, 1967-1976, February 26, 2009
Relevance of biallelic versus monoallelic TNFRSF13B mutations in distinguishing disease-causing from risk-increasing TNFRSF13B variants in antibody deficiency syndromes
Blood Salzer et al.
113: 1967
Supplemental materials for: Salzer et al
Files in this Data Supplement:
- Table S6. Scores for intrinsic disorder reported by IUPred (PDF, 244 KB) -
Each row of the table contains the disorder scores at a particular position in both wild-type TACI and in TACI with the amino acid substitution named in the first column. The score for wild-type TACI is in the second column and the score for TACI with the corresponding substitution is in the third column. Bold entries indicate positions predicted by IUPred to be disordered. The cutoff used is 0.5.
- Table S7. Scores for intrinsic disorder reported by RONN (PDF, 211 KB) -
Each row of the table contains the disorder scores at a particular position in both wild-type TACI and in TACI with the amino acid substitution named in the first column. The score for wild-type TACI is in the second column and the score for TACI with the corresponding substitution is in the third column. Bold entries indicate positions predicted by RONN to be disordered. The cutoff used is 0.5.
- Table S8. Summary of predictions of intrinsic disorder in wild-type TACI by six methods (PDF, 142 KB) -
Column one names an amino acid and position in wild-type TACI. Columns two through seven contain a “Y” if the named method predicts intrinsic disorder at that position and a “N” otherwise. Column eight contains a “Y” if four or more methods predict disorder at a position and “N” if two or fewer methods predict disorder. At positions A149 and P251, precisely three methods predict disorder and we did not find any compelling evidence to break the tie.
- Table S9. Substitutions predicted to cause changes in intrinsic disorder within TACI (PDF, 136 KB) -
The first column names an amino acid substitution, and columns two through five contain an “X” if the corresponding method either increases the prediction of disorder at a position having low intrinsic disorder or decreases the prediction at a position having high intrinsic disorder. A position is predicted to have low or high intrinsic disorder if at least four of six disorder prediction methods agree at that position (see Table S8). Column six contains an “X” if at least three of columns two through five contain an “X.”
- Table S10. Changes in stability for certain amino acid substitutions, as predicted by Dmutant (PDF, 129 KB) -
The first column lists amino substitutions that may be performed in chains R, S, and T of PDB structure 1xu1. The second through fourth columns are the changes in energy for each substitution in kcal/mol. Those numbers in parentheses are substitutions of an amino acid with a larger amino acid; Dmutant warns that its results are “not reliable” for such substitutions. A positive change implies that the mutant protein is predicted to be less stable.
- Table S11. Total energy and change in energy computed by FoldX for five amino acid substitutions in three chains of the PDB structure 1xu1 (PDF, 144 KB) -
The first column of the table names a substitution in the CRD2 domain of TACI. The second through fourth columns are the total energy, and in parentheses the change in energy in kcal/mol, if the substitution is performed in the specified chain of 1xu1. In computations with amino acid substitutions, the other two chains of TACI are wild-type. Change in energy is with respect to the energy of 1xu1 if all three chains of TACI are wild-type, which is −143.7 kcal/mol. Negative changes indicate stabilizing substitutions.
- Table S12. Energy change predicted by PoPMuSiC for five amino acid substitutions in TACI (JPG, 101 KB) -
The first column indicates an amino acid substitution. The second column is the change in energy if that substitution is made in chain R of PDB structure 1xu1. The third and forth columns contain similar changes in energy for substitutions in chain S and chain T, respectively. Energy is given in units of kcal/mol with negative values indicating stabilizing substitutions. The asterisks in the row for column Y79C indicate that the PoPMuSiC considers the energy computations at these positions to be unreliable, because the solvent accessible area for the residue is between 40 and 50% of the surface area.
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