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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 S13. Energy and rank as computed by RankViaContact for both the wild type TACI and TACI with amino acid substitutions at five positions (PDF, 188 KB) -
The first column in the table is the name of an amino acid substitution. Columns two, three, and four show the effect of each amino acid substitution on one of the three chains TACI contained in the structure 1xu1. Each cell of the columns two, three, and four contains two lines. The first line in each cell shows the energy in RT units (approximately 0.59 kcal/mol) computed by RankViaContact for wild-type TACI and for TACI with the corresponding amino acid substitution. The second line in each cell shows the rank of the corresponding position among the positions in the same chain of TACI in the wild-type structure and in the structure with the named amino acid substitution. The most negative energy is assigned rank one.
- Table S14. Summary of methods based on changes in energy (PDF, 90 KB) -
Column one lists a substitution in the CRD2 domain of TACI. Columns two through five are marked with an X if the named method predicts a large change in energy due to the substitution. Column six summarizes the preceding four columns. For I87N, C104R, and C104Y, column six receives two X marks because all four methods predict a destabilizing change due to the substitution. We mark Y79C with an X in columns four and six because RankViaContact predicts that the introduction of a C(ysteine) at position 79 creates stabilizing contacts with the Cysteines at positions 71 and 86, fundamentally altering structure.
- Table S15. Clash scores reported by probe for five amino acid substitutions in the three chains of TACI in the PDB structure 1xu1 (PDF, 121 KB) -
The first column in the table names a substitution. The second through fourth columns list the clash score computed by Probe and, in parenthesis, the number of serious clashes (non H-bond overlaps greater 0.4 Ã or greater) at the position of the substitution if the substitution is performed in chain R, S, or T of 1xu1, respectively.
- Table S16. Change in the cumulative β-aggregation compared to wild-type TACI for 17 amino acid substitutions as computed by TANGO (PDF, 142 KB) -
The first column of the table names an amino acid substitution. A positive number in the second column indicates an increase in β-aggregation and a negative number a decrease. Changes of magnitude less than one are reported as zero.
- Table S17. Clinical information on all 50 TACI deficient patients (PDF, 51.9 KB)
- Figure S1. TACI expression and APRIL binding on EBV cell lines of patients with heterozygous TNFRSF13B mutations (JPG, 94.4 KB)
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Upper panels: EBV transformed B-cell lines of patients were stained with a polyclonal antibody directed against the TACI extracellular domain. Middle panels: EBV transformed B-cell lines of patients were stained with a monoclonal antibody recognizing TNFRSF13B extracellular domain. Lower panels: EBV transformed B-cell lines of patients were stained with a flag-tagged APRIL construct. The colour code for all panels is as follows: blue histograms, patients; red histograms, healthy donors; grey filled histograms, patient with TNFRSF13B null mutation (S144X homozygous) serving as a negative control.
- Figure S2. Structural models of APRIL interacting with TACI CRD2 extracellular domain (JPG, 49.2 KB)
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Position of mutated amino acids in the structure of TACI bound to APRIL. (A) ribbon and sticks representation and (B) space filling representation of a monomeric TACI:APRIL interaction. Blue: APRIL. Green: TACI. Yellow: disulfide bridges of TACI. Orange: side chains of TACI residues making direct contact with APRIL. Red: residues within the CRD2 of TACI found mutated in CVID patients. Pictures were drawn from 1xu1 pdb coordinates32 using PyMol.
- Figure S3. Expression of TACI full-length (1293) and TACI extracellular domain (ED) TRAIL-R3 fusion proteins in 293T cells (JPG, 67.7 KB)
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Upper three panels 293T cells transfected with TACI ED TRAIL-R3 fusion proteins. Red lines: 293T cells transfected with empty vector; Blue: 293T cells transfected with TACI wt ED TRAIL-R3; Green: 293T cells transfected with TACI C104R ED TRAIL-R3; Lower three panels 293T cells transfected with TACI full-length (1293) proteins. Red lines: 293T cells transfected with empty vector; Blue: 293T cells transfected with TACI-full length (1293) wildtype; Green: 293T cells transfected with TACI-full length (1293) C104R. Left row: Staining of transfected 293T cells with monoclonal anti-TACI antibody (1A1); middle row: Staining of transfected 293T cells with polyclonal anti-TACI antibody; right row: Staining of transfected 293T cells with monoclonal antiTRAIL-R3 antibody (clone 572.11).
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