Additional file 1: Table S1. of Tapering and discontinuation of TNF-Îą blockers without disease relapse using ultrasonography as a tool to identify patients with rheumatoid arthritis in clinical and histological remission

Demographic, immunological, and US characteristics of patients with RA included in the observational study cohort. (DOC 51 kb

Additional file 1: of Characterization of inflammatory cell infiltrate of scleroderma skin: B cells and skin score progression

Table S1. Autoantibody characteristics according to scleroderma skin disease extension. (DOCX 14 kb

Computational alanine scanning-based free energies for the TCR-VB1^OE/huCollp261/HLA-DR4 complex.

<p>Computational alanine scanning-based free energies for the TCR-VB1^OE/huCollp261/HLA-DR4 complex.</p

Model of huCollp261 peptide in the HLA-DR4 binding cleft.

<p>The computationally generated model closely resembles the hypothetical model suggested by Dessen et al. (22) for the DR4 recognition of huCollp261. Phe263 fits into the P1 pocket and Glu266 (P4) hydrogen bonds to Lys71β. The MHC peptide-binding groove is represented with Connolly solid surface, whereas the ligand peptide is shown in stick representation.</p

Intermolecular hydrogen bonds between VB1^OE and huCollp261/HLA-DR4.

†<p>Interactions were statistically monitored throughout the MD trajectory for a total of 5000 conformations.</p

Hotspots predictions in the TCR VB1^OE -huCollp261/HLA-DR4 interface.

<p>Residues predicted to be hotspots (ΔΔG>1.0 kcal/mol) are shown in <i>red</i>, the huCollp261 peptide in <i>green</i> and the TCR is represented as a <i>yellow</i> ribbon. A) Unbound huCollp261/HLA-DR4 surface; B) Unbound TCR-VB1^OE surface; C) TCR-VB1^OE/huCollp261/HLA-DR4 complex.</p

Interaction energy and interface Accessible Surface Area (ASA) for the VB1^OE/huCollp261/HLA-DR4 complexes averaged over the MD simulation runs.

<p>Interaction energy and interface Accessible Surface Area (ASA) for the VB1^OE/huCollp261/HLA-DR4 complexes averaged over the MD simulation runs.</p

Interaction energy and interface Accessible Surface Area (ASA) in the minimized complexes emerging from docking calculations.

<p>Interaction energy and interface Accessible Surface Area (ASA) in the minimized complexes emerging from docking calculations.</p

Molecular PDF and protein structure analysis for the twenty models of DR4/huCollp261.

<p>Molecular PDF and protein structure analysis for the twenty models of DR4/huCollp261.</p

Molecular docking results.

<p>Structural comparison of overall structures of TCR-Vβ/huCollp261/HLA-DR4 complex models #36 (VB1^VB), #8 (VB1^OE) and #33 (VB1^OE) emerging from the docking study. Color coding is as follows: <i>magenta</i>, TCR-Vβ domain; <i>blue</i>, HLA-DR4; <i>green</i>, peptide.</p