Journal: Journal of autoimmunity

Article Title: FLEXIBLE PEPTIDE RECOGNITION BY HLA-DR TRIGGERS SPECIFIC AUTOIMMUNE T-CELL RESPONSES IN AUTOIMMUNE THYROIDITIS AND DIABETES

doi: 10.1016/j.jaut.2016.09.007

Figure Lengend Snippet: Diagram depicting the APS3v HLA-DR protein construct we produced. The α chain construct contained the DRα chain fused to the coiled coil region of the basic Leucine zipper domain of Fos. The β chain construct contained the coiled coil region of the basic Leucine zipper domain of JunB. The Jun and Fos dimerization motifs allowed the protein to dimerize to form the APS3v HLA-DR protein. The α chain has a His6 tag while the β chain has a V5 epitope tag for purification purposes.

Article Snippet: This resulted in the 36 predicted peptide binders listed in . table ft1 table-wrap mode="anchored" t5 caption a7 Peptide Sequence Tg.2098 LSSVVVDPSIRHFDV Tg.726 CPTPCQLQAEQAFLRTV Tg.1951 FRKKVILEDKVKNF Tg.1571 EKVPESKVIFDANAPVAVRSKVPDSEF Tg.202 VNTTDMMIFDLVHSYNRFPD TSHR.132 GIFNTGLKMFPDLTKVYST TSHR.197 FNGTKLDAVYLNKNKYLTVI Ins B9-23 SHLVEALYLVCGERG Ins.44 GERGFFYTPKTR Ins.25 FVNQHLCGSHLVEA Ins.76 PGAGSLQPLALEGSLQKRG Ins.89 RGIVEQCCTSICSL Ins.98 SICSLYQLENYCN GAD.378 SRKHKWKLSGVERANSVTW GAD.492 REGYEMVFDGKPQHTNVCF GAD.116 QDVMNILLQYVVKSFDRST GAD.247 NMYAMMIARFKMFPEVKEKG GAD.260 PEVKEKGMAALPRLIAFTSE GAD.274 IAFTSEHSHFSLK GAD.379 WKLSGVERANSV GAD.555 NFFRMVISNPAAT GAD.192 AADWLTSTANTNMFT GAD.456 WLMWRAKGTTGFEAH TPO.763 SGRRVLVYSCRHGYELQGR TPO.489 AAFRFGHATIHPLVRRLDASFQEH TPO.122 ALSEDLLSIIANMSGCLPY TPO.28 SRGKELLWGKPEESRVSSV TPO.423 ALNAHWSADAVYQEARKVV TPO.758 ESGRRVLVYSCRHGYELQG TPO.405 ALHTLWLREHNRLAAALKA TPO.338 RQLRNWTSAEGLLRVHARL TPO.513 DLPGLWLHQAFFSPWTLLR TPO.589 PGYNEWREFCGLPRLETPA TPO.161 RDHPRWGASNTALARWLPP TPO.344 TSAEGLLRVHARLRDSGRA TPO.351 RVHARLRDSGRAYLPFVPP APO (positive control) IPDNLFLKSDGRIKYTLNK scr2098 (negative control) HDLFSRIDSSVVVVP Open in a separate window Sequences of peptides tested in vitro for binding to APS3v HLA-DR. 2.4 Peptide synthesis The peptides used in this study were synthesized by Genscript (Piscataway, NJ).

Techniques: Construct, Produced, Purification

Journal: Journal of autoimmunity

Article Title: FLEXIBLE PEPTIDE RECOGNITION BY HLA-DR TRIGGERS SPECIFIC AUTOIMMUNE T-CELL RESPONSES IN AUTOIMMUNE THYROIDITIS AND DIABETES

doi: 10.1016/j.jaut.2016.09.007

Figure Lengend Snippet: Sequences of peptides tested in vitro for binding to APS3v HLA-DR.

Article Snippet: This resulted in the 36 predicted peptide binders listed in . table ft1 table-wrap mode="anchored" t5 caption a7 Peptide Sequence Tg.2098 LSSVVVDPSIRHFDV Tg.726 CPTPCQLQAEQAFLRTV Tg.1951 FRKKVILEDKVKNF Tg.1571 EKVPESKVIFDANAPVAVRSKVPDSEF Tg.202 VNTTDMMIFDLVHSYNRFPD TSHR.132 GIFNTGLKMFPDLTKVYST TSHR.197 FNGTKLDAVYLNKNKYLTVI Ins B9-23 SHLVEALYLVCGERG Ins.44 GERGFFYTPKTR Ins.25 FVNQHLCGSHLVEA Ins.76 PGAGSLQPLALEGSLQKRG Ins.89 RGIVEQCCTSICSL Ins.98 SICSLYQLENYCN GAD.378 SRKHKWKLSGVERANSVTW GAD.492 REGYEMVFDGKPQHTNVCF GAD.116 QDVMNILLQYVVKSFDRST GAD.247 NMYAMMIARFKMFPEVKEKG GAD.260 PEVKEKGMAALPRLIAFTSE GAD.274 IAFTSEHSHFSLK GAD.379 WKLSGVERANSV GAD.555 NFFRMVISNPAAT GAD.192 AADWLTSTANTNMFT GAD.456 WLMWRAKGTTGFEAH TPO.763 SGRRVLVYSCRHGYELQGR TPO.489 AAFRFGHATIHPLVRRLDASFQEH TPO.122 ALSEDLLSIIANMSGCLPY TPO.28 SRGKELLWGKPEESRVSSV TPO.423 ALNAHWSADAVYQEARKVV TPO.758 ESGRRVLVYSCRHGYELQG TPO.405 ALHTLWLREHNRLAAALKA TPO.338 RQLRNWTSAEGLLRVHARL TPO.513 DLPGLWLHQAFFSPWTLLR TPO.589 PGYNEWREFCGLPRLETPA TPO.161 RDHPRWGASNTALARWLPP TPO.344 TSAEGLLRVHARLRDSGRA TPO.351 RVHARLRDSGRAYLPFVPP APO (positive control) IPDNLFLKSDGRIKYTLNK scr2098 (negative control) HDLFSRIDSSVVVVP Open in a separate window Sequences of peptides tested in vitro for binding to APS3v HLA-DR. 2.4 Peptide synthesis The peptides used in this study were synthesized by Genscript (Piscataway, NJ).

Techniques: In Vitro, Binding Assay, Sequencing, Positive Control, Negative Control

Journal: Journal of autoimmunity

Article Title: FLEXIBLE PEPTIDE RECOGNITION BY HLA-DR TRIGGERS SPECIFIC AUTOIMMUNE T-CELL RESPONSES IN AUTOIMMUNE THYROIDITIS AND DIABETES

doi: 10.1016/j.jaut.2016.09.007

Figure Lengend Snippet: In vitro binding results of peptide binding to APS3v HLA-DR. 5 Tg, 2 TSHR, 6 Ins, 10 GAD65 and 13 TPO peptides were tested for binding to APS3v HLA-DR protein. APO was used as a positive control and scr2098 was used as a negative control. Peptides binding with greater than 2 fold (>10 standard deviations over the average for peptide alone with no HLA) were considered as positive and are indicated with black arrows.

Article Snippet: This resulted in the 36 predicted peptide binders listed in . table ft1 table-wrap mode="anchored" t5 caption a7 Peptide Sequence Tg.2098 LSSVVVDPSIRHFDV Tg.726 CPTPCQLQAEQAFLRTV Tg.1951 FRKKVILEDKVKNF Tg.1571 EKVPESKVIFDANAPVAVRSKVPDSEF Tg.202 VNTTDMMIFDLVHSYNRFPD TSHR.132 GIFNTGLKMFPDLTKVYST TSHR.197 FNGTKLDAVYLNKNKYLTVI Ins B9-23 SHLVEALYLVCGERG Ins.44 GERGFFYTPKTR Ins.25 FVNQHLCGSHLVEA Ins.76 PGAGSLQPLALEGSLQKRG Ins.89 RGIVEQCCTSICSL Ins.98 SICSLYQLENYCN GAD.378 SRKHKWKLSGVERANSVTW GAD.492 REGYEMVFDGKPQHTNVCF GAD.116 QDVMNILLQYVVKSFDRST GAD.247 NMYAMMIARFKMFPEVKEKG GAD.260 PEVKEKGMAALPRLIAFTSE GAD.274 IAFTSEHSHFSLK GAD.379 WKLSGVERANSV GAD.555 NFFRMVISNPAAT GAD.192 AADWLTSTANTNMFT GAD.456 WLMWRAKGTTGFEAH TPO.763 SGRRVLVYSCRHGYELQGR TPO.489 AAFRFGHATIHPLVRRLDASFQEH TPO.122 ALSEDLLSIIANMSGCLPY TPO.28 SRGKELLWGKPEESRVSSV TPO.423 ALNAHWSADAVYQEARKVV TPO.758 ESGRRVLVYSCRHGYELQG TPO.405 ALHTLWLREHNRLAAALKA TPO.338 RQLRNWTSAEGLLRVHARL TPO.513 DLPGLWLHQAFFSPWTLLR TPO.589 PGYNEWREFCGLPRLETPA TPO.161 RDHPRWGASNTALARWLPP TPO.344 TSAEGLLRVHARLRDSGRA TPO.351 RVHARLRDSGRAYLPFVPP APO (positive control) IPDNLFLKSDGRIKYTLNK scr2098 (negative control) HDLFSRIDSSVVVVP Open in a separate window Sequences of peptides tested in vitro for binding to APS3v HLA-DR. 2.4 Peptide synthesis The peptides used in this study were synthesized by Genscript (Piscataway, NJ).

Techniques: In Vitro, Binding Assay, Positive Control, Negative Control

Journal: Journal of autoimmunity

Article Title: FLEXIBLE PEPTIDE RECOGNITION BY HLA-DR TRIGGERS SPECIFIC AUTOIMMUNE T-CELL RESPONSES IN AUTOIMMUNE THYROIDITIS AND DIABETES

doi: 10.1016/j.jaut.2016.09.007

Figure Lengend Snippet: Decomposition analysis of the core sequence (Seq.) of peptides that bind to APS3v. Numerical values for each residue are interaction energies (Int. E) between the residue and the APS3v protein (in kcal/mol).

Article Snippet: This resulted in the 36 predicted peptide binders listed in . table ft1 table-wrap mode="anchored" t5 caption a7 Peptide Sequence Tg.2098 LSSVVVDPSIRHFDV Tg.726 CPTPCQLQAEQAFLRTV Tg.1951 FRKKVILEDKVKNF Tg.1571 EKVPESKVIFDANAPVAVRSKVPDSEF Tg.202 VNTTDMMIFDLVHSYNRFPD TSHR.132 GIFNTGLKMFPDLTKVYST TSHR.197 FNGTKLDAVYLNKNKYLTVI Ins B9-23 SHLVEALYLVCGERG Ins.44 GERGFFYTPKTR Ins.25 FVNQHLCGSHLVEA Ins.76 PGAGSLQPLALEGSLQKRG Ins.89 RGIVEQCCTSICSL Ins.98 SICSLYQLENYCN GAD.378 SRKHKWKLSGVERANSVTW GAD.492 REGYEMVFDGKPQHTNVCF GAD.116 QDVMNILLQYVVKSFDRST GAD.247 NMYAMMIARFKMFPEVKEKG GAD.260 PEVKEKGMAALPRLIAFTSE GAD.274 IAFTSEHSHFSLK GAD.379 WKLSGVERANSV GAD.555 NFFRMVISNPAAT GAD.192 AADWLTSTANTNMFT GAD.456 WLMWRAKGTTGFEAH TPO.763 SGRRVLVYSCRHGYELQGR TPO.489 AAFRFGHATIHPLVRRLDASFQEH TPO.122 ALSEDLLSIIANMSGCLPY TPO.28 SRGKELLWGKPEESRVSSV TPO.423 ALNAHWSADAVYQEARKVV TPO.758 ESGRRVLVYSCRHGYELQG TPO.405 ALHTLWLREHNRLAAALKA TPO.338 RQLRNWTSAEGLLRVHARL TPO.513 DLPGLWLHQAFFSPWTLLR TPO.589 PGYNEWREFCGLPRLETPA TPO.161 RDHPRWGASNTALARWLPP TPO.344 TSAEGLLRVHARLRDSGRA TPO.351 RVHARLRDSGRAYLPFVPP APO (positive control) IPDNLFLKSDGRIKYTLNK scr2098 (negative control) HDLFSRIDSSVVVVP Open in a separate window Sequences of peptides tested in vitro for binding to APS3v HLA-DR. 2.4 Peptide synthesis The peptides used in this study were synthesized by Genscript (Piscataway, NJ).

Techniques: Sequencing, Residue, Binding Assay

Journal: Journal of autoimmunity

Article Title: FLEXIBLE PEPTIDE RECOGNITION BY HLA-DR TRIGGERS SPECIFIC AUTOIMMUNE T-CELL RESPONSES IN AUTOIMMUNE THYROIDITIS AND DIABETES

doi: 10.1016/j.jaut.2016.09.007

Figure Lengend Snippet: A representative structure of the interaction between APS3v and TPO.758, the strongest binding peptide. The surface of the proximal residues to the peptide is colored by the electrostatic potential – red represent negative and blue positive potential. The binding pockets P1, P4, P6 and P9 are noted to highlight the mode of peptide binding. P1 is filled with the residue Leu and P9 with Tyr. Pockets P4, P5 and P6 create a polar arrangement characterized by positive potential from Arg-β74 near Ser4 and opposing negative potential due to Glu-α11, Asp-α66 and Glu-β9 next to Arg6.

Article Snippet: This resulted in the 36 predicted peptide binders listed in . table ft1 table-wrap mode="anchored" t5 caption a7 Peptide Sequence Tg.2098 LSSVVVDPSIRHFDV Tg.726 CPTPCQLQAEQAFLRTV Tg.1951 FRKKVILEDKVKNF Tg.1571 EKVPESKVIFDANAPVAVRSKVPDSEF Tg.202 VNTTDMMIFDLVHSYNRFPD TSHR.132 GIFNTGLKMFPDLTKVYST TSHR.197 FNGTKLDAVYLNKNKYLTVI Ins B9-23 SHLVEALYLVCGERG Ins.44 GERGFFYTPKTR Ins.25 FVNQHLCGSHLVEA Ins.76 PGAGSLQPLALEGSLQKRG Ins.89 RGIVEQCCTSICSL Ins.98 SICSLYQLENYCN GAD.378 SRKHKWKLSGVERANSVTW GAD.492 REGYEMVFDGKPQHTNVCF GAD.116 QDVMNILLQYVVKSFDRST GAD.247 NMYAMMIARFKMFPEVKEKG GAD.260 PEVKEKGMAALPRLIAFTSE GAD.274 IAFTSEHSHFSLK GAD.379 WKLSGVERANSV GAD.555 NFFRMVISNPAAT GAD.192 AADWLTSTANTNMFT GAD.456 WLMWRAKGTTGFEAH TPO.763 SGRRVLVYSCRHGYELQGR TPO.489 AAFRFGHATIHPLVRRLDASFQEH TPO.122 ALSEDLLSIIANMSGCLPY TPO.28 SRGKELLWGKPEESRVSSV TPO.423 ALNAHWSADAVYQEARKVV TPO.758 ESGRRVLVYSCRHGYELQG TPO.405 ALHTLWLREHNRLAAALKA TPO.338 RQLRNWTSAEGLLRVHARL TPO.513 DLPGLWLHQAFFSPWTLLR TPO.589 PGYNEWREFCGLPRLETPA TPO.161 RDHPRWGASNTALARWLPP TPO.344 TSAEGLLRVHARLRDSGRA TPO.351 RVHARLRDSGRAYLPFVPP APO (positive control) IPDNLFLKSDGRIKYTLNK scr2098 (negative control) HDLFSRIDSSVVVVP Open in a separate window Sequences of peptides tested in vitro for binding to APS3v HLA-DR. 2.4 Peptide synthesis The peptides used in this study were synthesized by Genscript (Piscataway, NJ).

Techniques: Binding Assay, Residue

Journal: Journal of autoimmunity

Article Title: FLEXIBLE PEPTIDE RECOGNITION BY HLA-DR TRIGGERS SPECIFIC AUTOIMMUNE T-CELL RESPONSES IN AUTOIMMUNE THYROIDITIS AND DIABETES

doi: 10.1016/j.jaut.2016.09.007

Figure Lengend Snippet: Two potential explanations by which HLA class II molecules can predispose to both AITD and T1D. First hypothesis (A), alleles predisposing to AITD and T1D are distinct but in tight LD. Two distinct pocket structures present thyroid and islet peptides respectively and are expressed on APCs together. Second hypothesis (B), APS3v HLA-DR pocket on APCs is flexible to accommodate both thyroid and islet peptides and present them to T-cells for immune response.

Article Snippet: This resulted in the 36 predicted peptide binders listed in . table ft1 table-wrap mode="anchored" t5 caption a7 Peptide Sequence Tg.2098 LSSVVVDPSIRHFDV Tg.726 CPTPCQLQAEQAFLRTV Tg.1951 FRKKVILEDKVKNF Tg.1571 EKVPESKVIFDANAPVAVRSKVPDSEF Tg.202 VNTTDMMIFDLVHSYNRFPD TSHR.132 GIFNTGLKMFPDLTKVYST TSHR.197 FNGTKLDAVYLNKNKYLTVI Ins B9-23 SHLVEALYLVCGERG Ins.44 GERGFFYTPKTR Ins.25 FVNQHLCGSHLVEA Ins.76 PGAGSLQPLALEGSLQKRG Ins.89 RGIVEQCCTSICSL Ins.98 SICSLYQLENYCN GAD.378 SRKHKWKLSGVERANSVTW GAD.492 REGYEMVFDGKPQHTNVCF GAD.116 QDVMNILLQYVVKSFDRST GAD.247 NMYAMMIARFKMFPEVKEKG GAD.260 PEVKEKGMAALPRLIAFTSE GAD.274 IAFTSEHSHFSLK GAD.379 WKLSGVERANSV GAD.555 NFFRMVISNPAAT GAD.192 AADWLTSTANTNMFT GAD.456 WLMWRAKGTTGFEAH TPO.763 SGRRVLVYSCRHGYELQGR TPO.489 AAFRFGHATIHPLVRRLDASFQEH TPO.122 ALSEDLLSIIANMSGCLPY TPO.28 SRGKELLWGKPEESRVSSV TPO.423 ALNAHWSADAVYQEARKVV TPO.758 ESGRRVLVYSCRHGYELQG TPO.405 ALHTLWLREHNRLAAALKA TPO.338 RQLRNWTSAEGLLRVHARL TPO.513 DLPGLWLHQAFFSPWTLLR TPO.589 PGYNEWREFCGLPRLETPA TPO.161 RDHPRWGASNTALARWLPP TPO.344 TSAEGLLRVHARLRDSGRA TPO.351 RVHARLRDSGRAYLPFVPP APO (positive control) IPDNLFLKSDGRIKYTLNK scr2098 (negative control) HDLFSRIDSSVVVVP Open in a separate window Sequences of peptides tested in vitro for binding to APS3v HLA-DR. 2.4 Peptide synthesis The peptides used in this study were synthesized by Genscript (Piscataway, NJ).

Techniques: