1. CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS BiC BioCentrum-DTU Technical University of Denmark Creation of a functional B cell receptor/Antibody

2. CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS BiC BioCentrum-DTU Technical University of Denmark Germ line gene organisation © 2001 by Garland Publishing

3. CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS BiC BioCentrum-DTU Technical University of Denmark Gene organisation © 2001 by Garland Publishing

4. CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS BiC BioCentrum-DTU Technical University of Denmark Number of functional gene segments © 2001 by Garland Publishing

5. CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS BiC BioCentrum-DTU Technical University of Denmark Rearrangement © 2001 by Garland Publishing

6. CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS BiC BioCentrum-DTU Technical University of Denmark P- and N-nucleotide introduction

7. CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS BiC BioCentrum-DTU Technical University of Denmark Somatic Hypermutations © 2001 by Garland Publishing

8. CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS BiC BioCentrum-DTU Technical University of Denmark The translated fuctional rearrangement

9. CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS BiC BioCentrum-DTU Technical University of Denmark Numbering Schemes

10. CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS BiC BioCentrum-DTU Technical University of Denmark Numbering Schemes  The Kabat numbering scheme is a widely adopted standard for numbering the residues in an antibody in a consistent manner. However the scheme has problems!  The Chothia numbering scheme is identical to the Kabat scheme, but places the insertions in CDR-L1 and CDR-H1 at the structurally correct positions. This means that topologically equivalent residues in these loops do get the same label (unlike the Kabat scheme).  The IMGT unique numbering for all IG and TR V-REGIONs of all species relies on the high conservation of the structure of the variable region [1-6]. This numbering, set up after aligning more than 5 000 sequences, takes into account and combines the definition of the framework (FR) and complementarity determining regions (CDR) [8], structural data from X-ray diffraction studies [9], and the characterization of the hypervariable loops [10]. http://www.bioinf.org.uk/abs/#kabatnum http://imgt.cines.fr/

11. CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS BiC BioCentrum-DTU Technical University of Denmark Identification of CDR regions Indentifying the CDRs CDR-L1 StartApprox residue 24 Residue beforeis always C Residue afteris always W. Typically WYQ, but also, WLQ, WFQ, WYL Length10 to 17 residues CDR-L2 Startalways 16 residues after the end of CDR-L1 Residues beforegenerally IY, but also, VY, IK, IF Lengthalways 7 residues CDR-L3 Startalways 33 residues after end of CDR-L2 Residue beforeis always C Residues afteralways FGXG Length7 to 11 residues CDR-H1 StartApproximately residue 31 (always 9 after a C) (Chothia/AbM defintion starts 5 residues earlier) Residues beforealways CXXXXXXXX Residues afteralways W. Typically WV, but also WI, WA Length5 to 7 residues (Kabat definition); 7 to 9 residues (Chothia definition); 10 to 12 residues (AbM definition) CDR-H2 Startalways 15 residues after the end of Kabat/AbM definition of CDR-H1 Residues beforetypically LEWIG, but a number of variations Residues afterK[RL]IVFT[AT]SIA (where residues in square brackets are alternatives at that position) LengthKabat definition 16 to 19 residues (AbM definition and most recent Chothia definition ends 7 residues earlier; earlier Chothia definition starts 2 residues later and ends 9 earlier) CDR-H3 Startalways 33 residues after end of CDR-H2 (always 3 after a C) Residues beforealways CXX (typically CAR)

12. CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS BiC BioCentrum-DTU Technical University of Denmark Phage Display http://www.bio.anl.gov/combinatorialbiology/reagents.html