University:
Boston University
Course:
CAS BI 525 | Biology of Neurodegenerative Diseases
Academic year:

2022
Views:

336

Pages:

19
Author:

Daniela Larson

Antibody Structure: Prediction and Design Rosetta       Rosetta consists of multiple modules: protein folding, comparative modeling, ligand docking, protein design, antibody/antigen interactions, etc. Rosetta is developed in a consortium of twelve laboratories by around 50 developers Rosetta is free for academic us; user guide and tutorials are available PyRosetta is a python interface that allows integration with Pymol FoldIt is the better video game for you and your kids Rosetta@home uses your computer for our research RosettaCon 2017, Leavenworth, WA, USA Bender, B. J..; et al. “Protocols for Molecular Modeling with Rosetta3 and RosettaScripts."" Biochemistry 2016. 2 What is an antibody? (Structurally) ated by RAG J ded by TdT J DNA repair J What is an antibody? (Structurally) Heavy Chain Antigen Variable Region Constant Region Light Chain Antibody terminology: Ig “Immunoglobulin” or “full length antibody” Antibody terminology: Fab “Fragment antigen-binding” Antibody terminology: Fv “Fragment variable” What is an antibody? (Structurally) Heavy Chain Light Chain The immunoglobulin domain fold Anthony S. Serianni Complementarity determining regions HCDR3 LCDR3 HCDR2 LCDR1 HCDR1 LCDR2 CH65 PDBID: 3SM5 Framework Recognition of antigens Protein-protein interactions are determined by shape and physicochemical properties of solvent exposed loops, such as CDR loops. Ab Ag PDB ID: 3SM5 Sequence Structure Function Antibody diversification is achieved primarily through four mechanisms Locus IGH IGK IGL V Genes 38-46 34-38 29-33 V D Genes J Genes 23 6 0 5 0 4-5 D ‘P’ nucleotides generated by RAG D J J ‘N’ nucleotides added by TdT D J Hybridization and DNA repair D J Heavy Chain V(D)J Recombination Junctional Diversity Light Chain Heavy/Light Chain Pairing … and affinity maturation. V(D)J recombination Locus IGH IGK IGL V Genes 38-46 34-38 29-33 V D Genes J Genes 23 6 0 5 0 4-5 D ‘P’ nucleotides gene D J ‘N’ nucleotides ad D Hybridization and D V(D)J Recombination Junctional Di Junctional diversity nes 46 38 33 D Genes J Genes 23 6 0 5 0 4-5 D Recombination ‘P’ nucleotides generated by RAG D J J ‘N’ nucleotides added by TdT D J Hybridization and DNA repair D J Heavy Chain Junctional Diversity Heavy/Light Cha V(D)J gene sequences mapped to CDRs V FR1 CDR 1 FR2 CDR 2 FR3 N D N J CDR3 FR4 Sequence/structure relationship V GENE D GENE J GENE IMGT DomainGapAlign Prediction of Antibody Structures: Match Sequences with Known Structures Identify homologous framework regions Graft canonical CDR loops De novo model HCDR3 Very Long HCDR3 Sequences are Rare but Present Raw Reads Unique Reads (Nuc) Productive CDR3s (no stop) Unique CDR3s (AA) 30-Length CDR3s Unique 30-Length CDR3s 514,312,664 167,667,706 118,440,255 23,357,390 74,457 24,917 18 HCDR3 torso domain conformations ~80% ~20% Bulged or kinked Non-bulged or extended