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

2022
Views:

493

Pages:

17
Author:

Reed Lloyd

RosettaAntibodyDesign  Monte Carlo Algorithm.  Whole CDR Sampling (GraftDesign)  Sample structures from database  Insert and optimize peptide bond without CDR disruption  New Graft Algorithm  100% Closure  Roughly mimics Somatic Recombination  Sequence Sampling (SeqDesign)  Sample amino acid types  According to CDR Cluster Profiles  Roughly mimics somatic hypermutation RosettaAntibodyDesign Top Decoy H3 Variability H1 H1 L2 L2 H3 H3 2j88 2dqc Re-elicitation of neutralizing antibodies Antigen Design Example Scaffold Grafting Other Structural Modeling Examples 44 Single Particle EM Indicative of Binding over Receptor Binding Site Receptor Binding Site H/D Exchange Peptide Lysine-193 rdt Residues N. J. Thornburg, et al., J Clin Invest; 2013; Vol. 123 (10): p. 4405-9. 45 Relative Orientation of H5.3 Fab is Ambiguous by EM Density Fitting Orientation A CCC=0.895 Orientation B CCC=0.868 Initial Cross Correlation Coefficient Model Cross Correlation Coefficient Predicted Binding Energy (REU) Orientation A 0.895 0.903 -21.0 Orientation B 0.868 0.911 -26.1 N. J. Thornburg, et al., J Clin Invest; 2013; Vol. 123 (10). A. Sircar and J. J. Gray, PLoS Comput Biol; 2010; Vol. 6 (1). 46 Mutational Analysis Indicates H5.3 Binding in Orientation B N. J. Thornburg, et al., J Clin Invest; 2013; Vol. 123 (10): p. 4405-9. 47 PG9-like is a Broadly Neutralizing HIV Antibody  30 residue long HCDR3 loop accounts for neutralization functionality  Variable chain has few mutations relative to other broadly neutralizing Abs  Germline reversion of the variable chain retains neutralization 48 VH Mutations (AA %) HIV Antibodies have Long HCDR3 loops and/or many Somatic Mutation Classical Vaccination Somatic mutation - Uncharacteristically high levels of somatic mutation - Uncharacteristically long heavy chain HCDR3 loops 49 Do HIV-Naïve Humans have PG9like Antibodies? Willis JR, et al. Proc Natl Acad Sci U S A. 2016;113(16):4446-51. 50 “Thread” Long HCDR3 Sequences over PG9 co-crystal Structure 51 Rapid Screening of 25,000 HCDR3s using Rosetta-Inspired PSSMs 30 𝐴𝑝𝑝𝑟𝑜𝑥𝑖𝑚𝑎𝑡𝑒𝑑 𝑅𝑜𝑠𝑒𝑡𝑡𝑎 𝑆𝑐𝑜𝑟𝑒 = 𝑠𝑡𝑎𝑏𝑖𝑙𝑖𝑡𝑦𝑖,𝑗 + 𝑎𝑓𝑓𝑖𝑛𝑖𝑡𝑦𝑖,𝑗 𝑖=1 52 Threading of Top 1000 HCDR3s Discriminates Unlikely Matches 53 Threading of Top 1000 HCDR3s Discriminates Unlikely Matches 54 Threading of Top 1000 HCDR3s Discriminates Unlikely Matches 55 Energetic Gap Between PG9 and Top Naïve Donor HCDR3 Sequences 56