Revisiting antibody modeling assessment for CDR-H3 loop

Abstract

The antigen-binding site of antibodies, also known as complementarity-determining region (CDR), has hypervariable sequence properties. In particular, the third CDR loop of the heavy chain, CDR-H3, has such variability in its sequence, length, and conformation that ordinary modeling techniques cannot build a high-quality structure. At Stage 2 of the Second Antibody Modeling Assessment (AMA-II) held in 2013, the model structures of the CDR-H3 loops were submitted by the seven modelers and were critically assessed. After our participation in AMA-II, we rebuilt one of the long CDR-H3 loops with 13 residues (A52 antibody) by a more precise method, using enhanced conformational sampling with the explicit water model, as compared to our previous method employed at AMA-II. The current stable models obtained from the free energy landscape at 300 K include structures similar to the X-ray crystal structures. Those models were not built in our previous work at AMA-II. The current free energy landscape suggested that the CDR-H3 loop structures in the crystal are not stable in solution, but they are stabilized by the crystal packing effect.

Cryptic-site binding mechanism of medium-sized Bcl-xL inhibiting compounds elucidated by McMD-based dynamic docking simulations

“…We have developed a dynamic docking implementation based on multicanonical molecular dynamics (McMD, see Section S1 for an explanation of the McMD theory) 16 , which we have applied to a number of cases 17 – 21 . Besides dynamic docking, we have also applied McMD 22 , 23 simulations to the conformational sampling of proteins and peptides 24 , 25 and the loop structure prediction of an antibody 26 . With McMD, the bias is correlated with the temperature, enabling McMD simulations to adaptively modulate the bias given the density of states.…”

Ensembles in solution as a new paradigm for antibody structure prediction and design

“…Thus, the accurate prediction of CDR-H3 loop structure remains challenging. [21][22][23] The CDR-H3 loop is also known to play a central role in antigen-binding and recognition as it has on average the highest counts of contacts with the antigen. 21 Additionally, the length and structure of the CDR-H3 loop can directly influence the antigen-binding patterns, and thereby have an effect on the specificity of the paratope.…”

“…21 Additionally, the length and structure of the CDR-H3 loop can directly influence the antigen-binding patterns, and thereby have an effect on the specificity of the paratope. 21,22 Recent studies that investigated the conformational diversity of the CDR-H3 loop in solution have shown that, in particular, CDR-H3 loop conformations in unbound antibody X-ray structures can be distorted by crystal packing effects and that the actual dominant CDR-H3 loop conformation in solution is optimized to bind the antigen. Thus, special care has to be taken when characterizing antibody CDR-H3 loops based on "unbound" Fab X-ray structures.…”

Methods for sequence and structural analysis of B and T cell receptor repertoires

“…CDR3 modeling has been tackled by a wide range of approaches [47] . Software for CDR3 modeling ( Table 2 ) spans the range from simple sequence alignment methods [48] , to fragment assembly [49] , molecular dynamics (MD) [50] and robotics-based loop closure algorithms [51] . In the most recent antibody modeling assessment (AMA-II) [52] , the lowest heavy-chain CDR3 (CDRH3) errors were obtained by our own group using a combination of MD, fragment assembly and manual selection [53] .…”