The human antibody sequence space and structural design of the V, J regions, and CDRH3 with Rosetta.

The human adaptive immune response enables the targeting of epitopes on pathogens with high specificity. Infection with a pathogen induces somatic hyper-mutation and B-cell selection processes that govern the shape and diversity of the antibody sequence landscape. To date, even the largest immunome repertoires of adaptive immune receptors acquired by next-generation sequencing cannot fully capture the vast antibody sequence space of a single individual, which is estimated to be at least 1012 potential sequences. Degeneracy of the genetic code means that the number of possible nucleotide triplets (64) is greater than the number of canonical amino acids (20), resulting in some amino acids being encoded by multiple triplets and different amino acids sharing the same nucleotide in 1 or 2 positions in the triplet. We hypothesize that the degeneracy of the genetic code can be used to statistically model an enlarged space of human antibody amino acid sequences, accommodating for the discrepancy between the observed and the hypothesized antibody sequence space. Facilitated by Bayesian statistics and immunome repertoire clustering, we calculated amino acid probabilities from single nucleotide frequencies to infer a human amino acid sequence space that is used to design human-like antibodies with Rosetta. We show that antibodies designed with our restraints are on average up to 16.6% more human-like in the V and J regions compared to the Rosetta designs produced without constraints. The human-likeness of the heavy-chain CDR3 region (CDRH3) could be increased for 8 of 27 antibodies compared to Rosetta designs with a similar number of mutations and could be successfully applied on Mus musculus antibodies to demonstrate humanization.

Structural basis for activation and gating of IP3 receptors.

A pivotal component of the calcium (Ca2+) signaling toolbox in cells is the inositol 1,4,5-triphosphate (IP3) receptor (IP3R), which mediates Ca2+ release from the endoplasmic reticulum (ER), controlling cytoplasmic and organellar Ca2+ concentrations. IP3Rs are co-activated by IP3 and Ca2+, inhibited by Ca2+ at high concentrations, and potentiated by ATP. However, the underlying molecular mechanisms are unclear. Here we report cryo-electron microscopy (cryo-EM) structures of human type-3 IP3R obtained from a single dataset in multiple gating conformations: IP3-ATP bound pre-active states with closed channels, IP3-ATP-Ca2+ bound active state with an open channel, and IP3-ATP-Ca2+ bound inactive state with a closed channel. The structures demonstrate how IP3-induced conformational changes prime the receptor for activation by Ca2+, how Ca2+ binding leads to channel opening, and how ATP modulates the activity, providing insights into the long-sought questions regarding the molecular mechanism underpinning receptor activation and gating.