Molecular evolution is an important step in the development of therapeutic antibodies. However, the current method of affinity maturation is overly costly and labor-intensive because of the repetitive mutation experiments needed to adequately explore sequence space. Here, we employed a long short term memory network (LSTM)—a widely used deep generative model—based sequence generation and prioritization procedure to efficiently discover antibody sequences with higher affinity. We applied our method to the affinity maturation of antibodies against kynurenine, which is a metabolite related to the niacin synthesis pathway. Kynurenine binding sequences were enriched through phage display panning using a kynurenine-binding oriented human synthetic Fab library. We defined binding antibodies using a sequence repertoire from the NGS data to train the LSTM model. We confirmed that likelihood of generated sequences from a trained LSTM correlated well with binding affinity. The affinity of generated sequences are over 1800-fold higher than that of the parental clone. Moreover, compared to frequency based screening using the same dataset, our machine learning approach generated sequences with greater affinity.

Here, we report molecular chaperone GroELs that carry, at their apical domains, multiple DNA strands (ideally 28 DNA strands in total) with defined oligonucleotide (nt) sequences. This design strategy allows for the preparation of GroEL and GroEL carrying 10-nt DNA strands of 10a and 10b with complementary sequences, respectively, at their apical domains. One-dimensional coassembly of these GroELs is possible to form protein nanotube NT with an anomalous thermodynamic stability due to the exceptionally large multivalency for the coassembly. Likewise, comparably stable nanotube NT was obtained even when the apical-domain DNA strands (15c and 10d) were partially complementary to one another. Nevertheless, in sharp contrast with NT, NT, when incubated with DNA 15d, dissociates rapidly and completely because 15d preferentially hybridizes with the DNA strands of 15c in NT by displacing those of 10d, to afford a mixture of GroEL and GroEL. Even in the presence of NT, 15d cleaved off NT selectively, indicating the potential utility of NTs for targeted delivery.

Herein, we report the synthesis and isolation of a shape-persistent Janus protein nanoparticle derived from biomolecular machine chaperonin GroEL (A GroEL B) and its application to DNA-mediated ternary supramolecular copolymerization. For synthesizing A GroEL B with two different DNA strands A and B at its opposite apical domains, we utilized the unique biological property of GroEL, i.e., "Mg 2+ /ATPmediated ring exchange" between A GroEL A and B GroEL B with their hollow cylindrical doubledecker architectures. This exchange event was reported more than 24 years ago but has never been utilized for molecular engineering of GroEL. We leveraged DNA nanotechnology to purely isolate Janus A GroEL B and succeeded in its precision ternary supramolecular copolymerization with two DNA comonomers A** and B* that are partially complementary to A and B in A GroEL B , respectively, and programmed to self-dimerize on the other side. Transmission electron microscopy allowed us to confirm the formation of an expected dual-periodic copolymer sequence-(B*/B GroEL A/A**/A**/A GroEL B/B*)-in the form of a laterally connected lamellar assembly, rather than a single-chain copolymer.

Herein, we report an ATP‐responsive nanoparticle (GroELNP) whose surface is fully covered with the biomolecular machine “chaperonin protein GroEL”. GroELNP was synthesized by DNA hybridization between a gold NP with DNA strands on its surface and GroEL carrying complementary DNA strands at its apical domains. The unique structure of GroELNP was visualized by transmission electron microscopy including under cryogenic conditions. The immobilized GroEL units retain their machine‐like function and enable GroELNP to capture denatured green fluorescent protein and release it in response to ATP. Interestingly, the ATPase activity of GroELNP per GroEL was 4.8 and 4.0 times greater than those of precursor cysGroEL and its DNA‐functionalized analogue, respectively. Finally, we confirmed that GroELNP could be iteratively extended to double‐layered (GroEL)2 ${{^{({\rm GroEL}){_{2}}}}}$ NP.

Herein, we report an ATP-responsive nanoparticle ( GroEL NP) whose surface is fully covered with the biomolecular machine "chaperonin protein GroEL". GroEL NP was synthesized by DNA hybridization between a gold NP with DNA strands on its surface and GroEL carrying complementary DNA strands at its apical domains. The unique structure of GroEL NP was visualized Angewandte Chemie