Arjun Aditham
@arjunine.bsky.social
new here. my handle is pronounced like arginine.
Thank you! I hope it will be a helpful platform for the research community.
December 20, 2024 at 2:59 PM
Thank you! I hope it will be a helpful platform for the research community.
As noted, please navigate to dms-vep.org/RABV_Pasteur... to view all of the data in an interactive format.
Deep mutational scanning of rabies G (Pasteur strain)
Pseudovirus deep mutational scanning to measure how rabies G mutations affect cell entry and escape from a panel of monoclonal antibodies
dms-vep.org
December 19, 2024 at 8:08 PM
As noted, please navigate to dms-vep.org/RABV_Pasteur... to view all of the data in an interactive format.
A huge thank you to Jesse, Caelan, Caleb, Naveen Jasti and @neilpking.bsky.social (especially bringing me up to speed on this protein!). Also thank you to the Bloom Lab for the valuable feedback and steadfast support to bring this project up off the ground.
December 19, 2024 at 8:08 PM
A huge thank you to Jesse, Caelan, Caleb, Naveen Jasti and @neilpking.bsky.social (especially bringing me up to speed on this protein!). Also thank you to the Bloom Lab for the valuable feedback and steadfast support to bring this project up off the ground.
Overall, I really enjoyed using DMS to study antibodies for prospective breadth as @jbloomlab.bsky.social describes extensively. I’m also excited by the mechanistic hypotheses this study generates, a cause near and dear to my heart.
December 19, 2024 at 8:08 PM
Overall, I really enjoyed using DMS to study antibodies for prospective breadth as @jbloomlab.bsky.social describes extensively. I’m also excited by the mechanistic hypotheses this study generates, a cause near and dear to my heart.
Note that Figure 5 goes into more details about comparing escape sites versus antibody-G contact sites for structures that have been solved by others.
December 19, 2024 at 8:08 PM
Note that Figure 5 goes into more details about comparing escape sites versus antibody-G contact sites for structures that have been solved by others.
CTB012 (Chao et al. doi.org/10.1371/jour...) escape sites are only contiguous in pre-fusion rabies G. Also, escape mutations are at H270, which is mutated in a vaccine candidate (doi.org/10.1016/j.ch... and doi.org/10.1016/j.va...)
December 19, 2024 at 8:08 PM
CTB012 (Chao et al. doi.org/10.1371/jour...) escape sites are only contiguous in pre-fusion rabies G. Also, escape mutations are at H270, which is mutated in a vaccine candidate (doi.org/10.1016/j.ch... and doi.org/10.1016/j.va...)
Can DMS insights antibodies lacking structures in complex? RVC68 was discovered (Debenedicitis, et al doi.org/10.15252/emm...) to bind a novel site and is very broad-spectrum against lyssaviruses, and here we’ve mapped it to the base of the fusion domain.
December 19, 2024 at 8:08 PM
Can DMS insights antibodies lacking structures in complex? RVC68 was discovered (Debenedicitis, et al doi.org/10.15252/emm...) to bind a novel site and is very broad-spectrum against lyssaviruses, and here we’ve mapped it to the base of the fusion domain.
We also looked at several antibodies that don’t have structures in complex with G. Getting structures of these complexes is a major challenge. Even fewer have full rabies G, many others use fragments of rabies G for structures. (Too many to cite here—sorry!).
December 19, 2024 at 8:08 PM
We also looked at several antibodies that don’t have structures in complex with G. Getting structures of these complexes is a major challenge. Even fewer have full rabies G, many others use fragments of rabies G for structures. (Too many to cite here—sorry!).
Of course, with cell entry measurements, these are hypotheses, but I hope will provide additional useful avenues for biochemically characterizing rabies G and engineering rabies vaccines, for example by trying to destabilize the extended intermediate.
December 19, 2024 at 8:08 PM
Of course, with cell entry measurements, these are hypotheses, but I hope will provide additional useful avenues for biochemically characterizing rabies G and engineering rabies vaccines, for example by trying to destabilize the extended intermediate.
We saw other hydrophobic residues cluster in the extended intermediate, and most only tolerate hydrophobic substitutions. A couple of these are solvent-facing in the pre-fusion conformation, suggesting hydrophobicity requirements originate from the extended intermediate.
December 19, 2024 at 8:08 PM
We saw other hydrophobic residues cluster in the extended intermediate, and most only tolerate hydrophobic substitutions. A couple of these are solvent-facing in the pre-fusion conformation, suggesting hydrophobicity requirements originate from the extended intermediate.
When looking at the extended intermediate, we recapitulate prior information of some known contacts. But we also observe other residues that are also highly mutationally constrained. They may play a role in scaffolding known important residues in this conformation.
December 19, 2024 at 8:08 PM
When looking at the extended intermediate, we recapitulate prior information of some known contacts. But we also observe other residues that are also highly mutationally constrained. They may play a role in scaffolding known important residues in this conformation.
We wondered if our DMS could help here and are grateful to have access to both pre-fusion and extended intermediate structures. Both conformations require substantial rearrangements, and some residues form contacts in the extended intermediate. (Prefusion PDB: 7U9G, Extended PDB: 6LGW)
December 19, 2024 at 8:08 PM
We wondered if our DMS could help here and are grateful to have access to both pre-fusion and extended intermediate structures. Both conformations require substantial rearrangements, and some residues form contacts in the extended intermediate. (Prefusion PDB: 7U9G, Extended PDB: 6LGW)
As noted, rabies G exchanges between pre-fusion and extended conformation states, making vaccine development difficult. Stabilizing pre-fusion rabies G is actively studied (eg doi.org/10.1016/j.ch... and doi.org/10.1126/scia...).
Redirecting
doi.org
December 19, 2024 at 8:08 PM
As noted, rabies G exchanges between pre-fusion and extended conformation states, making vaccine development difficult. Stabilizing pre-fusion rabies G is actively studied (eg doi.org/10.1016/j.ch... and doi.org/10.1126/scia...).
As noted, please navigate to dms-vep.org/RABV_Pasteur... to view all of the data in an interactive format.
December 19, 2024 at 8:00 PM
As noted, please navigate to dms-vep.org/RABV_Pasteur... to view all of the data in an interactive format.
A huge thank you to Jesse, Caelan, Caleb, Naveen Jasti and @neilpking.bsky.social (especially bringing me up to speed on this protein!). Also thank you to the Bloom Lab for the valuable feedback and steadfast support to bring this project up off the ground.
December 19, 2024 at 8:00 PM
A huge thank you to Jesse, Caelan, Caleb, Naveen Jasti and @neilpking.bsky.social (especially bringing me up to speed on this protein!). Also thank you to the Bloom Lab for the valuable feedback and steadfast support to bring this project up off the ground.
I really enjoyed using DMS to study antibodies for prospective breadth as @jbloomlab.bsky.social describes extensively. I’m also excited by the mechanistic hypotheses this study can generate, a cause near and dear to my heart.
December 19, 2024 at 8:00 PM
I really enjoyed using DMS to study antibodies for prospective breadth as @jbloomlab.bsky.social describes extensively. I’m also excited by the mechanistic hypotheses this study can generate, a cause near and dear to my heart.
(Figure 5 goes into more details about comparing escape sites versus antibody-G contact sites for structures that have been solved by others.)
December 19, 2024 at 8:00 PM
(Figure 5 goes into more details about comparing escape sites versus antibody-G contact sites for structures that have been solved by others.)
CTB012 (Chao et al. doi.org/10.1371/jour...) escape sites are only contiguous in pre-fusion rabies G. Also, escape mutations are at H270, which is mutated in a vaccine candidate (doi.org/10.1016/j.ch... and doi.org/10.1016/j.va...)
December 19, 2024 at 8:00 PM
CTB012 (Chao et al. doi.org/10.1371/jour...) escape sites are only contiguous in pre-fusion rabies G. Also, escape mutations are at H270, which is mutated in a vaccine candidate (doi.org/10.1016/j.ch... and doi.org/10.1016/j.va...)
Can DMS insights antibodies lacking structures in complex? RVC68 was discovered (Debenedicitis, et al doi.org/10.15252/emm...) to bind a novel site and is very broad-spectrum against lyssaviruses, and here we’ve mapped it to near the base of the fusion domain.
December 19, 2024 at 8:00 PM
Can DMS insights antibodies lacking structures in complex? RVC68 was discovered (Debenedicitis, et al doi.org/10.15252/emm...) to bind a novel site and is very broad-spectrum against lyssaviruses, and here we’ve mapped it to near the base of the fusion domain.
We also looked at several antibodies that don’t have structures in complex with G. Getting structures of these complexes is a major challenge. Even fewer have full rabies G, many others use fragments of rabies G for structures. (Too many to cite here—sorry!).
December 19, 2024 at 8:00 PM
We also looked at several antibodies that don’t have structures in complex with G. Getting structures of these complexes is a major challenge. Even fewer have full rabies G, many others use fragments of rabies G for structures. (Too many to cite here—sorry!).
Of course, with cell entry measurements, these are hypotheses, but I hope will provide additional useful avenues for mechanistically characterizing rabies G and engineering rabies vaccines, for example by trying to destabilize the extended intermediate and bias the pre-fusion state.
December 19, 2024 at 8:00 PM
Of course, with cell entry measurements, these are hypotheses, but I hope will provide additional useful avenues for mechanistically characterizing rabies G and engineering rabies vaccines, for example by trying to destabilize the extended intermediate and bias the pre-fusion state.