Many protein functions are coupled to proton transfer, yet the underlying mechanisms remain extremely difficult to resolve by experiment or conventional molecular dynamics (MD) simulations. The human voltage-gated proton channel HV1 (hHV1) plays key roles in human physiology, but how voltage and pH together drive its a...
Ming-Zhe Shen, Daniel Kortzak, Christophe Jardin et al.· bioRxiv· 0 citations
These studies show that a well-characterized sE1E2 platform compatible with multiple genotypes can be coupled to nanoparticles for use as a vaccine candidate and sets the stage for further exploration of nanoparticles and other multivalent platforms for the development of E1E2-based vaccines.
Liudmila Kulakova, Sarah Jeong, Dong-Xiu Zhang et al.· bioRxiv· 0 citations
The structures explain how the NRASQ61K mutation rendered a self-antigen visible to T cells and provide stringent tests for computational modeling of TCR-peptide-MHC interactions relevant to cancer immunotherapy.
V. Sharma, D. T. Gallagher, S. Saravanakumar et al.· Structure· 0 citations
It is shown that increased sampling and AlphaFold3 generally improve performance relative to default sampling and AlphaFold2, however predictive accuracy and improvement levels varied considerably among interface classes, with antibody-peptide complexes representing a challenge despite their small antigen size.
Rui Yin, S. Saravanakumar, S. Shi et al.· bioRxiv· 1 citation
A systematic NMR-characterized dataset of mutants of the GA/GB model fold-switching system is presented and it is found that this benchmark revealed variable and position-dependent performance across methods, with certain AlphaFold2-based algorithms able to predict mutant effects at individual sites, indicating some un...
Nathaniel R. Felbinger, K. Carillo, Yihong Chen et al.· bioRxiv· 0 citations
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