Base editing: advances and therapeutic opportunities

EM Porto, AC Komor, IM Slaymaker… - Nature Reviews Drug …, 2020 - nature.com
Base editing—the introduction of single-nucleotide variants (SNVs) into DNA or RNA in
living cells—is one of the most recent advances in the field of genome editing. As around …

[HTML][HTML] Recent advances in de novo protein design: Principles, methods, and applications

X Pan, T Kortemme - Journal of Biological Chemistry, 2021 - ASBMB
The computational de novo protein design is increasingly applied to address a number of
key challenges in biomedicine and biological engineering. Successes in expanding …

[HTML][HTML] Design of protein-binding proteins from the target structure alone

L Cao, B Coventry, I Goreshnik, B Huang, W Sheffler… - Nature, 2022 - nature.com
The design of proteins that bind to a specific site on the surface of a target protein using no
information other than the three-dimensional structure of the target remains a challenge …

Protein sequence design by conformational landscape optimization

C Norn, BIM Wicky, D Juergens, S Liu… - Proceedings of the …, 2021 - National Acad Sciences
The protein design problem is to identify an amino acid sequence that folds to a desired
structure. Given Anfinsen's thermodynamic hypothesis of folding, this can be recast as …

Top-down design of protein architectures with reinforcement learning

ID Lutz, S Wang, C Norn, A Courbet, AJ Borst, YT Zhao… - Science, 2023 - science.org
As a result of evolutionary selection, the subunits of naturally occurring protein assemblies
often fit together with substantial shape complementarity to generate architectures optimal …

Catalysis and Electron Transfer in De Novo Designed Metalloproteins

KJ Koebke, TBJ Pinter, WC Pitts, VL Pecoraro - Chemical reviews, 2022 - ACS Publications
One of the hallmark advances in our understanding of metalloprotein function is showcased
in our ability to design new, non-native, catalytically active protein scaffolds. This review …

Reconfigurable asymmetric protein assemblies through implicit negative design

DD Sahtoe, F Praetorius, A Courbet, Y Hsia, BIM Wicky… - Science, 2022 - science.org
Asymmetric multiprotein complexes that undergo subunit exchange play central roles in
biology but present a challenge for design because the components must not only contain …

[HTML][HTML] De novo design of obligate ABC-type heterotrimeric proteins

S Bermeo, A Favor, YT Chang, A Norris… - Nature Structural & …, 2022 - nature.com
The de novo design of three protein chains that associate to form a heterotrimer (but not any
of the possible two-chain heterodimers) and that can drive the assembly of higher-order …

[HTML][HTML] De novo design of modular peptide-binding proteins by superhelical matching

K Wu, H Bai, YT Chang, R Redler, KE McNally… - Nature, 2023 - nature.com
General approaches for designing sequence-specific peptide-binding proteins would have
wide utility in proteomics and synthetic biology. However, designing peptide-binding …

De novo design of small beta barrel proteins

DE Kim, DR Jensen, D Feldman… - Proceedings of the …, 2023 - National Acad Sciences
Small beta barrel proteins are attractive targets for computational design because of their
considerable functional diversity despite their very small size (< 70 amino acids). However …