GGAssembler: Precise and economical design and synthesis of combinatorial mutation libraries DOI Creative Commons
Shlomo Yakir Hoch, Ravit Netzer, Jonathan J. Weinstein

et al.

Protein Science, Journal Year: 2024, Volume and Issue: 33(10)

Published: Sept. 16, 2024

Abstract Golden Gate assembly (GGA) can seamlessly generate full‐length genes from DNA fragments. In principle, GGA could be used to design combinatorial mutation libraries for protein engineering, but creating accurate, complex, and cost‐effective has been challenging. We present GGAssembler, a graph‐theoretical method economical of fragments that assemble library encodes any desired diversity. GGAssembler one‐pot in vitro camelid antibody comprising >10 5 variants with costs <0.007$ per variant dropping significantly increased complexity. >93% the were product >99% represented within expected order magnitude as verified by deep sequencing. The workflow is, therefore, an accurate approach generating complex may drastically reduce accelerate discovery optimization antibodies, enzymes other proteins. is accessible through Google Colab notebook at https://github.com/Fleishman-Lab/GGAssembler .

Language: Английский

htFuncLib: Designing libraries of active-site multipoint mutants for protein optimization DOI Creative Commons
Rosalie Lipsh‐Sokolik, Sarel J. Fleishman

Journal of Molecular Biology, Journal Year: 2025, Volume and Issue: unknown, P. 169011 - 169011

Published: Feb. 1, 2025

Language: Английский

Citations

1
A novel directed evolution approach for co-evolution of β-glucosidase activity and organic acid tolerance DOI
Bei Ouyang, Guoping Wang,

Ziyan Hu

et al.

Journal of Biotechnology, Journal Year: 2025, Volume and Issue: 401, P. 1 - 10

Published: Feb. 19, 2025

Language: Английский

Citations

0
Inference and visualization of complex genotype-phenotype with gpmap-tools DOI Creative Commons
Carlos Martí‐Gómez, Juannan Zhou, Wei-Chia Chen

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: March 13, 2025

Multiplex assays of variant effect (MAVEs) allow the functional characterization an unprecedented number sequence variants in both gene regulatory regions and protein coding sequences. This has enabled study nearly complete combinatorial libraries mutational revealed widespread influence higher-order genetic interactions that arise when multiple mutations are combined. However, lack appropriate tools for exploratory analysis this high-dimensional data limits our overall understanding main qualitative properties complex genotype-phenotype maps. To fill gap, we have developed gpmap-tools ( https://github.com/cmarti/gpmap-tools ), a python library integrates Gaussian process models inference, phenotypic imputation, error estimation from incomplete noisy MAVE collections natural sequences, together with methods summarizing patterns epistasis non-linear dimensionality reduction techniques visualization maps containing up to millions genotypes. Here, used map Shine-Dalgarno sequence, motif modulates binding 16S rRNA 5' untranslated region (UTR) mRNAs through base pair complementarity during translation initiation prokaryotes. We inferred full landscapes 262,144 different sequences 5,311 5'UTRs E. coli genome experimental data. Visualizations were largely consistent each other, unveiled simple molecular mechanism underlying highly epistatic sequence.

Language: Английский

Citations

0
Evolutionary paths that link orthogonal pairs of binding proteins DOI

Ziv Avizemer,

Carlos Martí‐Gómez, Shlomo Yakir Hoch

et al.

Cell Systems, Journal Year: 2025, Volume and Issue: unknown, P. 101262 - 101262

Published: April 1, 2025

Language: Английский

Citations

0
Encoding and decoding selectivity and promiscuity in the human chemokine-GPCR interaction network DOI Creative Commons
Andrew B. Kleist, Martyna Szpakowska, Lindsay J. Talbot

et al.

Cell, Journal Year: 2025, Volume and Issue: unknown

Published: April 1, 2025

Language: Английский

Citations

0
Protein folding: From physico-chemical rules and cellular machineries of protein quality control to AI solutions DOI Creative Commons
Ulyana Shimanovich, F. Ulrich Hartl

Proceedings of the National Academy of Sciences, Journal Year: 2024, Volume and Issue: 121(34)

Published: Aug. 12, 2024

Large volumes of liquid water transiently existed on the surface Mars more than 3 billion years ago. Much this is hypothesized to have been sequestered in subsurface or lost space. We use rock physics models and Bayesian inversion ...

Language: Английский

Citations

1
GGAssembler: Precise and economical design and synthesis of combinatorial mutation libraries DOI Creative Commons
Shlomo Yakir Hoch, Ravit Netzer, Jonathan J. Weinstein

et al.

Protein Science, Journal Year: 2024, Volume and Issue: 33(10)

Published: Sept. 16, 2024

Abstract Golden Gate assembly (GGA) can seamlessly generate full‐length genes from DNA fragments. In principle, GGA could be used to design combinatorial mutation libraries for protein engineering, but creating accurate, complex, and cost‐effective has been challenging. We present GGAssembler, a graph‐theoretical method economical of fragments that assemble library encodes any desired diversity. GGAssembler one‐pot in vitro camelid antibody comprising >10 5 variants with costs <0.007$ per variant dropping significantly increased complexity. >93% the were product >99% represented within expected order magnitude as verified by deep sequencing. The workflow is, therefore, an accurate approach generating complex may drastically reduce accelerate discovery optimization antibodies, enzymes other proteins. is accessible through Google Colab notebook at https://github.com/Fleishman-Lab/GGAssembler .

Language: Английский

Citations

1