{
  "abstract": "Abactstr: Loop engineering of enzymes remains challenging due to high flexibility and conformational complexity, posing a bottleneck for deep-learning-based design. Here, we constructed mutant libraries for three loops of TEV protease to assess combining directed evolution with deep learning. Using an M13 phagemid-based selection system, the three libraries were screened, resulting in a Loop 1 variant (HyperTEV60/L1) that significantly enhanced the Michaelis constant ( K m ) of the HyperTEV60 scaffold, a highly active mutant identified by ProteinMPNN. Structural modeling suggested that a single-residue deletion and substitution in Loop 1 expands the substrate binding pocket, accounting for the improved K m . Although the catalytic efficiency k cat / K m of HyperTEV60/L1 was only marginally higher than HyperTEV60, due to a k cat decrease, our results reveal that the phagemid-based selection system tended to find variants optimizing K m . This study demonstrates that combining deep-learning-based global optimization with localized directed evolution maximizes the probability of discovering distinct, high-performance enzyme variants.",
  "abstract_shown": true,
  "affiliations": [],
  "article_type": null,
  "arxiv": null,
  "author_total": 2,
  "authors": [
    {
      "name": "Hiroki Yamaguchi",
      "orcid": "0000-0003-1274-1589"
    },
    {
      "name": "Mark Isalan",
      "orcid": "0000-0002-4652-0365"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/2a6xt4ryf5qct.bib",
  "cited_by": 0,
  "doi": "10.1038/s41598-026-74102-5",
  "fulltext_url": null,
  "id": "2a6xt4ryf5qct",
  "issns": [
    "2045-2322"
  ],
  "landing_url": "https://www.nature.com/articles/s41598-026-74102-5",
  "language": null,
  "licence": "CC-BY-4.0",
  "licence_label": "CC BY 4.0",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0",
  "metadata_licence": null,
  "native_subjects": [
    [
      "openalex",
      "1312|Enzyme Catalysis and Immobilization"
    ]
  ],
  "openalex": "W7219573256",
  "pdf_url": "https://www.nature.com/articles/s41598-026-74102-5_reference.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-10-04",
  "publisher": "Springer Science and Business Media LLC",
  "ris": "https://research.draconitic.com/paper/2a6xt4ryf5qct.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:17:22Z",
      "native_id": "10.1038/s41598-026-74102-5",
      "source": "crossref",
      "url": "https://www.nature.com/articles/s41598-026-74102-5"
    }
  ],
  "subjects": [
    {
      "field": "biochemistry",
      "origin": "openalex:1312|Enzyme Catalysis and Immobilization",
      "subfield": "molecular-biology"
    }
  ],
  "title": "Loop engineering and activity improvement of TEV protease by a phagemid-based selection system",
  "title_text": "Loop engineering and activity improvement of TEV protease by a phagemid-based selection system",
  "type": "peer-reviewed",
  "updated_at": "2026-10-30T12:17:22Z",
  "url": "https://research.draconitic.com/paper/2a6xt4ryf5qct",
  "venue": "Scientific Reports",
  "versions": []
}