{
  "abstract": "Introduction\n\nEngineered hemoglobin variants offer therapeutic promise for artificial blood substitutes and oxygen therapeutics, but rational design is constrained by protein stability and heme-binding. Protein language models (pLMs) predict mutation fitness, yet their integration with biophysical validation remains limited.Methods\n\nWe developed a hybrid pipeline combining pLM (ESM3) with molecular docking, Monte Carlo simulation, molecular dynamics, MM-GBSA/PBSA binding free energy calculations, and density functional theory (DFT) to engineer a stabilized hemoglobin variant (esmHb) with enhanced oxygen affinity, benchmarking against the clinically characterized Hb Fort de France mutation (α45 His→Arg).Results\n\nESM3 accurately assessed the fitness effect of the Hb Fort de France mutation and generated structurally stable esmHb models. Compared with the wild-type variant (wtHb), esmHb exhibited improved thermodynamic stability (ΔG: -18.48 vs. -12.22 kcal/mol), increased heme-binding affinity (ΔGbind: -11.79 vs. -8.42 kcal/mol), and greater thermodynamic favorability of oxidation according to DFT calculations (ΔE: -173.1 vs. -149.9 kcal/mol). MM-GBSA and MM-PBSA binding free energy calculations further supported improved protein-heme and protein-protein interactions, with esmHb showing more favorable values in both implicit solvation models. Statistical significance (p < 0.05) was reached for protein-protein interactions via both methods and for protein-heme interactions via MM-PBSA. We interpret the MM-GBSA results as a suggestive trend rather than definitive evidence.Discussion\n\nThis work establishes a generalizable framework for pLM-driven protein engineering applicable to therapeutic Hb variants and beyond.",
  "abstract_shown": true,
  "affiliations": [
    "Laboratory of Chemoinformatics, Infochemistry Scientific Center, ITMO University, Saint Petersburg, Russia.",
    "Department of Bioinformatics, Biocenter, Am Hubland, Julius-Maximilians University of Würzburg, Würzburg, Germany.",
    "Department of Biology and General Genetics, Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia."
  ],
  "article_type": "research article",
  "arxiv": null,
  "author_total": 4,
  "authors": [
    {
      "affs": [
        0,
        1,
        2
      ],
      "name": "Sergey Shityakov"
    },
    {
      "affs": [
        0
      ],
      "name": "Alexander S Novikov"
    },
    {
      "affs": [
        0
      ],
      "name": "Ekaterina V Skorb"
    },
    {
      "affs": [
        1
      ],
      "name": "Thomas Dandekar"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/fwvn5qkjfnva6.bib",
  "cited_by": 0,
  "doi": "10.3389/fchem.2026.1898272",
  "fulltext_url": "https://europepmc.org/articles/PMC13678298",
  "id": "fwvn5qkjfnva6",
  "issns": [
    "2296-2646"
  ],
  "landing_url": "https://europepmc.org/article/MED/42898797",
  "language": "eng",
  "licence": "CC-BY",
  "licence_label": "CC BY",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "openalex",
      "1307|Hemoglobin structure and function"
    ]
  ],
  "openalex": "W7220417726",
  "pdf_url": "https://europepmc.org/articles/PMC13678298?pdf=render",
  "pmcid": "PMC13678298",
  "pmid": "42898797",
  "published": "2026-10-05",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/fwvn5qkjfnva6.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:19:37Z",
      "native_id": "MED:42898797",
      "source": "europepmc",
      "url": "https://europepmc.org/article/MED/42898797"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "openalex:1307|Hemoglobin structure and function",
      "subfield": "cell-biology"
    }
  ],
  "title": "Engineering a hemoglobin variant with enhanced stability and oxygen affinity using a protein language model.",
  "title_text": "Engineering a hemoglobin variant with enhanced stability and oxygen affinity using a protein language model.",
  "type": "peer-reviewed",
  "updated_at": "2026-10-30T12:19:37Z",
  "url": "https://research.draconitic.com/paper/fwvn5qkjfnva6",
  "venue": "Frontiers in chemistry",
  "versions": []
}