{
  "abstract": "The navigational prowess of migratory birds is thought to arise from light-dependent radical-pair chemistry in cryptochrome 4 (CRY4), yet the slow structural transitions that couple photochemistry to signaling remain elusive. Here, we combine temperature-controlled steady-state UV-visible spectroscopy and hydrogen-deuterium exchange mass spectrometry (HDX-MS) to elucidate the photochemical and conformational dynamics of pigeon CRY4 (ClCRY4). Steady-state measurements at 5-25 {degrees}C reveal that lower temperatures slow FAD photoreduction and prolong the FAD neutral semiquinone signaling state. This occurs without a solvent kinetic isotope effect, implicating a conformational change rather than proton transfer as the rate determining step in FAD neutral semiquinone formation. Simultaneous HDX-MS under blue-light exposure identifies protection near the FAD-binding site and C-terminal region. To enhance sensitivity, we developed a pump-probe HDX-MS approach at 10 {degrees}C. This reveals eight peptides (within the phosphate-binding loop, protrusion motif, electron-transfer-chain loops and C-terminal tail) that exhibit rapid ([≤]10 s) and sustained light-induced protection, delineating early conformational rearrangements as a prerequisite for FAD neutral semiquinone accumulation. The findings of slower onset HDX protection as well as a bimodal pattern of deuterium uptake in the phosphate-binding loop further identify a local redistribution of conformational substates on the time scale of the accumulation of the signaling species. Site specific mutagenesis within the CTT supports the findings, which lead to a model in which blue light triggers rapid clamping down of protein near the two regions of spin pair separation, followed by a rate limiting closure of a surface loop. The resolution of time-dependent structural transitions that follow photoactivation of CRY4 resolves the interface between quantum radical-pair formation and classical conformational changes, while providing an enhanced structural framework for the molecular events that underlie avian magnetoreception.",
  "abstract_shown": true,
  "affiliations": [
    "University of California, Berkeley"
  ],
  "article_type": "New results",
  "arxiv": null,
  "author_total": 7,
  "authors": [
    {
      "name": "G. S. Jagdale"
    },
    {
      "name": "V. Fan"
    },
    {
      "name": "P. Dubey"
    },
    {
      "name": "A. Pham"
    },
    {
      "name": "E. Jiang"
    },
    {
      "name": "A. T. Iavarone"
    },
    {
      "affs": [
        0
      ],
      "name": "J. P. Klinman"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/b4n2zk7gnbknc.bib",
  "cited_by": 0,
  "doi": "10.64898/2026.08.27.747556",
  "fulltext_url": "https://www.biorxiv.org/content/10.64898/2026.08.27.747556v1.full",
  "id": "b4n2zk7gnbknc",
  "issns": [],
  "landing_url": "https://www.biorxiv.org/content/10.64898/2026.08.27.747556v1",
  "language": null,
  "licence": "CC-BY-NC-ND",
  "licence_label": "CC BY-NC-ND",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by-nc-nd/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "biorxiv",
      "biophysics"
    ],
    [
      "openalex",
      "2807|Circadian rhythm and melatonin"
    ]
  ],
  "openalex": "W7204971142",
  "pdf_url": "https://www.biorxiv.org/content/10.64898/2026.08.27.747556v1.full.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-08-27",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/b4n2zk7gnbknc.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:17:57Z",
      "native_id": "10.64898/2026.08.27.747556",
      "source": "biorxiv",
      "url": "https://www.biorxiv.org/content/10.64898/2026.08.27.747556v1"
    }
  ],
  "subjects": [
    {
      "field": "biochemistry",
      "origin": "biorxiv:biophysics",
      "subfield": "biophysics"
    }
  ],
  "title": "Mapping Light-Induced Conformational Dynamics of Pigeon Cryptochrome 4 by HDX-MS: Structural Transitions from Spin Pair Formation to Activated Conformational States",
  "title_text": "Mapping Light-Induced Conformational Dynamics of Pigeon Cryptochrome 4 by HDX-MS: Structural Transitions from Spin Pair Formation to Activated Conformational States",
  "type": "preprint",
  "updated_at": "2026-10-30T12:17:57Z",
  "url": "https://research.draconitic.com/paper/b4n2zk7gnbknc",
  "venue": "bioRxiv",
  "versions": []
}