2025-03-12 オークリッジ国立研究所 (ORNL)
The Summit supercomputer revealed how damaged strands of DNA are surgically repaired by a molecular pathway called nucleotide excision repair, or NER. NER’s protein components can change shape to perform different functions of repair on broken strands of DNA (blue and red helix). Credit: Tanmoy Paul, Georgia State University
<関連情報>
- https://www.ornl.gov/news/summit-supercomputer-draws-molecular-blueprint-repairing-damaged-dna
- https://www.nature.com/articles/s41467-024-52860-y
核酸切断修復におけるプレインシジョン複合体の分子構造と機能ダイナミクス Molecular architecture and functional dynamics of the pre-incision complex in nucleotide excision repair
Jina Yu,Chunli Yan,Tanmoy Paul,Lucas Brewer,Susan E. Tsutakawa,Chi-Lin Tsai,Samir M. Hamdan,John A. Tainer & Ivaylo Ivanov
Nature Communications Published:01 October 2024
DOI:https://doi.org/10.1038/s41467-024-52860-y
Abstract
Nucleotide excision repair (NER) is vital for genome integrity. Yet, our understanding of the complex NER protein machinery remains incomplete. Combining cryo-EM and XL-MS data with AlphaFold2 predictions, we build an integrative model of the NER pre-incision complex(PInC). Here TFIIH serves as a molecular ruler, defining the DNA bubble size and precisely positioning the XPG and XPF nucleases for incision. Using simulations and graph theoretical analyses, we unveil PInC’s assembly, global motions, and partitioning into dynamic communities. Remarkably, XPG caps XPD’s DNA-binding groove and bridges both junctions of the DNA bubble, suggesting a novel coordination mechanism of PInC’s dual incision. XPA rigging interlaces XPF/ERCC1 with RPA, XPD, XPB, and 5′ ssDNA, exposing XPA’s crucial role in licensing the XPF/ERCC1 incision. Mapping disease mutations onto our models reveals clustering into distinct mechanistic classes, elucidating xeroderma pigmentosum and Cockayne syndrome disease etiology.
