Biophysical Society Thematic Meeting | Trieste 2024

Emerging Theoretical Approaches to Complement Single-Particle Cryo-EM

Tuesday Speaker Abstracts

MOLECULAR ARCHITECTURE AND FUNCTIONAL DYNAMICS OF THE PRE INCISION COMPLEX IN THE NUCLEOTIDE EXCISION DNA REPAIR PATHWAY Ivaylo Ivanov 1 ; Jina Yu 1 ; Chunli Yan 1 ; Tanmoy Paul 1 ; Susan E Tsutakawa 2 ; Chi-Lin Tsai 3 ; Samir Hamdan 4 ; John A Tainer 3 ; 1 Georgia State University, Atlanta, GA, USA 2 Lawrence Berkeley National Laboratory, Berkeley , CA, USA 3 University of Texas MD Anderson Cancer Center, Houston, TX, USA 4 King Abdullah University of Science and Technology, Thuwal, Saudi Arabia Nucleotide excision repair (NER) is a genome maintenance pathway critical for human health. NER repairs a vast array of structurally unrelated DNA lesions caused by ultraviolet radiation, reactive oxygen species, environmental carcinogens, and chemotherapeutic agents such as cis platinum. Despite numerous biochemical and genetic studies, knowledge of the inner workings of the complex NER protein machinery remains fragmentary. By synthesizing cryo-EM and cross-linking mass spectrometry (XL-MS) data with computational modeling, MD simulations and AlphaFold2 predictions, we elucidate the structure and dynamics of a critically important state of the NER machinery – the pre-incision complex (PInC). Our analyses yield key mechanistic insights into PInC’s assembly and regulation, the structural basis of XPF and XPG nuclease coordination, and the licensing of the NER dual incision. Using graph-theoretical algorithms we also build dynamic network models of the PInC, which powerfully elucidate the etiology of devastating human genetic syndromes. Notably, we find that xeroderma pigmentosum (XP) and Cockayne syndrome (CS) disease mutations cluster at key interfaces of PInC’s dynamic communities, impacting NER protein stability, functional dynamics, DNA binding, nuclease licensing, and community integrity.

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