Congratulations to Tanmoy Paul, Chunli Yan and Grant Derdeyn-Blackwell who are co-authors on a just published paper in the journal Nature Communications entitled “Translocation mechanism of xeroderma pigmentosum group D protein on single-stranded DNA and genetic disease etiology”. We investigated the molecular basis of translocation by the xeroderma pigmentosum group D (XPD) helicase on single-stranded […]
Oak Ridge National Lab highlights our work on the mechanisms of global genome nucleotide excision repair: “Summit Supercomputer Draws Molecular Blueprint for Repairing Damaged DNA”. Related articles: Yu, J., Yan, C., Paul, T. et al. Molecular architecture and functional dynamics of the pre-incision complex in nucleotide excision repair. Nat Commun 15, 8511 (2024). Yu, J., Yan, C., Dodd, T. et […]
Congratulations to Tanmoy Paul, Chunli Yan and Jina Yu who are co-authors on a just published paper in the journal Nature Communications. The paper is entitled “Molecular model of TFIIH recruitment to the transcription-coupled repair machinery“. Transcription-coupled repair is a vital nucleotide excision repair sub-pathway that removes DNA lesions from actively transcribed DNA strands. Binding of the […]
Congratulations to Jina Yu, Chunli Yan, Tanmoy Paul and Lucas Brewer who are co-authors on a just published paper in the journal Nature Communications. The paper is entitled “Molecular architecture and functional dynamics of the pre-incision complex in nucleotide excision repair.” The nucleotide excision repair (NER) pathway is vital for genome integrity. By synthesizing cryo-EM and XL-MS […]
Ivaylo Ivanov receives a new R01 grant from the National Institute of Environmental Health Sciences.
Oak Ridge National Lab highlights our recent work on the mechanisms of transcription-coupled nucleotide excision repair: “Decoding the Role of CSB Protein in DNA Repair“. Below is a recent video recording on the same topic:
Congratulations to Chunli Yan, Tom Dodd and Jina Yu who are co-authors on a just accepted paper in the journal Nature Communications. The paper is entitled “Mechanism of Rad26-assisted rescue of stalled RNA polymerase II in transcription-coupled repair.” Our integrative modeling study elucidates the mechanism by which Cockayne Syndrome B protein (CSB) binds to lesion-arrested RNA Polymerase […]
Oak Ridge National Lab highlights our recent work on pathways for conformational switching in high fidelity DNA polymerases: “Simulations reveal Nature’s design for error correction during DNA replication“.
Congratulation to Chunli Yan and Tom Dodd who published a new paper in the journal Nature Structural & Molecular Biology on the molecular architecture and functional dynamics of the transcription preinitiation complex (PIC). Yan, C.; Dodd, T.; Tainer, J.A.; He, Y.; Tsutakawa, S.E.; & Ivanov, I.* Transcription preinitiation complex structure and dynamics provide insight into genetic diseases Nature Structural […]
Our project on the base extrusion mechanism of thymine DNA glycosylase (TDG) was highlighted by the San Diego Supercomputer Center. How an Enzyme Repairs DNA via a “Pinch-Push-Pull” Mechanism
Congratulation to Tom Dodd, Chunli Yan, Kurt Martin and Brad Kossmann who published a new paper in the journal Proceedings of the National Academy of Sciences USA. Dodd, T.; Yan, C.; Kossmann, B.R.; Martin, K.; & Ivanov I. Uncovering universal rules governing the selectivity of the archetypal DNA glycosylase TDG Proceedings of the National Academy of Sciences USA (2018) doi:10.1073/pnas.1803323115 […]
Ivaylo visited Lawrence Berkeley National Lab in Feb. 2018 and gave a talk “DNA sculpting as a strategy for base extrusion and damage selection by the repair glycosylase TDG” at the Advanced Light Source synchrotron facility.
Ivaylo gave a talk “DNA sculpting as a strategy for base extrusion and damage selection by the repair glycosylase TDG” at the 3rd DNA Replication/Repair Structures and Cancer Conference in Cancun Mexico.
Our paper ‘Alkylpurine Glycosylase D Employs DNA Sculpting as a Strategy to Extrude and Excise Damaged Bases’ was published in PLOS Computational Biology. We employed chain-of-replicas path optimization strategy to determine a minimum energy path (MEP) for flipping out a 3-methyl adenine lesion by the DNA glycosylase AlkD. The path showed that AlkD acts by […]
Integrative Biomolecular Modeling 