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:
Congratulation to Dr. Chunli Yan who published a new paper combining computational modeling and cryo-electron microscopy to unveil structures of pre-initiation complexes of RNA Polymerase III. Han, Y.; Yan, C.; Fishbain, S.; Ivanov, I. & He, Y. Structural visualization of RNA polymerase III transcription machineries. Cell Discovery (2018) (in press)
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 attended the 2018 Annual Meeting of the Biophysical Society and presented our new findings on the transcription initiation by RNA polymerase I.
Our project on transcription pre-initiation complexes was highlighted by the Texas Advanced Computing Center. https://www.tacc.utexas.edu/-/how-to-see-living-machines
Congratulations to Chunli Yan who published as a co-author on a new paper in the journal Nature Communications entitled “Rational design of a protein that binds integrin αvβ3 outside the ligand binding site”. The paper reports a new desinged protein which targets integrn at a novel site outside the canonocal Arg-Gly-Asp (RGD) binding site.
Congratulations to Brad Kossmann who published a new paper in the journal Bioorganic & Medicinal Chemistry Letters entitled “Discovery of selective inhibitors of tyrosyl-DNA phosphodiesterase 2 by targeting the enzyme DNA-binding cleft”. The paper details the characterization of three new selective inhibitors of the enzyme tyrosyl-DNA phosphodiesterase 2 (TDP2). TDP2processes protein/DNA adducts resulting from abortive DNA topoisomerase II […]
Our project on transcription pre-initiation complexes was picked up by the Science360 site of the National Science Foundation. https://news.science360.gov/archives/20160513/
An unprecedented molecular view of the critical early events in gene expression, a process essential for all life, has been provided by researchers at Georgia State University, the University of California at Berkeley and Northwestern University. Source: Researchers unveil new, detailed images of DNA transcription
Scientists reveal how evolutionary fine-tuning has obscured the origin of the glucocorticoid receptor’s ability to adopt different shapes. It highlights how proteins that evolve ‘new’ functions may have had those capacities — in some cases, for millions of years — because of their flexibility. Source: Ancient protein flexibility can drive ‘new’ functions
An unprecedented molecular view of the critical early events in gene expression, a process essential for all life, has been provided by researchers in a new study. Cryo-electron microscopy (cryo-EM), a technique that studies samples at cryogenic temperatures, combined with state-of-the-art computational modeling, allowed researchers to visualize large transcription pre-initiation complexes (PIC) at near-atomic resolution. […]
Computation and experiment reveal how protein switching provides right tool for the job Source: Researchers Show How Proteins Help DNA Replicate Past a Damaged Site
The Journal of Computational and Structural Biotechnology has just published our invited review paper ‘Integrative Modeling of Macromolecular Assemblies from Low to Near-Atomic Resolution’.
Another paper, ‘Functional Dynamics in Replication Protein A DNA Binding and Protein Recruitment Domains’ has also appeared in Structure.
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 […]
Our paper ‘Opening Pathways of the DNA Clamps Proliferating Cell Nuclear Antigen and Rad9-Rad1-Hus1’ has just been accepted by the journal Nucleic Acids Research. The recently solved structures of the DNA clamp protein 9-1-1 led to competing proposals regarding how 9-1-1 is loaded onto DNA. Through detailed subunit interface analysis, we identified the subunit interface […]
Our paper ‘Probing DNA clamps with single-molecule force spectroscopy’ has just been published in Nucleic Acids Research and sheds light on the mechanisms of DNA clamp opening under external forces by combining molecular simulation with single-molecule micromanipulation experiments.
Oak Ridge National Lab highlights our recent work on Replication Protein A:‘Neutrons help shed light on critical protein activity that protects our DNA’.
Our paper ‘A new structural framework for integrating replication protein A into DNA processing machinery’, which is currently in press in Nucleic Acids Research, has been selected as a ‘featured paper’ in the top 5% of NAR submissions.
Our collaborative efforts with Berkeley/LBNL have led to a combined experimental/computational publication ‘Repair complexes of FEN1, DNA and Rad9-Hus1-Rad1 are distinguished from their PCNA counterparts by functionally important stability’ currently in press in Proceedings of the National Academy of Science U.S.A.
Our PNAS paper on PCNA ubiquitylation has been selected and evaluated by the post-publication peer review service Faculty of 1000 (F1000). According to the F1000 service this places our work in “.. the top 2% of published articles in biology and medicine”. The Oak Ridge Leadership Computing Facility at Oak Ridge National Laboratory highlights our […]
Our proposal for computational time on the special purpose Anton machine at the National Resource for Biomedical Supercomputing (NRBSC) in Pittsburgh is approved.
Our collaborative efforts on PCNA ubiquitination with Berkeley Lab, Univ. of Iowa and Univ. of Delaware led to a combined experimental/computational publication currently in press in Proceedings of the National Academy of Science U.S.A.
Our collaboration with the group of Prof. Zheng on histone acetylation has led to a combined experimental/computational paper available from the Journal of Biological Chemistry.
Two recent papers on ligand-gated ion channels (LGICs) have been published and available from the Biophysical Journal and Proteins: Structure, Function and Bioinformatics.
Our work on PCNA highlighted by the NCCS at Supercomputing 2010 Conference in New Orleans.
Scientists use Jaguar to model replisome components to understand their role in health and disease. Source: Supercomputers Simulate the Molecular Machines that Replicate and Repair DNA
Our first paper from GSU is published and available from the web site of the Journal of the American Chemical Society.
Our renewal proposal through the DOE INCITE initiative was awarded 4,000,000 CPU hours at the leadership computing facility at ORNL. We are gratified that the award exceeded our original request by 400,000 units For more details about the award refer to the new DOE Office of Science.
A renewal proposal for computational resources through the DOE INCITE initiative has been submitted (07/01/2009). In 2009 our research project entitled “Interplay of AAA+ molecular machines, DNA repair enzymes and sliding clamps at the replication fork: A multiscale approach to modeling replisome assembly and function” was competitively chosen to receive 2,600,000 CPU hours of supercomputing […]
Integrative Biomolecular Modeling 