New paper in Nature Communications

Congratulations to Tom Dodd who is the first author on a just accepted paper in the journal Nature Communications. The paper is entitled “Polymerization and editing modes of a high-fidelity DNA polymerase are linked by a well-defined path” and addresses a grand challenge for the DNA replication field by demonstrating through combined computational and biochemical analyses […]

DEPARTMENT OF ENERGY ISSUES A PRESS RELEASE ABOUT OUR 2020 INCITE AWARD

Our group was among the 47 recipients of INCITE Awards from the U.S. Department of Energy’s Office of Science. The projects originate in national laboratories, academia, and industry, and encompass a remarkable range of scientific inquiry. Ours was among the projects in the areas of Biological Sciences/Biophysics. Here are the 2020 INCITE Announcement and the list of 2020 […]

NEW INCITE POJECT AWARDED FOR 2020

Our INCITE Award was competitively renewed for 2020 by the DOE Office of Science. The Innovative and Novel Computational Impact on Theory and Experiment (INCITE) program accelerates scientific discoveries and technological innovations by awarding, on a competitive basis, time on the world’s fastest supercomputers to researchers with large-scale, computationally intensive projects that address “grand challenges” in science and engineering. Our […]

NEW PAPER IN NATURE STRUCTURAL & MOLECULAR BIOLOGY

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 […]

NEW PAPER IN THE JOURNAL OF MOLECULAR BIOLOGY

Congratulation to group alumnus Dr. Max Xu and Dr. Chunli Yan and who published a new paper in the Journal of Molecular Biology that unravels the common origins of DNA clamp proteins’ subunit interface stability with implications for the function of these proteins in DNA replication. Perumal, S.K.; Xu, X.; Yan, C.; Ivanov, I. & Benkovic, S.J. Recognition of a […]

NEW PAPER IN THE JOURNAL PCCP

Congratulation to Dr. Kathleen Carter who published a new paper in the jounal Physical Chemistry Chemical Physics detailing the mechanism of sequence-specific DNA binding of a designed small molecule binder DB2277. Carter, E.K.; Laughlin, S.; Dodd, T.; Wilson, W.D. & Ivanov, I* Small molecule binders recognize DNA microstructural variations via an induced fit mechanism Physical Chemistry […]

Department of Energy issues a press release about the 2019 INCITE Awards

Our group was among the 62 recipients of INCITE Awards from the U.S. Department of Energy’s Office of Science. The projects originate in national laboratories, academia, and industry, and encompass a remarkable range of scientific inquiry. Ours was among 8 projects in the areas of Biological Sciences/Biophysics awarded nationwide. Here are the 2019INCITEAnnouncement and the […]

New INCITE Award provides access to the Oak Ridge Leadership Computing Facility

Ivaylo received a new INCITE Award from the DOE Office of Science. The Innovative and Novel Computational Impact on Theory and Experiment (INCITE) program accelerates scientific discoveries and technological innovations by awarding, on a competitive basis, time on the world’s fastest supercomputers to researchers with large-scale, computationally intensive projects that address “grand challenges” in science […]

GROUP MEMBERS PRESENT AT THE 2018 SERMACS MEETING IN AUGUSTA

Group members recently traveled to Augusta, GA to present at the 2018 Southeastern Regional Meeting of the American Chemical Society. Many thanks to all who presented! (Chunli Yan, Ashutosh Shandilya, Tom Dodd, Kurt Martin and Zhenyu Wang) At the meeting Ivaylo gave two invited talks: Emerging unified description of transcription initiation from cryo-EM and integrative computational […]

GROUP MEMBERS PRESENT AT THE ACS NATIONAL MEETING IN BOSTON

Group members recently traveled to Boston, MA to present at the 2018 National Meeting of the American Chemical Society. Ivaylo gave a talk entitled “Emerging unified description of transcription initiation from cryo-EM and integrative computational modeling ” in the COMP division (New Frontiers in Flexible Fitting, Image Processing & Refinement of Cryo-EM Data session). Many […]

New Paper in the Journal Cell Discovery

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)

New Paper in Proceedings of the National Academy of Sciences USA

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 […]

Visit to Berkeley National Lab

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.

KEYSTONE SYMPOSIUM ON CRYO-EM

Ivaylo attended the 2018 Keystone Symposium “Cryo-EM from Cells to Molecules: Multi-Scale Visualization of Biological Systems” and presented our new findings on the transcription initiation by RNA polymerase I.

New Paper in the Journal eLife

Congratulation to Dr. Chunli Yan who published a new paper on combining computational modeling and Cryo-electron microscopy to uncover the mechanisms of transcription initiation. Han, Y.; Yan, C.; Nguyen, K.; Jackobel, A.; Ivanov, I.; Knutson, B.A.; He, Y. Structural mechanism of ATP-independent transcription initiation by RNA polymerase I. eLife (2017) 6, e27414, doi:10.7554/eLife.27414

Group members present at two conferences

Group members recently attended and presented at two conferences: Nucleic Acids Research Gordon Conference in Biddeford, ME and CBSB2017: From Compuational Biophysics to Systems Biology 2017.  Many thanks to all who presented! (Kathleen Carter, Chunli Yan and Tom Dodd)

New paper in Nucleic Acids Research

Congratulations to Kathleen Carter who published a new paper in the journal Nucleic Acids Research: Laughlin S.; Carter E.K.; Ivanov, I* & Wilson, W.D. DNA microstructure influences selective binding of small molecules designed to target mixed-site DNA sequences Nucleic Acids Research (2016) doi:10.1093/nar/gkw1232

A new paper in Nature Communications

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.

Ivaylo Ivanov joins the Editorial Board of the Frontiers Journals in Physics, Physiology and Molecular Biosciences

Ivaylo Ivanov was selected to join the Editorial Board of Frontiers in Molecular Biosciences (Biophysics specialty section). Frontiers publishes several of the most cited Open-access journals in the world, is today one the largest and fastest-growing open-access publishers, receives millions of monthly page views, received the ALPSP Gold Award for Innovation in Publishing in 2014, has publishing agreements […]

Bernard Scott selected for the XSEDE Scholars Program

Congratulations to Bernard Scott who has won a fellowship from the XSEDE Scholars Program. The XSEDE Scholars Program (XSP) is a selective year-long program for U.S. students from underrepresented groups in the computing sciences who receive opportunities to learn more about high performance computing and XSEDE resources. XSEDE, the Extreme Science and Engineering Discovery Environment, is the most […]

A new drug discovery paper published in Bioorganic & Medicinal Chemistry Letters

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 […]

Ancient protein flexibility can drive ‘new’ functions

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

Researchers unveil new, detailed images of DNA transcription

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. […]

Georgia State scientist gets $1.675 million to study link between cancer and DNA replication, repair

Ivaylo Ivanov, associate professor of chemistry at Georgia State University, has received a five-year, $1.675 million federal grant to study how problems with DNA replication and repair may lead to cancer susceptibility and inheritable genetic diseases. Source: Georgia State scientist gets $1.675 million to study link between cancer and DNA replication, repair

New paper in PLOS Computational Biology

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 […]

New paper in the Journal of Medicinal Chemistry

Our paper ‘Diamidine Compounds for Selective Inhibition of Protein Arginine Methyltransferase 1’ has just been accepted by the Journal of Medicinal Chemistry. Misregulation of protein arginine methyltransferase enzymes (PRMTs) have been linked to many pathological conditions. In collaboration with Dr. Zheng’s group at UGA we report diamidine compounds as specific inhibitors of PRMT1, the primary […]

Another paper in Nucleic Acids Research

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 […]

New paper in Nucleic Acids Research

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.

New PNAS paper on FEN1/DNA clamp complexes

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.