From Oak Ridge Lab: “Researchers Show How Proteins Help DNA Replicate Past a Damaged Site” 

Computation and experiment reveal how protein switching provides right tool for the job


Dawn Levy
November 9, 2011

“Ultraviolet light, oxidants, and environmental toxins constantly assault the genome of a cell. Consequences in the absence of DNA repair could be severe—accelerated aging, degenerative disease, or cancer. Fortunately, cells have evolved sophisticated mechanisms for dealing with DNA damage, stabilizing their genomes, and ensuring their survival. Recently, a multi-institutional research team led by Ivaylo Ivanov of Georgia State University has employed the Jaguar XT4 supercomputer at Oak Ridge National Laboratory (ORNL) and x-rays a billion times brighter than the sun, produced at Lawrence Berkeley National Laboratory (LBNL), to illuminate how DNA replication continues past a damaged site so a lesion can be repaired later. The combination of computation and experiment reveals conformations that ubiquitin (Ub), a small protein that binds and orients DNA-editing enzymes, can assume when it associates with a molecular “tool belt” called proliferating cell nuclear antigen (PCNA). The results appear in the October 17, 2011, online issue of Proceedings of the National Academy of Sciences.


‘The tool belt model is a longstanding model in the PCNA field, although it has not been conclusively proven,’ said Ivanov, whose collaborators include Susan Tsutakawa of LBNL; John Tainer of LBNL and the Scripps Research Institute; Adam Van Wynsberghe of Hamilton College; Bret Freudenthal, M. Todd Washington, and Lokesh Gakhar of the University of Iowa College of Medicine; and Christopher Weinacht and Zhihao Zhuang of the University of Delaware.

Through the Innovative and Novel Computational Impact on Theory and Experiment (INCITE) program, the researchers received 2.6 million processor hours in 2009 on the Department of Energy Office of Science’s Jaguar XT4 to conduct their simulations. They also used the Intel 64 cluster Abe at the University of Illinois at Urbana-Champaign and its National Center for Supercomputing Applications through the National Science Foundation’s Teragrid.


A model of ubiquitinated PCNA, refined using multiscale dynamics simulations and protein-docking experiments, shows ubiquitin (orange) binding in a groove above a PCNA subunit interface. Mutations known to interfere with translesion synthesis (blue and green) are directly beneath. The conformation of the J-loop (purple), a structural element of PCNA, is affected by mutations at the subunit interface. Image courtesy Ivaylo Ivanov.

See the full article here.