October 02, 2020
In two new collaborative studies, researchers in the Mellon College of Science’s biological physics group used advanced neutron scattering techniques to further the understanding of proteins crucial to the development of cancer.
“We have developed the scattering methodology, the preparation of suitable membrane mimics, the protein handling and the analysis of the scattering data to a point that we are now able to provide useful information to biomedical groups that work on important disease-related systems,” said Associate Research Professor of Physics Frank Heinrich of the work Carnegie Mellon University’s Supramolecular Structures Lab completed in collaboration with the National Institute of Standards and Technology.
Led by Professor of Physics Mathias Lösche, the lab contributed to two new studies seeking to better understand the biophysical foundation of cancer.
In research published in the Proceedings of the National Academy of Sciences, Heinrich and his collaborators were able to characterize the structure and dynamics of the signaling protein KRAS, a member of the Ras family of Small GTPase proteins located at the cell membrane that can mutate to contribute to the development of many cancers.
“KRAS acts as a molecular switch regulating cell survival and proliferation, and when mutated it is put in a permanent on-position, leading to the characteristic tumor growth in cancer,” Heinrich said. Researchers have long attempted to develop cancer drugs targeted at KRAS, he noted, but have had little success.
“It was recognized that previous efforts might have failed in part because insufficient biophysical information about the structure and function of KRAS at the membrane was available,” Heinrich said, noting that researchers had predominantly studied the protein with traditional biochemical methods in solution and crystalline form.
Heinrich and Lösche’s team, however, was able to harness the power of “more than a decade of method developments” in neutron reflectometry to change that. The technique, which involves sending neutrons at a material and tracking how they scatter from it, can measure the structures of peripherally bound membrane proteins in conditions resembling those in actual cells.
“We found that contrary to previous beliefs, KRAS is very dynamic at the lipid membrane in that it frequently takes on conformations that move the main protein body, the G-domain, away from the membrane,” Heinrich said. “This flexibility allows KRAS to effectively bind to effector proteins and, distinct from previous observations in computer simulation studies, it is not significantly restrained by the proximity of the lipid membrane in doing so.”
In another study published in Science Advances on Sept. 30, the researchers characterized a different protein, ASAP1, which is essential for the activation of a distinct Small GTPase, Arf, a signaling protein that is also associated with a variety of human cancers.
“We were interested in the membrane-bound conformation of one particular ASAP1 domain, known as the PH domain, that held important clues on the structure of the entire protein at the membrane,” Heinrich said. “We determined the orientation of the PH domain and measured how many and what kind of membrane lipids it recruits to the protein upon binding. Those are fundamental properties of the ASAP1 protein that sheds new light on the molecular mechanism of signaling.”
Heinrich, Lösche and their collaborators are continuing to refine their techniques in studying the structural biology of membrane-bound proteins and are pushing forward further studies of these proteins and others.
Other authors on the study “Uncovering a membrane-distal conformation of KRAS available to recruit RAF to the plasma membrane” in the Proceedings of the National Academy of Sciences included: Daniel Scott with Carnegie Mellon; Que N. Van, Troy Taylor, Timothy H. Tran, Peter H. Frank, Simon Messing, Patrick Alexander, Xiaoying Ye, Matt Drew, Oleg Chertov, Dhirenda K. Simanshu, Dwight V. Nissey, William K. Gillette, Dominic Esposito, Frank McCormick and Andrew G. Stephen with the National Cancer Institute RAS Initiative; Cesar A. López, Nicolas W. Hengartner and S. Gnanakaran with the Los Alamos National Laboratory; Marco Tonelli, William M. Westler and John L. Markley with the University of Wisconsin-Madison; Ben Niu and Michael L. Gross with Washington University in St. Louis; Christopher B. Stanley and Debsindhu Bhowmik with Oak Ridge National Laboratory and Arvind Ramanathan with Argonne National Laboratory. Funding was provided by grants from the National Cancer Institute, NIH Contract HHSN261200800001E, the Spatiotemporal Modeling Center at the University of New Mexico and the U.S. Department of Commerce.
Other authors on the study “Membrane Surface Recognition by the ASAP1 PH Domain and Consequences for Interactions with the Small GTPase Arf1” in Science Advances included: Olivier Soubias, Yue Zhang, Jess Li and R. Andrew Byrd with the National Cancer Institute; Shashank Pant and Emad Tajkhorshid with the University of Illinois at Urbana-Champaign; Neeladri S. Roy, Xiaoying Jian, Marielle E. Yohe and Paul A. Randazzo with the National Institutes of Health. Funding was provided by grants from the National Cancer Institute (Projects ZIA BC 011419, ZIA BC 011131, ZIA BC 011132 and BC007365), the U.S. Department of Commerce and the National Institutes of Health (award numbers P41-GM104601 and R01-GM123455).