New method enables structure determination of flexible biomolecules.
The shapes and assemblies of biological macromolecules such as proteins and nucleic acids (including RNA and DNA) help explain and predict how these large molecules perform and determine specific functions within living cells and organisms. However, many of these molecules are highly flexible, making their structures difficult to characterize by standard techniques such as X-ray crystallography. A new approach developed at Lawrence Berkeley National Laboratory (LBNL) overcomes these limitations.
The new technique will enable researchers will sharpen researchers’ ability to understand the structure of flexible biomolecules.
Small-angle scattering (SAS) of X-rays or neutrons reveals information about the conformations and assemblies of such molecules in solution, but these time-consuming experiments are difficult to analyze and often provide models of unknown accuracy. The novel LBNL approach employs metrics based upon the discovery of a SAS invariant, meaning its value does not change regardless of how or where the measurement was performed. This new invariant, termed the volume of correlation (Vc), can be calculated from a single scattering dataset. LBNL scientists Robert Rambo and John Tainer used Vc to define metrics for conformation, mass, and model accuracy from experimentally measured parameters. They then tested the definition on several proteins and RNAs with known structures using small-angle X-ray scattering (SAXS) at the Advanced Light Source’s Structurally Integrated Biology for the Life Sciences (SIBYLS) station. They found that the Vc invariant and the derived metrics calculated from the experimental data agreed with known characteristics of the test molecules. Further experiments identified changes in the shape of biological macromolecules when solution conditions were altered, for example showing a smaller Vc when a metal ion was added that tightly bound to the macromolecule causing it to become more compact.
John A. Tainer
Department of Integrative Structural and Computational Biology, The Skaggs Institute for Chemical Biology, The Scripps Research Institute
La Jolla, CA 92037
This work is supported in part by funding to foster collaboration with Bruker and LBNL’s Laboratory Directed Research and Development (LDRD) program on Novel Technology for Structural Biology provided by the U.S. Department of Energy (DOE) Office of Science. The SIBYLS Beamline 12.3.1 facility and team at the Advanced Light Source are supported by DOE’s Integrated Diffraction Analysis Technologies program (DEAC02-05CH11231) and by the National Institutes of Health (grant R01GM105404).
Rambo, R., and Tainer, J. “Accurate assessment of mass, models and resolution by small-angle scattering.” Nature 496, 477-481 (2013). [DOI: 10.1038/nature12070]
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