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Mapping Single-Molecule Protein Complexes in 3D with DNA Nanoswitch Calipers
Prakash Shrestha1,2,3, Darren Yang1,2,3, Andrew Ward1,2
1Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts 02115, United States.
Journal of the American Chemical Society
|December 14, 2023
Summary
We developed a new method using DNA nanoswitch calipers to map the 3D structure of single protein complexes. This technique accurately determined the geometry of streptavidin, advancing single-molecule structural proteomics.
Area of Science:
- Structural biology
- Molecular biophysics
- Nanotechnology
Background:
- Mapping 3D geometry of single-molecule complexes in trace samples is difficult.
- Understanding molecular mechanics and structural proteomics requires precise structural data.
Purpose of the Study:
- To develop a high-resolution force spectroscopy method for measuring distances in protein complexes.
- To enable accurate 3D reconstruction of single-molecule structures.
Main Methods:
- Utilized reconfigurable nanoscale devices called DNA nanoswitch calipers.
- Employed a force-based barcoding system for distinct measurement locations.
- Applied high-resolution force spectroscopy to natively folded protein complexes.
Main Results:
- Successfully reconstructed the tetrahedral geometry of biotin-binding sites in streptavidin.
- Achieved 1.5-2.5 Å agreement with previously reported streptavidin structures.
- Demonstrated the capability of the DNA nanoswitch caliper method for precise structural mapping.
Conclusions:
- The developed DNA nanoswitch caliper method provides accurate 3D structural information for single-molecule complexes.
- This approach advances single-molecule structural proteomics and molecular mechanics studies.
- The technique shows promise for analyzing trace samples and complex biological structures.
