DOI: 10.1073/pnas.1205945109. Multiscale natural moves refine macromolecules using single-particle electron microscopy projection images

Multiscale natural moves refine macromolecules using single-particle electron microscopy projection images

10.1073/pnas.1205945109

Crossref journal-article

Proceedings of the National Academy of Sciences

Proceedings of the National Academy of Sciences (341)

Abstract

The method presented here refines molecular conformations directly against projections of single particles measured by electron microscopy. By optimizing the orientation of the projection at the same time as the conformation, the method is well-suited to two-dimensional class averages from cryoelectron microscopy. Such direct use of two-dimensional images circumvents the need for a three-dimensional density map, which may be difficult to reconstruct from projections due to structural heterogeneity or preferred orientations of the sample on the grid. Our refinement protocol exploits Natural Move Monte Carlo to model a macromolecule as a small number of segments connected by flexible loops, on multiple scales. After tests on artificial data from lysozyme, we applied the method to the Methonococcus maripaludis chaperonin . We successfully refined its conformation from a closed-state initial model to an open-state final model using just one class-averaged projection. We also used Natural Moves to iteratively refine against heterogeneous projection images of Methonococcus maripaludis chaperonin in a mix of open and closed states. Our results suggest a general method for electron microscopy refinement specially suited to macromolecules with significant conformational flexibility. The algorithm is available in the program Methodologies for Optimization and Sampling In Computational Studies.

Bibliography

Zhang, J., Minary, P., & Levitt, M. (2012). Multiscale natural moves refine macromolecules using single-particle electron microscopy projection images. Proceedings of the National Academy of Sciences, 109(25), 9845â9850.

Authors 3

Junjie Zhang (first)
Peter Minary (additional)
Michael Levitt (additional)

References 38 Referenced 32

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Dates

Type	When
Created	13 years, 2 months ago (June 5, 2012, 10:05 a.m.)
Deposited	3 years, 4 months ago (April 15, 2022, 2:44 a.m.)
Indexed	1 year, 3 months ago (May 9, 2024, 12:38 a.m.)
Issued	13 years, 2 months ago (June 4, 2012)
Published	13 years, 2 months ago (June 4, 2012)
Published Online	13 years, 2 months ago (June 4, 2012)
Published Print	13 years, 2 months ago (June 19, 2012)

Funders 0

None

BibTeX

@article{Zhang_2012, title={Multiscale natural moves refine macromolecules using single-particle electron microscopy projection images}, volume={109}, ISSN={1091-6490}, url={http://dx.doi.org/10.1073/pnas.1205945109}, DOI={10.1073/pnas.1205945109}, number={25}, journal={Proceedings of the National Academy of Sciences}, publisher={Proceedings of the National Academy of Sciences}, author={Zhang, Junjie and Minary, Peter and Levitt, Michael}, year={2012}, month=jun, pages={9845–9850} }

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