Solving the structure of Lgl2, a difficult blind test of unsupervised structure determination
| Autor: | Lior Almagor, William I. Weis, Michael Levitt, Ivan S. Ufimtsev |
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| Rok vydání: | 2019 |
| Předmět: |
Models
Molecular crystal structure Phase (waves) Structure (category theory) Derivative Crystallography X-Ray 010403 inorganic & nuclear chemistry 01 natural sciences 03 medical and health sciences symbols.namesake unsupervised Humans Molecular replacement 030304 developmental biology Mathematics 0303 health sciences Multidisciplinary Resolution (electron density) Biological Sciences Lgl 0104 chemical sciences Biophysics and Computational Biology Cytoskeletal Proteins Range (mathematics) Fourier transform symbols Protein crystallization Algorithm Algorithms |
| Zdroj: | Proceedings of the National Academy of Sciences of the United States of America |
| ISSN: | 1091-6490 0027-8424 |
| Popis: | Significance Determination of macromolecular crystal structures by molecular replacement (MR) uses a related structure to generate approximate phases for the unknown crystal. MR fails if the search model is too dissimilar to the unknown structure. In an accompanying paper, we described a method that generates many ensembles of possible solutions and refines them against the diffraction data without human intervention, and demonstrated its ability to solve test cases of known structure. Here, we apply this method to crystals of the epithelial cell polarity protein lethal giant larvae, which had resisted structure solution using conventional MR or experimental phasing. The results show that our method of unsupervised protein structure solution can be applied to a very large and difficult phasing problem. In the companion paper by Ufimtsev and Levitt [Ufimtsev IS, Levitt M (2019) Proc Natl Acad Sci USA, 10.1073/pnas.1821512116], we presented a method for unsupervised solution of protein crystal structures and demonstrated its utility by solving several test cases of known structure in the 2.9- to 3.45-Å resolution range. Here we apply this method to solve the crystal structure of a 966-amino acid construct of human lethal giant larvae protein (Lgl2) that resisted years of structure determination efforts, at 3.2-Å resolution. The structure was determined starting with a molecular replacement (MR) model identified by unsupervised refinement of a pool of 50 candidate MR models. This initial model had 2.8-Å RMSD from the solution. The solved structure was validated by comparison with a model subsequently derived from an alternative crystal form diffracting to higher resolution. This model could phase an anomalous difference Fourier map from an Hg derivative, and a single-wavelength anomalous dispersion phased density map made from these sites aligned with the refined structure. |
| Databáze: | OpenAIRE |
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