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Published April 1, 2005 | public
Journal Article

Dioxane contributes to the altered conformation and oligomerization state of a designed engrailed homeodomain variant


Our goal was to compute a stable, full-sequence design of the Drosophila melanogaster engrailed homeodomain. Thermal and chemical denaturation data indicated the design was significantly more stable than was the wild-type protein. The data were also nearly identical to those for a similar, later full-sequence design, which was shown by NMR to adopt the homeodomain fold: a three-helix, globular monomer. However, a 1.65 Å crystal structure of the design described here turned out to be of a completely different fold: a four-helix, rodlike tetramer. The crystallization conditions included approximately ~25% dioxane, and subsequent experiments by circular dichroism and sedimentation velocity analytical ultracentrifugation indicated that dioxane increases the helicity and oligomerization state of the designed protein. We attribute at least part of the discrepancy between the target fold and the crystal structure to the presence of a high concentration of dioxane.

Additional Information

© 2005 The Protein Society. Received December 8, 2004; Final Revision December 16, 2004; Accepted December 20, 2004. Article first published online: 1 Jan 2009. We are grateful to Premal Shah, Rhonda Digiusto, Scott Ross, and Karin Crowhurst for assistance with NMR; Doug Rees, James Holton, and J.J. Plecs for assistance with crystallography; Po-Ssu Huang for assistance with sedimentation velocity experiments and PyMOL; and Marie Ary and Jessica Mao for assistance with the manuscript. This work was supported by the Howard Hughes Medical Institute, the Ralph M. Parsons Foundation, the Defense Advanced Research Projects Agency, and an IBM Shared University Research Grant. Portions of this research were carried out at the Stanford Synchrotron Radiation Laboratory (SSRL), a national user facility operated by Stanford University on behalf of the U.S. Department of Energy, Office of Basic Energy Sciences. The SSRL Structural Molecular Biology Program is supported by the Department of Energy, Office of Biological and Environmental Research, and by the NIH, National Center for Research Resources, Biomedical Technology Program, and the National Institute of General Medical Sciences. We thank the Gordon and Betty Moore Foundation for their support of the crystallographic resources of the Molecular Observatory for Structural Molecular Biology used in this study.

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