Computational design and experimental verification of a symmetric protein homodimer
Homodimers are the most common type of protein assembly in nature and have distinct features compared with heterodimers and higher order oligomers. Understanding homodimer interactions at the atomic level is critical both for elucidating their biological mechanisms of action and for accurate modeling of complexes of unknown structure. Computation-based design of novel protein–protein interfaces can serve as a bottom-up method to further our understanding of protein interactions. Previous studies have demonstrated that the de novo design of homodimers can be achieved to atomic-level accuracy by β-strand assembly or through metal-mediated interactions. Here, we report the design and experimental characterization of a α-helix–mediated homodimer with C2 symmetry based on a monomeric Drosophila engrailed homeodomain scaffold. A solution NMR structure shows that the homodimer exhibits parallel helical packing similar to the design model. Because the mutations leading to dimer formation resulted in poor thermostability of the system, design success was facilitated by the introduction of independent thermostabilizing mutations into the scaffold. This two-step design approach, function and stabilization, is likely to be generally applicable, especially if the desired scaffold is of low thermostability.
© 2015 National Academy of Sciences. Freely available online through the PNAS open access option. Contributed by Stephen L. Mayo, May 18, 2015 (sent for review December 1, 2014). Published ahead of print August 12, 2015. We thank Justin Chartron for useful discussion about solution NMR structural determination and Marie Ary for assistance with the manuscript. NMR measurements were carried out at Instrumentation Center of National Taiwan University, Taiwan (NSC 102-2731-M-002-002-MY2). This work was supported by the Defense Advanced Research Projects Agency Protein Design Processes Program, a National Security Science and Engineering Faculty Fellowship (NSSEFF N00244-09-1-0011, N00244-09-1-0082), and the Gordon and Betty Moore Foundation through Grant GBMF2809 to the Caltech Programmable Molecular Technology Initiative. Author contributions: Y.M., P.-S.H., and S.L.M. designed research; Y.M., P.-S.H., F.-C.H., and S.-J.H. performed research; Y.M., P.-S.H., F.-C.H., S.-J.H., and S.L.M. analyzed data; and Y.M., P.-S.H., S.-J.H., and S.L.M. wrote the paper. The authors declare no conflict of interest. Data deposition: The atomic coordinates have been deposited in the Protein Data Bank, www.pdb.org (PDB ID codes 2MG4 and 4NDL). This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1505072112/-/DCSupplemental.
Published - PNAS-2015-Mou-10714-9.pdf
Supplemental Material - pnas.201505072SI.pdf