4NDL

Computational design and experimental verification of a symmetric homodimer

Summary for 4NDL

• Entry DOI: 10.2210/pdb4ndl/pdb
• Descriptor: ENH-c2b, computational designed homodimer (2 entities in total)
• Functional Keywords: helix-turn-helix, de novo protein
• Biological source: Drosophila melanogaster
• Total number of polymer chains: 3
• Total formula weight: 26546.72

Authors

Mou, Y.,Huang, P.S.,Hsu, F.C.,Huang, S.J.,Mayo, S.L. (deposition date: 2013-10-26, release date: 2014-11-05, Last modification date: 2024-02-28)

Primary citation

Mou, Y.,Huang, P.S.,Hsu, F.C.,Huang, S.J.,Mayo, S.L.
Computational design and experimental verification of a symmetric protein homodimer.
Proc.Natl.Acad.Sci.USA, 112:10714-10719, 2015

PubMed Abstract: 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.

PubMed: 26269568
DOI: 10.1073/pnas.1505072112

Experimental method

X-RAY DIFFRACTION (3.5 Å)