Metal-mediated affinity and orientation specificity in a computationally designed protein homodimer
By Bryan S. Der, M. Machius, M. Miley, Jeffrey L. Mills, Thomas Szyperski, Brian Kuhlman. 2011
115 citations recorded by the source corpus.
Computationally designing protein-protein interactions with high affinity and desired orientation is a challenging task. Incorporating metal-binding sites at the target interface may be one approach for increasing affinity and specifying the binding mode, thereby improving robustness of designed interactions for use as tools in basic research as well as in applications from biotechnology to medicine. Here we describe a Rosetta-based approach for the rational design of a protein monomer to form a zinc-mediated, symmetric homodimer. Our metal interface design, named MID1 (NESG target ID OR37), forms a tight dimer in the presence of zinc (MID1-zinc) with a dissociation constant <30 nM. Without zinc the dissociation constant is 4 μM. The crystal structure of MID1-zinc shows good overall agreement with the computational model, but only three out of four designed histidines coordinate zinc. However, a histidine-to-glutamate point mutation resulted in four-coordination of zinc, and the resulting metal binding site and dimer orientation closely matches the computational model (Cα RMSD = 1.4 Å).
Subfields: Molecular Biology
How researchers see this paper
The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.
In Molecular Biology
- Sagar D. Khare
- Gaetano T. Montelione
- Sarel Jacob Fleishman
- David Baker
- I. Samish
- Yuanpeng Janet Huang
- Nikolaos G. Sgourakis
- Oliver F. Lange
Citations in the corpus
- Design of a hyperstable 60-subunit protein icosahedron (2016, unknown): “Protein assemblies have been engineered using metals 9,10 , disulfide bonds 11–14 , genetic fusions 12,15–17 , and ideal helix-helix interactions 11,13,16 , but these approaches have generally yielded polydisperse or unanticipated products.”
- Emerging themes in the computational design of novel enzymes and protein–protein interfaces (2013, background): “Another approach for increasing the specificity of the designed binding mode utilized metal-mediated interactions, by designing a symmetric interaction incorporating a zinc ion binding site comprising residues on both partners [50].”
- The Protein Structure Initiative: achievements and visions for the future (2012, background): “PSI Centers are also involved in collaborative projects aimed at accelerating the field of protein NMR structure analysis [22-28] and computational protein design [29-31].”