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Diep P, Kell B, Yakunin A, Hilfinger A, Mahadevan R. Quantifying metal-binding specificity of CcNikZ-II from Clostridium carboxidivorans in the presence of competing metal ions. Anal Biochem 2023; 676:115182. [PMID: 37355028 DOI: 10.1016/j.ab.2023.115182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 04/25/2023] [Accepted: 05/08/2023] [Indexed: 06/26/2023]
Abstract
Many proteins bind transition metal ions as cofactors to carry out their biological functions. Despite binding affinities for divalent transition metal ions being predominantly dictated by the Irving-Williams series for wild-type proteins, in vivo metal ion binding specificity is ensured by intracellular mechanisms that regulate free metal ion concentrations. However, a growing area of biotechnology research considers the use of metal-binding proteins in vitro to purify specific metal ions from wastewater, where specificity is dictated by the protein's metal binding affinities. A goal of metalloprotein engineering is to modulate these affinities to improve a protein's specificity towards a particular metal; however, the quantitative relationship between the affinities and the equilibrium metal-bound protein fractions depends on the underlying binding mechanisms. Here we demonstrate a high-throughput intrinsic tryptophan fluorescence quenching method to validate binding models in multi-metal solutions for CcNikZ-II, a nickel-binding protein from Clostridium carboxidivorans. Using our validated models, we quantify the relationship between binding affinity and specificity in different classes of metal-binding models for CcNikZ-II. We further illustrate the potential relevance of data-informed models to predicting engineering targets for improved specificity.
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Affiliation(s)
- Patrick Diep
- BioZone Centre for Applied Bioscience and Bioengineering, Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada; Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA.
| | - Brayden Kell
- Department of Physics, University of Toronto, Toronto, ON, Canada; Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, ON, Canada; Department of Molecular Biosciences, Northwestern University, Evanston, IL, USA; NSF-Simons Center for Quantitative Biology, Northwestern University, Evanston, IL, USA
| | - Alexander Yakunin
- BioZone Centre for Applied Bioscience and Bioengineering, Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada; Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Gwynedd, UK
| | - Andreas Hilfinger
- Department of Physics, University of Toronto, Toronto, ON, Canada; Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, ON, Canada; Department of Mathematics, University of Toronto, Toronto, ON, Canada; Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Radhakrishnan Mahadevan
- BioZone Centre for Applied Bioscience and Bioengineering, Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON, Canada; Institute for Biomedical Engineering, University of Toronto, Toronto, ON, Canada
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