ArticleProtein engineering, design & selection : PEDS2016
Probing the minimal determinants of zinc binding with computational protein design.
Article in Protein engineering, design & selection : PEDS, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 21 citations in OpenAlex.
- Zero-shot design of abioRxiv : the preprint server for biology · 2026Article
- SuperMetal: a generative AI framework for rapid and precise metal ion location prediction in proteins.Journal of cheminformatics · 2025Article
- Metal3D: a general deep learning framework for accurate metal ion location prediction in proteins.Nature communications · 2023Article
- Inside-Out Design of Zinc-Binding Proteins with Non-Native Backbones.Biochemistry · 2023Article
- Design of a Flexible, Zn-Selective Protein Scaffold that Displays Anti-Irving-Williams Behavior.Journal of the American Chemical Society · 2022Article
- Article
- Second-Shell Amino Acid R266 Helps DetermineBiochemistry · 2021Article
- Step-by-step design of proteins for small molecule interaction: A review on recent milestones.Protein science : a publication of the Protein Society · 2021Review
- Engineering glycoside hydrolase stability by the introduction of zinc binding.Acta crystallographica. Section D, Structural biology · 2018Article
- Rapid Sampling of Hydrogen Bond Networks for Computational Protein Design.Journal of chemical theory and computation · 2018Article
- Benchmarking a computational design method for the incorporation of metal ion-binding sites at symmetric protein interfaces.Protein science : a publication of the Protein Society · 2017Article
- Binding Site Configurations Probe the Structure and Dynamics of the Zinc Finger of NEMO (NF-κB Essential Modulator).Biochemistry · 2017Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Structure-based protein design tests our understanding of the minimal determinants of protein structure and function. Previous studies have demonstrated that placing zinc binding amino acids (His, Glu, Asp or Cys) near each other in a folded protein in an arrangement predicted to be tetrahedral is often sufficient to achieve binding to zinc. However, few designs have been characterized with high-resolution structures. Here, we use X-ray crystallography, binding studies and mutation analysis to evaluate three alternative strategies for designing zinc binding sites with the molecular modeling program Rosetta. While several of the designs were observed to bind zinc, crystal structures of two designs reveal binding configurations that differ from the design model. In both cases, the modeling did not accurately capture the presence or absence of second-shell hydrogen bonds critical in determining binding-site structure. Efforts to more explicitly design second-shell hydrogen bonds were largely unsuccessful as evidenced by mutation analysis and low expression of proteins engineered with extensive primary and secondary networks. Our results suggest that improved methods for designing interaction networks will be needed for creating metal binding sites with high accuracy.
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