Metal binding site design

Microequilibrium constants for binding of metal to a protein. The iron-transport protein, transferrin, has two distinguishable metal-binding sites, designated a and b. The microequilibrium formation constants for each site are defined as follows ... 

Finally, in addition to structurally defined metal-binding sites, designing catalytically active metal centers will be another exciting area of research. It is the best way to realize the potentials of metalloprotein design. 

Regan, L. (1995) Protein design novel metal-binding sites. Trends Biochem. Sci. 20,280-285. 

He, M. M., Voss, J., Hubbell, W. L., and Kaback, H. R. (1995) Use of designed metal-binding sites to study helix proximity in the lactose permease of Escherichia coli. 2. Proximity of helix IX (Arg302) with helix X (His322 and Glu325). Biochemistry 34,15667-15670. 

In addition to structure stabilization and catalytic applications, transition metal-binding sites may be designed and exploited for regulatory purposes. For example, a regulatory metal-binding site has been engineered into the active site of trypsin, where metal binding inhibits proteo-... 

Compound (8) was designed to provide two proximate metal binding sites, similar to those that might be found in natural systems (Chang,... 

Lu, Y., Berry, S. M., and Pfister, T. D. (2001) Engineering novel metalloproteins Design of metal-binding sites into native protein scaffolds, Chem. Rev. 101, 3047-3080. 

Metallopeptide models refer to systems that are mostly unstructured in solntion in the absence of metal ions. It is applicable to design of metal-binding sites whose conserved residues appear mostly in a single peptide that is often much shorter than the whole protein. Designing metalloproteins using only the peptide with the consensus sequence, often called a motif, represents the minimalist approach in its purest sense. These motifs typically contain His, Cys, or both residues. In addition, metalloporphyrin-containing peptides have also been made to mimic basic features in heme proteins. 

Design of Metal-binding Sites into De Novo Designed Proteins... 

Figure 10 Incorporation of nonheme metal-binding sites into de novo designed proteins, (a) X-ray structure of a di-Zn derivative of Due Ferro 1. (Reprinted with permission from Ref. 57. 2000 the American Chemical Society) (b) Computer model of Zn (His)2(Cys)2 site in a four-helical bundle. (Reprinted with permission from Ref. 65. 1995 the American Chemical Society) (c) computer model of Ru -directed assembly of a four-helical bimdle. (Reprinted with permission from Ref. 66. 1992 the American Chemical Society) (d) Metal-ion induced assembly of a three-helcial bimdle. (Reprinted with permission from Ref. 67. 1998 the American Chemical Society)...

Redesign bypasses not only the design of the overall scaffold, but also the initial creation of the metal-binding site. In addition to being more technically feasible with a better chance of success than other methods, this approach best reveals the role of specific residues responsible for a particular structural or fimctional feature of the metal-binding site of interest. 

While redesign of existing metal-binding sites provides insight into the critical differences between the template and target proteins, it cannot address the roles of important residues that are common to both proteins. Designing new metal-binding sites provides such opportunities. 

A. Design Through Homology. New metal-binding sites can be created based on either sequence or structural homology... 

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