Sequence preference in DNA binding: de novo designed helix–turn–helix metallopeptides recognize a family of DNA target sites

DNA targeting and cleavage by an engineered metalloprotein dimer

Nature has illustrated through numerous examples that protein dimerization has structural and functional advantages. We previously reported the design and characterization of an engineered "metallohomeodomain" protein (C2) based on a chimera of the EF-hand Ca-binding motif and the helix-turn-helix motif of homeodomains (Lim and Franklin in Protein Sci. 15:2159-2165, 2004). This small metalloprotein binds the hard metal ions Ca(II) and Ln(III) and interacts with DNA with modest sequence preference and affinity, yet exhibits only residual DNA cleavage activity. Here we have achieved substantial improvement in function by constructing a covalent dimer of this C2 module (F2) to create a larger multidomain protein. As assayed via fluorescence spectroscopy, this F2 protein binds Ca(II) more avidly (25-fold) than C2 on a per-domain basis; in gel shift selection experiments, metallated F2 exhibits a specificity toward 5'-TAATTA-3' sequences. Finally, Ca(2)F2 cleaves plasmid DNA and generates a linear product in a Ca(II)-dependent way, unlike the CaC2 monomer. To the best of our knowledge this activation of Ca(II) in the context of an EF-hand binding motif is unique and represents a significant step forward in the design of artificial metallonucleases by utilizing biologically significant metal ions.

Towards artificial metallonucleases for gene therapy: recent advances and new perspectives

The process of DNA targeting or repair of mutated genes within the cell, induced by specifically positioned double-strand cleavage of DNA near the mutated sequence, can be applied for gene therapy of monogenic diseases. For this purpose, highly specific artificial metallonucleases are developed. They are expected to be important future tools of modern genetics. The present state of art and strategies of research are summarized, including protein engineering and artificial ‘chemical’ nucleases. From the results, we learn about the basic role of the metal ions and the various ligands, and about the DNA binding and cleavage mechanism. The results collected provide useful guidance for engineering highly controlled enzymes for use in gene therapy.

Of Folding and Function: Understanding Active-Site Context through Metalloenzyme Design

In the emerging field of biomolecular design, the introduction of metal-binding sites into loop or turn regions of known protein scaffolds has been utilized to create unique metalloprotein and metallopeptide systems for study. This Forum Article highlights examples of the modular-turn-substitution approach to design and the range of structural and mechanistic questions to which this tool can be applied. Examples from the authors' laboratory are given to show that lanthanide-binding metallopeptides, and now a full metallohomeodomain, can be generated by modular substitution of a Ca-binding EF-hand loop into the unrelated scaffold, the engrailed helix-turn-helix motif. We have previously shown that these peptides bind trivalent Ln(III) ions and promote DNA and phosphate hydrolysis, the targeted function. Here, a series of chimeric peptides are presented that differ only in the ninth loop position [given in parentheses; Peptides P3N (Asn), P3E (Glu), P3A (Ala), and P3W(D) (Asp]. This residue, a putative second-shell ligand stabilizing a coordinated water, was found to influence not only metal affinity but also peptide folding. The affinity for Tb(III) was determined by Trp-Tb fluorescence resonance energy transfer and followed the order Ka = P3W(D) > P3A approximately P3E > P3N. However, circular dichroism (CD) titrations with EuCl3 showed that only P3W(D) and P3N folded to any extent upon metal binding, indicating that the Asp/Asn side chains stabilize the central loop structure and thus propagate folding of the peripheral helices, whereas neither Ala nor Glu appears to be interacting with the metal to organize the loop. Finally, we investigated the longer range context of a given loop substitution by cloning and expressing a lanthanide-binding homeodomain (C2), whose loop insertion sequence is analogous to that of peptide P3W(D). We find by CD that apo-C2 has a significant helical structure (approximately 25% alphahelicity), which increases further upon the addition of Tb(III) (approximately 32% alpha helicity). The protein's Tb(III) affinity is similar to that of the chimeric peptides. However, unlike previously reported metallopeptides, we find that EuC2 does not appreciably promote phosphate or DNA cleavage, which suggests a difference in metal accessibility in the context of the full domain. We have demonstrated that substituting beta turns with metal-binding turns does not necessarily require homologous parental scaffolds or small flexible peptides but rather relies on the structural similarity of the motifs flanking the turn.

Engineered lanthanide-binding metallohomeodomains: designing folded chimeras by modular turn substitution

A series of chimeric metallohomeodomains are described, engineered by rational design of a flexible Ca/Ln binding site into a DNA-binding scaffold. A modular turn-substitution approach was used to create proteins that both bind DNA and lanthanide ions, while retaining the secondary structure of the full homeodomain (determined by circular dichroism [CD]). Four similar metallohomeodomains were designed (C1-C4), their structural stability predicted by molecular dynamics (MD) simulation of loop-mutations into the known homeodomain structure, and each designed protein cloned, expressed, and purified using standard molecular biology techniques. Two of the four loop insertions resulted in folded, metal- and DNA-binding proteins (EuC2 Kd = 2.1 +/- 0.4 microM; EuC4 Kd = 3.2 +/- 1.0 microM). These results show the successful incorporation of a metal site into a full protein domain, without compromising long-range structure. This is an important achievement in biomolecular design, as it provides a critical starting point for exploring metallonuclease function and substrate accessibility in a well-organized chimeric protein domain (rather than only in small HTH peptide systems).