Towards understanding the molecular recognition process in prokaryotic zinc-finger domain

The (unusual) aspartic acid in the metal coordination sphere of the prokaryotic zinc finger domain

“…We reported the structural and functional characterization of the protein Ros87_C27D, point mutant of Ros87 [23], minimal portion of the Ros protein capable to specifically interact with DNA [23,24,69] and of the double mutant Ros87_C27D_G29K. In Ros87_C27D the cysteine at position 27, which corresponds to the second position of coordination of the zinc ion in the wild type protein, is replaced by an aspartic acid.…”

“…The first helix is the secondary structure element most affected by the mutation but, overall, the general fold of the protein is maintained, most likely because the extensive hydrophobic core, for which differences are also observed (as shown Leu34 and Met61 are perturbed), compensates the perturbations caused by the mutation. In fact, the residues involved in the protein-DNA interaction [23,24,69] show in Ros87_C27D structure the same position and orientation observed in the wild type protein allowing this mutant protein to selectively bind its target DNA [12]. In Ros metal lacking homologues (Ml 4 and Ml 5 ), the presence of a basic residue in the turn connecting the second and third β-strand (position 29 in Ros87, occupied by a glycine) has been proved to confer stability to the protein [34]; such residue in this position has been shown to interact with the aspartate in the second position of the zinc-coordinating equivalent sites by driving it toward the interior of the globular domain, allowing the aspartate to achieve the correct orientation to make relevant stabilizing hydrogen bonds.…”

The prokaryotic zinc‐finger: structure, function and comparison with the eukaryotic counterpart

“…The molecular DNA recognition of prokaryotic ZF appears to be peculiar and very different to what is observed in eukaryota . NMR, molecular dynamics and mutagenesis data show that residues belonging to α 1 make extensive contacts with the bases and phosphate backbone of DNA (Fig.…”

Deciphering RGDechi peptide‐α5β1 integrin interaction mode in isolated cell membranes

“…In the last years, we have characterized the structures and functions of peptides recognizing membrane receptors either in vitro and on cellular membranes . Recently, we have also investigated the use of isolated cellular membranes and provided significant advantages in the structural study of the RGDechi interaction with α v β 3 integrin .…”

“…To elucidate the details of the α 5 β 1 integrin recognition mechanism by the RGDechi peptide, we performed a series of Molecular Dynamics simulations (MD) studies. To achieve a rigorous structural investigation of this interaction we applied a combined approach that includes in the Molecular Docking protocol data obtained by MD and Nuclear Magnetic Resonance (NMR) techniques. This strategy allows to take into account in the description of the binding mechanism not only the structural properties, but also the conformational heterogeneity of the RGDechi peptide.…”