Andrei T. Alexandrescu

NMR structure of a parallel homotrimeric coiled coil

Homeodomains are one of the key families of eukaryotic DNA-binding motifs and provide an important model system for studying protein–DNA interactions. We have crystallized the Antennapedia homeodomain–DNA complex and solved this structure at 2.4 Å resolution. NMR and molecular dynamics studies had implied that this homeodomain achieves specificity through an ensemble of rapidly fluctuating DNA contacts. The crystal structure is in agreement with the underlying NMR data, but our structure reveals a well-defined set of contacts and also reveals the locations and roles of water molecules at the protein–DNA interface. The synthesis of X-ray and NMR studies provides a unified, general model for homeodomain–DNA interactions.

An Intrahelical Salt Bridge within the Trigger Site Stabilizes the GCN4 Leucine Zipper

We previously reported that a helical trigger segment within the GCN4 leucine zipper monomer is indispensable for the formation of its parallel two-stranded coiled coil. Here, we demonstrate that the intrinsic secondary structure of the trigger site is largely stabilized by an intrahelical salt bridge. Removal of this surface salt bridge by a single amino acid mutation induced only minor changes in the backbone structure of the GCN4 leucine zipper dimer as verified by nuclear magnetic resonance. The mutation, however, substantially destabilized the dimeric structure. These findings support the proposed hierarchic folding mechanism of the GCN4 coiled coil in which local helix formation within the trigger segment precedes dimerization.

Contributions of the ionization states of acidic residues to the stability of the coiled coil domain of matrilin-1.

The pK a values of eight glutamic acid residues in the homotrimeric coiled coil domain of chicken matrilin‐1 have been determined from 2D H(CA)CO NMR spectra recorded as a function of the solution pH. The pK a values span a range between 4.0 and 4.7, close to or above those for glutamic acid residues in unstructured polypeptides. These results suggest only small favorable contributions to the stability of the coiled coil from the ionization of its acidic residues.