Response of a designed metalloprotein to changes in metal ion coordination, exogenous ligands, and active site volume determined by X-ray crystallography.

The de novo protein DF1 is a minimal model for diiron and dimanganese metalloproteins, such as soluble methane monooxygenase. DF1 is a homodimeric four-helix bundle whose dinuclear center is formed by two bridging Glu side chains, two chelating Glu side chains, and two monodentate His ligands. Here, we report the di-Mn(II) and di-Co(II) derivatives of variants of this protein.

Alpha-alpha linking motifs and interhelical orientations.

While the geometry and sequence preferences of turns that link two beta-strands have been exhaustively explored, the corresponding preferences for sequences that link helical structures have been less well studied. Here we examine the interhelical geometry of two connected helices as a function of their link's length. The interhelical geometry of a helical pair appears to be significantly influenced by the number of linking residues.

Analysis and design of turns in alpha-helical hairpins.

Although the analysis and design of turns that connect the strands in antiparallel beta-hairpins has reached an advanced state, much less is known concerning turns between antiparallel helices in helical hairpins. We have conducted an analysis of the structures and sequence preferences of two types of interhelical turns, each of which connects the two helices by a two-residue linker in an alphaL-beta conformation. Based on this analysis, it became apparent that the turn introduced into a designed four-helix bundle protein, DF1, did not occur within an optimal structural context.

Folding of helical membrane proteins: the role of polar, GxxxG-like and proline motifs.

Helical integral membrane proteins share several structural determinants that are widely conserved across their universe. The discovery of common motifs has furthered our understanding of the features that are important to stability in the membrane environment, while simultaneously providing clues about proteins that lack high-resolution structures. Motif analysis also helps to target mutagenesis studies, and other experimental and computational work.

Amino acid propensities are position-dependent throughout the length of alpha-helices.

The 20 commonly occurring amino acids have been shown to have distinct position-dependent, helix-forming propensities near the ends of alpha-helices. Here, we show that the amino acids also have very strong position-dependent propensities throughout the length of a helix. Most helices are amphiphilic, and they have a strong tendency to both begin and end on the solvent-inaccessible face of the helix.