Small-residue packing motifs modulate the structure and function of a minimal de novo membrane protein

Alpha-helical integral membrane proteins contain conserved sequence motifs that are known to be important in helix packing. These motifs are a promising starting point for the construction of artificial proteins, but their potential has not yet been fully explored. Here, we study the impact of introducing a common natural helix packing motif to the transmembrane domain of a genetically-encoded and structurally dynamic de novo membrane protein. The resulting construct is an artificial four-helix bundle with lipophilic regions that are defined only by the amino acids L, G, S, A and W. This minimal proto-protein could be recombinantly expressed by diverse prokaryotic and eukaryotic hosts and was found to co-sediment with cellular membranes. The protein could be extracted and purified in surfactant micelles and was monodisperse and stable in vitro, with sufficient structural definition to support the rapid binding of a heme cofactor. The reduction in conformational diversity imposed by this design also enhances the nascent peroxidase activity of the protein-heme complex. Unexpectedly, strains of Escherichia coli expressing this artificial protein specifically accumulated zinc protoporphyrin IX, a rare cofactor that is not used by natural metalloenzymes. Our results demonstrate that simple sequence motifs can rigidify elementary membrane proteins, and that orthogonal artificial membrane proteins can influence the cofactor repertoire of a living cell. These findings have implications for rational protein design and synthetic biology.

Analysis of the Torsion Angles between Helical Axes in Pairs of Helices in Protein Molecules

In this study, an analysis of distribution of the torsion angles Ω between helical axes in pairs of connected helices found in known proteins has been performed. The database for helical pairs was compiled using the Protein Data Bank taking into account the definite rules suggested earlier. The database was analyzed in order to elaborate its classification and find out novel structural features in helix packing. The database was subdivided into three subsets according to criterion of crossing helix projections on the parallel planes passing through the axes of the helices. It was shown that helical pairs not having crossing projections are distributed along whole range of angles Ω, although there are two maxima at Ω = 0° and Ω = 180°. Most of helical pairs of this subset are pairs formed by α-helices and 310- helices. It is shown that the distribution of all the helical pairs having the crossing helix projections has a maximum at 20° < Ω < 25°. In this subset, most helical pairs are formed by α-helices. The distribution of only α-helical pairs having crossing axes projections has three maxima, at –50° < Ω < –25°, 20° < Ω < 25°, and 70° < Ω < 110°.