A conserved trimerization motif controls the topology of short coiled coils

Abstract

In recent years, short coiled coils have been used for applications ranging from biomaterial to medical sciences. For many of these applications knowledge of the factors that control the topology of the engineered protein systems is essential. Here, we demonstrate that trimerization of short coiled coils is determined by a distinct structural motif that encompasses specific networks of surface salt bridges and optimal hydrophobic packing interactions. The motif is conserved among intracellular, extracellular, viral, and synthetic proteins and defines a universal molecular determinant for trimer formation of short coiled coils. In addition to being of particular interest for the biotechnological production of candidate therapeutic proteins, these findings may be of interest for viral drug development strategies.protein engineering ͉ sequence-to-structure rules ͉ protein-protein interaction ͉ salt bridges ͉ x-ray crystallography T he potential of short ␣-helical coiled coils for protein engineering, biotechnological, biomaterial, basic research, and medical applications has recently been recognized (1-12). The wide range of applications underscores the need for topological control of coiled-coil peptides. Although seemingly simple, coiled coils can form a variety of different assemblies ranging from dimers to pentamers (13,14). Furthermore, coiled coils can form homomers or heteromers with their chains arranged in a parallel or antiparallel fashion. To understand how side-chainside-chain interactions determine a particular structure, it is important to discriminate the factors responsible for specific interhelical interactions from those that are common to all coiled coils such as the heptad repeat.It is generally acknowledged that the detailed packing geometry of hydrophobic core residues correlates with the oligomerization state (15,16). In dimers the side chains of the residues at a and d positions pack in a manner termed parallel and perpendicular, respectively. In the four-stranded state the dimer mode is reversed. Trimeric coiled coils are characterized by an intermediate geometry of these residues, termed acute. Previous studies found that these oligomerization states are determined in particular by the distribution of isoleucine and leucine residues that prefer the parallel and acute, and the acute and perpendicular geometries, respectively (15, 16).Buried polar residues in hydrophobic interfaces also play an important role in determining the number and orientation of strands in coiled coils. Many two-stranded leucine zippers of transcription regulators contain at least one conserved polar residue. Frequently an asparagine or a lysine residue occupies heptad position a toward the center of the sequence, suggesting a common mechanism for determining dimer specificity in these molecules (17). Polar residues like glutamine and threonine at positions a and d, respectively, can favor trimer formation (18,19). Interhelical interactions between side chains of residues at the e and g positions as well as the packi...

Simultaneous prediction of protein folding and docking at high resolution

“…3A). These results demonstrate that the basic principles underlying Crick's ''knobs-into-holes''-based manual modeling (15,16), more constrained conformational searches (17), and other phenomenological rules (18) for the simplest coiled coils can be automatically and quite generally applied to the de novo modeling of complex symmetric helix interaction motifs.…”

Non-LTR retrotransposons encode noncanonical RRM domains in their first open reading frame

“…S1). This revealed conserved RhxxxhE motifs (h, hydrophobic; x, any amino acid) that were demonstrated in other proteins to induce a parallel trimeric coiled coil (42). Consequently, trimerization of type II ORF1p seems conserved for functional reasons.…”

Structural specificity in coiled-coil interactions

“…Straussman et al report that anti-parallel coiled coils in the PDB contain more charged residues in core positions than parallel ones, although it is not yet clear how to interpret this difference [36]. Kammerer et al previously described a short sequence motif that is common in parallel trimers in the PDB but rare in other types of coiled coils, and mutational data support this motif favoring trimer formation [37].…”