| Coiled coils are the most common oligomerization motif in naturally occurring proteins. An analysis of protein and DNA sequence databases has led to the estimate that 5–9% of proteins in sequenced genomes contain coiled coil domains and 1–3% of all amino acid residues in proteins occur in coiled coils. Given the growing importance of this class of proteins, it is necessary to understand the interactions that predict the structure and biological function of these proteins. This problem is complicated by the fact that coiled coils can self-associate or bind to heterologous partners; the helices can associate into two-, three-, or four-stranded structures; and finally, the helices can align in a parallel or antiparallel orientation.; We have made a series of model proteins to investigate the primary sequence features that lead to an increase in a parallel or antiparallel helix orientation preference. Residues at the a, d, e, and g positions define the interface between the helices and are important for determining coiled-coil specificity. In addition, the residues at these positions can participate in interhelical electrostatic and hydrophobic interactions. We have examined two different classes of interactions: interhelical Coulombic interactions between residues at the g and e positions and buried polar interactions.; We have explored the importance of Coulombic interactions between residues at the e and g positions. We used differential Coulombic interactions to set an antiparallel helix orientation preference. Our findings suggest that maintenance of all favorable electrostatic interactions and/or avoidance of two potentially repulsive interactions contributes approximately 2.1 kcal/mol to helix orientation preference.; We have also examined the importance of a salt bridge involving a buried charged residue. We have found that burying a polar Arg residue at an interior position has no influence on helix orientation, but does specify a dimeric state at a much lower thermodynamic cost than burial of a polar interaction. |
