| The coiled-coil protein oligomerization motif consists of two or more alpha-helices oriented parallel or antiparallel, which wrap around each other in a slight left-handed superhelical twist. The typical sequence of a coiled coil is characterized by a heptad repeat commonly denoted by the letters abcdefg, where residues in positions a and d are predominantly hydrophobic, while those in positions b, c, e, f, and g are usually charged or polar. Empirical rules have been established on the tendency of different core sequences to form a certain topology and oligomeric state but the physical forces behind this specificity are unclear. In this thesis we examine the ability of an effective energy function (EEF1.1) to discriminate the correct topology and oligomeric state for a given sequence using a molecular dynamics approach. We find that inclusion of entropic terms is necessary for discriminating the native structures from their misassembled counterparts. The decomposition of the effective energy into residue contributions yields theoretical values for the oligomeric propensity of different residue types at different heptad positions. We find that certain calculated residue propensities are general and consistent with existing rules, while other residue propensities are sequence context dependent. A variety of features contribute to the topological specificity of the motif, including electrostatics, side chain entropy change, steric matching, and the desolvation of hydrophobic side chains. Our results establish that the oligomeric state is dictated by similar rules in both parallel and antiparallel conformations but alignment of alpha-helices requires a broader set of both lateral and vertical interaction patterns. We found that the antiparallel topology can be directed by a/e' electrostatic attractions in the dimer, with e/e' and g/g' making minimal contributions. The antiparallel trimer topology is mainly the result of steric matching a/e' and d/g' side chain pairs in two antiparallel faces. The antiparallel tetramer is stabilized by similar interactions as the trimer in addition to b/e' electrostatics, which are only available in this oligomeric state. This work provides useful methodology and rules for designing coiled coils with a well defined and predictable three-dimensional structure. |
