S. Potluri, A.K. Yan, J.J. Chou, B.R. Donald, and C. Bailey-Kellogg, "Extended Abstract: Structure determination of symmetric protein complexes by a complete search of symmetry configuration space using NMR distance restraints", Proc. WAFR, 2006. [preprint]

Structural studies of symmetric homo-oligomers (protein complexes with similar subunits arranged symmetrically) provide mechanistic insights into their roles in essential biological processes. We have developed a novel algorithm for homo-oligomeric structure determination that is both complete, in that it evaluates all possible conformations and data-driven, in that it evaluates conformations separately for consistency with experimental data and for quality of packing. Our algorithm determines homo-oligomeric structures by performing a branch-and-bound search in the symmetry configuration space, the space of symmetry axis parameters (positions and orientations) defining all possible C_n homo-oligomeric complexes for a fixed subunit structure. It eliminates those symmetry axes inconsistent with experimental inter-subunit distance restraints, and then identifies conformations representing any consistent, well-packed structure to within a user-defined similarity level. Our tests demonstrate the power of our method to provide an unbiased determination and evaluation of homo-oligomeric complex structures.