Structure calculation strategies for helical membrane proteins; a comparison study

Structure predictions of helical membrane proteins have been designed to take advantage of the structural autonomy of secondary structure elements, as postulated by the two-stage model of Engelman and Popot. In this context, we investigate structure calculation strategies for two membrane proteins with different functions, sizes, aminoacid compositions, and topologies: the glycophorin A homodimer (a paradigm for close inter-helical packing in membrane proteins) and aquaporin (a channel protein). Our structure calculations are based on two alternative folding schemes: a one-step simulated annealing from an extended chain conformation, and a two-step procedure inspired by the grid-search methods traditionally used in membrane protein predictions. In this framework, we investigate rationales for the utilization of sparse NMR data such as distance-based restraints and residual dipolar couplings in structure calculations of helical membrane proteins.