Biology – Quantitative Biology – Biomolecules
Scientific paper
2005-05-06
Biology
Quantitative Biology
Biomolecules
Scientific paper
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.
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