2005/05/06 by Ileana Stoica, Stoica, Ileana
Biochemistry, Genetics and Molecular Biology · Physics and Astronomy · #Biomolecules (q-bio.BM) #FOS: Biological sciences #Lipid Membrane Structure and Behavior #Origins and Evolution of Life #q-bio.BM
paper · pdf · doi:10.48550/arxiv.q-bio/0505014
openalex publication_date 2005/05/06 · arxiv created 2005/08/21 · arxiv updated 2009/12/01 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
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.