title: Normal-mode refinement of anisotropic thermal parameters for potassium channel KcsA at 3.2 A crystallographic resolution.
abstract: We report a normal-mode method for anisotropic refinement of membrane-protein structures, based on a hypothesis that the global near-native-state disordering of membrane proteins in crystals follows low-frequency normal modes. Thus, a small set of modes is sufficient to represent the anisotropic thermal motions in X-ray crystallographic refinement. By applying the method to potassium channel KcsA at 3.2 A, we obtained a structural model with an improved fit with the diffraction data. Moreover, the improved electron density maps allowed for large structural adjustments for 12 residues in each subunit, including the rebuilding of 3 missing side chains. Overall, the anisotropic KcsA structure at 3.2 A was systematically closer to a 2.0 A KcsA structure, especially in the selectivity filter. Furthermore, the anisotropic thermal ellipsoids from the refinement revealed functionally relevant structural flexibility. We expect this method to be a valuable tool for structural refinement of many membrane proteins with moderate-resolution diffraction data.
authors: Graduate Program of Structural and Computational Biology and Molecular Biophysics, Rice University, Houston, TX 77005, USA.
authors: Xiaorui
authors: X
authors: Chen
authors: Billy K
authors: BK
authors: Poon
authors: Athanasios
authors: A
authors: Dousis
authors: Qinghua
authors: Q
authors: Wang
authors: Jianpeng
authors: J
authors: Ma
mesh_terms: D000595:Amino Acid Sequence; D016880:Anisotropy; D018360:Crystallography, X-Ray / Q000379:methods*; D008958:Models, Molecular; D015221:Potassium Channels / Q000737:chemistry* / Q000378:metabolism; D011487:Protein Conformation; D017433:Protein Structure, Secondary
chemical_list: D015221:Potassium Channels
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