ArticleStructure (London, England : 1993)2007
Normal-mode refinement of anisotropic thermal parameters for potassium channel KcsA at 3.2 A crystallographic resolution.
Article in Structure (London, England : 1993), 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- Mapping Enzyme Landscapes by Time-Resolved Crystallography with Synchrotron and X-Ray Free Electron Laser Light.Annual review of biophysics · 2022Review
- Analyzing Fluctuation Properties in Protein Elastic Networks with Sequence-Specific and Distance-Dependent Interactions.Biomolecules · 2019Article
- X-ray Scattering Studies of Protein Structural Dynamics.Chemical reviews · 2017Review
- Aligning experimental and theoretical anisotropic B-factors: water models, normal-mode analysis methods, and metrics.The journal of physical chemistry. B · 2014Article
- Structural basis of actin filament nucleation by tandem W domains.Cell reports · 2013Article
- Targeted molecular dynamics (TMD) of the full-length KcsA potassium channel: on the role of the cytoplasmic domain in the opening process.Journal of molecular modeling · 2013Article
- PIM: phase integrated method for normal mode analysis of biomolecules in a crystalline environment.Journal of molecular biology · 2013Article
- An emerging consensus on voltage-dependent gating from computational modeling and molecular dynamics simulations.The Journal of general physiology · 2012Article
- fSUB: normal mode analysis with flexible substructures.The journal of physical chemistry. B · 2012Article
- Normal-mode-analysis-guided investigation of crucial intersubunit contacts in the cAMP-dependent gating in HCN channels.Biophysical journal · 2012Article
- Some B(eq) are more equivalent than others.Acta crystallographica. Section A, Foundations of crystallography · 2011Article
- Normal mode analysis with molecular geometry restraints: bridging molecular mechanics and elastic models.Archives of biochemistry and biophysics · 2011Article
- Validation of crystallographic models containing TLS or other descriptions of anisotropy.Acta crystallographica. Section D, Biological crystallography · 2010Article
- Structure of the full-length Shaker potassium channel Kv1.2 by normal-mode-based X-ray crystallographic refinement.Proceedings of the National Academy of Sciences of the United States of America · 2010Article
- Recent developments in phasing and structure refinement for macromolecular crystallography.Current opinion in structural biology · 2009Review
- Application of normal-mode refinement to X-ray crystal structures at the lower resolution limit.Acta crystallographica. Section D, Biological crystallography · 2009Article
- Article
- Structural improvement of unliganded simian immunodeficiency virus gp120 core by normal-mode-based X-ray crystallographic refinement.Acta crystallographica. Section D, Biological crystallography · 2009Article
- A minimalist network model for coarse-grained normal mode analysis and its application to biomolecular x-ray crystallography.Proceedings of the National Academy of Sciences of the United States of America · 2008Article
- Use of normal modes for structural modeling of proteins: the case study of rat heme oxygenase 1.European biophysics journal : EBJ · 2008Article
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5 authors.
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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.
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