ArticleBiophysical journal2001
Calculation of rigid-body conformational changes using restraint-driven Cartesian transformations.
Article in Biophysical journal, 2001. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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10 citing papers in PubMed, 21 citations in OpenAlex.
- Molecular rearrangements in S6 during slow inactivation in Shaker-IR potassium channels.The Journal of general physiology · 2023Article
- Inferring functional units in ion channel pores via relative entropy.European biophysics journal : EBJ · 2021Article
- Molecular mechanism of Mg2+-dependent gating in CorA.Nature communications · 2014Article
- Broad disorder and the allosteric mechanism of myosin II regulation by phosphorylation.Proceedings of the National Academy of Sciences of the United States of America · 2011Article
- Normal mode analysis of biomolecular structures: functional mechanisms of membrane proteins.Chemical reviews · 2010Review
- Structural refinement of membrane proteins by restrained molecular dynamics and solvent accessibility data.Biophysical journal · 2008Article
- High-resolution structure of a Na+/H+ antiporter dimer obtained by pulsed electron paramagnetic resonance distance measurements.Biophysical journal · 2007Article
- Detection of the opening of the bundle crossing in KcsA with fluorescence lifetime spectroscopy reveals the existence of two gates for ion conduction.The Journal of general physiology · 2006Article
- Dipolar coupling between nitroxide spin labels: the development and application of a tether-in-a-cone model.Biophysical journal · 2006Article
- Intrinsic flexibility and gating mechanism of the potassium channel KcsA.Proceedings of the National Academy of Sciences of the United States of America · 2002Article
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Authors and funding
3 authors at 1 institution in 1 country.
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No grant is acknowledged in the PubMed record.
Abstract
We present an approach for calculating conformational changes in membrane proteins using limited distance information. The method, named restraint-driven Cartesian transformations, involves 1) the use of relative distance changes; 2) the systematic sampling of rigid body movements in Cartesian space; 3) a penalty evaluation; and 4) model refinement using energy minimization. As a test case, we have analyzed the structural basis of activation gating in the Streptomyces lividans potassium channel (KcsA). A total of 10 pairs of distance restraints derived from site-directed spin labeling and electron paramagnetic resonance (SDSL-EPR) spectra were used to calculate the open conformation of the second transmembrane domains of KcsA (TM2). The SDSL-EPR based structure reveals a gating mechanism consistent with a scissoring-type motion of the TM2 segments that includes a pivot point near middle of the helix. The present approach considerably reduces the amount of time and effort required to establish the overall nature of conformational changes in membrane proteins. It is expected that this approach can be implemented into restrained molecular dynamics protocol to calculate the structure and conformational changes in a variety of membrane protein systems.
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