Symmetry-Constrained Analysis of Pulsed Double Electron–Electron Resonance (DEER) Spectroscopy Reveals the Dynamic Nature of the KcsA Activation Gate
| Autor: | H. Clark Hyde, Raymond E. Hulse, Eduardo Perozo, Olivier Dalmas |
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| Rok vydání: | 2012 |
| Předmět: |
Models
Molecular Potassium Channels KcsA potassium channel Electron Biochemistry Resonance (particle physics) Article Catalysis Standard Model Tikhonov regularization Colloid and Surface Chemistry Nuclear magnetic resonance Bacterial Proteins Statistical physics Protein Structure Quaternary Spectroscopy Quantitative Biology::Biomolecules Chemistry Electron Spin Resonance Spectroscopy Reproducibility of Results General Chemistry Symmetry (physics) Protein Structure Tertiary Distribution (mathematics) Streptomyces lividans Protein Multimerization Ion Channel Gating |
| Zdroj: | Journal of the American Chemical Society. 134:16360-16369 |
| ISSN: | 1520-5126 0002-7863 |
| DOI: | 10.1021/ja3069038 |
| Popis: | Distance determination from an echo intensity modulation obtained by pulsed double electron-electron resonance (DEER) experiment is a mathematically ill-posed problem. Tikhonov regularization yields distance distributions that can be difficult to interpret, especially in system with multiple discrete distance distributions. Here, we show that by using geometric fit constraints in symmetric homo-oligomeric protein systems, we were able to increase the accuracy of a model-based fit solution based on a sum of Gaussian distributions. Our approach was validated on two different ion channels of known oligomeric states, KcsA (a tetramer) and CorA (a pentamer). Statistical analysis of the resulting fits was integrated within our method to help the experimenter evaluate the significance of a symmetry-constrained vs. standard model distribution fit and to examine multi-distance confidence regions. This approach was used to quantitatively evaluate the role of the C-terminal domain (CTD) on the flexibility and conformation of the activation gate of the K+ channel KcsA. Our analysis reveals a significant increase in the dynamics of the inner bundle gate upon opening. Also, it explicitly demonstrates the degree to which the CTD restricts the motion of the lower gate at rest and during activation gating. |
| Databáze: | OpenAIRE |
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