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Porin conformation in the absence of calcium. Refined structure at 2.5 A resolution
1Institut für Organische Chemie und Biochemie, Albert-Ludwigs-Universität, Freiburg im Breisgau, Germany.
Abstract:
The crystal structure of porin from Rhodobacter capsulatus in the absence of divalent calcium ions has been refined to convergence at a resolution of 2.5 A using the simulated annealing refinement method. The final model consists of all 301 amino acid residues, 77 solvent molecules, one tris(hydroxymethyl)-aminomethane molecule and one unknown ligand modeled as n-octyltetraoxyethylene. A superposition with the previously described model containing three calcium ions showed structural changes at the segment 108-116 of the inner loop beta 5-beta 6, and at loops beta 8-beta 9 and beta 11-beta 12 at the extracellular side of the porin molecule. Evidence is presented that the conformational changes depend on the presence or absence of calcium ions. A possible influence on porin function is discussed.
Insights
The crystal structure of Rhodobacter capsulatus porin without calcium ions reveals significant conformational changes. These structural alterations, dependent on calcium presence, may influence porin function.
Area of Science:
- Structural biology
- Biochemistry
- Microbiology
Background:
- Porins are essential outer membrane proteins involved in transport.
- Understanding porin structure is crucial for deciphering cellular transport mechanisms.
- Rhodobacter capsulatus porin serves as a model system for studying porin structure-function relationships.
Purpose of the Study:
- To refine the crystal structure of Rhodobacter capsulatus porin in the absence of divalent calcium ions.
- To investigate the structural impact of calcium ions on porin conformation.
- To explore potential functional implications of observed structural changes.
Main Methods:
- X-ray crystallography
- Simulated annealing refinement method
- Structural comparison of porin models with and without calcium ions
Main Results:
- The crystal structure of Rhodobacter capsulatus porin was refined to 2.5 A resolution.
- Significant structural changes were observed in specific loop regions (108-116, beta 5-beta 6, beta 8-beta 9, beta 11-beta 12) upon calcium ion removal.
- The final model included 301 amino acid residues, solvent molecules, and identified ligands.
Conclusions:
- The presence or absence of calcium ions demonstrably influences the conformation of Rhodobacter capsulatus porin.
- Observed conformational changes suggest a potential role for calcium ions in modulating porin function.
- Further studies are warranted to elucidate the functional consequences of calcium-dependent structural alterations.