1dwl
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(New page: 200px<br /><applet load="1dwl" size="450" color="white" frame="true" align="right" spinBox="true" caption="1dwl" /> '''THE FERREDOXIN-CYTOCHROME COMPLEX USING HETE...)
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Revision as of 11:31, 20 November 2007
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THE FERREDOXIN-CYTOCHROME COMPLEX USING HETERONUCLEAR NMR AND DOCKING SIMULATION
Overview
The combination of docking algorithms with NMR data has been developed, extensively for the studies of protein-ligand interactions. However, to, extend this development for the studies of protein-protein interactions, the intermolecular NOE constraints, which are needed, are more difficult, to access. In the present work, we describe a new approach that combines, an ab initio docking calculation and the mapping of an interaction site, using chemical shift variation analysis. The cytochrome c553-ferredoxin, complex is used as a model of numerous electron-transfer complexes. The, 15N-labeling of both molecules has been obtained, and the mapping of the, interacting site on each partner, respectively, has been done using HSQC, experiments. 1H and 15N chemical shift analysis defines the area of both, molecules involved in the recognition interface. Models of the complex, were generated by an ab initio docking software, the BiGGER program, (bimolecular complex generation with global evaluation and ranking). This, program generates a population of protein-protein docked geometries ranked, by a scoring function, combining relevant stabilization parameters such as, geometric complementarity surfaces, electrostatic interactions, desolvation energy, and pairwise affinities of amino acid side chains. We, have implemented a new module that includes experimental input (here, NMR, mapping of the interacting site) as a filter to select the accurate, models. Final structures were energy minimized using the X-PLOR software, and then analyzed. The best solution has an interface area (1037.4 A2), falling close to the range of generally observed recognition interfaces, with a distance of 10.0 A between the redox centers.
About this Structure
1DWL is a Protein complex structure of sequences from Desulfovibrio desulfuricans and Desulfovibrio vulgaris with SF4 and HEC as ligands. Full crystallographic information is available from OCA.
Reference
Heteronuclear NMR and soft docking: an experimental approach for a structural model of the cytochrome c553-ferredoxin complex., Morelli X, Dolla A, Czjzek M, Palma PN, Blasco F, Krippahl L, Moura JJ, Guerlesquin F, Biochemistry. 2000 Mar 14;39(10):2530-7. PMID:10704202
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