Name
Title | ||
|---|---|---|
Simulation of conformational changes occurring when a protein interacts with its receptor. |
Abstract | ||
|---|---|---|
In order to simulate the conformational changes occurring when a protein interacts with its receptor, we firstly evaluated the structural differences between the experimental unbound and bound conformations for selected proteins and created theoretical complexes by replacing, in each experimental complex, the protein-bound with the protein-unbound chain. The theoretical models were then subjected to additional modeling refinements to improve the side chain geometry. Comparing the theoretical and experimental complexes in term of structural and energetic factors is resulted that the refined theoretical complexes became more similar to the experimental ones. We applied the same procedure within an homology modeling experiment, using as templates the experimental structures of human interleukin-1beta (IL-1beta) unbound and bound with its receptor, to build models of the homologous proteins from mouse and trout in unbound and bound conformations and to simulate the interaction with the related receptors. Our results suggest that homology modeling techniques are sensitive to differences between bound and unbound conformations, and that modeling with accuracy the side chains in the complex improves the interaction and molecular recognition. Moreover, our refinement procedure could be used in protein-protein interaction studies and, also, applied in conjunction with rigid-body docking when is not available the protein-bound conformation. |
Year | DOI | Venue |
|---|---|---|
2007 | 10.1016/j.compbiolchem.2007.03.010 | Computational Biology and Chemistry |
Keywords | Field | DocType |
comparative assessment of structure prediction,theoretical complex,root mean square deviation,homology modeling technique,il-1β receptor,experimental structure,accessible surface area,fibroblast growth factor,protein data bank,fibroblast growth factor receptor,asa,fgf,additional modeling refinement,three-dimensional,rmsd,experimental complex,tgf,homology modeling experiment,pdb,interleukin-1 beta,conformational change,il-1β,granulocyte colony stimulating factor,casp,protein–receptor complex,experimental unbound,fgfr,g-csf,molecular modeling,conformational changes,refined theoretical complex,il-1r,theoretical model,bound conformation,transforming growth factor,protein interacts,3d,protein–protein interaction,homology modeling,rigid body,molecular recognition,protein protein interaction | Protein–protein interaction,Molecular recognition,Chemistry,Protein superfamily,Bioinformatics,Molecular model,Homology modeling,Protein Data Bank (RCSB PDB),Side chain,Protein structure | Journal |
Volume | Issue | ISSN |
31 | 3 | 1476-9271 |
Citations | PageRank | References |
0 | 0.34 | 2 |
Authors | ||
3 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| S Costantini | 1 | 0 | 0.34 |
| Giovanni Colonna | 2 | 4 | 3.38 |
| Angelo M. Facchiano | 3 | 2 | 4.04 |