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Preservation of protein clefts in comparative models

AutorPiedra, David; Lois, Sergi; Cruz, Xavier de la
Palabras claveProtein structure
Homology models
Protein clefts
Cleft quality
Sequence identity
Fecha de publicación16-ene-2008
EditorBioMed Central
CitaciónBMC Structural Biology 2008, 8:2
Resumen[Background] Comparative, or homology, modelling of protein structures is the most widely used prediction method when the target protein has homologues of known structure. Given that the quality of a model may vary greatly, several studies have been devoted to identifying the factors that influence modelling results. These studies usually consider the protein as a whole, and only a few provide a separate discussion of the behaviour of biologically relevant features of the protein. Given the value of the latter for many applications, here we extended previous work by analysing the preservation of native protein clefts in homology models. We chose to examine clefts because of their role in protein function/structure, as they are usually the locus of protein-protein interactions, host the enzymes' active site, or, in the case of protein domains, can also be the locus of domain-domain interactions that lead to the structure of the whole protein.
[Results] We studied how the largest cleft of a protein varies in comparative models. To this end, we analysed a set of 53507 homology models that cover the whole sequence identity range, with a special emphasis on medium and low similarities. More precisely we examined how cleft quality – measured using six complementary parameters related to both global shape and local atomic environment, depends on the sequence identity between target and template proteins. In addition to this general analysis, we also explored the impact of a number of factors on cleft quality, and found that the relationship between quality and sequence identity varies depending on cleft rank amongst the set of protein clefts (when ordered according to size), and number of aligned residues.
[Conclusion] We have examined cleft quality in homology models at a range of seq.id. levels. Our results provide a detailed view of how quality is affected by distinct parameters and thus may help the user of comparative modelling to determine the final quality and applicability of his/her cleft models. In addition, the large variability in model quality that we observed within each sequence bin, with good models present even at low sequence identities (between 20% and 30%), indicates that properly developed identification methods could be used to recover good cleft models in this sequence range.
DescripciónAdditional material: 5 supplementary files.
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Preservation_protein_clefts.pdfMain text of the paper860,4 kBAdobe PDFVista previa
Preservation_protein_clefts_suppl1.pdfRMSD vs. Cleft Sequence Identity21,8 kBAdobe PDFVista previa
Preservation_protein_clefts_suppl2.pdfSide-chain Contribution to GDT_4 and GDT_8 vs.Sequence Identity18,13 kBAdobe PDFVista previa
Preservation_protein_clefts_suppl3.pdfDependence of results on protein family39,04 kBAdobe PDFVista previa
Preservation_protein_clefts_suppl4.pdfDependence of results on cavity rank42,29 kBAdobe PDFVista previa
Preservation_protein_clefts_suppl5.gzList of target-template pairs used173,67 kBWinRAR (gz file)Visualizar/Abrir
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