title: Conformational characterization of disulfide bonds: a tool for protein classification.
abstract: BACKGROUND
  Throughout evolution, mutations in particular regions of some protein structures have resulted in extra covalent bonds that increase the overall robustness of the fold: disulfide bonds. The two strategically placed cysteines can also have a more direct role in protein function, either by assisting thiol or disulfide exchange, or through allosteric effects. In this work, we verified how the structural similarities between disulfides can reflect functional and evolutionary relationships between different proteins. We analyzed the conformational patterns of the disulfide bonds in a set of disulfide-rich proteins that included twelve SCOP superfamilies: thioredoxin-like and eleven superfamilies containing small disulfide-rich proteins (SDP).
  
  
  RESULTS
  The twenty conformations considered in the present study were characterized by both structural and energetic parameters. The corresponding frequencies present diverse patterns for the different superfamilies. The least-strained conformations are more abundant for the SDP superfamilies, while the "catalytic" +/-RHook is dominant for the thioredoxin-like superfamily. The "allosteric" -RHSaple is moderately abundant for BBI, Crisp and Thioredoxin-like superfamilies and less frequent for the remaining superfamilies. Using a hierarchical clustering analysis we found that the twelve superfamilies were grouped in biologically significant clusters.
  
  
  CONCLUSIONS
  In this work, we carried out an extensive statistical analysis of the conformational motifs for the disulfide bonds present in a set of disulfide-rich proteins. We show that the conformational patterns observed in disulfide bonds are sufficient to group proteins that share both functional and structural patterns and can therefore be used as a criterion for protein classification.
authors.affiliation: REQUIMTE/Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre 687, 4169-007 Porto, Portugal. zerui.marques@fc.up.pt
authors.forename: José Rui Ferreira
authors.initials: JR
authors.lastname: Marques
authors.forename: Rute R
authors.initials: RR
authors.lastname: da Fonseca
authors.forename: Brett
authors.initials: B
authors.lastname: Drury
authors.forename: André
authors.initials: A
authors.lastname: Melo
mesh_terms: D000465:Algorithms; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods*; D003553:Cystine / Q000737:chemistry; D004220:Disulfides / Q000737:chemistry*; D008958:Models, Molecular; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000145:classification*
chemical_list: D004220:Disulfides; D011506:Proteins; D003553:Cystine