In Search of Functional Advantages of Knots in Proteins.
We analysed the structure of deeply knotted proteins representing three unrelated families of knotted proteins. We looked at the correlation between positions of knotted cores in these proteins and such local structural characteristics as the number of intra-chain contacts, structural stability and solvent accessibility. We observed that the knotted cores and especially their borders showed strong enrichment in the number of contacts. These regions showed also increased thermal stability, whereas their solvent accessibility was decreased. Interestingly, the active sites within these knotted proteins preferentially located in the regions with increased number of contacts that also have increased thermal stability and decreased solvent accessibility. Our results suggest that knotting of polypeptide chains provides a favourable environment for the active sites observed in knotted proteins. Some knotted proteins have homologues without a knot. Interestingly, these unknotted homologues form local entanglements that retain structural characteristics of the knotted cores.
Centre of New Technologies, Banacha 2c, 02-097, Warsaw, Poland.|Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093, Warsaw, Poland.|Center for Integrative Genomics, University of Lausanne, 1015-Lausanne, Switzerland.
Pawel
P
Dabrowski-Tumanski
Center for Integrative Genomics, University of Lausanne, 1015-Lausanne, Switzerland.|SIB Swiss Institute of Bioinformatics, 1015-Lausanne, Switzerland.
Andrzej
http://orcid.org/0000-0002-0398-1989
A
Stasiak
Centre of New Technologies, Banacha 2c, 02-097, Warsaw, Poland.|Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093, Warsaw, Poland.
Joanna I
JI
Sulkowska
D020134:Catalytic Domain; D008958:Models, Molecular; D017510:Protein Folding; D055550:Protein Stability; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D012997:Solvents / Q000737:chemistry
D011506:Proteins; D012997:Solvents