Hydrogen-bond pattern and structural vulnerabilities (SEBHs) of the yeast SH3 domain and the human prion protein PrPC. (a) Hydrogen-bond pattern and structural vulnerabilities (SEBHs) of the yeast SH3 domain from a S. cerevisiae 40.4 kDa protein (PDB.1SSH) . The ribbon display is included as a visual aid. The protein backbone is shown as virtual bonds (blue) joining consecutive α-carbons in the peptide chain. Light-grey segments represent well protected backbone hydrogen bonds, and green segments represent SEBHs. The extent of solvent-exposure extent of a hydrogen bond was determined from atomic coordinates by calculating the number of nonpolar groups within its microenvironment (Materials and methods). SEBHs are those backbone hydrogen bonds protected by an insufficient number of nonpolar groups as statistically defined in Materials and methods. The level of structure vulnerability ν, defined as the ratio of SEBHs to the overall number of backbone hydrogen bonds, is 19.0% (ν = 4/21). (b) SEBH-pattern for the cellular structure of the human prion protein PrPC (PDB.1QM0) . Its vulnerability parameter is ν = 63.0%, making it the most vulnerable soluble folder of all structures of unbound proteins reported in the PDB.
Chen et al. Genome Biology 2008 9:R107 doi:10.1186/gb-2008-9-7-r107