Biochemical and Biophysical Research Communications
Amino acid propensities for secondary structures are influenced by the protein structural class
Section snippets
Methods
Database and definition of protein secondary structure. All analyses were performed using PDBselect [48] as a set of experimentally determined, non-redundant protein structures in the Protein Data Bank (see http://homepages.fh-giessen.de/~hg12640/pdbselect ). We used the PDBselect list with <25% sequence homology, released in December 2003, which contained 2216 protein chains.
The secondary structure for every PDB entry was assigned by the DSSP algorithm [49] based on the analysis of backbone
Analysis of PDBselect as a unique set
The PDBselect release of December 2003 included 2216 structures having homology percentage <25%. We assigned the secondary structure for 2168 proteins by using the DSSP program (the others report only α carbons and DSSP did not assign the secondary structure). We simplified the 8-state secondary structure as a three-state secondary structure, considering H, G, and I as helix, B and E as β structure, and the others as coil (see Methods for details about the 8 states).
We calculated the
Discussion
We calculated the amino acid propensities in helix, β-strand, and coil for all proteins in the PDBselect dataset and evaluated their reliability by using them to predict the secondary structure of proteins. The quality of these predictions was examined by resubstitution and jackknife tests. Results obtained with the two tests are in general very similar (differences of 0.1–0.2%), and in particular when the number of proteins in the dataset was higher. This may reflect the fact that in the
Acknowledgments
This work was partially supported by MIUR-FIRB project (Grant RBNE0157EH_003) and by Rete di Spettrometria di Massa (contract FERS n. 94.05.09.103, ARINCO N. 94.IT.16.028). Ph.D. fellowship of Dr. Susan Costantini is supported by E.U.
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