Prediction of strand pairing in antiparallel and parallel beta-sheets using information theory.
An information theory approach was developed to predict the alignment of interacting antiparallel and parallel beta-strands. Information scores were derived for the preference of a residue on a beta-strand to be opposite a sequence of residues on an adjacent beta-strand. These scores were used to predict the interstrand register of interacting beta-strands from 10 alternative offset positions either side of the experimentally observed beta-sheet register. The amino acid sequence of an internal beta-strand can be correctly aligned with two beta-strands in a fixed position either side of the strand in 45% of antiparallel and 48% of parallel arrangements. For comparison, when another beta-strand from a nonhomologous protein substitutes the internal beta-strand, the same register is predicted for only 24 and 36% of antiparallel and parallel arrangements. As expected, alignment of a single fixed strand with just a second beta-strand sequence was more difficult, and gave a correct register in 31 and 37% of antiparallel and parallel beta-pairs, respectively. These scores are 10% higher than for two randomly selected beta-strand sequences. In general, prediction accuracy was not improved by information tables that distinguished hydrogen-bonding patterns or beta-strand order. These results will contribute to predicting the arrangement of beta-strands in beta-pleated sheets and protein topology.
Steward
Robert E
RE
EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom. steward@ebi.ac.uk
Thornton
Janet M
JM
D000595:Amino Acid Sequence; D000596:Amino Acids / Q000737:chemistry; D006860:Hydrogen Bonding; D007257:Information Theory; D008958:Models, Molecular; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D015203:Reproducibility of Results; D016415:Sequence Alignment; D020539:Sequence Analysis, Protein / Q000379:methods*
D000596:Amino Acids; D011506:Proteins