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Prediction of strand pairing in antiparallel and parallel β‐sheets using information theory
Author(s) -
Steward Robert E.,
Thornton Janet M.
Publication year - 2002
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.10152
Subject(s) - antiparallel (mathematics) , coding strand , single strand , sequence (biology) , beta sheet , crystallography , mathematics , algorithm , combinatorics , physics , computer science , protein structure , chemistry , dna , genetics , biology , polymerase , nuclear magnetic resonance , quantum mechanics , magnetic field
An information theory approach was developed to predict the alignment of interacting antiparallel and parallel β‐strands. Information scores were derived for the preference of a residue on a β‐strand to be opposite a sequence of residues on an adjacent β‐strand. These scores were used to predict the interstrand register of interacting β‐strands from 10 alternative offset positions either side of the experimentally observed β‐sheet register. The amino acid sequence of an internal β‐strand can be correctly aligned with two β‐strands in a fixed position either side of the strand in 45% of antiparallel and 48% of parallel arrangements. For comparison, when another β‐strand from a nonhomologous protein substitutes the internal β‐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 β‐strand sequence was more difficult, and gave a correct register in 31 and 37% of antiparallel and parallel β‐pairs, respectively. These scores are 10% higher than for two randomly selected β‐strand sequences. In general, prediction accuracy was not improved by information tables that distinguished hydrogen‐bonding patterns or β‐strand order. These results will contribute to predicting the arrangement of β‐strands in β‐pleated sheets and protein topology. Proteins 2002;48:178–191. © 2002 Wiley‐Liss, Inc.