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An analysis of the helix‐to‐strand transition between peptides with identical sequence
Author(s) -
Zhou Xianghong,
Alber Frank,
Folkers Gerd,
Gonnet Gaston H.,
Chelvanayagam Gareth
Publication year - 2000
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 - 10.1002/1097-0134(20001101)41:2<248::aid-prot90>3.0.co;2-j
Subject(s) - peptide , sequence (biology) , peptide sequence , ambivalence , amino acid , transition (genetics) , protein secondary structure , biology , computational biology , protein structure , sequence analysis , preference , helix (gastropod) , alpha helix , genetics , evolutionary biology , biochemistry , psychology , mathematics , gene , ecology , social psychology , statistics , snail
Abstract An analysis of peptide segments with identical sequence but that differ significantly in structure was performed over non‐redundant databases of protein structures. We focus on those peptides, which fold into an α‐helix in one protein but a β‐strand in another. While the study shows that many such structurally ambivalent peptides contain amino acids with a strong helical preference collocated with amino acids with a strong strand preference, the results overwhelmingly indicate that the peptide's environment ultimately dictates its structure. Furthermore, the first naturally occurring structurally ambivalent nonapeptide from evolutionary unrelated proteins is described, highlighting the intrinsic plasticity of peptide sequences. We even find seven proteins that show structural ambivalence under different conditions. Finally, a computer algorithm has been implemented to identify regions in a given sequence where secondary structure prediction programs are likely to make serious mispredictions. Proteins 2000;41:248–256. © 2000 Wiley‐Liss, Inc.