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Inverse sequence similarity of proteins does not imply structural similarity
Author(s) -
Lorenzen Stephan,
Gille Christoph,
Preissner Robert,
Frömmel Cornelius
Publication year - 2003
Publication title -
febs letters
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.593
H-Index - 257
eISSN - 1873-3468
pISSN - 0014-5793
DOI - 10.1016/s0014-5793(03)00450-2
Subject(s) - protein data bank (rcsb pdb) , structural similarity , similarity (geometry) , inverse , pairwise comparison , protein structure , sequence (biology) , computational biology , superposition principle , protein secondary structure , structural alignment , protein design , protein folding , biology , peptide sequence , biological system , sequence alignment , mathematics , computer science , genetics , biochemistry , artificial intelligence , statistics , geometry , mathematical analysis , image (mathematics) , gene
There is a debate on the folding of proteins with inverted sequences. Theoretical approaches and experiments give contradictory results. Many proteins in the Protein Data Bank (PDB) show conspicuous inverse sequence similarity (ISS) to each other. Here we analyze whether this ISS is related to structural similarity. For the first time, we performed a large scale three‐dimensional (3‐D) superposition of corresponding Cα atoms of forwardly and inversely aligned proteins and tested the degree of secondary structure identity between them. Comparing proteins of less than 50% pairwise sequence identity, only 0.5% of the inversely aligned pairs had similar folds (99 out of 19 073), whereas about 9% of forwardly aligned proteins in the same score and length range show similar 3‐D structures (1731 out of 19 248). This observation strongly supports the view that the inversion of sequences in almost all cases leads to a different folding property of the protein. Inverted sequences are thus suitable as protein‐like sequences for control purposes without relations to existing proteins.