Homonyms and synonyms in the Dictionary of Interfaces in Proteins (DIP).
BACKGROUND
Should reports on molecular mimicry in particular cases, e.g. responsible for cross-reactivity, be considered as accidental or as a general principle in protein evolution? To answer this question, two types of similarity have to be considered: those in homologues (synonyms) and resemblance between patches from unrelated proteins (homonyms).


RESULTS
All interfaces from known protein structures were collected in a comprehensive data bank [Dictionary of Interfaces in Proteins (DIP)]. A fast, sequence-independent, three-dimensional superposition procedure was developed to search automatically for geometrically similar surface areas. Surprisingly, we found a large number of structurally similar interfaces on the surface of unrelated proteins. Even patches from different types of secondary structure were found resembling each other. The putative functional meaning of homonyms is demonstrated with striking examples.
Preissner
R
R
Medical Faculty, Humboldt University, Charité, Institute of Biochemistry, Berlin, Germany. preissner@rz.hu-berlin.de
Goede
A
A
Frömmel
C
C
D000465:Algorithms; D000595:Amino Acid Sequence; D019295:Computational Biology; D016208:Databases, Factual; D004015:Dictionaries, Chemical as Topic; D008958:Models, Molecular; D018716:Molecular Mimicry; D008969:Molecular Sequence Data; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000235:genetics*
D011506:Proteins