Analysis of insertions/deletions in protein structures.
An analysis of insertions and deletions (indels) occurring in a databank of multiple sequence alignments based on protein tertiary structure is reported. Indels prefer to be short (1 to 5 residues). The average intervening sequence length between them versus the percentage of residue identity in pairwise alignments shows an exponential behaviour, suggesting a stochastic process such that nearly every loop in an ancestral structure is a possible target for indels during evolution. The results also suggest a limit to the average size of indels accommodated by protein structures. The preferred indel conformations are reverse turn and coil as are the preferred conformations at the indel edges (N- and C-terminal sides). Interruptions in helices and strands were observed as very rare events.
Pascarella
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European Molecular Biology Laboratory, Heidelberg, Germany.
Argos
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P
D000595:Amino Acid Sequence; D000818:Animals; D016208:Databases, Factual; D006801:Humans; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009154:Mutation; D011506:Proteins / Q000737:chemistry* / Q000235:genetics; D016415:Sequence Alignment
D011506:Proteins