J Mol Biol. 1992 Mar 20;224(2):461-71.

Analysis of insertions/deletions in protein structures.

Source

European Molecular Biology Laboratory, Heidelberg, Germany.

Abstract

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.

PMID:: 1560462; [PubMed - indexed for MEDLINE]

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Research Support, Non-U.S. Gov't

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Proteins

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