Abstract
We have carried out a systematic computational analysis on a representative dataset of proteins of known three-dimensional structure, in order to evaluate whether it would possible to ‘swap’ certain short peptide sequences in naturally occurring proteins with their corresponding ‘inverted’ peptides and generate ‘artificial’ proteins that are predicted to retain native-like protein fold. The analysis of 3,967 representative proteins from the Protein Data Bank revealed 102,677 unique identical inverted peptide sequence pairs that vary in sequence length between 5–12 and 18 amino acid residues. Our analysis illustrates with examples that such ‘artificial’ proteins may be generated by identifying peptides with ‘similar structural environment’ and by using comparative protein modeling and validation studies. Our analysis suggests that natural proteins may be tolerant to accommodating such peptides.
Highlights
The relationship between amino acid sequences to their corresponding three-dimensional structures continues to be of interest to biologists and bio-informaticians
We analyzed the conformations associated with hexapeptide and longer sequences that occur as continuous amino acid repeats in proteins (CARPs) [2]
We examined whether heptapeptide and large sequences that entirely correspond to a helix, strand or coil conformation in one protein may be associated with a different conformation in another protein, thereby representing some of the ‘chameleon’ sequences in proteins [3]
Summary
The relationship between amino acid sequences to their corresponding three-dimensional structures continues to be of interest to biologists and bio-informaticians In this context, we have earlier developed a relational database – PSSARD, that can be used to query the conformations associated with any given peptide sequence in proteins of known three-dimensional structure [1]. While comparing proteins of less than 50% pair-wise sequence identity, only 0.5% of inversely aligned proteins had similar folds, whereas 9% of forwardly aligned proteins in the same range showed similar 3-D structures, supporting the view that the inversion of protein sequences in almost all cases lead to a different folding property of the protein It was suggested, that the inverted sequences were suitable as protein-like sequences for control purposes without relation to existing proteins. We provide a list of natural proteins containing potentially ‘swappable’ peptide sequences with ‘inverted’ peptide sequences
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