title: Can natural proteins designed with 'inverted' peptide sequences adopt native-like protein folds?
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.
authors.affiliation: Bioinformatics, Centre for Cellular and Molecular Biology, Hyderabad, Telangana, India.
authors.forename: Settu
authors.initials: S
authors.lastname: Sridhar
authors.affiliation: Bioinformatics, Centre for Cellular and Molecular Biology, Hyderabad, Telangana, India.
authors.forename: Kunchur
authors.initials: K
authors.lastname: Guruprasad
mesh_terms: D000595:Amino Acid Sequence; D003198:Computer Simulation; D008958:Models, Molecular; D015202:Protein Engineering; D017510:Protein Folding; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D012984:Software
chemical_list: D011506:Proteins