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PubMed · 12351823

Secondary structures at polypeptide-chain termini and their features.

Rajasri Bhattacharyya·Debnath Pal·Pinak Chakrabarti
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Abstract

An analysis of secondary structures (alpha-helices and beta-strands) in the two terminal regions of polypeptide chains reveals features different from those observed over the whole protein structure. Compared with the overall distribution, the helices in the N-terminal region tend to be smaller and have higher propensities to contain Gln and Leu, while the C-terminal helices are longer and have a greater proportion of Lys and Glu. As a strand, the C-terminal region is never found in the interior of parallel beta-sheets and has a higher propensity to be at the edge of antiparallel beta-sheets. In contrast, compared with the whole structure the N-terminal region has a higher propensity to be in the interior of parallel beta-sheets. Compared with the overall distributions, terminal helices and strands show distinct periodicities in length. The Schellman motif, which is a prevalent C-capping motif in helices, is not common in C-terminal helices. There are other observations that can be used in the design of helical peptides: more residues beyond the C-terminus of helices are used for capping interactions than residues before the N-terminus. Consideration of the distribution of terminal strands in the interior and at the edge of beta-sheets suggests a sequential folding mechanism beginning at the N-terminus of the polypeptide chain.

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Amino Acid SequenceAmino AcidsCrystallography, X-RayHydrogen BondingModels, MolecularPeptidesProtein FoldingProtein Structure, SecondaryJournal ArticleResearch Support, Non-U.S. Gov't

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Rajasri Bhattacharyya, Debnath Pal, Pinak Chakrabarti. 2002-09-28. Secondary structures at polypeptide-chain termini and their features.. https://doi.org/10.1107/s0907444902013069

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