Secondary structures at polypeptide-chain termini and their features

Acta Crystallographica. Section D, Biological Crystallography
Rajasri BhattacharyyaP Chakrabarti

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 bet...Continue Reading

Citations

Jan 20, 2005·Proceedings of the National Academy of Sciences of the United States of America·Mallela M G Krishna, S W Englander
Nov 11, 2005·Proteins·Alessandro Laio, Cristian Micheletti
Nov 16, 2013·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·M LundgrenAntti J Niemi

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