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Influence of charge and size of terminal amino‐acid residues on local conformational states and shape of alanine‐based peptides
Author(s) -
Makowska Joanna,
Bagińska Katarzyna,
Skwierawska Agnieszka,
Liwo Adam,
Chmurzyński Lech,
Scheraga Harold A.
Publication year - 2008
Publication title -
peptide science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.21077
Subject(s) - polyproline helix , chemistry , alanine , peptide , circular dichroism , crystallography , amino acid , molecular dynamics , stereochemistry , computational chemistry , biochemistry
We present results of conformational studies by Circular dichroism and NMR spectroscopy, differential scanning calorimetry, and molecular dynamics, of three alanine‐based peptides: Ac‐KK‐(A) 7 ‐KK‐NH 2 (KAK), Ac‐OO‐(A) 7 ‐DD‐NH 2 (OAD), and Ac‐KK‐(A) 7 ‐EE‐NH 2 (KAE), where A, K, O, D, and E, denote alanine, lysine, ornithine, aspartic acid, and glutamic acid residues, respectively. For OAD and KAE, canonical MD simulations with time‐averaged NMR‐derived restraints demonstrate the presence of an ensemble of structures with a variety of conformational states (polyproline II, α‐helical, α′, and extended, turn); for KAK the conformational states are predominantly polyproline II and extended. The OAD peptide exhibits a bent shape with its ends close to each other, whereas KAK and KAE are more extended. The bent shape was also observed in our earlier study of the Ac‐XX‐(A) 7 ‐OO‐NH 2 (XAO) peptide, where X denotes the diaminobutyric acid residue; therefore, the shape seems to depend on the size of the charged side chains at the ends of the alanine sequence and not on their kind. This suggests that the bent shape of the alanine sequence is formed to enable screening of this nonpolar sequence from the solvent by sufficiently short charged side chains. As in our previous study of the XAO peptide, no long polyproline II segments were observed. © 2008 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 85:772‐782, 2008. This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com