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Equilibrium unfolding of the poly(glutamic acid) 20 helix
Author(s) -
Finke John M.,
Jennings Patricia A.,
Lee Jennifer C.,
Onuchic José N.,
Winkler Jay R.
Publication year - 2007
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.20719
Subject(s) - chemistry , helix (gastropod) , circular dichroism , intramolecular force , polyproline helix , alpha helix , crystallography , förster resonance energy transfer , random coil , polyglutamic acid , molecular dynamics , stereochemistry , peptide , fluorescence , computational chemistry , physics , ecology , biochemistry , quantum mechanics , snail , biology
Abstract The equilibrium structural ensemble of a 20‐residue polyglutamic acid peptide (E 20 ) was studied with FRET, circular dichroism, and molecular dynamics (MD) simulations. A FRET donor, o ‐aminobenzamide, and acceptor, 3‐nitrotyrosine, were introduced at the N‐ and C‐termini, respectively. Circular dichroism, steady state FRET, and time‐resolved FRET measurements were employed to characterize the fraction helix and end‐to‐end distance under different pH conditions: pH 4 (60% α‐helix), pH 6 (0% α‐helix), and pH 9 (0% α‐helix). At pH 4, the end‐to‐end distance was measured at 24 Å and determined to be considerably less than the 31 Å predicted for an α‐helix of the same length. At pH 6 and 9, the end‐to‐end distance was measured at > 31 and 39 Å respectively, both which are determined to be considerably greater than the 27 Å predicted for a freely jointed random coil of the same length. To better understand the physical forces underlying the unusual helix‐coil transition in this peptide, three theoretical MD models of E 20 were constructed: (1) a pure α‐helix, (2) an α‐helix with equivalent attractive intramolecular contacts, and (3) a weak α‐helix with termini‐weighted intramolecular contacts (“sticky ends”). Using MD simulations, the bent helix structure calculated from Model 3 was found to be the closest in agreement with the experimental data. © 2007 Wiley Periodicals, Inc. Biopolymers 86: 193–211, 2007. 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