Journal
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
Volume 99, Issue 14, Pages 9190-9195Publisher
NATL ACAD SCIENCES
DOI: 10.1073/pnas.112193999
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- NIGMS NIH HHS [GM29458, R01 GM029458] Funding Source: Medline
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A sequence of seven alanine residues-too short to form an a-helix and whose side chains do not interact with each other-is a particularly simple model for testing the common description of denatured proteins as structureless random coils. The (3)J(HNalpha) coupling constants of individual alanine residues have been measured from 2 to 56degreesC by using isotopically labeled samples. The results display a thermal transition between different backbone conformations, which is confirmed by CD spectra. The NMR results suggest that polyproline H is the dominant conformation at 2degreesC and the content of p strand is increased by approximately 10% at 55degreesC relative to that at 2degreesC. The polyproline II conformation is consistent with recent studies of short alanine peptides, including structure prediction by ab initio quantum mechanics and solution structures for both a blocked alanine dipeptide and an alanine tripeptide. CD and other optical spectroscopies have found structure in longer random coil peptides and have implicated polyproline II, which is a major backbone conformation in residues within loop regions of protein structures. Our result suggests that the backbone conformational entropy in alanine peptides is considerably smaller than estimated by the random coil model. New thermodynamic data confirm this suggestion: the entropy loss on alanine helix formation is only 2.2 entropy units per residue.
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