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BIOPHYSICS
The polyproline II
conformation in short alanine peptides is noncooperative
Department of Chemistry, New York University, New York, NY 10003
Communicated by Robert L. Baldwin, Stanford University Medical Center, Stanford, CA, September 8, 2004 (received for review July 15, 2004)
The finding that short alanine peptides possess a high
fraction of polyproline II (PII) structure (
= -75°, 
= +145°) at low temperature has broad implications for
unfolded states of proteins. An important question concerns whether
or not this structure is locally determined or cooperative. We have
monitored the conformation of alanine in a series of model peptides
AcGG(A)nGGNH2 (n = 1–3) over a temperature range
from -10°C to +80°C. Use of 15N-labeled alanine
substitutions makes it possible to measure 3J
N coupling constants
accurately over the full temperature range. Based on a 1D
next-neighbor model, the cooperative parameter 
of PII nucleation is evaluated from the
coupling constant data. The finding that is close to unity (1 ± 0.2) indicates
a noncooperative role for alanine in PII structure formation,
consistent with statistical surveys of the Protein Data Bank
that suggest that most PII structure occurs in isolated residues.
Lack of cooperativity in these models implies that hydration
effects that influence PII conformation in water are highly
localized. Using a nuclear Overhauser effect ratio strategy to
define the alanine angle, we
estimate that, at 40°C, the time-averaged alanine conformation ( = -80°, = +170°) deviates from canonical PII
structure, indicating that PII melts at high temperature. Thus, the
high-temperature state of short alanine peptides seems to be an
unfolded ensemble with higher distribution in the extended 
structure basin, but not a
coil.
Abbreviations: PII, polyproline II; NOE, nuclear Overhauser effect.
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To whom correspondence should be addressed. E-mail: nrk1{at}nyu.edu
.
© 2004 by The National Academy of Sciences of the USA
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