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Biophys J, January 2001, p. 31-44, Vol. 80, No. 1
*Department of Chemistry, Boston University, Boston, Massachusetts
02215; and Protein NMR Group, Vertex Pharmaceutical
Inc., 130 Waverly Street, Cambridge, Massachusetts 02139 USA
The amyloid A
(10-35)-NH2 peptide is
simulated in an aqueous environment on the nanosecond time scale. One
focus of the study is on the validation of the computational model
through a direct comparison of simulated statistical averages with
experimental observations of the peptide's structure and dynamics.
These measures include (1) nuclear magnetic resonance
spectroscopy-derived amide bond order parameters and
temperature-dependent H
proton chemical shifts, (2) the
peptide's radius of gyration and end-to-end distance, (3) the rates of
peptide self-diffusion in water, and (4) the peptide's hydrodynamic
radius as measured by quasielastic light scattering experiments. A
second focus of the study is the identification of key intrapeptide
interactions that stabilize the central structural motif of the
peptide. Particular attention is paid to the structure and fluctuation
of the central LVFFA hydrophobic cluster (17-21) region and the VGSN
turn (24-27) region. There is a strong correlation between
preservation of the structure of these elements and interactions
between the cluster and turn regions in imposing structure on the
peptide monomer. The specific role of these interactions in relation to
proposed mechanisms of amyloidosis is discussed.
Biophys J, January 2001, p. 31-44, Vol. 80, No. 1
© 2001 by the Biophysical Society 0006-3495/01/01/31/14 $2.00
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