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PDBsum entry 2d3f
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Structural protein
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PDB id
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2d3f
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References listed in PDB file
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Key reference
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Title
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High-Resolution structures of collagen-Like peptides [(pro-Pro-Gly)4-Xaa-Yaa-Gly-(Pro-Pro-Gly)4]: implications for triple-Helix hydration and hyp(x) puckering.
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Authors
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K.Okuyama,
C.Hongo,
G.Wu,
K.Mizuno,
K.Noguchi,
S.Ebisuzaki,
Y.Tanaka,
N.Nishino,
H.P.Bächinger.
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Ref.
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Biopolymers, 2009,
91,
361-372.
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PubMed id
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Abstract
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Structures of (Pro-Pro-Gly)4-Xaa-Yaa-Gly-(Pro-Pro-Gly)4 (ppg9-XYG) where (Xaa,
Yaa)=(Pro, Hyp), (Hyp, Pro) or (Hyp, Hyp) were analyzed at high resolution using
synchrotron radiation. Molecular and crystal structures of these peptides are
very similar to those of the (Pro-Pro-Gly)9 peptide. The results obtained in
this study, together with those obtained from related compounds, indicated the
puckering propensity of the Hyp in the X position: (1) Hyp(X) residues involved
in the Hyp(X):Pro(Y) stacking pairs prefer the down-puckering conformation, as
in ppg9-OPG, and ppg9-OOG; (2) Hyp(X) residues involved in the Hyp(X):Hyp(Y)
stacking pairs prefer the up-puckering conformation if there is no specific
reason to adopt the down-puckering conformation. Water molecules in these
peptide crystals are classified into two groups, the 1st and 2nd hydration
waters. Water molecules in the 1st hydration group have direct hydrogen bonds
with peptide oxygen atoms, whereas those in the 2nd hydration group do not.
Compared with globular proteins, the number of water molecules in the 2nd
hydration shell of the ppg9-XYG peptides is very large, likely due to the unique
rod-like molecular structure of collagen model peptides. In the collagen helix,
the amino acid residues in the X and Y positions must protrude outside of the
triple helix, which forces even the hydrophobic side chains, such as Pro, to be
exposed to the surrounding water molecules. Therefore, most of the waters in the
2nd hydration shell are covering hydrophobic Pro side chains by forming
clathrate structures.
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