2D3H

Crystal structures of collagen model peptides (Pro-Pro-Gly)4-Hyp-Hyp-Gly-(Pro-Pro-Gly)4

Summary for 2D3H

• Entry DOI: 10.2210/pdb2d3h/pdb
• Related: 1V4F 1V6Q 1V7H 1X1K 1YM8 2CUO 2D3F
• Descriptor: COLLAGEN MODEL PEPTIDES (PRO-PRO-GLY)4-HYP-HYP-GLY-(PRO-PRO-GLY)4 (2 entities in total)
• Functional Keywords: collagen, triple-helix, hydroxyproline, structural protein
• Total number of polymer chains: 6
• Total formula weight: 13869.28

Authors

Wu, G.,Noguchi, K.,Okuyama, K.,Mizuno, K.,Bachinger, H.P. (deposition date: 2005-09-28, release date: 2006-09-19, Last modification date: 2023-10-25)

Primary citation

Okuyama, K.,Hongo, C.,Wu, G.,Mizuno, K.,Noguchi, K.,Ebisuzaki, S.,Tanaka, Y.,Nishino, N.,Bachinger, H.P.
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.
Biopolymers, 91:361-372, 2009

PubMed Abstract: 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.

PubMed: 19137577
DOI: 10.1002/bip.21138

Experimental method

X-RAY DIFFRACTION (1.22 Å)