Crystal structure of the collagen triple helix model [(Pro-Pro-Gly)(10)](3)

Abstract

The first report of the full-length structure of the collagen-like polypeptide [(Pro-Pro-Gly)(10)](3) is given. This structure was obtained from crystals grown in a microgravity environment, which diffracted up to 1.3 A, using synchrotron radiation. The final model, which was refined to an R(factor) of 0.18, is the highest-resolution description of a collagen triple helix reported to date. This structure provides clues regarding a series of aspects related to collagen triple helix structure and assembly. The strict dependence of proline puckering on the position inside the Pro-Pro-Gly triplets and the correlation between backbone and side chain dihedral angles support the propensity-based mechanism of triple helix stabilization/destabilization induced by hydroxyproline. Furthermore, the analysis of [(Pro-Pro-Gly)(10)](3) packing, which is governed by electrostatic interactions, suggests that charges may act as locking features in the axial organization of triple helices in the collagen fibrils.

Fig. 1.

(A) Organization of the [(Pro-Pro-Gly)₁₀]₃ triple helices in the ac plane. Chains are colored with a ramping code from blue (N-termini) to red (C-termini). The two molecules in the asymmetric unit are the top-center (molecule 1) and the bottom-center (molecule 2) molecules. (B) Average model obtained in the subcell approximation (Vitagliano et al. 2001a) in the ac` plane. The c` corresponds to a ninth of the full-length c axis. (C) Electron density map (2Fo-Fc), extended to the whole unit cell, contoured at 2.0 σ. (D) Omit map (Fo-Fc) of a representative triplet contoured at 3.5 σ.

Fig. 1.

(A) Organization of the [(Pro-Pro-Gly)₁₀]₃ triple helices in the ac plane. Chains are colored with a ramping code from blue (N-termini) to red (C-termini). The two molecules in the asymmetric unit are the top-center (molecule 1) and the bottom-center (molecule 2) molecules. (B) Average model obtained in the subcell approximation (Vitagliano et al. 2001a) in the ac` plane. The c` corresponds to a ninth of the full-length c axis. (C) Electron density map (2Fo-Fc), extended to the whole unit cell, contoured at 2.0 σ. (D) Omit map (Fo-Fc) of a representative triplet contoured at 3.5 σ.

Fig. 1.

(A) Organization of the [(Pro-Pro-Gly)₁₀]₃ triple helices in the ac plane. Chains are colored with a ramping code from blue (N-termini) to red (C-termini). The two molecules in the asymmetric unit are the top-center (molecule 1) and the bottom-center (molecule 2) molecules. (B) Average model obtained in the subcell approximation (Vitagliano et al. 2001a) in the ac` plane. The c` corresponds to a ninth of the full-length c axis. (C) Electron density map (2Fo-Fc), extended to the whole unit cell, contoured at 2.0 σ. (D) Omit map (Fo-Fc) of a representative triplet contoured at 3.5 σ.

Fig. 2.

Values of ϕ versus χ₁ for proline rings in X (•) and Y (▪) positions in [(Pro-Pro-Gly)₁₀]₃ and derived from a statistical survey on trans proline rings in protein structures (○) (Vitagliano et al. 2001b).

Fig. 3.

Distribution of water molecules as a function of their distance from the nearest protein atom.

Fig. 4.

Solvent accessibility, averaged over the two molecules in the asymmetric unit, of the Pro side chain atoms in X positions(A) and Y positions (B).

Fig. 4.

Solvent accessibility, averaged over the two molecules in the asymmetric unit, of the Pro side chain atoms in X positions(A) and Y positions (B).

Fig. 5.

Lateral packing: (A) Electrostatic potential surface of a charged layer. The color code is blue for positive and red for negative electrostatic potential. (B) Pseudotetragonal packing of the triple helices. The triple helices shown in red are directed upward from the paper, whereas those shown in blue are directed downward from the paper.

Fig. 5.

Lateral packing: (A) Electrostatic potential surface of a charged layer. The color code is blue for positive and red for negative electrostatic potential. (B) Pseudotetragonal packing of the triple helices. The triple helices shown in red are directed upward from the paper, whereas those shown in blue are directed downward from the paper.

Fig. 6.

Average main chain e.s.d. values versus residue number for the three chains of molecule 1 (A) and molecule 2 (B) in the asymmetric unit. The insets show the stagger of the three chains in each triple helix.

Fig. 6.

Average main chain e.s.d. values versus residue number for the three chains of molecule 1 (A) and molecule 2 (B) in the asymmetric unit. The insets show the stagger of the three chains in each triple helix.