Figure 1.
Greatly simplified organizational hierarchy of fibrillar collagen structure (from polypeptide to fibril)
A. The collagen-forming polypeptide chains contain a large helix-forming domain with the repeat amino acid sequence Gly-X-Y, where X and Y are occupied by Pro or Hyp more frequently than other residues, but only account for approximately 1/6 of the total amino acid content (see for instance human sequence: ExPASy sequence data bank codes; P02452 and P08123). An arrow points to the figure element that shows that three polypeptides form the collagen monomer. The large triple-helix (super-helix) domain of approximately 300 nm in length is flanked by non-helical telopeptides (N and C, shown). The 6–8.6 nm dimension indicates the repeat of the triple-helix (36; 37). B. Collagen molecules are staggered approximately 67 nm from one another in the formation of microfibril aggregates. The microfibrils are D-periodic (D = 67 nm), and in each D-period, two monomers coil, or partially coil, around each other giving the appearance of another helix-like feature in the structural hierarchy (3). C. Cross-sectional view of the collagen molecular packing of a type I collagen fibril (11). Each circle represents one collagen molecule in cross-section (at the axial level of 0.44D). at the 0.44 D position. Next to B to C arrow, cross-section of an isolated microfibril. D) Archival image (Orgel laboratory) of the wide angle fiber diffraction pattern of type I collagen from rat tail tendon. The distinctly different but superimposed non-crystalline and crystalline diffraction patterns are indicated. Previous fiber diffraction studies of collagen's helical structure have concentrated on the non-crystalline part of the pattern, in this present study, we analyze crystalline diffraction data.
Figure 2.
Helical and non-helical organization of collagen.
The non-helical, folded C-terminal end of the collagen molecule (top) extending from the triple-helical region (below). The electron density of neighboring collagen molecules can be seen along side the chain traced segment (red). The GPO5 domain is indicated in white.
Figure 3.
Thermal stability versus α chain triple-helical dissociation.
A) Thermal stability plot [25]. B) Comparison of local predicted stability variations with local helical dissociation. Blue lines mark a noteworthy correlation between peaks that indicate thermal instability of the helix and where the helix is also dissociated (see part C). Red lines indicate noteworthy areas where there is not a correlation. The helix is calculated to be thermally stable but the low resolution structural data indicates the triple-helix to be relatively dissociated at room temperature. Or vice versa, the stability plot indicates a well formed helix while the structural data shows a relatively disassociated one. Some of the places were there is no correlation (stable helix but structure shows a dissociated one) are located at points of molecular inflection (bends, see Figure 1 and 3 and electron density [4]). Thicker lines indicate more significant discrepancy/correlation, unmarked areas are thought to show more or less expected similarity between the two plots (A and C). C) dissociation of peptide chains: difference between the calculated relaxed model (via force field calculations against diffraction data) and the starting stringent model (from high resolution model peptide data) of the collagen triple-helix. Sequence numbering includes the N-telopeptide residues. This is an estimate of triple-helix dissociation. The magnitude of dissociation of the three peptide chains are shown as a local average (black line), along with the global average (blue line) and two times standard deviation (2*σ, light blue line). 1–6 and * indicate significant bends in the collagen molecule as determined from the electron density of in situ fibrillar collagen data.
Figure 4.
Helix net map of the 10/3 (A) and 7/2 (B) triple-helix models.
The unit height of the α-peptide chain (h) and the superhelix (hsh), the pitch and helix true repeat periods of each helical symmetry is as indicated.
Figure 5.
Patterson functions of the type I and II collagen 00L (meridional) series.
A) Patterson function from 0.0–0.5D, the inverse (0.5–1.0) half of the Patterson function is not shown. The fractional distances between periodicities indicated in the functions has been multiplied by 67 nm (the length of the one dimensional unit cell – the D-period) for comparison with the helix symmetry periods. B) Enhanced view of the Patterson function range of interest for the helix symmetry periodicities. C) Table of key helix periodicities for comparison with A and B (see also Figure 4).
Figure 6.
Patterson functions of collagen model structure factors 00L (meridional) series.
A) Comparison of GPO (7/2 model) and GPO with collagen sequence threaded to check if amino acid sequence effects periodicities detected by the Patterson function. It does not appear so. B) As (A) except for GAA (10/3 model). C) Patterson functions of collagen types I and II are compared with those from the GAA and GPO coordinate models with the collagen sequence threaded onto them. The semi-transparent arrows mark: red, the maximum of the GAA (10/3) helix model pitch and repeat periods, the black arrows mark the collagen I and II respective positions for these periods. Note that the collagen experimental data show periods that are longer then the 7/2 and do seem to almost reach the 10/3 expected range. This could be interpreted to mean that both helical symmetries are found in native fibrillar collagen in addition to other possible conformations.
Table 1.
Patterson function periodicities and correlation between observed and ‘perfect’ helical symmetry periodicities (see also Figure 5).