## 2 Results and Discussion
### Interpretations from AFM and XRD Studies
This site is also neighboring (within \(\sim\)2 nm) the collagenase interaction domain and fibronectin binding domain of its nearest packing neighbor on monomer 4. As Table 4 summarizes, in the collagen fibril D-period, the antibody probe binding positions indicated by the XRD Fourier and Patterson functions are as follows:  
* 0.32 which is just prior to the C-terminal telopeptide region with a cluster of modestly exposed GPP/GPR sequences on M4 and M5;
* 0.42 is at the end of the highly exposed GPO/GPP(4/5) region and the start of the non-helical telopeptide (M5), the middle of the fibronectin binding/MMP interaction domain of which the C-terminal portion is also a DDR interaction site (M4);
* 0.85 is a highly accessible area in the gap region with GPP/GAP sequences, just before the decoron D-band binding site and directly over the DDR2/von Willebrand factor (vWF) binding site, a region of known helical stability [9; 22];
* 0.99-1.0/0.0 is the lowest trough of the up/down formation of the collagen fibril surface (Figure 6) and rich in lysine residues and some reoccurring GDK sequences. Its trough-like features could lead to more unspecific type interactions with the probe. Figure 6: Fibril and microfibril views, colored by binding domain or amino acid features. Number scale is fractional percentage along D-period (aligned parts (A–C)). (**A**) Selected functional binding domains (fibril surface view); (**B**) Selected functional binding domains microfibril/lateral view inside fibril interior; (**C**) Amino acid sequences (fibril surface view). This includes C-telopeptide sequence in its tight turn configuration, GPO/GPP repeats, immuno-rich triplets (GPY or GXP), GDK triplets, and K residues; (**D**) Color keys for parts (A–C). The common theme between these sites is that GPP or GPO are closely related sequences for triple-helical stability ([23]) and repeats of GPP/GPO are the interaction sequence for these immunologically associated molecules. Regarding the major 0.42D binding site, it is interesting to note that it was previously reported that this specific antibody did not bind rat tail collagen I samples prepared via proteolytic treatment. Our data clearly show that the antibody binds (both AFM and X-ray) when the samples are left intact without removal of the telopeptides. In addition to the presence of the longest GPP/GPO repeat in the type I collagen primary structure, this could indicate a role for the C-telopeptide in interaction with the immunoglobulin or possibly, because of its tight fold confirmation [2; 3], which brings several tyrosine residues into close proximity with the GPO5 repeat. Significantly, the role of tyrosine residues has been found to be highly relevant in OSCAR function. Since our methodology does not work well for non-native/non-intact preparations of fibrillar collagen, we are unable to perform an adequate control experiment to test this hypothesis directly. However, this would be almost paradoxically a negative control, that is, in using an atelo artificial fibril to replicate the non-binding result of [PERSON] and [PERSON] (2007) [24] which was performed for rat skin with pepsinized collagen isolates, as opposed to intact rat tail tendon isolates used in this study. However, this speculation does not affect the observation that the binding location of the antibody is clearly shown at the interdomain location of the GPO/C-telopeptide region (Figures 6 and 7). The remaining binding sites seem comparatively minor, however, it seems noteworthy that they are in close proximity to a fibronectin binding domain (\(\sim\)0.32D) and DDR binding domain (0.85D), see Figures 6 and 7. However, these sites lack the exposure to the environment of the 0.42D site GPO sequence and, presumably, the triple-helical rigidity that GPO5 repeat possesses. There is evidence that the triple helices are relatively stable and well formed in these regions, with the possible exception towards the end of the \(\alpha\)2 collagen peptide [9; 22].