Editing Collagen (section)

==Molecular structure==
{{More citations needed section|date=April 2021}}
A single collagen molecule, tropocollagen, is used to make up larger collagen aggregates, such as fibrils. It is approximately 300&nbsp;[[nanometre|nm]] long and 1.5&nbsp;nm in diameter, and it is made up of three [[polypeptide]] strands (called alpha peptides, see step 2), each of which has the conformation of a left-handed [[helix]] – this should not be confused with the right-handed [[alpha helix]]. These three left-handed helices are twisted together into a right-handed triple helix or "super helix", a cooperative [[quaternary structure]] stabilized by many [[hydrogen bond]]s. With type I collagen and possibly all fibrillar collagens, if not all collagens, each triple-helix associates into a right-handed super-super-coil referred to as the collagen microfibril. Each microfibril is [[wikt:interdigitate|interdigitated]] with its neighboring microfibrils to a degree that might suggest they are individually unstable, although within collagen fibrils, they are so well ordered as to be crystalline.

[[File:Collagen biosynthesis (en).png|thumb|upright=1.3|Three [[polypeptide]]s coil to form tropocollagen. Many tropocollagens then bind together to form a fibril, and many of these then form a fibre.]]

A distinctive feature of collagen is the regular arrangement of amino acids in each of the three chains of these collagen subunits. The sequence often follows the pattern [[glycine|Gly]]-[[proline|Pro]]-X or Gly-X-[[hydroxyproline|Hyp]], where X may be any of various other amino acid residues.<ref name="SzpakJAS"/> Proline or hydroxyproline constitute about 1/6 of the total sequence. With glycine accounting for the 1/3 of the sequence, this means approximately half of the collagen sequence is not glycine, proline or hydroxyproline, a fact often missed due to the distraction of the unusual GX<sub>1</sub>X<sub>2</sub> character of collagen alpha-peptides. The high glycine content of collagen is important with respect to stabilization of the collagen helix, as this allows the very close association of the collagen fibers within the molecule, facilitating hydrogen bonding and the formation of intermolecular cross-links.<ref name="SzpakJAS"/> This kind of regular repetition and high glycine content is found in only a few other fibrous proteins, such as silk [[fibroin]].

Collagen is not only a structural protein. Due to its key role in the determination of cell phenotype, cell adhesion, tissue regulation, and infrastructure, many sections of its non-proline-rich regions have cell or matrix association/regulation roles. The relatively high content of proline and hydroxyproline rings, with their geometrically constrained [[carboxyl]] and (secondary) [[amino]] groups, along with the rich abundance of glycine, accounts for the tendency of the individual polypeptide strands to form left-handed helices spontaneously, without any intrachain hydrogen bonding.

Because glycine is the smallest amino acid with no side chain, it plays a unique role in fibrous structural proteins. In collagen, Gly is required at every third position because the assembly of the triple helix puts this residue at the interior (axis) of the helix, where there is no space for a larger side group than glycine's single [[hydrogen]] atom. For the same reason, the rings of the Pro and Hyp must point outward. These two amino acids help stabilize the triple helix – Hyp even more so than Pro because of a stereoelectronic effect;<ref>{{cite journal | vauthors = Holmgren SK, Taylor KM, Bretscher LE, Raines RT | title = Code for collagen stability deciphered | journal = Nature | volume = 392 | pages = 666-667 | date = 1998 | pmid = 9565027 | doi = 10.1038/33573 }}</ref> a lower concentration of them is required in animals such as fish, whose [[thermoregulation|body temperatures]] are lower than most warm-blooded animals. Lower proline and hydroxyproline contents are characteristic of cold-water, but not warm-water fish; the latter tend to have similar proline and hydroxyproline contents to mammals.<ref name="SzpakJAS"/> The lower proline and hydroxyproline contents of cold-water fish and other [[poikilothermic|poikilotherm]] animals lead to their collagen having a lower thermal stability than mammalian collagen.<ref name="SzpakJAS"/> This lower thermal stability means that [[gelatin]] derived from fish collagen is not suitable for many food and industrial applications.

The tropocollagen [[protein subunit|subunits]] spontaneously [[molecular self-assembly|self-assemble]], with regularly staggered ends, into even larger arrays in the [[extracellular]] spaces of tissues.<ref>{{cite journal | vauthors = Hulmes DJ | title = Building collagen molecules, fibrils, and suprafibrillar structures | journal = Journal of Structural Biology | volume = 137 | issue = 1–2 | pages = 2–10 | year = 2002 | pmid = 12064927 | doi = 10.1006/jsbi.2002.4450 }}</ref><ref name="Hulmes, D.J. 1992. p. 49">{{cite journal | vauthors = Hulmes DJ | title = The collagen superfamily--diverse structures and assemblies | journal = Essays in Biochemistry | volume = 27 | pages = 49–67 | year = 1992 | pmid = 1425603 }}</ref> Additional assembly of fibrils is guided by fibroblasts, which deposit fully formed fibrils from fibripositors. In the fibrillar collagens, molecules are staggered to adjacent molecules by about 67&nbsp;[[Nanometre|nm]] (a unit that is referred to as 'D' and changes depending upon the hydration state of the aggregate). In each D-period repeat of the microfibril, there is a part containing five molecules in cross-section, called the "overlap", and a part containing only four molecules, called the "gap".<ref name="Orgel" /> These overlap and gap regions are retained as microfibrils assemble into fibrils, and are thus viewable using electron microscopy. The triple helical tropocollagens in the microfibrils are arranged in a quasihexagonal packing pattern.<ref name="Orgel" /><ref name="Hulmes Miller 1979" />
[[File:Collagen fibrils in rabbit skin.jpg|thumb|upright|The D-period of collagen fibrils results in visible 67nm bands when observed by electron microscopy.]]
There is some [[covalent bond|covalent]] crosslinking within the triple helices and a variable amount of covalent crosslinking between tropocollagen helices forming well-organized aggregates (such as fibrils).<ref>{{cite journal | vauthors = Perumal S, Antipova O, Orgel JP | title = Collagen fibril architecture, domain organization, and triple-helical conformation govern its proteolysis | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 105 | issue = 8 | pages = 2824–2829 | date = February 2008 | pmid = 18287018 | pmc = 2268544 | doi = 10.1073/pnas.0710588105 | doi-access = free | bibcode = 2008PNAS..105.2824P }}</ref> Larger fibrillar bundles are formed with the aid of several different classes of proteins (including different collagen types), glycoproteins, and proteoglycans to form the different types of mature tissues from alternate combinations of the same key players.<ref name="Hulmes, D.J. 1992. p. 49"/> Collagen's [[soluble|insolubility]] was a barrier to the study of monomeric collagen until it was found that tropocollagen from young animals can be extracted because it is not yet fully [[cross-link|crosslinked]]. However, advances in microscopy techniques (i.e. electron microscopy (EM) and atomic force microscopy (AFM)) and X-ray diffraction have enabled researchers to obtain increasingly detailed images of collagen structure ''in situ''.<ref>{{Cite journal| vauthors = Buchanan JK, Zhang Y, Holmes G, Covington AD, Prabakar S |date=2019|title=Role of X-ray Scattering Techniques in Understanding the Collagen Structure of Leather|journal=ChemistrySelect|language=en|volume=4|issue=48|pages=14091–102|doi=10.1002/slct.201902908|s2cid=212830367|issn=2365-6549|url=http://nectar.northampton.ac.uk/15330/1/Role_Xray_Scattering_Leather_Covington_etel_2019.pdf |archive-url=https://web.archive.org/web/20220127190335/http://nectar.northampton.ac.uk/15330/1/Role_Xray_Scattering_Leather_Covington_etel_2019.pdf |archive-date=2022-01-27 |url-status=live}}</ref> These later advances are particularly important to better understanding the way in which collagen structure affects cell–cell and cell–matrix communication and how tissues are constructed in growth and repair and changed in development and disease.<ref>{{cite journal | vauthors = Sweeney SM, Orgel JP, Fertala A, McAuliffe JD, Turner KR, Di Lullo GA, Chen S, Antipova O, Perumal S, Ala-Kokko L, Forlino A, Cabral WA, Barnes AM, Marini JC, San Antonio JD | title = Candidate cell and matrix interaction domains on the collagen fibril, the predominant protein of vertebrates | journal = The Journal of Biological Chemistry | volume = 283 | issue = 30 | pages = 21187–21197 | date = July 2008 | pmid = 18487200 | pmc = 2475701 | doi = 10.1074/jbc.M709319200 | doi-access = free }}</ref><ref>{{cite journal | vauthors = Twardowski T, Fertala A, Orgel JP, San Antonio JD | title = Type I collagen and collagen mimetics as angiogenesis promoting superpolymers | journal = Current Pharmaceutical Design | volume = 13 | issue = 35 | pages = 3608–3621 | year = 2007 | pmid = 18220798 | doi = 10.2174/138161207782794176 }}</ref> For example, using AFM–based nanoindentation it has been shown that a single collagen fibril is a heterogeneous material along its axial direction with significantly different mechanical properties in its gap and overlap regions, correlating with its different molecular organizations in these two regions.<ref>{{cite journal | vauthors = Minary-Jolandan M, Yu MF | title = Nanomechanical heterogeneity in the gap and overlap regions of type I collagen fibrils with implications for bone heterogeneity | journal = Biomacromolecules | volume = 10 | issue = 9 | pages = 2565–2570 | date = September 2009 | pmid = 19694448 | doi = 10.1021/bm900519v }}</ref>

Collagen fibrils/aggregates are arranged in different combinations and concentrations in various tissues to provide varying tissue properties. In bone, entire collagen triple helices lie in a parallel, staggered array. 40&nbsp;nm gaps between the ends of the tropocollagen subunits (approximately equal to the gap region) probably serve as nucleation sites for the deposition of long, hard, fine crystals of the mineral component, which is hydroxylapatite (approximately) Ca<sub>10</sub>(OH)<sub>2</sub>(PO<sub>4</sub>)<sub>6</sub>.<ref>Ross, M. H. and Pawlina, W. (2011) ''Histology'', 6th ed., Lippincott Williams & Wilkins, p. 218.</ref> Type I collagen gives bone its [[tensile strength]].