Extracellular matrix organization

Mosher DF, Adams JC. Adhesion-modulating/matricellular ECM protein families: a structural, functional and evolutionary appraisal. Matrix Biol. 2012 Apr;31(3):155–61. doi: 10.1016/j.matbio.2012.01.003. PMID: 22265890.; Lu P, Takai K, Weaver VM, Werb Z. Extracellular Matrix Degradation and Remodeling in Development and Disease. Cold Spring Harbor Perspectives in Biology. 2011 Sep 14;3(12):a005058. doi: 10.1101/cshperspect.a005058.; Frantz C, Stewart KM, Weaver VM. The extracellular matrix at a glance. J Cell Sci. 2010 Dec 15;123(Pt 24):4195–200. PMID: 21123617; PMCID: PMC2995612.; Brew K, Nagase H. The tissue inhibitors of metalloproteinases (TIMPs): An ancient family with structural and functional diversity. Biochimica et Biophysica Acta (BBA) - Molecular Cell Research. 2010 Jan;1803(1):55–71. doi: 10.1016/j.bbamcr.2010.01.003.; Hynes RO. The extracellular matrix: not just pretty fibrils. Science. 2009 Nov 27;326(5957):1216–9. PMID: 19965464; PMCID: PMC3536535.; Cawston TE, Young DA. Proteinases involved in matrix turnover during cartilage and bone breakdown. Cell Tissue Res. 2010 Jan;339(1):221–35. doi: 10.1007/s00441-009-0887-6. PMID: 19915869.; Bornstein P. Matricellular proteins: an overview. Journal of Cell Communication and Signaling. 2009 Sep 25;3(3-4):163. doi: 10.1007/s12079-009-0069-z.; Daley WP, Peters SB, Larsen M. Extracellular matrix dynamics in development and regenerative medicine. J Cell Sci. 2008 Feb 01;121(Pt 3):255–64. doi: 10.1242/jcs.006064. PMID: 18216330.; Page-McCaw A, Ewald AJ, Werb Z. Matrix metalloproteinases and the regulation of tissue remodelling. Nature Reviews Molecular Cell Biology. 2007 Mar;8(3):221–33. doi: 10.1038/nrm2125.; Roughley PJ. The structure and function of cartilage proteoglycans. Eur Cell Mater. 2006 Nov 30;12():92–101. doi: 10.22203/ecm.v012a11. PMID: 17136680.; Bosman FT, Stamenkovic I. Functional structure and composition of the extracellular matrix. The Journal of Pathology. 2003 Jul;200(4):423–8. doi: 10.1002/path.1437.; Ameye L, Young MF. Mice deficient in small leucine-rich proteoglycans: novel in vivo models for osteoporosis, osteoarthritis, Ehlers-Danlos syndrome, muscular dystrophy, and corneal diseases. Glycobiology. 2002 Sep;12(9):107R–16R. doi: 10.1093/glycob/cwf065. PMID: 12213783.; Yang Z, Strickland DK, Bornstein P. Extracellular Matrix Metalloproteinase 2 Levels Are Regulated by the Low Density Lipoprotein-related Scavenger Receptor and Thrombospondin 2. Journal of Biological Chemistry. 2001 Mar;276(11):8403–8. doi: 10.1074/jbc.m008925200.; Iozzo RV. Matrix proteoglycans: from molecular design to cellular function. Annu Rev Biochem. 1998;67():609–52. doi: 10.1146/annurev.biochem.67.1.609. PMID: 9759499.; MUKHERJEE BB, NEMIR M, BENINATI S, CORDELLA-MIELE E, SINGH K, CHACKALAPARAMPIL I, SHANMUGAM V, DeVOUGE MW, MUKHERJEE AB. Interaction of Osteopontin with Fibronectin and Other Extracellular Matrix Moleculesa. Annals of the New York Academy of Sciences. 1995 Aug;760(1):201–12. doi: 10.1111/j.1749-6632.1995.tb44631.x.; Hardingham TE, Fosang AJ. Proteoglycans: many forms and many functions. The FASEB Journal. 1992 Feb;6(3):861–70. doi: 10.1096/fasebj.6.3.1740236.; Scott JE. Proteoglycan-collagen interactions and sub-fibrillar structure in collagen fibrils: implications in the development and remodelling of connective tissues. Biochem Soc Trans. 1990 Jun;18(3):489–90. doi: 10.1042/bst0180489a. PMID: 2373244.; Scott JE, Haigh M. 'Small'-proteoglycan:collagen interactions: keratan sulphate proteoglycan associates with rabbit corneal collagen fibrils at the 'a' and 'c' bands. Biosci Rep. 1985 Sep;5(9):765–74. doi: 10.1007/bf01119875. PMID: 2935202.; Scott JE, Orford CR. Dermatan sulphate-rich proteoglycan associates with rat tail-tendon collagen at the d band in the gap region. Biochem J. 1981 Jul 01;197(1):213–6. PMID: 7317031; PMCID: PMC1163072.

Metabolites

Ascorbate

Formula: C6H8O6 (176.0320868)

CAS ID: 50-81-7

Bromide

Formula: Br (78.918336)

CAS ID: 24959-67-9

Calcium cation

Formula: Ca (39.962591)

CAS ID: 14127-61-8

CO2

Formula: CO2 (43.98983)

CAS ID: 124-38-9

Copper

Formula: Cu (62.929599)

CAS ID: 7440-50-8

Fe2+

Formula: Fe (55.934939)

CAS ID: 15438-31-0

H2O

Formula: H2O (18.0105642)

CAS ID: 7732-18-5

Hydrogen peroxide

Formula: H2O2 (34.0054792)

CAS ID: 7722-84-1

Magnesium cation

Formula: Mg (23.98505)

CAS ID: 22537-22-0

Manganese(2+)

Formula: Mn (54.938046)

CAS ID: 7439-96-5

Oxygen

Formula: O2 (31.98983)

CAS ID: 7782-44-7

2-oxoglutarate(2-)

Formula: C5H4O5 (144.00587339999998)

CAS ID: 64-15-3

succinate(2-)

Formula: C4H4O4 (116.01095839999999)

CAS ID: 56-14-4

UDP(3-)

Formula: C9H11N2O12P2 (400.9787246)

CAS ID: 86527-70-0



Enzyme

EC Number name full name note
3.4.21.-
1.14.11.4 procollagen-lysine 5-dioxygenase L-lysine-[procollagen],2-oxoglutarate:oxygen oxidoreductase (5-hydroxylating)
1.14.11.7 procollagen-proline 3-dioxygenase [procollagen]-L-proline,2-oxoglutarate:oxygen oxidoreductase (3-hydroxylating)
2.4.1.50 procollagen galactosyltransferase UDP-galactose:procollagen-5-hydroxy-L-lysine D-galactosyltransferase
2.4.1.66 procollagen glucosyltransferase UDP-glucose:(2S,5R)-5-O-(beta-D-galactosyl)-5-hydroxy-L-lysine-[procollagen] D-glucosyltransferase
2.7.10.1 receptor protein-tyrosine kinase ATP:[protein]-L-tyrosine O-phosphotransferase (receptor-type)
2.7.11.13 protein kinase C ATP:protein phosphotransferase (diacylglycerol-dependent)
3.4.21.20 cathepsin G
3.4.21.75 Furin
3.4.24.17 stromelysin 1
3.4.24.23 matrilysin
3.4.24.24 gelatinase A
3.4.24.34 neutrophil collagenase
3.4.24.35 gelatinase B
3.4.24.80 membrane-type matrix metalloproteinase-1
5.2.1.8 peptidylprolyl isomerase Peptidylproline cis-trans-isomerase
5.3.4.1 protein disulfide-isomerase Protein disulfide-isomerase


Proteins

Protein ID name full name