Sandbox Reserved 1645

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== Structure ==
== Structure ==
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The protein contains multiple subunits called epidermal growth factor (EGF) and transforming growth factor β binding protein-like domain (7 TGF-bp). EGF are repeated in tandem along the whole protein which represents about 75% of the total fibrillin-1 lenght and they are interrupted by the insertion of TGF-bp unit. In total, there are 47 motifs of EGF in one fibrillin-1, but only 43 of them contain calcium binding sequences. In consequence, these EGF are named cb-EGF for their ability to bind calcium cations (Proteopedia 3D visualization of two tandem cb-EGF). Each of EGF or cb-EGF unit contains 6 residues of cysteine which form <scene name='86/868178/Disulfide_bridges/1'>3 disulfide bridges</scene> (CYS1-CYS3,CYS2-CYS4,CYS5-CYS6)(Proteopedia 3D visualization of disulfide bridges) stabilizing the secondary structure of the protein. cb-EGF units contain also a <scene name='86/868178/Ca_binding_site/1'>Ca2+ binding site</scene> composed by aminoacids D,N,Q,E,Y and F which participate into the cation bonding and which can be seperated by different number of other aminoacids (D/N-x-D/N-E/Q-xm-D/N-xn-Y/F represents the binding site of Ca2+,x, xm, and xn represent certain number of amino acids). Amino acids which participate in the Ca2+ binding D, N, E, Q contain oxygen in their lateral chains and Y with F which contain an aromatic cycle. Oxygen atoms of D/N/Q/E are involved in the Ca2+ binding and create the binding site with the pentagonal bipyramidal geometry.
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The protein contains multiple subunits called epidermal growth factor (EGF) and transforming growth factor β binding protein-like domain (7 TGF-bp). EGF are repeated in tandem along the whole protein which represents about 75% of the total fibrillin-1 lenght and they are interrupted by the insertion of TGF-bp unit. In total, there are 47 motifs of EGF in one fibrillin-1, but only 43 of them contain calcium binding sequences. In consequence, these EGF are named cb-EGF for their ability to bind calcium cations (Proteopedia 3D visualization of two tandem cb-EGF). Each of EGF or cb-EGF unit contains 6 residues of cysteine which form <scene name='86/868178/Disulfide_bridges/1'>3 disulfide bridges</scene> (CYS1-CYS3,CYS2-CYS4,CYS5-CYS6)(Proteopedia 3D visualization of disulfide bridges) stabilizing the secondary structure of the protein. Cb-EGF units contain also a <scene name='86/868178/Ca_binding_site/1'>Ca2+ binding site</scene> composed especially by aminoacids which contain an atom of oxygen or groups with azote in their lateral chains (D,N,S,Q,E). These amino acids stabilate the calcium cation by interactions between positivly charged cation and hetero atoms (oxygen or azote) of amino acid's lateral chain. Consequently, a pentagonal bipyramidal binding site is created in which one calcium cation is bound in every cb-EGF subunit of the fibrillin-1 protein.
3D model represents these parts of fibrillin-1: <scene name='86/868178/Cbegf9/2'>cb-EGF9</scene>, second hybrid domain and <scene name='86/868178/Cbegf10/1'>cb-EGF10</scene>.
3D model represents these parts of fibrillin-1: <scene name='86/868178/Cbegf9/2'>cb-EGF9</scene>, second hybrid domain and <scene name='86/868178/Cbegf10/1'>cb-EGF10</scene>.

Revision as of 12:28, 30 December 2020

This Sandbox is Reserved from 26/11/2020, through 26/11/2021 for use in the course "Structural Biology" taught by Bruno Kieffer at the University of Strasbourg, ESBS. This reservation includes Sandbox Reserved 1643 through Sandbox Reserved 1664.
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Fibrillin - 1

3D structure of fibrillin-1

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References

  1. ↑ Hanson, R. M., Prilusky, J., Renjian, Z., Nakane, T. and Sussman, J. L. (2013), JSmol and the Next-Generation Web-Based Representation of 3D Molecular Structure as Applied to Proteopedia. Isr. J. Chem., 53:207-216. doi:http://dx.doi.org/10.1002/ijch.201300024
  2. ↑ Herraez A. Biomolecules in the computer: Jmol to the rescue. Biochem Mol Biol Educ. 2006 Jul;34(4):255-61. doi: 10.1002/bmb.2006.494034042644. PMID:21638687 doi:10.1002/bmb.2006.494034042644
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