Sandbox Reserved 1103
From Proteopedia
(Difference between revisions)
| Line 13: | Line 13: | ||
== Structure == | == Structure == | ||
| + | |||
| + | === The TRF1 TRFH binding domain === | ||
The [https://en.wikipedia.org/wiki/TERF1 TRF1] TRFH domain is a sequence motif of about 200 amino acids located in the centre of TRF1. It is entirely constituted of α helices and binds to another TRF1 TRFH to form a homodimer. The two monomers are antiparallel and form a homodimer which is symmetrical. There are three α-helices from each monomer involved in this homodimerization: <scene name='82/829356/Helices_1/1'>the helices 1</scene>, <scene name='82/829356/Helices_2/1'>2</scene> <scene name='82/829356/Helices_9/1'>9</scene>. To form a dimer, the helix 1 of one monomer comes into contact with helix 1 of the other monomer, its helix 2 does it with the helix 2, and so does the helix 9. The two helices 9 stabilize the dimer interface and are perpendicular to the helices 1, forming a cross brace at the top and the bottom of it. The two helices 1 are the core of the dimer interface. This interface involves many hydrophobic interactions and a few hydrogen bonds. The amino acids <scene name='82/829356/Trp77/3'>Trp77</scene> of each helix 1 are central to the formation of the hydrophobic core. “Trp77 packs against <scene name='82/829356/Phe255/1'>Phe255</scene> (helix 9) within the monomer and between <scene name='82/829356/Ala259/1'>Ala259</scene> and <scene name='82/829356/Ala259/1'>Ala260</scene> and against <scene name='82/829356/Val263/1'>Val263</scene> of helix 9 from its partner” (Fairall L et al Mol Cell.<ref>PMID: 11545737</ref>) The hydrogen bonds involved in the dimer interface are formed between <scene name='82/829356/Glu71/1'>Glu71</scene> of one monomer with <scene name='82/829356/Ser85/1'>Ser85</scene> of the other monomer. Overall, this dimer interface is highly hydrophobic and packed. | The [https://en.wikipedia.org/wiki/TERF1 TRF1] TRFH domain is a sequence motif of about 200 amino acids located in the centre of TRF1. It is entirely constituted of α helices and binds to another TRF1 TRFH to form a homodimer. The two monomers are antiparallel and form a homodimer which is symmetrical. There are three α-helices from each monomer involved in this homodimerization: <scene name='82/829356/Helices_1/1'>the helices 1</scene>, <scene name='82/829356/Helices_2/1'>2</scene> <scene name='82/829356/Helices_9/1'>9</scene>. To form a dimer, the helix 1 of one monomer comes into contact with helix 1 of the other monomer, its helix 2 does it with the helix 2, and so does the helix 9. The two helices 9 stabilize the dimer interface and are perpendicular to the helices 1, forming a cross brace at the top and the bottom of it. The two helices 1 are the core of the dimer interface. This interface involves many hydrophobic interactions and a few hydrogen bonds. The amino acids <scene name='82/829356/Trp77/3'>Trp77</scene> of each helix 1 are central to the formation of the hydrophobic core. “Trp77 packs against <scene name='82/829356/Phe255/1'>Phe255</scene> (helix 9) within the monomer and between <scene name='82/829356/Ala259/1'>Ala259</scene> and <scene name='82/829356/Ala259/1'>Ala260</scene> and against <scene name='82/829356/Val263/1'>Val263</scene> of helix 9 from its partner” (Fairall L et al Mol Cell.<ref>PMID: 11545737</ref>) The hydrogen bonds involved in the dimer interface are formed between <scene name='82/829356/Glu71/1'>Glu71</scene> of one monomer with <scene name='82/829356/Ser85/1'>Ser85</scene> of the other monomer. Overall, this dimer interface is highly hydrophobic and packed. | ||
| + | === The TRF1 TRFH-TIN2 interaction === | ||
The interaction between TRF1 TRFH and the TIN2 peptide involves the C-terminus of the peptide which is called TIN2 TBM (TIN2-TRFH binding motif). TIN2 TBM is the sequence of the peptide that goes from amino acid 256 to the amino acid 276. In the homodimer of TRF1 TRFH, each TRF1 TRFH interacts with one TIN2 peptide. There are not many differences between the conformation of unliganded TRF1 TRFH and TRF1 TRFH bound to TIN2, the only one is the loop L34. When “TIN2 TBM is bound, loop L34 folds back upon helices 3 and 4, sandwiched between the helices and TIN2 TBM”. “The N-terminus of TIN2 TBM (H257-F-N-L-A-Phe262) adopts an extended conformation stabilized by an extensive intermolecular hydrogen-bonding network. The side chain of L260 is therefore positioned into a deep hydrophobic pocket of TRF1 TRFH. In addition, F258 and P262 also make hydrophobic contacts with TRF1 TRFH: F258 sits on concave surface, whereas P262 stacks with TRF1-F142.” (Chen Y et al Science <ref>PMID:18202258</ref>) C-terminus of TIN2 TBM (L263-G-R-R-R-V268) and D139-A-Q141 of TRF1 TRFH form an antiparallel β sheet. This arrangement positions the C-terminus of TIN2 TBM on the surface of loop L34, allowing R265-R-R267 of TIN2 TBM to be in contact with TRF1 TRFH through electrostatic interactions. “, R266 is nested within an acidic depression on the surface of loop L34 through a network of salt bridges and hydrogen bonds.” (Chen Y et al Science <ref>PMID:18202258</ref>) TIN2 TBM also has the sequence F-X-L-X-P at its N-terminus, the sequence F/Y-X-L-X-P being involved in the binding of several [https://en.wikipedia.org/wiki/Shelterin shelterin]-associated proteins to TRF1 TRFH. | The interaction between TRF1 TRFH and the TIN2 peptide involves the C-terminus of the peptide which is called TIN2 TBM (TIN2-TRFH binding motif). TIN2 TBM is the sequence of the peptide that goes from amino acid 256 to the amino acid 276. In the homodimer of TRF1 TRFH, each TRF1 TRFH interacts with one TIN2 peptide. There are not many differences between the conformation of unliganded TRF1 TRFH and TRF1 TRFH bound to TIN2, the only one is the loop L34. When “TIN2 TBM is bound, loop L34 folds back upon helices 3 and 4, sandwiched between the helices and TIN2 TBM”. “The N-terminus of TIN2 TBM (H257-F-N-L-A-Phe262) adopts an extended conformation stabilized by an extensive intermolecular hydrogen-bonding network. The side chain of L260 is therefore positioned into a deep hydrophobic pocket of TRF1 TRFH. In addition, F258 and P262 also make hydrophobic contacts with TRF1 TRFH: F258 sits on concave surface, whereas P262 stacks with TRF1-F142.” (Chen Y et al Science <ref>PMID:18202258</ref>) C-terminus of TIN2 TBM (L263-G-R-R-R-V268) and D139-A-Q141 of TRF1 TRFH form an antiparallel β sheet. This arrangement positions the C-terminus of TIN2 TBM on the surface of loop L34, allowing R265-R-R267 of TIN2 TBM to be in contact with TRF1 TRFH through electrostatic interactions. “, R266 is nested within an acidic depression on the surface of loop L34 through a network of salt bridges and hydrogen bonds.” (Chen Y et al Science <ref>PMID:18202258</ref>) TIN2 TBM also has the sequence F-X-L-X-P at its N-terminus, the sequence F/Y-X-L-X-P being involved in the binding of several [https://en.wikipedia.org/wiki/Shelterin shelterin]-associated proteins to TRF1 TRFH. | ||
Revision as of 20:38, 16 January 2020
TRF1 TRFH domain and TIN2 peptide complex, pdb=3BQO
The TRFH (Telomeric Repeat Factor Homology) is a domain which is in the centre of the TRF1(Telomeric Repeat-Binding Factor) and of about 200 amino acids.In humans TERF1 is encoded by the TERF1 gene. TIN2(TERF1-interacting Nuclear Factor) is a protein encoded in humans by the TINF2 gene that can bind to TRFH TRF1.
| |||||||||||
