Sandbox Reserved 815: Difference between revisions
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=Structure= | =Structure= | ||
The 3HAF structure results from a work leaded by Lee S. in 2010, in which | The 3HAF structure results from a work leaded by Lee S. in 2010, in which the team has characterized seven variants of the human prion. The structure was determined by XRAY diffraction in a 2.26-Angstrom resolution. | ||
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==Secondary Structure== | ==Secondary Structure== | ||
The unique chain of 3HAF is constituted of 7 | The unique chain of 3HAF is constituted of 7 helices (Alpha helix 112-135, Alpha helix 144-153, 3/10 helix 154-156, 3/10 helix 165-169, Alpha helix 172-192, Alpha helix 194-197, Alpha helix 200-227) and of 2 beta-sheets (129-130 and 160-163). | ||
The proportion of each structure is 43% of <scene name='56/568013/Alpha_helix/9'>Alpha Helix</scene>(7 | The proportion of each structure is 43% of <scene name='56/568013/Alpha_helix/9'>Alpha Helix</scene>(7 helices, 62 residues) and 2% of <scene name='56/568013/Beta_sheet/1'>Beta Sheet</scene> (2 strands, 4 residues). | ||
3 residues can have a contact with metals; S132, H140 and D147. | 3 residues can have a contact with metals; S132, H140 and D147. | ||
A lot of empty structures are present between | A lot of empty structures are present between helices. | ||
One of the structure is called 3/10 helix (Each amino acid corresponds to a 120° turn in the helix). | One of the structure is called 3/10 helix (Each amino acid corresponds to a 120° turn in the helix). | ||
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Between the Cysteine 179 and the Cysteine 214 we can find a <scene name='56/568013/B/1'>disulphide | Between the Cysteine 179 and the Cysteine 214 we can find a <scene name='56/568013/B/1'>disulphide bond</scene> which links helix 2 and the helix 3. | ||
It exists also a specific loop at R164-S170 residues. This loop aim to stabilize the 129-130 beta-sheet. The R164 is able to make a hydrogen bond with G126, creating a conformational bridge. | It exists also a specific loop at R164-S170 residues. This loop aim to stabilize the 129-130 beta-sheet. The R164 is able to make a hydrogen bond with G126, creating a conformational bridge. | ||
The structure shows moreover a hairpin structure at the N-ter domain. | The structure shows moreover a hairpin structure at the N-ter domain. | ||
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The protein exists in majority in its dimer form. | The protein exists in majority in its dimer form. | ||
Between each <scene name='User:Erin_May/Sandbox_1/Nonpolar_at_dimer_interface/2'> helix 144-156</scene> of the two proteins, it exists many interactions whose stabilize the dimer interface. It can be retain acidic and mostly negative residues, or basic and positive residues. | Between each <scene name='User:Erin_May/Sandbox_1/Nonpolar_at_dimer_interface/2'> helix 144-156</scene> of the two proteins, it exists many interactions whose stabilize the dimer interface. It can be retain acidic and mostly negative residues, or basic and positive residues. | ||
Each is linked to the C-terminal <scene name='User:Erin_May/Sandbox_1/Helix_2_with_helix_3/1'> helix 200-225</scene> of the other monomer. [http://en.wikipedia.org/wiki/Van_der_Waals_forces Van der Waals] forces are here between such nonpolar residues as | Each is linked to the C-terminal <scene name='User:Erin_May/Sandbox_1/Helix_2_with_helix_3/1'> helix 200-225</scene> of the other monomer. [http://en.wikipedia.org/wiki/Van_der_Waals_forces Van der Waals] forces are here between such nonpolar residues as Valine, Isoleucine, and nonpolar sections as Histadine, Methionine, and Glutamic acid. | ||
It occurs hydrogen | It occurs hydrogen bond between the dimers at <scene name='User:Erin_May/Sandbox_1/Interface_hydrogen_bonding/1'> Thr188 O −Gly195 N</scene>, Thr190 O−Lys194 N and Thr192 O−Thr192 N. | ||
On each monomer, a | On each monomer, a hydrogen bond between <scene name='User:Erin_May/Sandbox_1/Hydrogen_bond_asp_202/1'> Asp 202 and Thr 199</scene> stabilizes the dimeric structure. | ||
<scene name='User:Erin_May/Sandbox_1/Hydrogen_bonding/1'> Arg 220 and Ser 132</scene> form a | <scene name='User:Erin_May/Sandbox_1/Hydrogen_bonding/1'> Arg 220 and Ser 132</scene> form a hydrogen bond located at the end of helix 3 which permit inter-chain interactions to be specific. | ||
