RiAFP: Difference between revisions

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== Overall Structure ==

The crystallographic structure of RiAFP was defined recently<ref>DOI 10.1074/jbc.M113.450973</ref>. ~~It reveals~~ a ~~new~~ β-solenoid architecture that forms <scene name='60/607864/Beta_sheets/1'>β-sandwich</scene> of <scene name='60/607864/Beta_sheets_colored/1'>two parallel 6 and 7 stranded-sheets</scene> of remarkable regularity. The β-sheets lie on top of each other with the upper and lower strands parallel but in the opposite orientation. Two ends deviate from β helix regularity by forming <scene name='60/607864/Beta_sheets_capping/2'>capping structures</scene>. These capping structures help to prevent end-to-end associations that would spoil the solubility of RiAFP and lead to oligomerization and aggregation.

The crystallographic structure of RiAFP was defined recently<ref>DOI 10.1074/jbc.M113.450973</ref>. RiAFP has a novel β-solenoid architecture that forms <scene name='60/607864/Beta_sheets/1'>β-sandwich</scene>. This sandwich is composed of <scene name='60/607864/Beta_sheets_colored/1'>two parallel 6 and 7 stranded-sheets</scene> of remarkable regularity. The β-sheets lie on top of each other with the upper and lower strands parallel but in the opposite orientation. Two ends deviate from β helix regularity by forming <scene name='60/607864/Beta_sheets_capping/2'>capping structures</scene>. These capping structures help to prevent end-to-end associations that would spoil the solubility of RiAFP and lead to oligomerization and aggregation.

The three residues in β-strand 11 at the C terminus <scene name='60/607864/Gln110_gln112_ile114/1'>(Gln110, Gln112, and Ile114)</scene> that are too bulky to be accommodated into the core may also contribute to the capping structure to prevent amyloid-like polymerization. RiAFP solenoid possesses compressed nature with average distance between the sheets of only 6 Å. In the core of RiAFP, the side chains within apposed β-strands from the two β-sheets are staggered, allowing the side chains to interdigitate and pack tightly against one another. Most of the <scene name='60/607864/Core_structure/1'>side chains</scene> in the core are from Ala, Ser and Thr. Those residues create a more compact fold that may contribute to the high stability and antifreeze activity of RiAFP. Within the core there are <scene name='60/607864/Hydrogen_bonds/2'>hydrogen bonds</scene> between Thr-Ser (65-55, 85-75, 132-124 respectively) and one <scene name='60/607864/S-s_bond/1'>disulfide bond</scene> between Cys4-Cys21, that contributes to stabilization of the whole structure. The β-turns in the structure contain mostly Gly or Pro residues.

The asymmetric unit comprises two RiAFP molecules juxtaposed with their ice-binding surfaces, however the protein is monomer in the solutio

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 == Overall Structure ==
-The crystallographic structure of RiAFP was defined recently<ref>DOI 10.1074/jbc.M113.450973</ref>. It reveals a new β-solenoid architecture that forms <scene name='60/607864/Beta_sheets/1'>β-sandwich</scene> of <scene name='60/607864/Beta_sheets_colored/1'>two parallel 6 and 7 stranded-sheets</scene>  of remarkable regularity. The β-sheets lie on top of each other with the upper and lower strands parallel but in the opposite orientation. Two ends deviate from β helix regularity by forming <scene name='60/607864/Beta_sheets_capping/2'>capping structures</scene>. These capping structures help to prevent end-to-end associations that would spoil the solubility of RiAFP and lead to oligomerization and aggregation.
+The crystallographic structure of RiAFP was defined recently<ref>DOI 10.1074/jbc.M113.450973</ref>. RiAFP has a novel β-solenoid architecture that forms <scene name='60/607864/Beta_sheets/1'>β-sandwich</scene>. This sandwich is composed of <scene name='60/607864/Beta_sheets_colored/1'>two parallel 6 and 7 stranded-sheets</scene>  of remarkable regularity. The β-sheets lie on top of each other with the upper and lower strands parallel but in the opposite orientation. Two ends deviate from β helix regularity by forming <scene name='60/607864/Beta_sheets_capping/2'>capping structures</scene>. These capping structures help to prevent end-to-end associations that would spoil the solubility of RiAFP and lead to oligomerization and aggregation.
 The three residues in β-strand 11 at the C terminus <scene name='60/607864/Gln110_gln112_ile114/1'>(Gln110, Gln112, and Ile114)</scene> that are too bulky to be accommodated into the core may also contribute to the capping structure to prevent amyloid-like polymerization. RiAFP solenoid possesses compressed nature with average distance between the sheets of only 6 Å. In the core of RiAFP, the side chains within apposed β-strands from the two β-sheets are staggered, allowing the side chains to interdigitate and pack tightly against one another. Most of the <scene name='60/607864/Core_structure/1'>side chains</scene> in the core are from <span style="color:pink;background-color:black;font-weight:bold;">Ala</span>, <span style="color:green;background-color:black;font-weight:bold;">Ser</span> and <span style="color:yellow;background-color:black;font-weight:bold;">Thr</span>. Those residues create a more compact fold that may contribute to the high stability and antifreeze activity of RiAFP. Within the core there are <scene name='60/607864/Hydrogen_bonds/2'>hydrogen bonds</scene> between Thr-Ser (65-55, 85-75, 132-124 respectively) and one <scene name='60/607864/S-s_bond/1'>disulfide bond</scene> between Cys4-Cys21, that contributes to stabilization of the whole structure. The β-turns in the structure contain mostly Gly or Pro residues.
 The asymmetric unit comprises two RiAFP molecules juxtaposed with their ice-binding surfaces, however the protein is monomer in the solutio