Sandbox 154: Difference between revisions

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[[image:2zwh_domain_colours2.png|thumb|Domains of F-actin monomer|frame|left]]

==== Polymer ====

F-actin has the appearance of two right-handed helices, with a gradual twist around one another. It is actually composed of repeats of 13 actin units for every 6 left-handed turns, spanning a length of 350 Å<ref name="Holmes2"/>. Including the ADP and Ca2+, the F-actin molecule as shown here consists of 377 residues (43kDa), two major domains separated by a nucleotide-binding cleft<ref name="oda" />. Depending on the state of the bound nucleotide, the most stable conformation of F-actin changes. In its ATP and ADP + Pi nucleotide bound states, it has a closed binding cleft. In its ADP only bound state, it has a wider binding cleft<ref~~>pfaendtner</ref~~>. A characteristic trait of actin is that the domains remain twisted relative to one another, despite the nucleotide-state-dependent conformational changes<ref name="oda" />.

F-actin has the appearance of two right-handed helices, with a gradual twist around one another. It is actually composed of repeats of 13 actin units for every 6 left-handed turns, spanning a length of 350 Å<ref name="Holmes2"/>. Including the ADP and Ca2+, the F-actin molecule as shown here consists of 377 residues (43kDa), two major domains separated by a nucleotide-binding cleft<ref name="oda" />. Depending on the state of the bound nucleotide, the most stable conformation of F-actin changes. In its ATP and ADP + Pi nucleotide bound states, it has a closed binding cleft. In its ADP only bound state, it has a wider binding cleft<ref name="Pfaendtner">. A characteristic trait of actin is that the domains remain twisted relative to one another, despite the nucleotide-state-dependent conformational changes<ref name="oda" />.

=== Nucleotide-State-Dependent Conformational Changes ===

The state of the bound phosphorylated nucleotide affects what conformation the F-actin monomer undertakes. The presence of a gamma-phosphate in the active site causes the rotation of a Ser14 residue. This change leads to HIC73 (4-methyl histidine) becoming shifted, which alters the F-actin active site and causes a conformational change in the D-loop. The HIC73 is located in the sensor loop, or the "switch" for linking changes in bound nucleotide to conformational changes<ref name="Graceffa"/>. In ATP-actin and ADP-Pi-actin, the D-loop is unstructured. In the ADP-bound form of F-actin, an alpha helix is commonly apparent in the D-loop of the monomer<ref name="pfaendter"/><ref name="Graceffa"/>. Although the alpha-helix is not observed in this Oda model of F-actin, it is acknowkledged by Oda et. al that the experimental results could have lead to an extended alpha-helix in the model<ref name="oda"/>.

Sandbox 154: Difference between revisions

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@@ Line 25: / Line 25: @@
 [[image:2zwh_domain_colours2.png|thumb|Domains of F-actin monomer|frame|left]]
 ==== Polymer ====
-F-actin has the appearance of two right-handed helices, with a gradual twist around one another. It is actually composed of repeats of 13 actin units for every 6 left-handed turns, spanning a length of 350 Å<ref name="Holmes2"/>. Including the ADP and Ca<sup>2+</sup>, the F-actin molecule as shown here consists of 377 residues (43kDa), two major domains separated by a nucleotide-binding cleft<ref name="oda" />. Depending on the state of the bound nucleotide, the most stable conformation of F-actin changes. In its ATP and ADP + Pi nucleotide bound states, it has a closed binding cleft. In its ADP only bound state, it has a wider binding cleft<ref>pfaendtner</ref>. A characteristic trait of actin is that the domains remain twisted relative to one another, despite the nucleotide-state-dependent conformational changes<ref name="oda" />.
+F-actin has the appearance of two right-handed helices, with a gradual twist around one another. It is actually composed of repeats of 13 actin units for every 6 left-handed turns, spanning a length of 350 Å<ref name="Holmes2"/>. Including the ADP and Ca<sup>2+</sup>, the F-actin molecule as shown here consists of 377 residues (43kDa), two major domains separated by a nucleotide-binding cleft<ref name="oda" />. Depending on the state of the bound nucleotide, the most stable conformation of F-actin changes. In its ATP and ADP + Pi nucleotide bound states, it has a closed binding cleft. In its ADP only bound state, it has a wider binding cleft<ref name="Pfaendtner">. A characteristic trait of actin is that the domains remain twisted relative to one another, despite the nucleotide-state-dependent conformational changes<ref name="oda" />.
 === Nucleotide-State-Dependent Conformational Changes ===
 The state of the bound phosphorylated nucleotide affects what conformation the F-actin monomer undertakes. The presence of a gamma-phosphate in the active site causes the rotation of a Ser14 residue. This change leads to HIC73 (4-methyl histidine) becoming shifted, which alters the F-actin active site and causes a conformational change in the D-loop. The HIC73 is located in the sensor loop, or the "switch" for linking changes in bound nucleotide to conformational changes<ref name="Graceffa"/>. In ATP-actin and ADP-P<sub>i</sub>-actin, the D-loop is unstructured. In the ADP-bound form of F-actin, an alpha helix is commonly apparent in the D-loop of the monomer<ref name="pfaendter"/><ref name="Graceffa"/>. Although the alpha-helix is not observed in this Oda model of F-actin, it is acknowkledged by Oda et. al that the experimental results could have lead to an extended alpha-helix in the model<ref name="oda"/>.