Sandbox 154: Difference between revisions

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Formation of F-actin is a dynamic process of assembly and disassembly which has been termed “treadmilling”.

The transition between G- and F-actin begins with a stabilized oligomer of ATP-actin units formed through a nucleation-condensation type fold pattern<ref>pfaendtner</ref>. Addition of ATP-monomeric units to either end subsequently occurs, however, because of a difference in charge polarity in the two ends, there is preferential addition to what is termed the "plus (+) end" or the "barbed-end". On the opposite end, the "minus (-) end" or the "pointed end", there is preferential dissociation of actin units<ref>mitchinson</ref>. After attachment of the ATP-bound actin, hydrolysis of the ATP occurs yielding the ADP+Pi bound state. Subsequent loss of a Pi leaves the ADP-actin state<ref>chen</ref>. Because of the potential for addition or removal of monomeric units to occur at both ends, the assembly of F-actin may be described in terms of equilibrium. However, because the rate of ATP-actin association is ten-fold that of ADP-actin dissociation, the f-actin has the appearance of moving forward, or "treadmilling"<ref>clasier</ref>. ADP-actin monomers dissociate at the minus end and become recycled to ATP-actin so polymerization at the plus end may occur once again.

According to Oda et al.<ref>Oda</ref>, there is a 20 degree tilt in one of the domains of F-actin as compared to G-actin which gives F-actin the much flatter structure as compared to G-actin. It is not certain whether this flattening occurs before or after ATP hydrolysis.

== Structure ==

=== Domains of F-actin Unit ===

[[Image:2zwh_domain_colours.png]]

Structure of a unit of F-actin with domains from a single polypeptide chain. Note the cleft between the two domains houses the nucleotide phosphate ligand and the Ca2+ metal ion ligand.

Domain movement is made possible by rotation about the <scene name='Sandbox_154/2zwh_helix_domains_2/1'> 141-142 and 335-336 peptide bonds</scene>, shown in purple. According to Oda et al.<ref>oda</ref>Domain 2 is believed to tilt 20 degrees and fit itself with Domain 1, thus giving a flatter conformation than the free G-actin. It is not certain whether this flattening occurs before or after ATP hydrolysis.

=== Stability ===

The flattened folded form of F-actin requires different stabilization mechanisms than the free monomeric G-actin form. Stability of the F-actin complex is achieved by a series of salt bridge formations involving polar and charged residues, including HIC73, a methylated histidine residue. Additional stability is believed to arise from cross-subunit interactions between Leu110 and Thr194<ref>oda</ref>.

==== Active Site ====

The cleavage of the gamma-phosphoryl from the bound ATP is a result of a conformational change upon binding that moves the Gln137 residue closer to the ATP-Ca2+ ligand. Release of the inorganic phosphate occurs via the conformational change of the flexible "D-loop" into an ordered alpha-helix<ref>graceffa</ref>.

=== History of the structure ===

The F-actin protein was discovered by Straub in 1942. The structure was speculated based on a low-resolution x-ray crystallograph found in 1990 by Holmes et al. and over this time, despite the importance of F-actin in eukaryotic cells, this speculated structure was accepted. A higher resolution structure was only recently deposited in the PDB databank in Decemeber 2008 by Oda et al. <ref> Oda T, Iwasa M, Aihara T, Maéda Y, and Narita A. 2009. The nature of the globular-to fibrous actin transition. Nature,457(7228):441-445. PMID: [http://www.ncbi.nlm.nih.gov/pubmed/19158791/ 19158791]</ref>.

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=== Polymer F-actin ===

~~[[image:f-actin.png]]~~

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> Holmes, K.C., Popp, D., Gebhard, W. and Kabsch, W. 1990. Atomic model of the actin filament. Nature,347(6288):44-49. PMID: [http://www.ncbi.nlm.nih.gov/pubmed/2395461/ 2395461]</ref>. 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>oda</ref>. 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>oda</ref>.

~~=== Domains ===~~

Domain movement is made possible by rotation about the <scene name='Sandbox_154/2zwh_helix_domains_2/1'> 141-142 and 335-336 residue bonds</scene> shown in purple. These occur in an alpha-helix (Ile136-Gly146) sequence that does not belong to either domain<ref>graceffa</ref>.

~~=== Stability ===~~

The flattened folded form of F-actin requires different stabilization mechanisms than the free monomeric G-actin form. Stability of the f-actin complex is achieved by a series of salt bridge formations involving polar and charged residues, including HIC73, a methylated histidine residue. Additional stability is believed to arise from cross-subunit interactions between Leu110 and Thr194<ref>oda</ref>.

~~==== Active Site ====~~

The cleavage of the gamma-phosphoryl from the bound ATP is a result of a conformational change upon binding that moves the Gln137 residue closer to the ATP-Ca2+ ligand. Release of the inorganic phosphate occurs via the conformational change of the flexible "D-loop" into an ordered alpha-helix<ref>graceffa</ref>.

== Function ==

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@@ Line 14: / Line 14: @@
 Formation of F-actin is a dynamic process of assembly and disassembly which has been termed “treadmilling”.
 The transition between G- and F-actin begins with a stabilized oligomer of ATP-actin units formed through a nucleation-condensation type fold pattern<ref>pfaendtner</ref>. Addition of ATP-monomeric units to either end subsequently occurs, however, because of a difference in charge polarity in the two ends, there is preferential addition to what is termed the "plus (+) end" or the "barbed-end". On the opposite end, the "minus (-) end" or the "pointed end", there is preferential dissociation of actin units<ref>mitchinson</ref>. After attachment of the ATP-bound actin, hydrolysis of the ATP occurs yielding the ADP+Pi bound state. Subsequent loss of a Pi leaves the ADP-actin state<ref>chen</ref>. Because of the potential for addition or removal of monomeric units to occur at both ends, the assembly of F-actin may be described in terms of equilibrium. However, because the rate of ATP-actin association is ten-fold that of ADP-actin dissociation, the f-actin has the appearance of moving forward, or "treadmilling"<ref>clasier</ref>. ADP-actin monomers dissociate at the minus end and become recycled to ATP-actin so polymerization at the plus end may occur once again.
-According to Oda et al.<ref>Oda</ref>, there is a 20 degree tilt in one of the domains of F-actin as compared to G-actin which gives F-actin the much flatter structure as compared to G-actin. It is not certain whether this flattening occurs before or after ATP hydrolysis.
 == Structure ==
+=== Domains of F-actin Unit ===
 [[Image:2zwh_domain_colours.png]]
 Structure of a unit of F-actin with domains from a single polypeptide chain. Note the cleft between the two domains houses the nucleotide phosphate ligand and the Ca2+ metal ion ligand.
+Domain movement is made possible by rotation about the <scene name='Sandbox_154/2zwh_helix_domains_2/1'> 141-142 and 335-336 peptide bonds</scene>, shown in purple. According to Oda et al.<ref>oda</ref>Domain 2 is believed to tilt 20 degrees and fit itself with Domain 1, thus giving a flatter conformation than the free G-actin. It is not certain whether this flattening occurs before or after ATP hydrolysis.
+=== Stability ===
+The flattened folded form of F-actin requires different stabilization mechanisms than the free monomeric G-actin form. Stability of the F-actin complex is achieved by a series of salt bridge formations involving polar and charged residues, including HIC73, a methylated histidine residue. Additional stability is believed to arise from cross-subunit interactions between Leu110 and Thr194<ref>oda</ref>.
+==== Active Site ====
+The cleavage of the gamma-phosphoryl from the bound ATP is a result of a conformational change upon binding that moves the Gln137 residue closer to the ATP-Ca2+ ligand. Release of the inorganic phosphate occurs via the conformational change of the flexible "D-loop" into an ordered alpha-helix<ref>graceffa</ref>.
 === History of the structure ===
 The F-actin protein was discovered by Straub in 1942. The structure was speculated based on a low-resolution x-ray crystallograph found in 1990 by Holmes et al. and over this time, despite the importance of F-actin in eukaryotic cells, this speculated structure was accepted. A higher resolution structure was only recently deposited in the PDB databank in Decemeber 2008 by Oda et al. <ref> Oda T, Iwasa M, Aihara T, Maéda Y, and Narita A. 2009. The nature of the globular-to fibrous actin transition. Nature,457(7228):441-445. PMID: [http://www.ncbi.nlm.nih.gov/pubmed/19158791/ 19158791]</ref>.
@@ Line 26: / Line 32: @@
 === Polymer F-actin ===
 <applet load='2zwh' size='222' color='black' frame='true' align='left' caption='Filamentous Actin (F-actin)' scene='Sandbox_154/2zwh_black_domains/1'/>
-[[image:f-actin.png]]
 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> Holmes, K.C., Popp, D., Gebhard, W. and Kabsch, W. 1990. Atomic model of the actin filament. Nature,347(6288):44-49. PMID: [http://www.ncbi.nlm.nih.gov/pubmed/2395461/ 2395461]</ref>. 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>oda</ref>. 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>oda</ref>.
-=== Domains ===
-Domain movement is made possible by rotation about the <scene name='Sandbox_154/2zwh_helix_domains_2/1'> 141-142 and 335-336 residue bonds</scene> shown in purple. These occur in an alpha-helix (Ile136-Gly146) sequence that does not belong to either domain<ref>graceffa</ref>.
-=== Stability ===
-The flattened folded form of F-actin requires different stabilization mechanisms than the free monomeric G-actin form. Stability of the f-actin complex is achieved by a series of salt bridge formations involving polar and charged residues, including HIC73, a methylated histidine residue. Additional stability is believed to arise from cross-subunit interactions between Leu110 and Thr194<ref>oda</ref>.
-==== Active Site ====
-The cleavage of the gamma-phosphoryl from the bound ATP is a result of a conformational change upon binding that moves the Gln137 residue closer to the ATP-Ca2+ ligand. Release of the inorganic phosphate occurs via the conformational change of the flexible "D-loop" into an ordered alpha-helix<ref>graceffa</ref>.
 == Function ==