Sandbox 154: Difference between revisions

==== Monomer ====

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

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="holmes"><ref>PMID:2395461</ref>. 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" />.

<applet load='2zwh' size='275' color='black' frame='true' align='right' caption='Filamentous Actin (F-actin)' scene='Sandbox_154/2zwh_black_domains/1'/>

The structure of a single unit of F-actin arises from one polypeptide chain with two domains, as observed by the figure on the left. The nucleotide binding cleft, site of ATP hydrolysis, can be observed between the two domains. Movement of the domains allows for the open and closed F-actin conformations.  

Domain movement is made possible by rotation about the <scene name='Sandbox_154/2zwh_helix_domains_2/1'> peptide bonds of residues 141-142 and 335-336</scene>, shown in purple. According to Oda et al., during the transition from G- to F- actin, Domain 2 is believed to tilt 20&deg; 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<ref name="oda" />.

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 <scene name='Sandbox_154/2zwh_saltbridge/1'>salt bridge</scene> formations involving arginine 206, 183, 177 (purple); glutamate 72(blue), aspartate 187(green), 179 and 4-methyl histidine 73(yellow). Additional stability is believed to arise from a break in the interaction between residues <scene name='Sandbox_154/2zwh_leu_val/2'>108-111 and Val165 and Ile175</scene> in the same half of their respective domains to a new interaction between <scene name='Sandbox_154/2zwh_leu_thr/2'>Leu110 and Thr194</scene> where a much greater distance is observed between them<ref name="oda" />.

Upon actin binding on the plus end of the actin filament, the ATPase function is activated. The conformational change from G- to F- actin promotes the catalytic activity because of the 20&deg; shift leading to a more closed binding site; this conformational change is stabilized also by the diagonal subdomain interaction between Leu110 and Thr194.  

Upon binding changes, the Gln137 residue of actin is moved closer to the ATP-Ca2+ ligand. Gln137 holds a water molecule, and placing it in close proximity to ATP allows for the gamma-phosphate to become cleaved. Release of the inorganic phosphate occurs via the conformational change of the flexible "D-loop" into an ordered alpha-helix<ref>graceffa</ref>.