Sandbox 154: Difference between revisions
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=== Domains of F-actin Unit === | === Domains of F-actin Unit === | ||
Structure of a unit of F-actin with domains from a single polypeptide chain. Note that the nucleotide binding cleft occurs between the two domains and is also the region of ATP hydrolysis. | Structure of a unit of F-actin with domains from a single polypeptide chain. Note that the nucleotide binding cleft occurs between the two domains and is also the region of ATP hydrolysis. | ||
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> | 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 === | === 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 <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> | 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>oda</ref>. | ||
=== Active Site === | === Active Site === | ||
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=== Polymer F-actin === | === Polymer F-actin === | ||
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> | 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>. | ||
== Function == | == Function == | ||
