Non-polymerizable monomeric actin: Difference between revisions

The actin fold consists of a two five-stranded β-sheets surrounded by 3 helices. These sheets are present in subdomain 1 and subdomain 3 and consist of both parallel and antiparallel β-strands. Two β-strands in subdomain 1 form a β-hairpin (residues 8-21). The loop connecting the two β-strands is the S-loop which contains Serine 14, a critical residue that responds to changes in bound nucleotide.  

Two β-strands within the subdomain 3 β-sheet also form a β-hairpin (residues 150-166). The loop connecting the β-strands form the G-loop which contain residues in the nucleotide-binding cleft. These β-sheet structures are highly conserved in the actin superfamily and contain residues critical for nucleotide binding and catalysis.  

Residues 70-77 in subdomain 1 make up the H-loop. This loop is also known as the sensor loop because structural changes in the nucleotide binding cleft, such as tortional movement of serine 14, are propagated to these amino acids. Thus, the H-loop undergoes the largest nucleotide-dependent conformational changes as seen above. The H-loop is a good example of a type I’ β-turn. β-turns are comprised of four consecutive residues whose distance between the α-carbons of residue i and i+3 is less than 7 Å. Typically, β-turns form hydrogen bonds between the carboxyl group of residue i and the amide group of residue i+3. Here, the carbonyl of glutamic acid-72 (i) forms a hydrogen bond with the amide group of isoleucine 75 (i+3). In addition, another hydrogen bond is formed between the carbonyl of isoleucine 75 and the amide of glutamic acid 72, indicating a capping box motif. β-turns can be further classified by the dihedral angles of the i+1 and i+2 residues as well as the distance between the α-carbons of residue i and i+3. This turn is consistent with a type I’ β-turn.

Helix capping describes the interruption of hydrogen bonds between amide hydrogen’s and carbonyl oxygen’s at the termini of an α-helix. This occurs when amide hydrogen’s form hydrogen bonds with alternative binding partners such as side chains. A number of helix capping motifs have been described to form these alternative hydrogen bonding patterns. The N-terminus of α-helix eight (residues 202-217) in AP-actin is capped by a “capping box” motif. This motif caps two (threonine-202 and glutamic acid-205) of the initial four amide hydrogen donors in the helix. <ref name="Aurora">PMID: 9514257</ref>

Domain 1 in actin contains a helix-loop-helix motif (residues 333-357). The helices are interrupted by loop residues 346-352. The break in helicity appears to be due to two glutamates (Q353 and Q354) that hydrogen bind with the carbonyl carbons of adjacent residues in the helix (L349, A347 and T351). In addition to this, there appears to be a hydrophobic staple between residues L346 and F352 However, this doesn’t follow the i, i+5 rule that is normally seen with a hydrophobic staple.  

Subomain 1 contains a right handed β-α-β motif (residues 103-136). Here, two parallel β-strands are linked by an α-helix. These β-strands are part of the β-sheet motif in subdomain 1.