User:SSN21/SNARE motif sandbox

Information below was taken from two review papers and I still need to compile it into more "digestible" form...

SNARE motif - Their complex-forming regions are located adjacent to their respective C-terminal membrane anchors and consist of homologous coiled coil regions of approximately 60 residues, termed SNARE motifs

all SNAREs share a homologous domain of ~60 amino acids that is referred to as the SNARE motif. The SNARE motif is the defining feature of all SNAREs and is also functionally important because it mediates the association SNAREs into core complexes

SNAREs can be divided into subfamilies on the basis of whether they contain one or two SNARE motifs, on the sequences of the SNARE motifs, and on the type and sequences of the flanking domains. Most SNAREs contain a single SNARE motif that is preceded by a variable N-terminal sequence and is followed by a C-terminal transmembrane region

SNAREs are classified into Q- and R-SNAREs because the crystal structure showed that a central residue in the SNARE motif is either an arginine or a glutamine. These central arginine and glutamines form an ionic layer in which three Q-SNAREs bind to one R-SNARE. The classification into Q- and R-SNAREs is preferable over the v- and t-SNARE terminology because, as discussed in more detail below, localization on trafficking vesicles vs. target membranes does not always correlate with structurally identified SNARE subfamilies

The neuronal SNAREs synaptobrevin 2, syntaxin 1a, and SNAP-25 assemble into a stable ternary complex with a 1:1:1 stoichiometry that is referred to as the core complex. The ternary complex is unusually stable. Under laboratory conditions, assembly is virtually irreversible. The complex is not denatured by heat or by the detergent SDS, and it is resistant to proteolysis by botulinum and tetanus neurotoxins. Resistance to SDS and neurotoxins is therefore often used to demonstrate the presence of ternary core complexes. Site-directed mutagenesis and limited proteolysis revealed that synaptobrevin, syntaxin, and SNAP-25 bind to each other exclusively via their SNARE motifs. A core complex formed by the isolated four SNARE motifs without surrounding sequences (one SNARE motif each from syntaxin and synaptobrevin and two from SNAP-25) exhibits most of the biophysical and biochemical properties of complexes formed by the intact proteins. CD-spectroscopy and site-specific labeling showed that the core complex is composed of a helical bundle with the transmembrane regions emerging from the C-terminal end of the rod-shaped particle. The N-terminal domain of syntaxin emerges from this particle as a mobile, separately folded domain. Although not yet studied in similar detail, the exocytotic fusion complex from yeasts (consisting of corresponding fragments of Sec9p, Snc1p, and Sso1p) exhibits very similar properties, suggesting that the features of the neuronal SNARE complex are paradigmatic for all SNARE complexes. The crystal structure of the synaptic core complex has recently been solved. It consists of a twisted four-helical bundle with an overall length of 12 nm. All chains are aligned in parallel, a finding that was independently confirmed by sitespecific labeling. The linker domain of SNAP-25, which connects the two helical SNARE motifs and contains the cysteine-rich membrane anchor domain, is not part of the crystal structure; it probably forms a loop that connects the two SNARE motifs of the molecule. Interactions in the core of the bundle are mostly hydrophobic, resembling that of other helix bundles with coiled-coil structures. Interestingly, an ionic layer is formed in the center of the four-helical bundle. This ionic layer is constructed from an arginine residue contributed by the SNARE motif of synaptobrevin and three glutamine residues contributed by each of the three SNARE motifs of syntaxin and SNAP-25, respectively. Together with the peptide backbones, the flanking leucine-zipper layers form a water-tight seal around the ionic layer, thereby shielding the ionic interactions from the aqueous surroundings that may increase the stability of the complex. Furthermore, the asymmetric ionic layer fixes the positions of the hydrophobic layers in the center of the helix bundle. This ensures that the long helices of the SNARE motifs are placed into the correct “register” during assembly. The amino acids contributing to the ionic layer are the most highly conserved residues throughout the SNARE superfamily. Apparently, SNARE core complexes generally consist of four-helix bundles, formed from one R-SNARE and three Q-SNAREs with an ionic layer sandwiched between hydrophobic layers, although complexes consisting of only Q-SNAREs have been invoked in special cases. The functional significance of the four-helix bundle is highlighted by the phenotypes of mutations in SNARE proteins in various organisms. Single amino acid substitutions mapping to the core of the bundle generally result in loss, or at least severe impairment, of SNARE function.

The surface of the complex includes four shallow grooves that contain patches of charged and hydrophobic regions. It is possible that this surface provides a scaffold for the binding of regulatory proteins. The amino acids exposed on the surface are the least conserved residues. Hydrogen-bonding and surface electrostatic interactions further stabilize the helix bundle. Interestingly, there are significantly fewer of such interactions originating from synaptobrevin than from the other three helices.