SNAREs (soluble N-ethylmaleimide-sensitive factor attachment receptors) represent an evolutionarily conserved protein family that mediates membrane fusion in the secretory and endocytic pathways of eukaryotic cells 1–3. Upon membrane contact, these proteins assemble in trans between the membranes as a bundle of four α-helices, with the energy released upon assembly being thought to drive fusion 4–6. However, it is unclear how the energy is transferred to the membranes and whether assembly is conformationally linked to fusion. Here, we report the X-ray structure of the neuronal SNARE complex, consisting of syntaxin 1A, SNAP-25 and synaptobrevin 2, with the C-terminal linkers and transmembrane regions at a resolution of 3.4 Å. The structure shows that assembly proceeds beyond the already known core-SNARE complex 7, resulting in a continuous helical bundle that is further stabilized by side-chain interactions in the linker region. Our results suggest that the final phase of SNARE assembly is directly coupled to membrane merger.

VOLUME 29 NUMBER 10 OCTOBER 2011 nature biotechnology A r t i c l e sFluorescent proteins (FPs) 1 whose fluorescence can be reversibly or irreversibly switched by optical irradiation have opened new opportunities for the imaging of cells. They have facilitated in vivo protein-tracking schemes 2,3 , applications based on singlemolecule observations 4,5 and fluorescence microscopy with subdiffraction resolution [6][7][8][9][10] .Still, photoswitchable proteins have not displayed their full potential, because proteins that are just photoactivatable 11-13 can be switched only once, which implies that repeated measurements with the same molecule are impossible. On the other hand, photochromic or reversibly switchable fluorescent proteins (RSFPs) can be repeatedly photoswitched between a fluorescent and a nonfluorescent state by irradiation with light of two different wavelengths. However, in all previously characterized RSFPs, the wavelength used for generating the fluorescence emission is identical to one of the wavelengths used for switching the fluorescence on or off. The result is a complex interlocking of switching and fluorescence readout [14][15][16][17][18][19][20][21][22] , impeding or even precluding many applications, including fluorescence nanoscopy (super-resolution microscopy). Hence, the identification of an RSFP in which the generation of fluorescence is disentangled from switching has long been pursued. RESULTS Generation of the RSFP DreiklangNumerous GFP variants exhibit some degree of (generally undesirable) reversible photoswitching 4,23,24 . We found that the fluorescence of the yellow fluorescent protein Citrine 25,26 , a derivative of GFP, can be reversibly modulated to a small extent by alternate irradiation with light of 365 nm (on switching) and 405 nm (off switching), whereas fluorescence is excited at 515 nm. However, the achievable contrast was low, especially at pH values >6, rendering the reversible switching of Citrine unusable (Supplementary Fig. 1).To further develop this unusual switching behavior, we performed extensive random mutagenesis as well as directed PCR-mediated mutagenesis on a plasmid encoding Citrine. We transformed Escherichia coli with the plasmid, and screened with an automated home-built fluorescence microscope for bacterial colonies expressing fluorescent proteins whose fluorescence was excited with green light (515 nm) and which could be reversibly photoswitched from a fluorescent state to a long-lived nonfluorescent state by irradiation with near-UV (405 nm) light and back to a fluorescent state by UV (365 nm) light (Fig. 1a). In several consecutive screening rounds ~70,000 individual clones were analyzed. Finally, we identified a mutant differing from Citrine at four positions (Citrine-V61L, F64I, Y145H, N146D) ( Supplementary Fig. 2), which can be effectively switched and excited to fluoresce. We named this switchable fluorescent protein Dreiklang, the German word for a three-note chord in music.At thermal equilibrium, Dreiklang adopts the brightly fluorescent ...

Dronpa is a novel GFP-like fluorescent protein with exceptional light-controlled switching properties. It may be reversibly switched between a fluorescent on-state and a nonfluorescent off-state by irradiation with light. To elucidate the molecular basis of the switching mechanism, we generated reversibly switchable Dronpa protein crystals. Using these crystals we determined the elusive dark-state structure of Dronpa at 1.95-Å resolution. We found that the photoswitching results in a cis-trans isomerization of the chromophore accompanied by complex structural rearrangements of four nearby amino acid residues. Because of this cascade of intramolecular events, the chromophore is exposed to distinct electrostatic surface potentials, which are likely to influence the protonation equilibria at the chromophore. We suggest a comprehensive model for the light-induced switching mechanism, connecting a cascade of structural rearrangements with different protonation states of the chromophore. The recently discovered reversibly switchable FPs (RSFPs) are a further powerful class of FPs for cell biology and beyond. Other than the photoactivatable FPs, RSFPs may be repeatedly and reversibly switched by irradiation between a fluorescent and a nonfluorescent state. Hence they exhibit unique advantages for protein tracking applications, subdiffraction microscopy, and several novel applications that had not been addressable previously (8-13). Dronpa (14) and asFP595 (asulCP, asCP) (15) are the most prominent RSFPs. Like all FPs, they exhibit a GFP-like fold, namely a ␤-barrel enclosing an ␣-helix containing the autocatalytically formed chromophore. Because of its low quantum yield, the tetrameric asFP595 is only of limited use for cell biology applications, whereas Dronpa has been successfully used for several protein tracking studies (14,16,17). Dronpa is monomeric, displays favorable switching properties, and shows bright fluorescence with a remarkable fluorescence quantum yield of 0.85. Furthermore, several new Dronpa variants with accelerated switching kinetics have been described (18).Despite its tremendous potential for many applications, little is known about the molecular basis of the switching in Dronpa. Thus far competing models discussing either the light-driven regulation of the chromophoric protonation state by the surrounding protein matrix (19, 20) or postulating a cis-trans isomerization of the chromophore indirectly determining its own protonation state (18) have been suggested.To unravel this problem we generated Dronpa protein crystals that were reversibly switchable with visible light at ambient conditions. After switching the whole Dronpa crystals we determined its thus far elusive off-state structure by x-ray crystallography. We found that the primary event of the switching is a light-activated cis-trans isomerization of the chromophore together with a cascade of residue rearrangements. Because the electrostatic surface potentials in the chromophoric cis and trans cavities differ substantially, we postulate ...

Proteins that can be reversibly photoswitched between a fluorescent and a nonfluorescent state bear enormous potential in diverse fields, such as data storage, in vivo protein tracking, and subdiffraction resolution light microscopy. However, these proteins could hitherto not live up to their full potential because the molecular switching mechanism is not resolved. Here, we clarify the molecular photoswitching mechanism of asFP595, a green fluorescent protein (GFP)-like protein that can be transferred from a nonfluorescent ''off'' to a fluorescent ''on'' state and back again, by green and blue light, respectively. To this end, we establish reversible photoswitching of fluorescence in whole protein crystals and show that the switching kinetics in the crystal is identical with that in solution. Subsequent x-ray analysis demonstrated that upon the absorption of a green photon, the chromophore isomerizes from a trans (off) to a cis (on) state. Molecular dynamics calculations suggest that isomerization occurs through a bottom hula twist mechanism with concomitant rotation of both bonds of the chromophoric methine ring bridge. This insight into the switching mechanism should facilitate the targeted design of photoswitchable proteins. Reversible photoswitching of the protein chromophore system within intact crystals also constitutes a step toward the use of fluorescent proteins in three-dimensional data recording.photoisomerization ͉ asCP ͉ photochromism ͉ optical bistability ͉ asulCP F luorescent proteins have been widely used as genetically encodable tags to monitor protein localizations and dynamics in live cells (1-3). Recently, novel GFP-like fluorescent proteins have been discovered (4-6) that can be reversibly photoswitched between a fluorescent (on) and nonfluorescent (off) state, that is, they are optically bistable and fluorescent. This feature is remarkable, because the reversible photoswitching occurring in photochromic organic compounds, such as in fulgides and diarylethenes, is usually not accompanied by fluorescence (7). Therefore, not surprisingly, these proteins hold great promise in many areas of science reaching out far beyond their prominent use as triggerable protein markers in live cells. For example, the reversible photoswitching of fluorescent markers should provide nanoscale resolution in fluorescence microscopy by using lenses and regular illumination, which was hardly conceivable only a few years ago (8-10). As fluorescence can be sensitively read out from a bulky crystal, the prospect of erasable three-dimensional data storage is equally intriguing.The GFP-like protein asFP595 (asCP or asulCP) from the sea anemone Anemonia sulcata is such a protein: It can be transferred by green light from a nonfluorescent off into a fluorescent on state from which it reverts back eventually, but this transition can also be promptly stimulated by gentle irradiation with blue light (6). The ''on-off'' cycle can be repeated many times. However, with its low quantum yield (Ͻ0.001, ref. 6) and comparatively slo...