Molecular basis of lipid-linked oligosaccharide recognition and processing by bacterial oligosaccharyltransferase.

Oligosaccharyltransferase (OST) is a membrane-integral enzyme that catalyzes the transfer of glycans from lipid-linked oligosaccharides (LLOs) onto asparagine side chains, the first step in protein N-glycosylation. Here, we report the X-ray structure of a single-subunit OST, PglB from Campylobacter lari, trapped in an intermediate state bound to an acceptor peptide and a synthetic LLO analog. The structure reveals the role of the external loop EL5, present in all OST enzymes, in substrate recognition. Whereas the N-terminal half of EL5 binds LLO, the C-terminal half interacts with the acceptor peptide. The glycan moiety of LLO must thread under EL5 to access the active site. Reducing EL5 mobility decreases the catalytic rate of OST when full-size heptasaccharide LLO is provided, but not for a monosaccharide-containing LLO analog. Our results define the chemistry of a ternary complex state, assign functional roles to conserved OST motifs, and provide opportunities for glycoengineering by rational design of PglB.

Barrierless Photoisomerization of 11-cis Retinal Protonated Schiff Base in Solution.

A hallmark of the primary visual event is the barrierless, ultrafast, and efficient 11-cis to all-trans photoisomerization of the retinal protonated Schiff base (RPSB) chromophore. The remarkable reactivity of RPSB in the visual pigment rhodopsin has been attributed to potential energy surface modifications enabled by evolution-optimized chromophore-protein interactions. Here, we use a combined synthetic and ultrafast spectroscopic approach to show that barrierless photoisomerization is an intrinsic property of 11-cis RPSB, suggesting that the protein may merely adjust the ratio between fast reactive and slow unreactive decay channels. These results call for a re-evaluation of our understanding and theoretical description of RPSB photochemistry.

Synthetic control of retinal photochemistry and photophysics in solution.

Understanding how molecular structure and environment control energy flow in molecules is a requirement for the efficient design of tailor-made photochemistry. Here, we investigate the tunability of the photochemical and photophysical properties of the retinal-protonated Schiff base chromophore in solution. Replacing the n-butylamine Schiff base normally chosen to mimic the saturated linkage found in nature by aromatic amines results in the reproduction of the opsin shift and complete suppression of all isomerization channels. Modification of retinal by directed addition or removal of backbone substituents tunes the overall photoisomerization yield from 0 to 0.55 and the excited state lifetime from 0.4 to 7 ps and activates previously inaccessible reaction channels to form 7-cis and 13-cis products. We observed a clear correlation between the presence of polarizable backbone substituents and photochemical reactivity. Structural changes that increase reaction speed were found to decrease quantum yields, and vice versa, so that excited state lifetime and efficiency are inversely correlated in contrast to the trends observed when comparing retinal photochemistry in protein and solution environments. Our results suggest a simple model where backbone modifications and Schiff base substituents control barrier heights on the excited-state potential energy surface and therefore determine speed, product distribution, and overall yield of the photochemical process.

Backbone modification of retinal induces protein-like excited state dynamics in solution.

The drastically different reactivity of the retinal chromophore in solution compared to the protein environment is poorly understood. Here, we show that the addition of a methyl group to the C═C backbone of all-trans retinal protonated Schiff base accelerates the electronic decay in solution making it comparable to the proton pump bacteriorhodopsin. Contrary to the notion that reaction speed and efficiency are linked, we observe a concomitant 50% reduction in the isomerization yield. Our results demonstrate that minimal synthetic engineering of potential energy surfaces based on theoretical predictions can induce drastic changes in electronic dynamics toward those observed in an evolution-optimized protein pocket.

How to distinguish between feruloyl quinic acids and isoferuloyl quinic acids by liquid chromatography/tandem mass spectrometry.

All four regioisomers of feruloyl quinic acid and isoferuloyl quinic acid were synthesized and a liquid chromatography/tandem mass spectrometry (LC/MS/MS) method developed that resolves all eight regioisomers. All eight regioisomers can be readily distinguished by their MS/MS spectra in the negative ion mode, illustrating the power of tandem mass spectrometry to elucidate the structures of regioisomeric compounds. Compound identification is possible, either by direct comparison of spectral fingerprints or by rational probing of diagnostic fragment ions, thus allowing the identification of these important classes of natural products and potential human metabolites.

Profiling and characterization by LC-MSn of the chlorogenic acids and hydroxycinnamoylshikimate esters in maté (Ilex paraguariensis).

The chlorogenic acids of mate (Ilex paraguariensis) have been investigated qualitatively by LC-MS(n). Forty-two chlorogenic acids were detected and all characterized to regioisomeric level on the basis of their fragmentation pattern in tandem MS spectra, 24 of them for the first time from this source. Both chlorogenic acids based on trans- and cis-cinnamic acid substituents were identified. Assignment to the level of individual regioisomers was possible for eight caffeoylquinic acids (1-8), five dicaffeoylquinic acids (20-24), six feruloylquinic acids (9-14), two diferuloyl quinic acids (25 and 26), five p-coumaroylquinic acids (15-19), four caffeoyl-p-coumaroylquinic acids (34-37), seven caffeoyl-feruloylquinic acids (27-33), three caffeoyl-sinapoylquinic acids (38-40), one tricaffeoylquinic acid (41), and one dicaffeoyl-feruloylquinic acid (42). Furthermore, four caffeoylshikimates (43-46), three dicaffeoylshikimates (47-49), one tricaffeoylshikimate (51), and one feruloylshikimate (50) have been detected and shown to possess characteristic tandem MS spectra and were assigned by comparison to reference standards.