@article{14776,
  abstract     = {Soluble chaperones residing in the endoplasmic reticulum (ER) play vitally important roles in folding and quality control of newly synthesized proteins that transiently pass through the ER en route to their final destinations. These soluble residents of the ER are themselves endowed with an ER retrieval signal that enables the cell to bring the escaped residents back from the Golgi. Here, by using purified proteins, we showed that Nicotiana tabacum phytaspase, a plant aspartate-specific protease, introduces two breaks at the C-terminus of the N. tabacum ER resident calreticulin-3. These cleavages resulted in removal of either a dipeptide or a hexapeptide from the C-terminus of calreticulin-3 encompassing part or all of the ER retrieval signal. Consistently, expression of the calreticulin-3 derivative mimicking the phytaspase cleavage product in Nicotiana benthamiana cells demonstrated loss of the ER accumulation of the protein. Notably, upon its escape from the ER, calreticulin-3 was further processed by an unknown protease(s) to generate the free N-terminal (N) domain of calreticulin-3, which was ultimately secreted into the apoplast. Our study thus identified a specific proteolytic enzyme capable of precise detachment of the ER retrieval signal from a plant ER resident protein, with implications for the further fate of the escaped resident.},
  author       = {Teplova, Anastasiia and Pigidanov, Artemii A. and Serebryakova, Marina V. and Golyshev, Sergei A. and Galiullina, Raisa A. and Chichkova, Nina V. and Vartapetian, Andrey B.},
  issn         = {1422-0067},
  journal      = {International Journal of Molecular Sciences},
  keywords     = {Inorganic Chemistry, Organic Chemistry, Physical and Theoretical Chemistry, Computer Science Applications, Spectroscopy, Molecular Biology, General Medicine, Catalysis},
  number       = {22},
  publisher    = {MDPI},
  title        = {{Phytaspase Is capable of detaching the endoplasmic reticulum retrieval signal from tobacco calreticulin-3}},
  doi          = {10.3390/ijms242216527},
  volume       = {24},
  year         = {2023},
}

@article{11498,
  abstract     = {Rest-frame ultraviolet (UV) emission lines probe electron densities, gas-phase abundances, metallicities, and ionization parameters of the emitting star-forming galaxies and their environments. The strongest main UV emission line, Lyα, has been instrumental in advancing the general knowledge of galaxy formation in the early universe. However, observing Lyα emission becomes increasingly challenging at z ≳ 6 when the neutral hydrogen fraction of the circumgalactic and intergalactic media increases. Secondary weaker UV emission lines provide important alternative methods for studying galaxy properties at high redshift. We present a large sample of rest-frame UV emission line sources at intermediate redshift for calibrating and exploring the connection between secondary UV lines and the emitting galaxies’ physical properties and their Lyα emission. The sample of 2052 emission line sources with 1.5 < z < 6.4 was collected from integral field data from the MUSE-Wide and MUSE-Deep surveys taken as part of Guaranteed Time Observations. The objects were selected through untargeted source detection (i.e., no preselection of sources as in dedicated spectroscopic campaigns) in the three-dimensional MUSE data cubes. We searched optimally extracted one-dimensional spectra of the full sample for UV emission features via emission line template matching, resulting in a sample of more than 100 rest-frame UV emission line detections. We show that the detection efficiency of (non-Lyα) UV emission lines increases with survey depth, and that the emission line strength of He IIλ1640 Å, [O III] λ1661 + O III] λ1666, and [Si III] λ1883 + Si III] λ1892 correlate with the strength of [C III] λ1907 + C III] λ1909. The rest-frame equivalent width (EW0) of [C III] λ1907 + C III] λ1909 is found to be roughly 0.22 ± 0.18 of EW0(Lyα). We measured the velocity offsets of resonant emission lines with respect to systemic tracers. For C IVλ1548 + C IVλ1551 we find that ΔvC IV ≲ 250 km s−1, whereas ΔvLyα falls in the range of 250−500 km s−1 which is in agreement with previous results from the literature. The electron density ne measured from [Si III] λ1883 + Si III] λ1892 and [C III] λ1907 + C III] λ1909 line flux ratios is generally < 105 cm−3 and the gas-phase abundance is below solar at 12 + log10(O/H)≈8. Lastly, we used “PhotoIonization Model Probability Density Functions” to infer physical parameters of the full sample and individual systems based on photoionization model parameter grids and observational constraints from our UV emission line searches. This reveals that the UV line emitters generally have ionization parameter log10(U) ≈ −2.5 and metal mass fractions that scatter around Z ≈ 10−2, that is Z ≈ 0.66 Z⊙. Value-added catalogs of the full sample of MUSE objects studied in this work and a collection of UV line emitters from the literature are provided with this paper.},
  author       = {Schmidt, K. B. and Kerutt, J. and Wisotzki, L. and Urrutia, T. and Feltre, A. and Maseda, M. V. and Nanayakkara, T. and Bacon, R. and Boogaard, L. A. and Conseil, S. and Contini, T. and Herenz, E. C. and Kollatschny, W. and Krumpe, M. and Leclercq, F. and Mahler, G. and Matthee, Jorryt J and Mauerhofer, V. and Richard, J. and Schaye, J.},
  issn         = {1432-0746},
  journal      = {Astronomy & Astrophysics},
  keywords     = {Space and Planetary Science, Astronomy and Astrophysics, ultraviolet: galaxies / galaxies: high-redshift / galaxies: ISM / ISM: lines and bands / methods: observational / techniques: imaging spectroscopy},
  publisher    = {EDP Sciences},
  title        = {{Recovery and analysis of rest-frame UV emission lines in 2052 galaxies observed with MUSE at 1.5 < z < 6.4}},
  doi          = {10.1051/0004-6361/202140876},
  volume       = {654},
  year         = {2021},
}

@article{11526,
  abstract     = {We present the results from a MUSE survey of twelve z ≃ 3.15 quasars, which were selected to be much fainter (20 < iSDSS < 23) than in previous studies of giant Ly α nebulae around the brightest quasars (16.6 < iAB < 18.7). We detect H I Ly α nebulae around 100 per cent of our target quasars, with emission extending to scales of at least 60 physical kpc, and up to 190 pkpc. We explore correlations between properties of the nebulae and their host quasars, with the goal of connecting variations in the properties of the illuminating QSO to the response in nebular emission. We show that the surface brightness profiles of the nebulae are similar to those of nebulae around bright quasars, but with a lower normalization. Our targeted quasars are on average 3.7 mag (≃30 times) fainter in UV continuum than our bright reference sample, and yet the nebulae around them are only 4.3 times fainter in mean Ly α surface brightness, measured between 20 and 50 pkpc. We find significant correlations between the surface brightness of the nebula and the luminosity of the quasar in both UV continuum and Ly α. The latter can be interpreted as evidence for a substantial contribution from unresolved inner parts of the nebulae to the narrow components seen in the Ly α lines of some of our faint quasars, possibly from the inner circumgalactic medium or from the host galaxy’s interstellar medium.},
  author       = {Mackenzie, Ruari and Pezzulli, Gabriele and Cantalupo, Sebastiano and Marino, Raffaella A and Lilly, Simon and Muzahid, Sowgat and Matthee, Jorryt J and Schaye, Joop and Wisotzki, Lutz},
  issn         = {1365-2966},
  journal      = {Monthly Notices of the Royal Astronomical Society},
  keywords     = {Space and Planetary Science, Astronomy and Astrophysics, techniques: imaging spectroscopy, intergalactic medium, quasars: emission lines, quasars: general},
  number       = {1},
  pages        = {494--509},
  publisher    = {Oxford University Press},
  title        = {{Revealing the impact of quasar luminosity on giant Lyα nebulae}},
  doi          = {10.1093/mnras/staa3277},
  volume       = {502},
  year         = {2021},
}

@article{13386,
  abstract     = {Azobenzenealkanethiols in self-assembled monolayers (SAMs) on Au(111) exhibit reversible trans–cis photoisomerization when diluted with alkanethiol spacers. Using these mixed SAMs, we show switching of the linear optical and second-harmonic response. The effective switching of these surface optical properties relies on a reasonably large cross section and a high photoisomerization yield as well as a long lifetime of the metastable cis isomer. We quantified the switching process by X-ray absorption spectroscopy. The cross sections for the trans–cis and cis–trans photoisomerization with 365 and 455 nm light, respectively, are 1 order of magnitude smaller than in solution. In vacuum, the 365 nm photostationary state comprises 50–74% of the molecules in the cis form, limited by their rapid thermal isomerization back to the trans state. In contrast, the 455 nm photostationary state contains nearly 100% trans-azobenzene. We determined time constants for the thermal cis–trans isomerization of only a few minutes in vacuum and in a dry nitrogen atmosphere but of more than 1 day in ambient air. Our results suggest that adventitious water adsorbed on the surface of the SAM stabilizes the polar cis configuration of azobenzene under ambient conditions. The back reaction rate constants differing by 2 orders of magnitude underline the huge influence of the environment and, accordingly, its importance when comparing various experiments.},
  author       = {Moldt, Thomas and Przyrembel, Daniel and Schulze, Michael and Bronsch, Wibke and Boie, Larissa and Brete, Daniel and Gahl, Cornelius and Klajn, Rafal and Tegeder, Petra and Weinelt, Martin},
  issn         = {1520-5827},
  journal      = {Langmuir},
  keywords     = {Electrochemistry, Spectroscopy, Surfaces and Interfaces, Condensed Matter Physics, General Materials Science},
  number       = {42},
  pages        = {10795--10801},
  publisher    = {American Chemical Society},
  title        = {{Differing isomerization kinetics of azobenzene-functionalized self-assembled monolayers in ambient air and in vacuum}},
  doi          = {10.1021/acs.langmuir.6b01690},
  volume       = {32},
  year         = {2016},
}

@article{13396,
  abstract     = {Photoswitching in densely packed azobenzene self-assembled monolayers (SAMs) is strongly affected by steric constraints and excitonic coupling between neighboring chromophores. Therefore, control of the chromophore density is essential for enhancing and manipulating the photoisomerization yield. We systematically compare two methods to achieve this goal: First, we assemble monocomponent azobenzene–alkanethiolate SAMs on gold nanoparticles of varying size. Second, we form mixed SAMs of azobenzene–alkanethiolates and “dummy” alkanethiolates on planar substrates. Both methods lead to a gradual decrease of the chromophore density and enable efficient photoswitching with low-power light sources. X-ray spectroscopy reveals that coadsorption from solution yields mixtures with tunable composition. The orientation of the chromophores with respect to the surface normal changes from a tilted to an upright position with increasing azobenzene density. For both systems, optical spectroscopy reveals a pronounced excitonic shift that increases with the chromophore density. In spite of exciting the optical transition of the monomer, the main spectral change in mixed SAMs occurs in the excitonic band. In addition, the photoisomerization yield decreases only slightly by increasing the azobenzene–alkanethiolate density, and we observed photoswitching even with minor dilutions. Unlike in solution, azobenzene in the planar SAM can be switched back almost completely by optical excitation from the cis to the original trans state within a short time scale. These observations indicate cooperativity in the photoswitching process of mixed SAMs.},
  author       = {Moldt, Thomas and Brete, Daniel and Przyrembel, Daniel and Das, Sanjib and Goldman, Joel R. and Kundu, Pintu K. and Gahl, Cornelius and Klajn, Rafal and Weinelt, Martin},
  issn         = {1520-5827},
  journal      = {Langmuir},
  keywords     = {Electrochemistry, Spectroscopy, Surfaces and Interfaces, Condensed Matter Physics, General Materials Science},
  number       = {3},
  pages        = {1048--1057},
  publisher    = {American Chemical Society},
  title        = {{Tailoring the properties of surface-immobilized azobenzenes by monolayer dilution and surface curvature}},
  doi          = {10.1021/la504291n},
  volume       = {31},
  year         = {2015},
}

@article{8461,
  abstract     = {Solid-state NMR provides insight into protein motion over time scales ranging from picoseconds to seconds. While in solution state the methodology to measure protein dynamics is well established, there is currently no such consensus protocol for measuring dynamics in solids. In this article, we perform a detailed investigation of measurement protocols for fast motions, i.e. motions ranging from picoseconds to a few microseconds, which is the range covered by dipolar coupling and relaxation experiments. We perform a detailed theoretical investigation how dipolar couplings and relaxation data can provide information about amplitudes and time scales of local motion. We show that the measurement of dipolar couplings is crucial for obtaining accurate motional parameters, while systematic errors are found when only relaxation data are used. Based on this realization, we investigate how the REDOR experiment can provide such data in a very accurate manner. We identify that with accurate rf calibration, and explicit consideration of rf field inhomogeneities, one can obtain highly accurate absolute order parameters. We then perform joint model-free analyses of 6 relaxation data sets and dipolar couplings, based on previously existing, as well as new data sets on microcrystalline ubiquitin. We show that nanosecond motion can be detected primarily in loop regions, and compare solid-state data to solution-state relaxation and RDC analyses. The protocols investigated here will serve as a useful basis towards the establishment of a routine protocol for the characterization of ps–μs motions in proteins by solid-state NMR.},
  author       = {Haller, Jens D. and Schanda, Paul},
  issn         = {0925-2738},
  journal      = {Journal of Biomolecular NMR},
  keywords     = {Spectroscopy, Biochemistry},
  number       = {3},
  pages        = {263--280},
  publisher    = {Springer Nature},
  title        = {{Amplitudes and time scales of picosecond-to-microsecond motion in proteins studied by solid-state NMR: a critical evaluation of experimental approaches and application to crystalline ubiquitin}},
  doi          = {10.1007/s10858-013-9787-x},
  volume       = {57},
  year         = {2013},
}

@article{8479,
  abstract     = {Multidimensional NMR spectroscopy is a well-established technique for the characterization of structure and fast-time-scale dynamics of highly populated ground states of biological macromolecules. The investigation of short-lived excited states that are important for molecular folding, misfolding and function, however, remains a challenge for modern biomolecular NMR techniques. Off-equilibrium real-time kinetic NMR methods allow direct observation of conformational or chemical changes by following peak positions and intensities in a series of spectra recorded during a kinetic event. Because standard multidimensional NMR methods required to yield sufficient atom-resolution are intrinsically time-consuming, many interesting phenomena are excluded from real-time NMR analysis. Recently, spatially encoded ultrafast 2D NMR techniques have been proposed that allow one to acquire a 2D NMR experiment within a single transient. In addition, when combined with the SOFAST technique, such ultrafast experiments can be repeated at high rates. One of the problems detected for such ultrafast protein NMR experiments is related to the heteronuclear decoupling during detection with interferences between the pulses and the oscillatory magnetic field gradients arising in this scheme. Here we present a method for improved ultrafast data acquisition yielding higher signal to noise and sharper lines in single-scan 2D NMR spectra. In combination with a fast-mixing device, the recording of 1H–15N correlation spectra with repetition rates of up to a few Hertz becomes feasible, enabling real-time studies of protein kinetics occurring on time scales down to a few seconds.},
  author       = {Gal, Maayan and Kern, Thomas and Schanda, Paul and Frydman, Lucio and Brutscher, Bernhard},
  issn         = {0925-2738},
  journal      = {Journal of Biomolecular NMR},
  keywords     = {Spectroscopy, Biochemistry},
  pages        = {1--10},
  publisher    = {Springer Nature},
  title        = {{An improved ultrafast 2D NMR experiment: Towards atom-resolved real-time studies of protein kinetics at multi-Hz rates}},
  doi          = {10.1007/s10858-008-9284-9},
  volume       = {43},
  year         = {2009},
}

@article{8485,
  abstract     = {High signal to noise is a necessity for the quantification of NMR spectral parameters to be translated into accurate and precise restraints on protein structure and dynamics. An important source of long-range structural information is obtained from 1H–1H residual dipolar couplings (RDCs) measured for weakly aligned molecules. For sensitivity reasons, such measurements are generally performed on highly deuterated protein samples. Here we show that high sensitivity is also obtained for protonated protein samples if the pulse schemes are optimized in terms of longitudinal relaxation efficiency and J-mismatch compensated coherence transfer. The new sensitivity-optimized quantitative J-correlation experiment yields important signal gains reaching factors of 1.5 to 8 for individual correlation peaks when compared to previously proposed pulse schemes.},
  author       = {Schanda, Paul and Lescop, Ewen and Falge, Mirjam and Sounier, Rémy and Boisbouvier, Jérôme and Brutscher, Bernhard},
  issn         = {0925-2738},
  journal      = {Journal of Biomolecular NMR},
  keywords     = {Spectroscopy, Biochemistry},
  pages        = {47--55},
  publisher    = {Springer Nature},
  title        = {{Sensitivity-optimized experiment for the measurement of residual dipolar couplings between amide protons}},
  doi          = {10.1007/s10858-006-9138-2},
  volume       = {38},
  year         = {2007},
}

@article{13426,
  abstract     = {Photoswelling of thin films of dichromated gelatin provides a basis for fabrication of multilevel surface reliefs via sequential UV illumination through different photomasks. The remarkable feature of this simple, benchtop technique is that by adjusting irradiation times, film thickness, or its hydration state the heights of the developed features can be varied from few nanometers to tens of microns. After UV exposure, the surface structures can be replicated faithfully into either soft or hard PDMS stamps.},
  author       = {Paszewski, Maciej and Smoukov, Stoyan K. and Klajn, Rafal and Grzybowski, Bartosz A.},
  issn         = {1520-5827},
  journal      = {Langmuir},
  keywords     = {Electrochemistry, Spectroscopy, Surfaces and Interfaces, Condensed Matter Physics, General Materials Science},
  number       = {10},
  pages        = {5419--5422},
  publisher    = {American Chemical Society},
  title        = {{Multilevel surface nano- and microstructuring via sequential photoswelling of dichromated gelatin}},
  doi          = {10.1021/la062982c},
  volume       = {23},
  year         = {2007},
}

@article{8491,
  abstract     = {Fast multidimensional NMR with a time resolution of a few seconds provides a new tool for high throughput screening and site-resolved real-time studies of kinetic molecular processes by NMR. Recently we have demonstrated the feasibility to record protein 1H–15N correlation spectra in a few seconds of acquisition time using a new SOFAST-HMQC experiment (Schanda and Brutscher (2005) J. Am. Chem. Soc. 127, 8014). Here, we investigate in detail the performance of SOFAST-HMQC to record 1H–15N and 1H−13C correlation spectra of proteins of different size and at different magnetic field strengths. Compared to standard 1H–15N correlation experiments SOFAST-HMQC provides a significant gain in sensitivity, especially for fast repetition rates. Guidelines are provided on how to set up SOFAST-HMQC experiments for a given protein sample. In addition, an alternative pulse scheme, IPAP-SOFAST-HMQC is presented that allows application on NMR spectrometers equipped with cryogenic probes, and fast measurement of one-bond 1H–13C and 1H–15N scalar and residual dipolar coupling constants.},
  author       = {Schanda, Paul and Kupče, Ēriks and Brutscher, Bernhard},
  issn         = {0925-2738},
  journal      = {Journal of Biomolecular NMR},
  keywords     = {Spectroscopy, Biochemistry},
  number       = {4},
  pages        = {199--211},
  publisher    = {Springer Nature},
  title        = {{SOFAST-HMQC experiments for recording two-dimensional deteronuclear correlation spectra of proteins within a few seconds}},
  doi          = {10.1007/s10858-005-4425-x},
  volume       = {33},
  year         = {2005},
}

@article{13432,
  abstract     = {A new experimental technique is described that uses reaction−diffusion phenomena as a means of one-step microfabrication of complex, multilevel surface reliefs. Thin films of dry gelatin doped with potassium hexacyanoferrate are chemically micropatterned with a solution of silver nitrate delivered from an agarose stamp. Precipitation reaction between the two salts causes the surface to deform. The mechanism of surface deformation is shown to involve a sequence of reactions, diffusion, and gel swelling/contraction. This mechanism is established experimentally and provides a basis of a theoretical lattice-gas model that allows prediction surface topographies emerging from arbitrary geometries of the stamped features. The usefulness of the technique is demonstrated by using it to rapidly prepare two types of mold for passive microfluidic mixers.},
  author       = {Campbell, Christopher J. and Klajn, Rafal and Fialkowski, Marcin and Grzybowski, Bartosz A.},
  issn         = {1520-5827},
  journal      = {Langmuir},
  keywords     = {Electrochemistry, Spectroscopy, Surfaces and Interfaces, Condensed Matter Physics, General Materials Science},
  number       = {1},
  pages        = {418--423},
  publisher    = {American Chemical Society},
  title        = {{One-step multilevel microfabrication by reaction−diffusion}},
  doi          = {10.1021/la0487747},
  volume       = {21},
  year         = {2005},
}