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Scientific reports 9(1), 19281 (1-14) (2019). doi:10.1038/s41598-019-55777-5, Low-frequency vibrations are crucial for protein structure and function, but only a few experimental techniques can shine light on them. The main challenge when addressing protein dynamics in the terahertz domain is the ubiquitous water that exhibit strong absorption. In this paper, we observe the protein atoms directly using X-ray crystallography in bovine trypsin at 100 K while irradiating the crystals with 0.5 THz radiation alternating on and off states. We observed that the anisotropy of atomic displacements increased upon terahertz irradiation. Atomic displacement similarities developed between chemically related atoms and between atoms of the catalytic machinery. This pattern likely arises from delocalized polar vibrational modes rather than delocalized elastic deformations or rigid-body displacements. The displacement correlation between these atoms were detected by a hierarchical clustering method, which can assist the analysis of other ultra-high resolution crystal structures. These experimental and analytical tools provide a detailed description of protein dynamics to complement the structural information from static diffraction experiments., Published by Macmillan Publishers Limited, part of Springer Nature, [London]

This paper suggests a taxonomy for labeling deviating patterns in district heating (DH) customer data. The taxonomy contains several fault labels intended to register information about faults in the DH systems that cause deviations in customer data. This taxonomy is needed because the DH industry is currently missing a unanimous way to label identified faults. The lack of a taxonomy makes it hard to develop automated fault detection and diagnosis methods based on the analysis of DH customer data. Such methods usually require training on historical data sets known to contain deviating data patterns caused by specific faults. By developing a taxonomy for labeling these faults, this study aims to create value for DH utilities in current and future DH systems. The taxonomy structure was based on literature studies, workshops, and discussions with partners within the Swedish FutureHeat collaboration organization Smart Energi. Once the basic structure was decided, it was sent out for evaluation amongst Swedish DH utilities. The evaluation was carried out as a survey study. The results from the survey were compiled, and the finalized version of the deviation cause taxonomy was produced. The study includes the results of the survey study and the finalized version of the deviation cause taxonomy.

Low-frequency vibrations are crucial for protein structure and function, but only a few experimental techniques can shine light on them. The main challenge when addressing protein dynamics in the terahertz domain is the ubiquitous water that exhibit strong absorption. In this paper, we observe the protein atoms directly using X-ray crystallography in bovine trypsin at 100 K while irradiating the crystals with 0.5 THz radiation alternating on and off states. We observed that the anisotropy of atomic displacements increases upon terahertz irradiation. Atomic displacement similarities develop between chemically related atoms and between atoms of the catalytic machinery. This pattern likely arise from delocalized polar vibrational modes rather than delocalized elastic deformations or rigid-body displacements. This method can ultimately reveal how the alignment of chemically related atoms and the underlying polar vibrational dynamics make a protein structure stable.

A Bayesian model which uses a Markov chain Monte Carlo algorithm has been developed to estimate structure-factor amplitude differences., In experimental research referencing two or more measurements to one another is a powerful tool to reduce the effect of systematic errors between different sets of measurements. The interesting quantity is usually derived from two measurements on the same sample under different conditions. While an elaborate experimental design is essential for improving the estimate, the data analysis should also maximally exploit the covariance between the measurements. In X-ray crystallography the difference between structure-factor amplitudes carries important information to solve experimental phasing problems or to determine time-dependent structural changes in pump–probe experiments. Here a multivariate Bayesian method was used to analyse intensity measurement pairs to determine their underlying structure-factor amplitudes and their differences. The posterior distribution of the model parameter was approximated with a Markov chain Monte Carlo algorithm. The described merging method is shown to be especially advantageous when systematic and random errors result in recording negative intensity measurements.

Electrospray contaminant-free delivery of proteins to x-ray laser heralds the start of single-protein x-ray diffractive imaging., The possibility of imaging single proteins constitutes an exciting challenge for x-ray lasers. Despite encouraging results on large particles, imaging small particles has proven to be difficult for two reasons: not quite high enough pulse intensity from currently available x-ray lasers and, as we demonstrate here, contamination of the aerosolized molecules by nonvolatile contaminants in the solution. The amount of contamination on the sample depends on the initial droplet size during aerosolization. Here, we show that, with our electrospray injector, we can decrease the size of aerosol droplets and demonstrate virtually contaminant-free sample delivery of organelles, small virions, and proteins. The results presented here, together with the increased performance of next-generation x-ray lasers, constitute an important stepping stone toward the ultimate goal of protein structure determination from imaging at room temperature and high temporal resolution.

Photosynthetic reaction centers develop a stable charge separated state upon illumination. To investigate the molecular vibrations associated with the illuminated state of a reaction center we recorded terahertz absorption spectra of the photosynthetic reaction center from Rhodobacter sphaeroides in the dark and upon illumination and observed a small, but significant THz absorption increase in the 20 to 130 cm(-1) spectral region. Reaction centers show very similar terahertz absorption increase when solubilized in detergents and in a lipidic sponge phase indicating that the nature of the bulk solvent has limited influence on the vibrational spectrum. The absorption change of the isolated LM subunit is very similar to that of the intact reaction center. Through temperature control experiments we show that 89% of the absorption change is likely attributed to the non-thermal activation of the protein molecules. These results indicate that picosecond molecular vibrations change primarily in the cofactors and/or in the evolutionary conserved core of the reaction center upon illumination, whereas the nuclear motions of the H-subunit and the bulk solvent have limited impact on the terahertz spectral changes.

2016 41st International Conference on Infrared, Millimeter, and Terahertz waves (IRMMW-THz) : [Proceedings] - IEEE, 2016. - ISBN 978-1-4673-8485-8 - doi:10.1109/IRMMW-THz.2016.7758457 41st International Conference on Infrared, Millimeter, and Terahertz waves, IRMMW-THz 2016, Copenhagen, Denmark, 25 Sep 2016 - 30 Sep 2016; IEEE, 2 pp. (2016). doi:10.1109/IRMMW-THz.2016.7758457, We have periodically (25ms on - 25ms off) illuminated lysozyme crystals with 0.4 THz radiation and simultaneously monitored their X-ray diffraction intensity in order to study non-thermal structural changes in the protein. In this work we analyze the X-ray scaled and unmerged diffraction intensity observations using a multivariate Bayesian model in order to improve the accuracy of the intensity estimates. The diffraction intensity pairs of the illuminated and non-illuminated state show a predominantly positive correlation. The correlation decreases with increasing resolution suggesting that finer slicing and faster sampling of the rocking curve may further improve the accuracy and effect size of structure factor amplitude differences, making the interpretation of structural changes more straightforward. The improved analysis retains the most important structural features described previously (in helix 3) and provide addition details about the B-factor changes close to the substrate binding site., Published by IEEE

S100A4 or metastasin plays a central role in the progression of metastatic diseases. Like many other examples, the protein S100A4 contains ordered and disordered regions. The aim of this study was ...