| 1. |
- Ahlberg Gagnér, Viktor, 1989, et al.
(författare)
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Clustering of atomic displacement parameters in bovine trypsin reveals a distributed lattice of atoms with shared chemical properties
- 2019
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322 .- 2045-2322. ; 9:1
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Tidskriftsartikel (refereegranskat)abstract
- 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. © 2019, The Author(s).
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| 2. |
- Duelli, Annette, 1980, et al.
(författare)
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The C-Terminal Random Coil Region Tunes the Ca2+-Binding Affinity of S100A4 through Conformational Activation.
- 2014
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Ingår i: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 9:5
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Tidskriftsartikel (refereegranskat)abstract
- S100A4 interacts with many binding partners upon Ca2+ activation and is strongly associated with increased metastasis formation. In order to understand the role of the C-terminal random coil for the protein function we examined how small angle X-ray scattering of the wild-type S100A4 and its C-terminal deletion mutant (residues 1-88, Δ13) changes upon Ca2+ binding. We found that the scattering intensity of wild-type S100A4 changes substantially in the 0.15-0.25 Å-1 q-range whereas a similar change is not visible in the C-terminus deleted mutant. Ensemble optimization SAXS modeling indicates that the entire C-terminus is extended when Ca2+ is bound. Pulsed field gradient NMR measurements provide further support as the hydrodynamic radius in the wild-type protein increases upon Ca2+ binding while the radius of Δ13 mutant does not change. Molecular dynamics simulations provide a rational explanation of the structural transition: the positively charged C-terminal residues associate with the negatively charged residues of the Ca2+-free EF-hands and these interactions loosen up considerably upon Ca2+-binding. As a consequence the Δ13 mutant has increased Ca2+ affinity and is constantly loaded at Ca2+ concentration ranges typically present in cells. The activation of the entire C-terminal random coil may play a role in mediating interaction with selected partner proteins of S100A4.
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| 3. |
- Katona, Gergely, 1975, et al.
(författare)
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Bayesian analysis of non-thermal structural changes induced by terahertz radiation in protein crystals
- 2016
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Ingår i: 2016 41ST INTERNATIONAL CONFERENCE ON INFRARED, MILLIMETER, AND TERAHERTZ WAVES (IRMMW-THZ). - New York : IEEE conference proceedings. - 2162-2027 .- 2162-2035. - 9781467384858
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Konferensbidrag (refereegranskat)abstract
- 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.
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| 4. |
- Katona, Gergely, 1975, et al.
(författare)
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Estimating the difference between structure-factor amplitudes using multivariate Bayesian inference
- 2016
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Ingår i: Acta Crystallographica a-Foundation and Advances. - 2053-2733. ; 72, s. 406-411
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 5. |
- Lundholm, Ida, 1986, et al.
(författare)
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Terahertz absorption of illuminated photosynthetic reaction center solution: a signature of photoactivation?
- 2014
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Ingår i: Rsc Advances. - : Royal Society of Chemistry (RSC). - 2046-2069. ; 4:49, s. 25502-25509
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Tidskriftsartikel (refereegranskat)abstract
- 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.
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| 6. |
- Lundholm, Ida, 1986
(författare)
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Terahertz radiation as a pump and probe for studying low frequency vibrations in proteins
- 2015
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Many functionally important structural changes in proteins proceed along the direction of their lowest frequency vibrations. These vibrations correspond to picosecond collective dynamics. Establishing the fundamental relationship between these vibrations and protein function remains a challenge within biophysics. Electromagnetic radiation in the terahertz frequency range (0.1-10 THz) can excite collective picosecond vibrations which makes it suitable as a probe for direct observation as well as a pump for the selection of functionally relevant vibrations for detection by other methods. The use of terahertz radiation for biological applications is hampered by several technical difficulties such as water absorption and thermal effects. For these reasons, method development is an important aspect when applying terahertz radiation to biological problems. In this work, terahertz radiation has been used to identify and characterize low frequency vibrations in three different proteins by applying both novel experimental design and analysis methods. Terahertz absorption spectroscopy was used to identify the change in collective dynamics upon photoactivation of a photosynthetic reaction centre. The collective vibrations were of non thermal origin and localized to the chromophore containing subunits implying the involvement of collective dynamics in photosynthesis. By combining X-ray crystallography with 0.4 THz excitation the presence of collective dynamics was detected in both lysozyme and thermolysin. In lysozyme, the vibrational mode was localized to a central α-helix. The vibrational mode had a lifetime longer than expected which most likely arise from a hypothetical Fröhlich condensation process not previously observed. The interaction of terahertz radiation with thermolysin was identified through a Bayesian statistical analysis of X-ray diffraction data.
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| 7. |
- Lundholm, Ida, 1986, et al.
(författare)
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Terahertz radiation induces non-thermal structural changes associated with Fröhlich condensation in a protein crystal
- 2015
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Ingår i: Structural Dynamics. - : AIP Publishing. - 2329-7778 .- 2329-7778. ; 2:5
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Tidskriftsartikel (refereegranskat)abstract
- Whether long-range quantum coherent states could exist in biological systems, and beyond low-temperature regimes where quantum physics is known to be applicable, has been the subject to debate for decades. It was proposed by Fröhlich that vibrational modes within protein molecules can order and condense into a lowest-frequency vibrational mode in a process similar to Bose-Einstein condensation, and thus that macroscopic coherence could potentially be observed in biological systems. Despite the prediction of these so-called Fröhlich condensates almost five decades ago, experimental evidence thereof has been lacking. Here, we present the first experimental observation of Fröhlich condensation in a protein structure. To that end, and to overcome the challenges associated with probing low-frequency molecular vibrations in proteins (which has hampered understanding of their role in proteins’ function), we combined terahertz techniques with a highly sensitive X-ray crystallographic method to visualize low-frequency vibrational modes in the protein structure of hen-egg white lysozyme. We found that 0.4 THz electromagnetic radiation induces non-thermal changes in electron density. In particular, we observed a local increase of electron density in a long a-helix motif consistent with a subtle longitudinal compression of the helix. These observed electron density changes occur at a low absorption rate indicating that thermalization of terahertz photons happens on a micro- to milli-second time scale, which is much slower than the expected nanosecond time scale due to damping of delocalized low frequency vibrations. Our analyses show that the micro- to milli-second life time of the vibration can only be explained by Fröhlich condensation, a phenomenon predicted almost half a century ago, yet never experimentally confirmed.
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| 8. |
- Rodilla, Helena, 1982, et al.
(författare)
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Applying THz Technology in Life Science
- 2014
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Ingår i: Swedish Microwave Days. Gigahertz Symposium, March 11-12, 2014. Gothenburg, Sweden.
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Konferensbidrag (refereegranskat)abstract
- Bio-molecules, due to their structure and size, have vibrational and rotational resonances at THz frequencies (0.1 to 10 THz) [1]. This unique interaction promises a multitude of applications in life sciences, wherein the latest development of THz sources and detectors has enabled this field of research to grow. Although being at an early and mostly exploratory stage of development, this field is riddled with many challenges that should be overcome; measurements of inhomogeneous media, short interaction lengths with few molecules, strong water absorption, and also the cultural gap between medical and engineering communities. In this work we present our preliminary results for three experiments within this field.
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