| 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. |
- Garcia-Bonete, Maria-Jose, 1989, et al.
(författare)
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A practical guide to developing virtual and augmented reality exercises for teaching structural biology.
- 2019
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Ingår i: Biochemistry and molecular biology education : a bimonthly publication of the International Union of Biochemistry and Molecular Biology. - : Wiley. - 1539-3429. ; 47:1, s. 16-24
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Tidskriftsartikel (refereegranskat)abstract
- Although virtual and augmented reality (VR and AR) techniques have been used extensively in specialized laboratories, only recently did they become affordable, reaching wider consumer markets. With increased availability, it is timely to examine the roles that VR and AR may play in teaching structural biology and in experiencing complex data sets such as macromolecular structures. This guide is suitable for those teachers of structural biology who do not have a deep knowledge of information technologies. This study focuses on three questions: 1) How can teachers of structural biology produce and disseminate VR/AR-ready educational material with established and user-friendly software tools?; 2) What are the positive and negative experiences reported by test participants when performing identical learning tasks in the VR and AR environments?; and 3) How do the test participants perceive prerecorded narration during VR/AR exploration? © 2018 International Union of Biochemistry and Molecular Biology, 47(1):16-24, 2018.
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| 3. |
- Garcia-Bonete, Maria-Jose, 1989, et al.
(författare)
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Bayesian machine learning improves single-wavelength anomalous diffraction phasing
- 2019
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Ingår i: Acta Crystallographica a-Foundation and Advances. - : International Union of Crystallography (IUCr). - 2053-2733. ; 75, s. 851-860
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Tidskriftsartikel (refereegranskat)abstract
- Single-wavelength X-ray anomalous diffraction (SAD) is a frequently employed technique to solve the phase problem in X-ray crystallography. The precision and accuracy of recovered anomalous differences are crucial for determining the correct phases. Continuous rotation (CR) and inverse-beam geometry (IBG) anomalous data collection methods have been performed on tetragonal lysozyme and monoclinic survivin crystals and analysis carried out of how correlated the pairs of Friedel's reflections are after scaling. A multivariate Bayesian model for estimating anomalous differences was tested, which takes into account the correlation between pairs of intensity observations and incorporates the a priori knowledge about the positivity of intensity. The CR and IBG data collection methods resulted in positive correlation between I(+) and I(-) observations, indicating that the anomalous difference dominates between these observations, rather than different levels of radiation damage. An alternative pairing method based on near simultaneously observed Bijvoet's pairs displayed lower correlation and it was unsuccessful for recovering useful anomalous differences when using the multivariate Bayesian model. In contrast, multivariate Bayesian treatment of Friedel's pairs improved the initial phasing of the two tested crystal systems and the two data collection methods.
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| 4. |
- Garcia-Bonete, Maria-Jose, 1989
(författare)
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Structural and Interaction Studies of the Human Protein Survivin.
- 2019
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Cell division and cell death (apoptosis) are two essential processes to maintain the specific number of cells in all multicellular organisms. In humans, the misregulation of these processes leads to severe diseases, such as cancer, and neurological, inflammatory or autoimmune diseases. Proteins are the most versatile macromolecules in all living organisms and are the orchestra directors of the majority of cellular processes. Their three-dimensional structure and the interaction with other molecules are essential for their correct biological function. This work focus on small human protein survivin which plays an important role in cell division and apoptosis, and has been extensively reported in clinical research. Our aim was to discover new interaction partners of survivin, and to study their specific binding and structure to better understand its function. We successfully used microarray peptide technology to determine new possible interaction partners and microscale thermophoresis to confirm these interactions. The direct interaction between the shugoshin-like protein family and survivin has been reported and highlights its importance in cell division. In addition, this thesis exhibits the powerful multivariate Bayesian inference approach for data analysis by focussing on addressing X-ray crystallography problems of experimental phasing for molecular structure determination. This approach has also been successfully applied to determine the binding curve and to calculate the interaction strength between two molecules, and avoids manual treatment and human subjective bias.
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