| 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. |
- Ahlberg Gagnér, Viktor
(författare)
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Electromagnetic Field Induced Out-of-Equilibrium Structural Dynamics in Protein Crystals: From Picoseconds to Milliseconds
- 2022
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Light-induced interactions in biomolecules are strongly varying over different model systems. Most amino acids and proteins absorb ultraviolet light, but only a few with specialised chromophores or fluorophores, are able to absorb light in the visible spectrum. In the terahertz frequency spectrum, spectroscopy have revealed protein-light interactions which are attributed to low-frequency protein vibrations. Despite the fact that questions regarding a protein’s structure and function are integrally connected, only a small fraction have been answered. With the develop ment of ultra-fast facilities, the possibility to answer these questions at picosecond and sub-picosecond time scales are possible. The aim of this thesis is to demonstrate results from different aspects of the structural dynamics research field. This thesis show induced structural dynamics in the model protein bovine trypsin, while irradiated by a terahertz electromagnetic field at millisecond and at femtosecond timescales, during two different X-ray crystallography experiments. At millisecond timescales, differences in averages over the model parameters B-factors and anisotropy (’ANISO’) reveal structural dynamics which are not attributed to thermal vibrations. A clustering of the individual components of the anisotropic displacement parameter tensor, group atoms which have seemingly no spatial correlation. This indicates long range vibrations, oscillating over the entire protein scaffold. At femtosecond timescales, averages of distances of individual atom positions and individual B-factors, show structural differences which are distributed over the entire protein model, but localised to specific residues, or nearest neighbours. In addition, the structural dynamics in photosyntetic reaction center protein were demonstrated in a femtosecond optical pump-X-ray probe experiment. Average distance ratios of individual Cα atoms from photo-activated and ”dark” datasets were compared. The distances reveal a structural difference upon excitation with infrared light, attributed to an electron charge transfer from the special pair of chlorophyll molecules, to the menaquinone, via the cofactors of the L-subunit. The structural differences are supported by electron difference maps, time-resolved infrared spectroscopy and molecular modelling. Finally, this thesis demonstrate X-ray data, collected at a commissioning beamtime at the FemtoMAX beamline, of the short-pulse facility at MAX IV. Despite technical and practical difficulties, high resolution X-ray diffraction data were collected with good data reduction and refinement statistics. From this data, a satisfactory protein model was obtained
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| 3. |
- Ahlberg Gagnér, Viktor, et al.
(författare)
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Estimating the probability of coincidental similarity between atomic displacement parameters with machine learning
- 2021
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Ingår i: Machine Learning-Science and Technology. - : IOP Publishing. - 2632-2153. ; 2:3
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Tidskriftsartikel (refereegranskat)abstract
- High-resolution diffraction studies of macromolecules incorporate the tensor form of the anisotropic displacement parameter (ADP) of atoms from their mean position. The comparison of these parameters requires a statistical framework that can handle the experimental and modeling errors linked to structure determination. Here, a Bayesian machine learning model is introduced that approximates ADPs with the random Wishart distribution. This model allows for the comparison of random samples from a distribution that is trained on experimental structures. The comparison revealed that the experimental similarity between atoms is larger than predicted by the random model for a substantial fraction of the comparisons. Different metrics between ADPs were evaluated and categorized based on how useful they are at detecting non-accidental similarity and whether they can be replaced by other metrics. The most complementary comparisons were provided by Euclidean, Riemann and Wasserstein metrics. The analysis of ADP similarity and the positional distance of atoms in bovine trypsin revealed a set of atoms with striking ADP similarity over a long physical distance, and generally the physical distance between atoms and their ADP similarity do not correlate strongly. A substantial fraction of long- and short-range ADP similarities does not form by coincidence and are reproducibly observed in different crystal structures of the same protein.
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| 4. |
- Ahlberg, Viktor, et al.
(författare)
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Global transcriptional response to ISCOM-Matrix adjuvant at the site of administration and in the draining lymph node early after intramuscular injection in pigs
- 2012
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Ingår i: Developmental and Comparative Immunology. - : Elsevier BV. - 0145-305X .- 1879-0089. ; 38, s. 17-26
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Tidskriftsartikel (refereegranskat)abstract
- ISCOM vaccines induce a balanced Th1/Th2 response, long-lasting antibody responses and cytotoxic T lymphocytes. The mode of action for the adjuvant component, the ISCOM-Matrix, is known to some extent but questions remain regarding its mechanism of action. The Affymetrix GeneChip (R) Porcine Genome Array was applied to study the global transcriptional response to ISCOM-Matrix in pigs at the injection site and in the draining lymph node 24 h after i.m. injection. Gene enrichment analysis revealed inflammation, innate immunity and antigen processing to be central in the ISCOM-Matrix response. At the injection site, 594 genes were differentially expressed, including up-regulation of the cytokines osteopontin (SPP1), IL-10 and IL-18 and the chemokines CCL2, CCL19 and CXCL16. Of the 362 genes differentially expressed in the lymph node, IL-1 beta and CXCL11 were up-regulated whereas IL18, CCL15 and CXCL12 were down-regulated. ISCOM-Matrix also modulated genes for pattern recognition receptors at the injection site (TLR2, TLR4, MRC1, PTX3, LGALS3) and in the lymph node (TLR4, RIG-I, MDA5, OAS1, ElF2AK2, LGALS3). A high proportion of up-regulated interferon-regulated genes indicated an interferon response. Thus, several genes, genetic pathways and biological processes were identified that are likely to shape the early immune response elicited by ISCOM-based vaccines. (C) 2012 Elsevier Ltd. All rights reserved.
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| 5. |
- Ahlberg, Viktor, et al.
(författare)
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Global transcriptional response to ISCOM matrix at the site of administration and in draining lymph nodes after intramuscular injection in pigs
- 2011
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- ISCOM vaccines are characterised by a balanced Th1/Th2 response and induction of CTLs. The adjuvant component, ISCOM-matrix, consists of purified saponins, cholesterol and phospholipids. However, the mode of action for the ISCOM-matrix is still largely unknown, especially concerning its modulation of gene expression in the innate immunity. To address this, the early global transcriptional response to ISCOM-matrix was studied in pigs. ISCOM-matrix, Matrix M (AbISCO® 100), was given as intramuscular injection and the Affymetrix GeneChip® Porcine Genome Array was applied to analyse gene expression at the injection site and in the draining lymph node after 24 hours. A total of 594 and 362 genes were differentially expressed (fold change > 2; q < 0.05) at the injection site and in the lymph node, respectively. At the injection site, the cytokines osteopontin (SPP1), IL-10 and IL-18 and the chemokines CCL2, CCL19 and CXCL16 were up-regulated. In the draining lymph node, IL-1β and CXCL11 were up-regulated but IL18, CCL15 and CXCL12 were down-regulated. AbISCO® 100 also modulated genes for several pattern recognition receptors at the injection site (TLR2, TLR4, MRC1, PTX3) and in the draining lymph node (TLR4, RIG-I, MDA5, OAS1, PRKR). Furthermore, a strong interferon induction was indicated; 54.3 % (n = 50) and 28.1 % (n = 108) of the up-regulated genes in the lymph node and at the injection site, respectively, were identified as interferon-regulated genes, of which several are known to be involved in host response to pathogens. In conclusion, ISCOM-matrix, without any antigen added, has a clear immunomodulatory effect at the site of administration as well as in the draining lymph node. These findings could help to reveal yet unknown mechanisms for how the ISCOM-matrix and ISCOMs mediate their adjuvant activity
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| 6. |
- Ahlberg, Viktor, et al.
(författare)
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Innate immune responses induced by the saponin adjuvant Matrix-M in specific pathogen free pigs
- 2017
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Ingår i: Veterinary Research. - : Springer Science and Business Media LLC. - 0928-4249 .- 1297-9716. ; 48
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Tidskriftsartikel (refereegranskat)abstract
- Saponin-based adjuvants have been widely used to enhance humoral and cellular immune responses in many species, but their mode of action is not fully understood. A characterization of the porcine transcriptional response to Matrix-M was performed in vitro using lymphocytes, monocytes or monocyte-derived dendritic cells (MoDCs) and in vivo. The effect of Matrix-M was also evaluated in specific pathogen free (SPF) pigs exposed to conventionally reared pigs. The pro-inflammatory cytokine genes IL1B and CXCL8 were up-regulated in monocytes and lymphocytes after Matrix-M exposure. Matrix-M also induced IL12B, IL17A and IFNG in lymphocytes and IFN-a gene expression in MoDCs. Several genes were indicated as up-regulated by Matrix-M in blood 18 h after injection, of which the genes for IFN-a and TLR2 could be statistically confirmed. Respiratory disease developed in all SPF pigs mixed with conventional pigs within 1-3 days. Two out of four SPF pigs injected with saline prior to contact exposure displayed systemic symptoms that was not recorded for the four pigs administered Matrix-M. Granulocyte counts, serum amyloid A levels and transcription of IL18 and TLR2 coincided with disease progression in the pigs. These results support further evaluation of Matrix-M as a possible enhancer of innate immune responses during critical moments in pig management.
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| 7. |
- Ahlberg, Viktor
(författare)
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Innate immune responses to a saponin adjuvant in the pig : application of gene expression profiling
- 2016
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Vaccination is one of the most powerful ways to prevent infectious diseases. Successful vaccines produce a long-term immunity including effector T and B lymphocytes. In this context, adjuvants have a key role in vaccines by stimulating the innate immunity and thereby enhancing and shaping the subsequent adaptive immune response. The aim of this thesis was to elucidate the early innate immune response to the saponin-based adjuvant Matrix-M in the pig. Gene expression profiling was applied to monitor the global transcriptional response to Matrix-M in vivo. The innate immune response was further characterized by quantitative PCR analysis in vivo and in vitro and the early immunomodulatory effect of Matrix-M was evaluated in a contact exposure model. A mild inflammation and a cellular influx were recorded at the injection site and in the draining lymph node 24 hours after intramuscular injection of Matrix-M in pigs. In accordance, microarray analysis detected transcriptional alterations of genes for cytokines, chemokines and pattern recognition receptors in both tissues. Interferon- regulated genes were significantly overrepresented in these tissues, accompanied by increased gene expression for interferon-β in in the draining lymph node and interferon-α in blood. Transcriptional responses to Matrix-M in vitro were generally low but increased culture and exposure time affected genes for pro-inflammatory cytokines and TH cytokines in lymphocytes. Low levels of interferon-α gene expression were also detected in monocyte-derived dendritic cells. A contact exposure model was established to mimic field conditions when allocating grower pigs, by mixing pigs of various health statuses. After transport and mixing with conventionally reared pigs, all specific pathogen free (SPF) pigs in this model developed respiratory disease. Systemic symptoms that correlated with granulocyte counts, serum amyloid A levels and transcription of IL18 and TLR2 were provoked in two out of four SPF pigs that received saline prior to exposure, but not in those given Matrix-M. Taken together, the application of gene expression profiling successfully identified the induction of innate immune responses in porcine tissues and indicated that Matrix-M primes the host for further immune regulation. Thus, Matrix-M or similar saponin formulations are potentially useful clinical immunomodulators or adjuvants in emergency vaccines.
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| 8. |
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| 9. |
- Andersson, Märit, et al.
(författare)
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Intestinal gene expression in pigs experimentally co-infected with PCV2 and PPV
- 2011
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Ingår i: Veterinary Immunology and Immunopathology. - : Elsevier BV. - 0165-2427 .- 1873-2534. ; 142, s. 72-80
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Tidskriftsartikel (refereegranskat)abstract
- The objective of the present study was to characterize the local immune reaction in the intestine of pigs experimentally infected with PCV2 and PPV. Archived intestinal material from an experimental study in which pigs were co-infected with a Swedish isolate of PCV2 (S-PCV2) and PPV, or a reference isolate of PCV2 (PCV2-1010) and PPV, were used. The intestinal samples were analysed by qPCR for expression of a number of selected cytokines and the overall gene expression in the intestine was screened by cDNA microarray. Analyses by qPCR showed that pigs infected with PCV2-1010/PPV displayed a significantly increased mRNA expression for IL-6 (p < 0.05), IL-10 (p < 0.05) and IFN-gamma (p < 0.05). The microarray screening revealed a strong up-regulation of IFITM3 along with several other interferon-stimulated genes (ISGs) in pigs infected with PCV2/PPV. The analyses also indicated differences between the two isolates. Fewer pigs infected with S-PCV2/PPV expressed the cytokines detected by qPCR, compared to pigs infected with PCV2-1010/PPV, and pigs infected with S-PCV2/PPV displayed a higher proportion of down-regulated genes than PCV2-1010/PPV-infected pigs. (C) 2011 Elsevier B.V. All rights reserved.
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| 10. |
- Dods, Robert, 1989, et al.
(författare)
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Ultrafast structural changes within a photosynthetic reaction centre.
- 2021
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 589:7841, s. 310-314
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Tidskriftsartikel (refereegranskat)abstract
- Photosynthetic reaction centres harvest the energy content of sunlight by transporting electrons across an energy-transducing biological membrane. Here we use time-resolved serial femtosecond crystallography1 using an X-ray free-electron laser2 to observe light-induced structural changes in the photosynthetic reaction centre of Blastochloris viridis on a timescale of picoseconds. Structural perturbations first occur at the special pair of chlorophyll molecules of the photosynthetic reaction centre that are photo-oxidized by light. Electron transfer to the menaquinone acceptor on the opposite side of the membrane induces a movement of this cofactor together with lower amplitude protein rearrangements. These observations reveal how proteins use conformational dynamics to stabilize the charge-separation steps of electron-transfer reactions.
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