| 1. |
- Andersson, Anders G., et al.
(författare)
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Simulation of free surface flow in a spillway with the rigid lid and volume of fluid methods and validation in a scale model
- 2010
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Ingår i: Proceedings, Fifth European Conference on Computational Fluid Dynamics. - 9789899677814
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Konferensbidrag (refereegranskat)abstract
- Simulations on the spilling from a dam were performed and compared to experimental results from a physical scale model. Both mechanical and acoustic methods to measure the velocity were used. The model has three gates leading into the spillway that can be maneuvered separately. At first two of the gates were closed and the inlet flow was high enough to get a fully wetted outlet at the third gate. This case was simulated with a rigid lid approximation since the water surface was considered to be plane. The water surface level was taken from the scale model. In the second case, all three gates were open resulting in a free water surface through all the gates to the spillway. This case was simulated with the Volume of Fluids method were both water and air phase were considered. Water levels, velocities and the shape of the water surface were compared between simulations and experiments. The simulations capture both qualitative features such as a vortex near the outlet and show good quantitative agreement with the experiments.
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| 2. |
- Bergström, Ulf, et al.
(författare)
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Long-term effects of no-take zones in Swedish waters
- 2022
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- Marine protected areas (MPAs) are increasingly established worldwide to protect and restore degraded ecosystems. However, the level of protection varies among MPAs and has been found to affect the outcome of the closure. In no-take zones (NTZs), no fishing or extraction of marine organisms is allowed. The EU Commission recently committed to protect 30% of European waters by 2030 through the updated Biodiversity Strategy. Importantly, one third of these 30% should be of strict protection. Exactly what is meant by strict protection is not entirely clear, but fishing would likely have to be fully or largely prohibited in these areas. This new target for strictly protected areas highlights the need to evaluate the ecological effects of NTZs, particularly in regions like northern Europe where such evaluations are scarce. The Swedish NTZs made up approximately two thirds of the total areal extent of NTZs in Europe a decade ago. Given that these areas have been closed for at least 10 years and can provide insights into long-term effects of NTZs on fish and ecosystems, they are of broad interest in light of the new 10% strict protection by 2030 commitment by EU member states.In total, eight NTZs in Swedish coastal and offshore waters were evaluated in the current report, with respect to primarily the responses of focal species for the conservation measure, but in some of the areas also ecosystem responses. Five of the NTZs were established in 2009-2011, as part of a government commission, while the other three had been established earlier. The results of the evaluations are presented in a synthesis and also in separate, more detailed chapters for each of the eight NTZs. Overall, the results suggest that NTZs can increase abundances and biomasses of fish and decapod crustaceans, given that the closed areas are strategically placed and of an appropriate size in relation to the life cycle of the focal species. A meta-regression of the effects on focal species of the NTZs showed that CPUE was on average 2.6 times higher after three years of protection, and 3.8 times higher than in the fished reference areas after six years of protection. The proportion of old and large individuals increased in most NTZs, and thereby also the reproductive potential of populations. The increase in abundance of large predatory fish also likely contributed to restoring ecosystem functions, such as top-down control. These effects appeared after a 5-year period and in many cases remained and continued to increase in the longer term (>10 years). In the two areas where cod was the focal species of the NTZs, positive responses were weak, likely as an effect of long-term past, and in the Kattegat still present, recruitment overfishing. In the Baltic Sea, predation by grey seal and cormorant was in some cases so high that it likely counteracted the positive effects of removing fisheries and led to stock declines in the NTZs. In most cases, the introduction of the NTZs has likely decreased the total fishing effort rather than displacing it to adjacent areas. In the Kattegat NTZ, however, the purpose was explicitly to displace an unselective coastal mixed bottom-trawl fishery targeting Norway lobster and flatfish to areas where the bycatches of mature cod were smaller. In two areas that were reopened to fishing after 5 years, the positive effects of the NTZs on fish stocks eroded quickly to pre-closure levels despite that the areas remained closed during the spawning period, highlighting that permanent closures may be necessary to maintain positive effects.We conclude from the Swedish case studies that NTZs may well function as a complement to other fisheries management measures, such as catch, effort and gear regulations. The experiences from the current evaluation show that NTZs can be an important tool for fisheries management especially for local coastal fish populations and areas with mixed fisheries, as well as in cases where there is a need to counteract adverse ecosystem effects of fishing. NTZs are also needed as reference for marine environmental management, and for understanding the effects of fishing on fish populations and other ecosystem components in relation to other pressures. MPAs where the protection of both fish and their habitats is combined may be an important instrument for ecosystembased management, where the recovery of large predatory fish may lead to a restoration of important ecosystem functions and contribute to improving decayed habitats.With the new Biodiversity Strategy, EUs level of ambition for marine conservation increases significantly, with the goal of 30% of coastal and marine waters protected by 2030, and, importantly, one third of these areas being strictly protected. From a conservation perspective, rare, sensitive and/or charismatic species or habitats are often in focus when designating MPAs, and displacement of fisheries is then considered an unwanted side effect. However, if the establishment of strictly protected areas also aims to rebuild fish stocks, these MPAs should be placed in heavily fished areas and designed to protect depleted populations by accounting for their home ranges to generate positive outcomes. Thus, extensive displacement of fisheries is required to reach benefits for depleted populations, and need to be accounted for e.g. by specific regulations outside the strictly protected areas. These new extensive EU goals for MPA establishment pose a challenge for management, but at the same time offer an opportunity to bridge the current gap between conservation and fisheries management.
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| 3. |
- Lind, Hans, 1950-, et al.
(författare)
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Bostadsmarknad och ekonomisk tillväxt
- 2008
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- Snabbväxande regioner riskerar att hämmas i sin utveckling på grund av en bostadsmarknad som fungerar dåligt. I samhällsdebatten framhålls ofta att problemen står att finna i ett för lågt bostadsbyggande. I den här rapporten framtonar ett något annorlunda och mycket intressant perspektiv. Författarnas slutsats är att bostadsbristen inte enbart går att bygga bort. Istället är det ett ökat utbud av bostäder i det befintliga beståndet som är den stora utmaningen.
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| 4. |
- Lundström, Yasmin, et al.
(författare)
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Detection of Changes in Immunohistochemical Stains Caused by Postmortem Delay and Fixation Time
- 2019
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Ingår i: Applied immunohistochemistry & molecular morphology (Print). - 1541-2016 .- 1533-4058. ; 27:3, s. 238-245
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Tidskriftsartikel (refereegranskat)abstract
- In this study, we have systematically assessed the influence of postmortem delay (PMD) and fixation time (FT) on the immunohistochemical (IHC) staining outcome. The IHC method is frequently applied on surgical and postmortem samples in diagnostics and research. To replicate the routine situation, brain tissues from pigs were exposed to either storage in a refrigerator (+8°C), that is, PMD (1 to 168 h), or fixed in 10% buffered formalin, that is, FT (18 to 94 d). Subsequently, the tissue was routinely processed into paraffin blocks to enable construction of tissue microarrays (TMA). Sections cut from the TMA blocks were stained applying 13 different antibodies directed against neuronal and glial antigens. Immunoreactivity applying 5 antibodies was influenced by prolonged PMD and applying 2 antibodies by prolonged FT. None of the staining outcomes related to the PMD or FT were predictable. Loss of TMA cores during processing was primarily influenced by pretreatment and by tissue characteristics (gray/white matter). The test model described here confirmed that these 2 variables, PMD and FT, indeed influence the IHC outcome. The PMD and FT are particularly of importance while assessing tissue samples obtained at autopsy. The result above is also of importance while comparing the IHC outcomes seen in the postmortem setting (various PMD/FT) with surgical samples or with IHC outcome seen in experimental animal setting (controlled PMD/FT). Thus, we suggest that the test model described here is considered when assessing the reliability of the IHC outcome when analyzing tissues with various characteristics.
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| 5. |
- Ahlner, Alexandra, 1984-, et al.
(författare)
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Conformational Dynamics and Multimerization of Active Forms of the EphrinB Receptor 2 Kinase Domain
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Active and autoinhibited forms of the ephrinB receptor 2 (EphB2) kinase domain have been studied using NMR spectroscopy. The project was initiated because of the finding that the crystal structures of active forms of the kinase domain and previous NMR studies suggested that a change in inter-lobe flexibility and the sampling of catalytically competent excited states conformations are responsible for activity. Using Carr-Purcell-Meiboom-Gill relaxation dispersion experiments, we have measured millisecond dynamics to identify such states. We have also performed concentration dependent relaxation experiments and analytical ultracentrifugation experiments that report on the effective protein size to look for possible differences in self-association for active and autoinhibited forms of the EphB2 kinase domain. We show that the active but not autoinhibited forms exchange between a ground state and an excited state at a rate of 1900 s-1. Similar results were found for the S677/680A mutant of the protein. The nature and importance of the excited state is still unknown. Our most important finding is that active forms of the kinase domain self-associate in a concentration dependent manner and form tetramers and possibly larger oligomers. Multimerization of the kinase domain may enable the assembly of complexes of downstream proteins and could be important for Eph signaling.
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| 6. |
- Ahlner, Alexandra, 1984-, et al.
(författare)
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Fractional enrichment of proteins using [2-13C]-glycerol as the carbon source facilitates measurement of excited state 13Cα chemical shifts with improved sensitivity
- 2015
-
Ingår i: Journal of Biomolecular NMR. - : Springer Netherlands. - 0925-2738 .- 1573-5001. ; 62:3, s. 341-351
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Tidskriftsartikel (refereegranskat)abstract
- A selective isotope labeling scheme based on the utilization of [2-13C]-glycerol as the carbon source during protein overexpression has been evaluated for the measurement of excited state 13Cα chemical shifts using Carr–Purcell–Meiboom–Gill (CPMG) relaxation dispersion (RD) experiments. As expected, the fractional incorporation of label at the Cα positions is increased two-fold relative to labeling schemes based on [2-13C]-glucose, effectively doubling the sensitivity of NMR experiments. Applications to a binding reaction involving an SH3 domain from the protein Abp1p and a peptide from the protein Ark1p establish that accurate excited state 13Cα chemical shifts can be obtained from RD experiments, with errors on the order of 0.06 ppm for exchange rates ranging from 100 to 1000 s−1, despite the small fraction of 13Cα–13Cβ spin-pairs that are present for many residue types. The labeling approach described here should thus be attractive for studies of exchanging systems using 13Cα spin probes.
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| 7. |
- Ahlner, Alexandra, 1984-
(författare)
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Improved Methods for Characterization of Protein Dynamics by NMR spectroscopy and Studies of the EphB2 Kinase Domain
- 2015
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Proteins are essential for all known forms of life and in many lethal diseases protein failure is the cause of the disease. To understand proteins and the processes they are involved in, it is valuable to know their structures as well as their dynamics and interactions. The structures may not be directly inspected because proteins are too small to be visible in a light microscope, which is why indirect methods such as nuclear magnetic resonance (NMR) spectroscopy have to be utilized. This method provides atomic information about the protein and, in contrast to other methods with similar resolution, the measurements are performed in solution resulting in more physiological conditions, enabling analysis of dynamics. Important dynamical processes are the ones on the millisecond timeframe, which may contribute to interactions of proteins and their catalysis of chemical reactions, both of significant value for the function of the proteins.To better understand proteins, not only do we need to study them, but also develop the methods we are using. This thesis presents four papers about improved NMR techniques as well as a fifth where the kinase domain of ephrinB receptor 2 (EphB2) has been studied regarding the importance of millisecond dynamics and interactions for the activation process. The first paper presents the software COMPASS, which combines statistics and the calculation power of a computer with the flexibility and experience of the user to facilitate and speed up the process of assigning NMR signals to the atoms in the protein. The computer program PINT has been developed for easier and faster evaluation of NMR experiments, such as those that evaluate protein dynamics. It is especially helpful for NMR signals that are difficult to distinguish, so called overlapped peaks, and the soft- ware also converts the detected signals to the indirectly measured physical quantities, such as relaxation rate constants, principal for dynamics. Next are two new versions of the Carr-Purcell-Maiboom-Gill (CPMG) dispersion pulse sequences, designed to measure millisecond dynamics in a way so that the signals are more separated than in standard experiments, to reduce problems with overlaps. To speed up the collection time of the data set, a subset is collected and the entire data set is then reconstructed, by multi-dimensional decomposition co-processing. Described in the thesis is also a way to produce suitably labeled proteins, to detect millisecond dynamics at Cα positions in proteins, using the CPMG dispersion relaxation experiment at lower protein concentrations. Lastly, the kinase domain of EphB2 is shown to be more dynamic on the millisecond time scale as well as more prone to interact with itself in the active form than in the inactive one. This is important for the receptor function of the protein, when and how it mediates signals.To conclude, this work has extended the possibilities to study protein dynamics by NMR spectroscopy and contributed to increased understanding of the activation process of EphB2 and its signaling mechanism.
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| 8. |
- Ahlner, Alexandra, 1984-, et al.
(författare)
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Measurement of Protein Backbone 13CO and 15N Relaxation Dispersion at High Resolution
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Three-dimensional pulse sequences for the measurement of Carr-Purcell-Meiboom-Gill relaxation dispersions and new methods for co-processing non-uniformly sampled data are presented. The new methodology was validated for the disordered protein IgA and for an SH3 domain from Abp1p in exchange between its free form and bound to a peptide from the protein Ark1p. We show that the results are similar to ones obtained using traditional experiments and that accurate excited state chemical shifts can be determined. Furthermore, we show that jackknife analysis of down sampled spectra yields robust estimates of peak intensities errors, eliminating the need for recording duplicate data points. The methodology should be useful for characterization of millisecond dynamics in small to medium-sized proteins with poorly dispersed spectra.
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| 9. |
- Ahlner, Alexandra, et al.
(författare)
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PINT: a software for integration of peak volumes and extraction of relaxation rates
- 2013
-
Ingår i: Journal of Biomolecular NMR. - : Springer Verlag (Germany). - 0925-2738 .- 1573-5001. ; 56:3, s. 191-202
-
Tidskriftsartikel (refereegranskat)abstract
- We present the software Peak INTegration (PINT), designed to perform integration of peaks in NMR spectra. The program is very simple to run, yet powerful enough to handle complicated spectra. Peaks are integrated by fitting predefined line shapes to experimental data and the fitting can be customized to deal with, for instance, heavily overlapped peaks. The results can be inspected visually, which facilitates systematic optimization of the line shape fitting. Finally, integrated peak volumes can be used to extract parameters such as relaxation rates and information about low populated states. The utility of PINT is demonstrated by applications to the 59 residue SH3 domain of the yeast protein Abp1p and the 289 residue kinase domain of murine EphB2.
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| 10. |
- Akke, Mikael, et al.
(författare)
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Protein conformational dynamics by relaxation dispersion
- 2013
-
Ingår i: Encyclopedia of biophysics. - Berlin : Elsevier. - 9783642167126 ; , s. 1967-1979
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Bokkapitel (övrigt vetenskapligt/konstnärligt)abstract
- Protein dynamics is intimately connected to function. Many biochemical reactions are mediated by protein conformational transitions to high-energy states that are often populated at low levels undetectable by traditional methods in structural biology. Nuclear magnetic resonance ( NMR) relaxation dispersion methods ( Relaxation Dispersion) provide a unique means of characterizing this type of protein motion with rate constants ranging from approximately 1–105 s–1 and populations down to approximately 1%. Relaxation dispersion experiments yield a wealth of information about the exchanging system, including the kinetic rate constants, the relative populations of the exchanging states, and the chemical shift differences between these, which depend on the molecular structure. Temperature-dependent experiments enable mapping of the energy landscape in terms of the free energy barrier and the free energy difference between the exchanging states, broken down into enthalpy and entropy. Applications have addressed protein folding-unfolding ( Protein Folding), enzyme catalysis ( Protein Dynamics in Catalysis – Computational Studies), and ligand binding ( Protein–Ligand Dynamics) (Korzhnev and Kay 2008; Baldwin and Kay 2009). This chapter outlines the fundamental principles of relaxation dispersion experiments and their application to protein dynamics. The focus is on heteronuclear experiments performed on isotope-labeled proteins ( Protein NMR – Introduction), where the dynamics is typically probed by 15N or 13C spin relaxation, but experiments have also been developed for 1H.
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| 11. |
- Alnersson, Gustaf
(författare)
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Towards 3D modelling of Compression Moulding of SMC
- 2021
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Licentiatavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The automotive industry is facing ever increasing demands for reduced emissions, and lightweight solutions are thusly required. One field that has significant potential in this regard is composite materials, which can offer a good combination of weight reduction and mechanical properties. However, the rapid development cycles in the automotive industry mean that tools for numerical modeling are necessary, both regarding manufacturing processes and prediction of mechanical properties. The material that has been of interest for this work is Sheet Moulding Compound (SMC). SMC consists of sheets of resin and chopped fibres. When used for manufacturing the sheets are cut into appropriate size and shape. The cut sheets are then placed in a pre-heated mould. When this mould is closed, the sheets melt and the fibre-filled resin flows out and fills the mould cavity; the resin then cures and solidifies. A significant advantage of SMC compared to other composite solutions is that the process has comparatively short cycle times, which is a necessity for automotive applications. However, it is a rather complicated process to model numerically for a number of reasons, including the complex rheological properties of the charge, the often rather significant temperature gradients throughout the thickness, often complicated three-dimensional effects in the flow, and the chopped fibres present in the charge. These fibres will move and change orientation as the charge is pressed, which is a significant challenge to model properly.The first part of this work is a review and discussion of the difficulties described above, and some solutions that have been suggested. The second part concerns a suggestion for a three-dimensional flow model for the compression moulding process, which takes into account factors that have been suggested to influence the flow behavior, such as temperature distribution and shear strain rate. Some simulation results are presented along with comparison to previous experimental results, and similar flow patterns are observed serving as a qualitative validation. The third part concerns the expansion of this model to include the effects of the flow on the fibre orientation.
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| 12. |
- Anandapadmanaban, Madhanagopal, et al.
(författare)
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High-resolution structure of TBP with TAF1 reveals anchoring patterns in transcriptional regulation
- 2013
-
Ingår i: Nature Structural & Molecular Biology. - : NATURE PUBLISHING GROUP, 75 VARICK ST, 9TH FLR, NEW YORK, NY 10013-1917 USA. - 1545-9993 .- 1545-9985. ; 20:8, s. 1008-
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Tidskriftsartikel (refereegranskat)abstract
- The general transcription factor TFIID provides a regulatory platform for transcription initiation. Here we present the crystal structure (1.97 angstrom) and NMR analysis of yeast TAF1 N-terminal domains TAND1 and TAND2 bound to yeast TBP, together with mutational data. We find that yeast TAF1-TAND1, which in itself acts as a transcriptional activator, binds TBPs concave DNA-binding surface by presenting similar anchor residues to TBP as does Mot1 but from a distinct structural scaffold. Furthermore, we show how TAF1-TAND2 uses an aromatic and acidic anchoring pattern to bind a conserved TBP surface groove traversing the basic helix region, and we find highly similar TBP-binding motifs also presented by the structurally distinct TFIIA, Mot1 and Brf1 proteins. Our identification of these anchoring patterns, which can be easily disrupted or enhanced, provides insight into the competitive multiprotein TBP interplay critical to transcriptional regulation.
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| 13. |
- Anckarsäter, Henrik, 1966, et al.
(författare)
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The Child and Adolescent Twin Study in Sweden (CATSS).
- 2011
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Ingår i: Twin Research and Human Genetics. - : Cambridge University Press (CUP). - 1832-4274 .- 1839-2628. ; 14:6, s. 495-508
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Tidskriftsartikel (refereegranskat)abstract
- The Child and Adolescent Twin Study in Sweden (CATSS) is an ongoing longitudinal twin study targeting all twins born in Sweden since July 1, 1992. Since 2004, parents of twins are interviewed regarding the children's somatic and mental health and social environment in connection with their 9th or 12th birthdays (CATSS-9/12). By January 2010, 8,610 parental interviews concerning 17,220 twins had been completed, with an overall response rate of 80%. At age 15 (CATSS-15) and 18 (CATSS-18), twins and parents complete questionnaires that, in addition to assessments of somatic and mental health, include measures of personality development and psychosocial adaptation. Twin pairs in CATSS-9/12 with one or both twins screening positive for autism spectrum disorders, attention deficit/hyperactivity disorder, tic disorders, developmental coordination disorder, learning disorders, oppositional defiant disorder, conduct disorder, obsessive-compulsive disorder, and/or eating problems have been followed with in-depth questionnaires on family, social environment and personality, and subsequently by clinical assessments at age 15 together with randomly selected population controls, including 195 clinically assessed twin pairs from the first 2 year cohorts (CATSS-15/DOGSS). This article describes the cohorts and study groups, data collection, and measures used. Prevalences, distributions, heritability estimates, ages at onset, and sex differences of mental health problems in the CATSS-9/12, that were analyzed and found to be overall comparable to those of other clinical and epidemiological studies. The CATSS study has the potential of answering important questions on the etiology of childhood mental health problems and their role in the development of later adjustment problems.
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| 14. |
- Andersson, Anders G., et al.
(författare)
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A numerical study of the location and function of the entrance of a fishway in a regulated river
- 2010
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Ingår i: 8th International Symposium on ECOHYDRAULICS. ; , s. 277-284
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Konferensbidrag (refereegranskat)abstract
- Simulation driven design with Computational Fluid Dynamics has been used to evaluate the flow downstream a hydropower plant with regards to upstream migrating fish. Field measurements with an Acoustic Doppler Current Profiler were performed and the measurements were used to validate the simulations. The measurements indicate a more unstable flow than the simulations and the tailrace jet from the turbines is stronger in the simulations. The simulations are however considered to capture the important features of the flow in a way that makes them viable for attraction water simulations. A fishway entrance was included in the simulations and the subsequent attraction water was evaluated for two positions and two angles of the entrance at different turbine discharges. Results show that both positions are viable and that a position where the flow from the fishway does not have to compete with the flow from the power plant will generate superior attraction water. Simulations were also performed further downstream where the flow from the turbines meets the old river bed which is the current fish passage for upstream migrating fish. A modification of the old river bed was made in the model as one scenario to generate better attraction water. This considerably increases the attraction water although it cannot compete with the flow from the tailrace tunnel.
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| 15. |
- Andersson, Anders G., et al.
(författare)
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A study of the location of the entrance of a fishway in a regulated river with CFD and ADCP
- 2012
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Ingår i: Modelling and Simulation in Engineering. - : Hindawi Limited. - 1687-5591 .- 1687-5605. ; 2012
-
Tidskriftsartikel (refereegranskat)abstract
- Simulation-driven design with computational fluid dynamics has been used to evaluate the flow downstream of a hydropower plant with regards to upstream migrating fish. Field measurements with an Acoustic Doppler Current Profiler were performed, and the measurements were used to validate the simulations. The measurements indicate a more unstable flow than the simulations, and the tailrace jet from the turbines is stronger in the simulations. A fishway entrance was included in the simulations, and the subsequent attraction water was evaluated for two positions and two angles of the entrance at different turbine discharges. Results show that both positions are viable and that a position where the flow from the fishway does not have to compete with the flow from the power plant will generate superior attraction water. Simulations were also performed for further downstream where the flow from the turbines meets the old river bed which is the current fish passage for upstream migrating fish. A modification of the old river bed was made in the model as one scenario to generate better attraction water. This considerably increases the attraction water although it cannot compete with the flow from the tailrace tunnel.
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| 16. |
- Andersson, Anders G., et al.
(författare)
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CFD-modelling and validation of free surface flow during spilling of reservoir in down-scale model
- 2013
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Ingår i: Engineering Applications of Computational Fluid Mechanics. - : Informa UK Limited. - 1994-2060 .- 1997-003X. ; 7:1, s. 159-167
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Tidskriftsartikel (refereegranskat)abstract
- Fully three dimensional modelling of the spilling from a reservoir with relatively complex geometry were performed and compared to experimental results from a physical scale model with the aim to advance the science of numerical modelling of free surface flow of real reservoirs. In the set-up in focus the water was spilled from the reservoir through three gates that could be manoeuvred separately. In the first case two of the gates were closed and the third gate was partly opened. In this experimental set-up the water surface in the reservoir was close to horizontal. Therefore it was here meaningful to compare a rigid lid modelling approximation to the more computational heavy method of Volume of Fluids. In the second case, all three gates were open, resulting in a nonhorizontal varied flow surface profile in the reservoir upstream critical sections at the spillway crests. This case was simulated with Volume of Fluids and the position of the air-water interface was derived for two turbulence models, the standard k-ε and SSG. Water levels, velocities and the shape of the water surface were compared to experiments. The simulation results capture qualitative features such as a vortex near the outlet and show good quantitative agreement with the experiments regardless of method used to simulate the free surface. In general, simulations with the standard k-ε and the more advanced SSG turbulence models give the same results with respect to the averaged quantities measured.
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| 17. |
- Andersson, Anders G., et al.
(författare)
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Effect of spatial resolution of rough surfaces on numerically computed flow fields with application to hydraulic engineering
- 2014
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Ingår i: Engineering Applications of Computational Fluid Mechanics. - : Informa UK Limited. - 1994-2060 .- 1997-003X. ; 8:3, s. 373-381
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Tidskriftsartikel (refereegranskat)abstract
- In numerical simulations of flow over rough surfaces, the roughness is often not resolved but represented by a numerical model. The validity of such an assumption is investigated in this paper by Reynolds-Averaged Navier-Stokes simulations of flow over a surface with a large roughness. The surface was created from a high-resolution laser scanning of a real rock blasted tunnel. By reducing the geometrical resolution of the roughness in two steps, the importance of an appropriate surface description could be examined. The flow fields obtained were compared to a set-up with a geometrical flat surface where the roughness was represented by a modified form of the Launder and Spalding wall-function. The flow field over the surface with the lowest resolution was substantially different from those of the two finer resolutions and rather close to the results from the set-up with the wall-function. The results also yield that the finer the resolution is the more vorticity is formed close to the rough surface and more turbulence is generated.
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| 18. |
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| 19. |
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| 20. |
- Andersson, L. Robin, et al.
(författare)
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Characterization of Flow Structures Induced by Highly Rough Surface Using Particle Image Velocimetry, Proper Orthogonal Decomposition and Velocity Correlations
- 2018
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Ingår i: Engineering. - : Scientific Research Publishing. - 1947-3931 .- 1947-394X. ; 10, s. 399-416
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Tidskriftsartikel (refereegranskat)abstract
- High Reynolds number flow inside a channel of rectangular cross section is examined using Particle Image Velocimetry. One wall of the channel has been replaced with a surface of a roughness representative to that of real hydropower tunnels, i.e. a random terrain with roughness dimensions typically in the range of ≈10% - 20% of the channels hydraulic radius. The rest of the channel walls can be considered smooth. The rough surface was captured from an existing blasted rock tunnel using high resolution laser scanning and scaled to 1:10. For quantification of the size of the largest flow structures, integral length scales are derived from the auto-correlation functions of the temporally averaged velocity. Additionally, Proper Orthogonal Decomposition (POD) and higher-order statistics are applied to the instantaneous snapshots of the velocity fluctuations. The results show a high spatial heterogeneity of the velocity and other flow characteristics in vicinity of the rough surface, putting outer similarity treatment into jeopardy. Roughness effects are not confined to the vicinity of the rough surface but can be seen in the outer flow throughout the channel, indicating a different behavior than postulated by Townsend’s similarity hypothesis. The effects on the flow structures vary depending on the shape and size of the roughness elements leading to a high spatial dependence of the flow above the rough surface. Hence, any spatial averaging, e.g. assuming a characteristic sand grain roughness factor, for determining local flow parameters becomes less applicable in this case.
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| 21. |
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| 22. |
- Andersson, Robin, 1987-, et al.
(författare)
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Gävunda case study
-
Annan publikation (övrigt vetenskapligt/konstnärligt)
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| 23. |
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| 24. |
- Andersson, Robin, 1987-, et al.
(författare)
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Numerical investigation of a hydropower tunnel : Estimating localised head-loss using the manning equation
- 2019
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Ingår i: Water. - : MDPI. - 2073-4441. ; 11:8
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Tidskriftsartikel (refereegranskat)abstract
- The fluid dynamics within a water tunnel is investigated numerically using a RANS approach with the k-ε turbulence model. The computational model is based on a laser scan of a hydropower tunnel located in Gävunda, Sweden. The tunnel has a typical height of 6.9 m and a width of 7.2 m. While the average cross-sectional shape of the tunnel is smooth the local deviations are significant, where some roughness elements may be in the size of 5 m implying a large variation of the hydraulic radius. The results indicate that the Manning equation can successfully be used to study the localised pressure variations by taking into account the varying hydraulic radius and cross-sectional area of the tunnel. This indicates a dominant effect of the tunnel roughness in connection with the flow, which has the potential to be used in the future evaluation of tunnel durability. ANSYS-CFX was used for the simulations along with ICEM-CFD for building the mesh.
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| 25. |
- Andrésen, Cecilia, et al.
(författare)
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Biophysical characterization of the calmodulin-like domain of Plasmodium falciparum calcium dependent protein kinase 3
- 2017
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Ingår i: PLOS ONE. - : PUBLIC LIBRARY SCIENCE. - 1932-6203. ; 12:7
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Tidskriftsartikel (refereegranskat)abstract
- Calcium dependent protein kinases are unique to plants and certain parasites and comprise an N-terminal segment and a kinase domain that is regulated by a C-terminal calcium binding domain. Since the proteins are not found in man they are potential drug targets. We have characterized the calcium binding lobes of the regulatory domain of calcium dependent protein kinase 3 from the malaria parasite Plasmodium falciparum. Despite being structurally similar, the two lobes differ in several other regards. While the monomeric N-terminal lobe changes its structure in response to calcium binding and shows global dynamics on the sub-millisecond time-scale both in its apo and calcium bound states, the C-terminal lobe could not be prepared calcium-free and forms dimers in solution. If our results can be generalized to the full-length protein, they suggest that the C-terminal lobe is calcium bound even at basal levels and that activation is caused by the structural reorganization associated with binding of a single calcium ion to the N-terminal lobe.
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| 26. |
- Andrésen, Cecilia
(författare)
-
Protein Structure and Interaction in Health and Disease
- 2011
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- This thesis focuses on protein structure, dynamics and interaction and their relation to human disease. In particular, the biophysical and structural properties of both well-ordered and partially disordered proteins are studied using a range of biophysical techniques such as circular dichroism spectroscopy, fluorescence spectroscopy, mass spectrometry and nuclear magnetic resonance spectroscopy. Pseudomonas aeruginosa is a human pathogen due to its multidrug resistance (MDR) caused by overexpression of efflux pump systems. This thesis describes how MDR mutations within the MexR repressor of the MexAB-OprM system reduce the DNA affinity by altering its stability with maintained structure. The oncogenic protein c-Myc is involved in many essential biological functions such as cell proliferation, differentiation and apoptosis and is also highly associated with several forms of human cancers, and where the N-terminal domain is regulated by a plethora of protein interactions. In this thesis the intrinsically disordered N-terminal part of c-Myc and its interactions with the proteins Bin1 and TBP are described. Myc binds Bin1 with maintained disorder in a multivalent manner, which may explain why the onco-protein can interact with such a wide range of binding partners. A similarly dynamic interaction is observed for Myc with the TATA-binding protein (TBP). The essential human multidomain glutaredoxin Grx3 is associated with several biological functions such as redox signaling, proliferation and signal transduction. We have solved the structure and analyzed the dynamic properties in the ps-ns and ms time scale for the two N-terminal domains, providing a platform for further analysis of the Grx3 protein and its interactions. Taken together, this thesis emphasizes the importance of joint structural, biophysical and dynamic studies to better understand protein function in health and disease.
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| 27. |
- Andrésen, Cecilia, et al.
(författare)
-
Structural and dynamic analysis of human glutaredoxin 3
-
Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Human glutaredoxin (Grx3) is an essential protein associated with biological functions including embryonic development and immune response, and is involved in human disease such as lung, colon cancer and cardiovascular disorder. Grx3 can harbour a [2Fe-2S]2+ cluster and is most likely involved in oxidative stress response. Grx3 consists of an N-terminal thioredoxin-like domain and two additional monothiol glutaredoxin domains, and is thus classified as a multidomain monothiol glutaredoxin. The Grx3 thioredoxin domain lacks both a characteristic active-site and catalytic activity, but is still essential in the yeast homologue and presumably functions together with its monothiol glutaredoxin domains. We have characterised the structures of the two Nterminal domains in Grx3, which have thioredoxin and glutaredoxin folds. We have analysed their dynamic and structural interdependence by analysing NMR relaxation data together with chemical shift changes between isolated and covalently linked domains. We find that although the two domains show interdomain mobility around a semi-flexible linker, there are indications for a preferred interaction surface between the two domains. Millisecond internal dynamics in a suggested ligand binding site in the isolated thioredoxin domain is dampened in the domain pair, suggesting that the two domains mutually affect each other on a profound level. Our results present a platform for further detailed studies of multidomain thioredoxin-glutaredoxin containing proteins, and their function in human cells.
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| 28. |
- Andrésen, Cecilia, et al.
(författare)
-
Transient structure and dynamics in the disordered c-Myc transactivation domain affect Bin1 binding
- 2012
-
Ingår i: Nucleic Acids Research. - : Oxford University Press (OUP): Policy C / Oxford University Press. - 0305-1048 .- 1362-4962. ; 40:13, s. 6353-6366
-
Tidskriftsartikel (refereegranskat)abstract
- The crucial role of Myc as an oncoprotein and as a key regulator of cell growth makes it essential to understand the molecular basis of Myc function. The N-terminal region of c-Myc coordinates a wealth of protein interactions involved in transformation, differentiation and apoptosis. We have characterized in detail the intrinsically disordered properties of Myc-1-88, where hierarchical phosphorylation of S62 and T58 regulates activation and destruction of the Myc protein. By nuclear magnetic resonance (NMR) chemical shift analysis, relaxation measurements and NOE analysis, we show that although Myc occupies a very heterogeneous conformational space, we find transiently structured regions in residues 22-33 and in the Myc homology box I (MBI; residues 45-65); both these regions are conserved in other members of the Myc family. Binding of Bin1 to Myc-1-88 as assayed by NMR and surface plasmon resonance (SPR) revealed primary binding to the S62 region in a dynamically disordered and multivalent complex, accompanied by population shifts leading to altered intramolecular conformational dynamics. These findings expand the increasingly recognized concept of intrinsically disordered regions mediating transient interactions to Myc, a key transcriptional regulator of major medical importance, and have important implications for further understanding its multifaceted role in gene regulation.
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| 29. |
- Andrésen, Cecilia, et al.
(författare)
-
Transient structure and intrinsic disorder in the c-Myc transactivation domain and its effects on ligand binding
-
Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- The crucial role of c-Myc as an oncoprotein and as a key regulator of cell growth makes it essential to understand the molecular basis of c-Myc function. The transactivation domain of c-Myc coordinates a wealth of protein interactions involved in transformation, differentiation and apoptosis. We have characterized in detail the intrinsically disordered properties of c-Myc-1-88, where hierarchical phosphorylation of T58 and S62 regulates activation and destruction of the c-Myc protein. By NMR chemical shift analysis, relaxation measurements and NOE analysis, we show that both the MBI region (residues 45-65) and residues 22-33 are transiently structured regions, conserved also in other members of the Myc family. Binding of Bin1-SH3 to c-Myc-1-88 as assayed by NMR and SPR revealed primary binding to the S62 region, but also a dynamically disordered and multivalent complex in which intrinsic disorder of c-Myc-1-88 was retained while releasing transient intramolecular interactions. Our findings describe a novel mode of regulatory recognition of c-Myc that is in agreement with the increasingly recognized capability of intrinsically disordered regions to efficiently mediate transient interactions with a wide range of targets, with important implications towards understanding the unique multifaceted biological functions of c-Myc.
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| 30. |
- Auer, Renate, et al.
(författare)
-
Measuring the Signs of H-1(alpha) Chemical Shift Differences Between Ground and Excited Protein States by Off-Resonance Spin-Lock R-1 rho NMR Spectroscopy
- 2009
-
Ingår i: JOURNAL OF THE AMERICAN CHEMICAL SOCIETY. - : American Chemical Society (ACS). - 0002-7863 .- 1520-5126. ; 131:31, s. 10832-10833
-
Tidskriftsartikel (refereegranskat)abstract
- Analysis of Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion NMR profiles provides the kinetics and thermodynamics of millisecond-time-scale exchange processes involving the interconversion of populated ground and invisible excited states. In addition, the absolute values of chemical, shift differences between NMR probes in the exchanging states, vertical bar Delta(pi)vertical bar, are also extracted. Herein, we present a simple experiment for obtaining the sign of H-1(alpha) Delta(pi) values by measuring off-resonance H-1(alpha) decay rates, R-1 rho, using weak proton spin-lock fields. A pair of R-1 rho values is measured with a spin-lock field applied vertical bar Delta omega vertical bar downfield and upfield of the major-state peak. In many cases, these two relaxation rates differ substantially, with the larger one corresponding to the case where the spin-lock field coincides with the resonance frequency of the probe in the minor state. The utility of the methodology is demonstrated first on a system involving protein ligand exchange and subsequently on an SH3 domain exchanging between a folded state and its on-pathway folding intermediate. With this experiment, it thus becomes possible to determine H-1(alpha) chemical shifts of the invisible excited state, which can be used as powerful restraints in defining the structural properties of these elusive conformers.
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| 31. |
- Bach, Anders, et al.
(författare)
-
A high-affinity, dimeric inhibitor of PSD-95 bivalently interacts with PDZ1-2 and protects against ischemic brain damage
- 2012
-
Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 109:9, s. 3317-3322
-
Tidskriftsartikel (refereegranskat)abstract
- Inhibition of the ternary protein complex of the synaptic scaffolding protein postsynaptic density protein-95 (PSD-95), neuronal nitric oxide synthase (nNOS), and the N-methyl-D-aspartate (NMDA) receptor is a potential strategy for treating ischemic brain damage, but high-affinity inhibitors are lacking. Here we report the design and synthesis of a novel dimeric inhibitor, Tat-NPEG4(IETDV)(2) (Tat-N-dimer), which binds the tandem PDZ1-2 domain of PSD-95 with an unprecedented high affinity of 4.6 nM, and displays extensive protease-resistance as evaluated in vitro by stability-measurements in human blood plasma. X-ray crystallography, NMR, and small-angle X-ray scattering (SAXS) deduced a true bivalent interaction between dimeric inhibitor and PDZ1-2, and also provided a dynamic model of the conformational changes of PDZ1-2 induced by the dimeric inhibitor. A single intravenous injection of Tat-N-dimer (3 nmol/g) to mice subjected to focal cerebral ischemia reduces infarct volume with 40% and restores motor functions. Thus, Tat-N-dimer is a highly efficacious neuroprotective agent with therapeutic potential in stroke.
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| 32. |
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| 33. |
- Björklund, Emil, et al.
(författare)
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Analysis of protein-ligand interactions from titrations and nuclear magnetic resonance relaxation dispersions
- 2022
-
Ingår i: Protein Science. - : Wiley. - 0961-8368 .- 1469-896X. ; 31:1, s. 301-307
-
Tidskriftsartikel (refereegranskat)abstract
- We present PLIS, a publicly available, open-source software for the determination of protein-ligand dissociation constants that can be used to characterize biological processes or to shed light on biophysical aspects of interactions. PLIS can analyze data from titration experiments monitored by for instance fluorescence spectroscopy or from nuclear magnetic resonance relaxation dispersion experiments. In addition to analysis of experimental data, PLIS includes functionality for generation of synthetic data, useful for understanding how different parameters effect the data in order to better analyze experiments.
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| 34. |
- Björnsson, Jon Mar, et al.
(författare)
-
Proliferation of primitive myeloid progenitors can be reversibly induced by HOXA10
- 2001
-
Ingår i: Blood. - 1528-0020 .- 0006-4971. ; 98:12, s. 3301-3308
-
Tidskriftsartikel (refereegranskat)abstract
- Recent studies show that several Hox transcription factors are important for regulation of proliferation and differentiation in hematopoiesis. Among these is HOXA10, which is selectively expressed at high levels in the most primitive subpopulation of human CD34(+) bone marrow cells. When overexpressed, HOXA10 increases the proliferation of early progenitor cells and can lead to the development of myeloid leukemia. To study the effects of HOXA10 on primitive hematopoietic progenitors in more detail, transgenic mice were generated with regulatable HOXA10 expression. The transgenic mouse model, referred to as tetO-HOXA10, contains the HOXA10 gene controlled by a tetracycline-responsive element and a minimal promoter. Thus, the expression of HOXA10 is inducible and reversible depending on the absence or presence of tetracycline or its analog, doxycycline. A retroviral vector containing the tetracycline transactivator gene (tTA) was used to induce expression of the HOXA10 gene In bone marrow cells from the transgenic mice. Reverse transcription-polymerase chain reaction analysis confirmed regulatable HOXA10 expression in several transgenic lines. HOXA10 induction led to the formation of hematopoietic colonies containing blastlike cells and megakaryocytes. Moreover, the induction of HOXA10 resulted in significant proliferative advantage of primitive hematopoietic progenitors (spleen colony-forming units [CFU-S-12]), which was reversible on withdrawal of induction. Activation of HOXA10 expression in tet0-HOXA10 mice will therefore govern proliferation of primitive myeloid progenitors in a regulated fashion. This novel animal model can be used to identify the target genes of HOXA10 and better clarify, the specific role of HOXA10 in normal and malignant hematopoiesis.
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| 35. |
- Björnsson, Jon Mar, et al.
(författare)
-
Reduced proliferative capacity of hematopoietic stem cells deficient in hoxb3 and hoxb4
- 2003
-
Ingår i: Blood. - 0006-4971 .- 1528-0020. ; 23:11, s. 3872-3883
-
Tidskriftsartikel (refereegranskat)abstract
- Several homeobox transcription factors, such as HOXB3 and HOXB4, have been implicated in regulation of hematopoiesis. In support of this, studies show that overexpression of HOXB4 strongly enhances hematopoietic stem cell regeneration. Here we find that mice deficient in both Hoxb3 and Hoxb4 have defects in endogenous hematopoiesis with reduced cellularity in hematopoietic organs and diminished number of hematopoietic progenitors without perturbing lineage commitment. Analysis of embryonic day 14.5 fetal livers revealed a significant reduction in the hematopoietic stem cell pool, suggesting that the reduction in cellularity observed postnatally is due to insufficient expansion during fetal development. Primitive Lin(-) Scal(+) c-kit(+) hematopoietic progenitors lacking Hoxb3 and Hoxb4 displayed impaired proliferative capacity in vitro. Similarly, in vivo repopulating studies of Hoxb3/Hoxb4-deficient hematopoietic cells resulted in lower repopulating capability compared to normal littermates. Since no defects in homing were observed, these results suggest a slower regeneration of mutant HSC. Furthermore, treatment with cytostatic drugs demonstrated slower cell cycle kinetics of hematopoietic stem cells deficient in Hoxb3 and Hoxb4, resulting in increased tolerance to antimitotic drugs. Collectively, these data suggest a direct physiological role of Hoxb4 and Hoxb3 in regulating stem cell regeneration and that these genes are required for maximal proliferative response.
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| 36. |
- Bryhn, Andreas, et al.
(författare)
-
Fisk- och skaldjursbestånd i hav och sötvatten 2020 : Resursöversikt
- 2021
-
Rapport (övrigt vetenskapligt/konstnärligt)abstract
- I rapporten kan du ta del av bedömningen som görs av situationen för bestånd som regleras inom ramen för EU:s gemensamma fiskeripolitik (GFP). Bedömningarna baseras på det forskningssamarbete och den rådgivning som sker inom det Internationella Havsforskningsrådet (ICES). Totalt redovisas underlag och råd för 48 fisk- och skaldjursarter.De bestånd som förvaltas nationellt baseras på de biologiska underlagen, och rådgivningen i huvudsak på den forskning och övervakning samt analys som bedrivs av Institutionen för akvatiska resurser vid Sveriges lantbruksuniversitet (SLU Aqua) samt yrkesfiskets rapportering.
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| 37. |
- Cala, Juan, et al.
(författare)
-
Graded modules over object-unital groupoid graded rings
- 2021
-
Ingår i: Communications in Algebra. - : Taylor & Francis Group. - 0092-7872 .- 1532-4125. ; 50:2, s. 444-462
-
Tidskriftsartikel (refereegranskat)abstract
- In this article, we analyze the category(Formula presented) of unitary G-graded modules over object unital G -graded rings R, being G a groupoid. Here we consider the forgetful functor G - R- mod and determine many properties (Formula presented.) for which the following implications are valid for modules M in (Formula presented.) M is (Formula presented.) (Formula presented.) U(M) is (Formula presented.) U(M) is (Formula presented.) (Formula presented.) M is (Formula presented.) We treat the cases when (Formula presented.) is any of the properties: direct summand, projective, injective, free and semisimple. Moreover, graded versions of results concerning classical module theory are established, as well as some structural properties (Formula presented.).
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| 38. |
- Cala, Juan, et al.
(författare)
-
Object-unital groupoid graded rings, crossed products and separability
- 2021
-
Ingår i: Communications in Algebra. - : Informa UK Limited. - 0092-7872 .- 1532-4125. ; 44:4, s. 1676-1696
-
Tidskriftsartikel (refereegranskat)abstract
- We extend the classical construction by Noether of crossed product algebras, defined by finite Galois field extensions, to cover the case of separable (but not necessarily finite or normal) field extensions. This leads us naturally to consider non-unital groupoid graded rings of a particular type that we call object unital. We determine when such rings are strongly graded, crossed products, skew groupoid rings and twisted groupoid rings. We also obtain necessary and sufficient criteria for when object unital groupoid graded rings are separable over their principal component, thereby generalizing previous results from the unital case to a non-unital situation. © 2020 The Author(s). Published with license by Taylor and Francis Group, LLC.
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| 39. |
- Chi, Celestine N., 1978-, et al.
(författare)
-
Biophysical Characterization of the Complex between Human Papillomavirus E6 Protein and Synapse-associated Protein 97
- 2011
-
Ingår i: Journal of Biological Chemistry. - : The American Society for Biochemistry and Molecular Biology. - 0021-9258 .- 1083-351X. ; 286:5, s. 3597-3606
-
Tidskriftsartikel (refereegranskat)abstract
- The E6 protein of human papillomavirus (HPV) exhibits complex interaction patterns with several host proteins, and their roles in HPV-mediated oncogenesis have proved challenging to study. Here we use several biophysical techniques to explore the binding of E6 to the three PDZ domains of the tumor suppressor protein synapse-associated protein 97 (SAP97). All of the potential binding sites in SAP97 bind E6 with micromolar affinity. The dissociation rate constants govern the different affinities of HPV16 and HPV18 E6 for SAP97. Unexpectedly, binding is not mutually exclusive, and all three PDZ domains can simultaneously bind E6. Intriguingly, this quaternary complex has the same apparent hydrodynamic volume as the unliganded PDZ region, suggesting that a conformational change occurs in the PDZ region upon binding, a conclusion supported by kinetic experiments. Using NMR, we discovered a new mode of interaction between E6 and PDZ: a subset of residues distal to the canonical binding pocket in the PDZ(2) domain exhibited noncanonical interactions with the E6 protein. This is consistent with a larger proportion of the protein surface defining binding specificity, as compared with that reported previously.
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| 40. |
- Chi, Celestine N., et al.
(författare)
-
Conformational change and non-canonical interactions in the complex between human papillomavirus E6 protein and Synapse-Associated Protein 97
-
Tidskriftsartikel (refereegranskat)abstract
- The E6 protein of human papillomavirus exhibits complex interaction patterns with several host proteins and their roles in HPV mediated oncogensis have proved challenging to study. Here we use several biophysical techniques to explore the binding of E6 to the three PDZ domains of the tumor suppressor protein SAP97. All potential binding sites in SAP97 can bind E6 with low micromolar affinity. Unexpectedly,binding is not mutually exclusive and all three PDZ domains can simultaneously bind E6. Intriguingly, the quaternary complex has the same apparent hydrodynamic volume as the unliganded PDZ region, despite having a doubled mass, suggesting that a conformational change occurs in the PDZ region upon E6 binding. Further, using NMR, we discovered a new mode of interaction between E6 and PDZ, as a subset of residues distal to the binding pocket in the PDZ2 domain was found to exhibit non-canonical interactions with the E6 protein suggesting that a large proportion of the proteins surface defines binding specificity
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| 41. |
- Chi, Celestine N., et al.
(författare)
-
Interactions outside the Boundaries of the Canonical Binding Groove of a PDZ Domain Influence Ligand Binding
- 2012
-
Ingår i: Biochemistry. - : American Chemical Society (ACS). - 0006-2960 .- 1520-4995. ; 51:44, s. 8971-8979
-
Tidskriftsartikel (refereegranskat)abstract
- The postsynaptic density protein-95/discs large/zonula occludens-1 (PDZ) domain is a protein-protein interaction module with a shallow binding groove where protein ligands bind. However, interactions that are not part of this canonical binding groove are likely to modulate peptide binding. We have investigated such interactions beyond the binding groove for PDZ3 from PSD-95 and a peptide derived from the C-terminus of the natural ligand CRIPT. We found via nuclear magnetic resonance experiments that up to eight residues of the peptide ligand interact with the PDZ domain, showing that the interaction surface extends far outside of the binding groove as defined by the crystal structure. PDZ3 contains an extra structural element, a C-terminal helix (α3), which is known to affect affinity. Deletion of this helix resulted in the loss of several intermolecular nuclear Overhauser enhancements from peptide residues outside of the binding pocket, suggesting that α3 forms part of the extra binding surface in wild-type PDZ3. Site-directed mutagenesis, isothermal titration calorimetry, and fluorescence intensity experiments confirmed the importance of both α3 and the N-terminal part of the peptide for the affinity. Our data suggest a general mechanism in which different binding surfaces outside of the PDZ binding groove could provide sites for specific interactions.
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| 42. |
- Edvardsson Rasmussen, Jesper, et al.
(författare)
-
The Acute Effects of Furosemide on Na-K-Cl Cotransporter-1, Fetuin-A and Pigment Epithelium-Derived Factor in the Guinea Pig Cochlea
- 2022
-
Ingår i: Frontiers in Molecular Neuroscience. - : Frontiers Media S.A.. - 1662-5099. ; 15
-
Tidskriftsartikel (refereegranskat)abstract
- Background: Furosemide is a loop diuretic used to treat edema; however, it also targets the Na-K-Cl cotransporter-1 (NKCC1) in the inner ear. In very high doses, furosemide abolishes the endocochlear potential (EP). The aim of the study was to gain a deeper understanding of the temporal course of the acute effects of furosemide in the inner ear, including the protein localization of Fetuin-A and PEDF in guinea pig cochleae. Material and Method: Adult guinea pigs were given an intravenous injection of furosemide in a dose of 100 mg per kg of body weight. The cochleae were studied using immunohistochemistry in controls and at four intervals: 3 min, 30 min, 60 min and 120 min. Also, cochleae of untreated guinea pigs were tested for Fetuin-A and PEDF mRNA using RNAscope (R) technology. Results: At 3 min, NKCC1 staining was abolished in the type II fibrocytes in the spiral ligament, followed by a recovery period of up to 120 min. In the stria vascularis, the lowest staining intensity of NKCC1 presented after 30 min. The spiral ganglion showed a stable staining intensity for the full 120 min. Fetuin-A protein and mRNA were detected in the spiral ganglion type I neurons, inner and outer hair cells, pillar cells, Deiters cells and the stria vascularis. Furosemide induced an increased staining intensity of Fetuin-A at 120 min. PEDF protein and mRNA were found in the spiral ganglia type I neurons, the stria vascularis, and in type I and type II fibrocytes of the spiral ligament. PEDF protein staining intensity was high in the pillar cells in the organ of Corti. Furosemide induced an increased staining intensity of PEDF in type I neurons and pillar cells after 120 min. Conclusion: The results indicate rapid furosemide-induced changes of NKCC1 in the type II fibrocytes. This could be part of the mechanism that causes reduction of the EP within minutes after high dose furosemide injection. Fetuin-A and PEDF are present in many cells of the cochlea and probably increase after furosemide exposure, possibly as an otoprotective response.
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| 43. |
- Fernberg, Patrik, et al.
(författare)
-
Mechanisms controlling particle distribution in infusion molded composites
- 2006
-
Ingår i: Journal of reinforced plastics and composites (Print). - : SAGE Publications. - 0731-6844 .- 1530-7964. ; 25:1, s. 59-70
-
Tidskriftsartikel (refereegranskat)abstract
- This article presents results from an experimental investigation in which two grades of aluminatrihydroxide (ATH) particles are added to liquid resin and used in infusion molding experiments. Based on the results, potential key mechanisms controlling resin flow and hence also the final particle distribution are proposed. A pore doublet model is proposed to explain the seemingly random spatial distribution of particle-dense regions within the final material. These dense regions are found within flow channels, at locations where local shear strain rates are low. This suggests that they are formed as a consequence of a Bingham type of viscosity behavior observed for the suspension and/or due to filtering of particles during fiber bundle impregnation. © 2006 SAGE Publications.
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| 44. |
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| 45. |
- Ghasriani, Houman, et al.
(författare)
-
Appropriation of the MinD protein-interaction motif by the dimeric interface of the bacterial cell division regulator MinE
- 2010
-
Ingår i: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. - : National Academy of Sciences; 1999. - 0027-8424. ; 107:43, s. 18416-18421
-
Tidskriftsartikel (refereegranskat)abstract
- MinE is required for the dynamic oscillation of Min proteins that restricts formation of the cytokinetic septum to the midpoint of the cell in gram negative bacteria. Critical for this oscillation is MinD-binding by MinE to stimulate MinD ATP hydrolysis, a function that had been assigned to the first similar to 30 residues in MinE. Previous models based on the structure of an autonomously folded dimeric C-terminal fragment suggested that the N-terminal domain is freely accessible for interactions with MinD. We report here the solution NMR structure of the full-length MinE dimer from Neisseria gonorrhoeae, with two parts of the N-terminal domain forming an integral part of the dimerization interface. Unexpectedly, solvent accessibility is highly restricted for residues that were previously hypothesized to directly interact with MinD. To delineate the true MinD-binding region, in vitro assays for MinE-stimulated MinD activity were performed. The relative MinD-binding affinities obtained for full-length and N-terminal peptides from MinE demonstrated that residues that are buried in the dimeric interface nonetheless participate in direct interactions with MinD. According to results from NMR spin relaxation experiments, access to these buried residues may be facilitated by the presence of conformational exchange. We suggest that this concealment of MinD-binding residues by the MinE dimeric interface provides a mechanism for prevention of nonspecific interactions, particularly with the lipid membrane, to allow the free diffusion of MinE that is critical for Min protein oscillation.
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| 46. |
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| 47. |
- Hansen, Alexandar L, et al.
(författare)
-
Quantifying Millisecond Exchange Dynamics in Proteins by CPMG Relaxation Dispersion NMR Using Side-Chain H-1 Probes
- 2012
-
Ingår i: Journal of the American Chemical Society. - : American Chemical Society. - 0002-7863 .- 1520-5126. ; 134:6, s. 3178-3189
-
Tidskriftsartikel (refereegranskat)abstract
- A Carr-Purcell-Meiboom-Gill relaxation dispersion experiment is presented for quantifying millisecond time-scale chemical exchange at side-chain H-1 positions in proteins. Such experiments are not possible in a fully protonated molecule because of magnetization evolution from homonuclear scalar couplings that interferes with the extraction of accurate transverse relaxation rates. It is shown, however, that by using a labeling strategy whereby proteins are produced using {C-13,H-1}-glucose and D2O a significant number of isolated side-chain H-1 spins are generated, eliminating such effects. It thus becomes possible to record H-1 dispersion profiles at the beta positions of Ass, Cys, Ser, His, Phe, Tyr, and Trp as well as the gamma positions of Glx, in addition to the methyl side-chain moieties. This brings the total of amino acid side-chain positions that can be simultaneously probed using a single H-1 dispersion experiment to 16. The utility of the approach is demonstrated with an application to the four-helix bundle colicin E7 immunity protein, Im7, which folds via a partially structured low populated intermediate that interconverts with the folded, ground state on the millisecond time-scale. The extracted H-1 chemical shift differences at side-chain positions provide valuable restraints in structural studies of invisible, excited states, complementing backbone chemical shifts that are available from existing relaxation dispersion experiments.
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| 48. |
- Hansen, D. Flemming, et al.
(författare)
-
Probing chemical shifts of invisible states of proteins with relaxation dispersion NMR spectroscopy: How well can we do?
- 2008
-
Ingår i: Journal of the American Chemical Society. - : American Chemical Society. - 0002-7863 .- 1520-5126. ; 130:8, s. 2667-2675
-
Tidskriftsartikel (refereegranskat)abstract
- Carr−Purcell−Meiboom−Gill relaxation dispersion NMR spectroscopy has evolved into a powerful approach for the study of low populated, invisible conformations of biological molecules. One of the powerful features of the experiment is that chemical shift differences between the exchanging conformers can be obtained, providing structural information about invisible excited states. Through the development of new labeling approaches and NMR experiments it is now possible to measure backbone 13Cα and 13CO relaxation dispersion profiles in proteins without complications from 13C−13C couplings. Such measurements are presented here, along with those that probe exchange using 15N and 1HN nuclei. A key experimental design has been the choice of an exchanging system where excited-state chemical shifts were known from independent measurement. Thus it is possible to evaluate quantitatively the accuracy of chemical shift differences obtained in dispersion experiments and to establish that in general very accurate values can be obtained. The experimental work is supplemented by computations that suggest that similarly accurate shifts can be measured in many cases for systems with exchange rates and populations that fall within the range of those that can be quantified by relaxation dispersion. The accuracy of the extracted chemical shifts opens up the possibility of obtaining quantitative structural information of invisible states of the sort that is now available from chemical shifts recorded on ground states of proteins.
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| 49. |
- Haq, S Raza, et al.
(författare)
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Side-Chain Interactions Form Late and Cooperatively in the Binding Reaction between Disordered Peptides and PDZ Domains
- 2012
-
Ingår i: Journal of the American Chemical Society. - : American Chemical Society. - 0002-7863 .- 1520-5126. ; 134:1, s. 599-605
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Tidskriftsartikel (refereegranskat)abstract
- Intrinsically disordered proteins are very common and mediate numerous protein-protein and protein-DNA interactions. While it is clear that these interactions are instrumental for the life of the mammalian cell, there is a paucity of data regarding their molecular binding mechanisms. Here we have used short peptides as a model system for intrinsically disordered proteins. Linear free energy relationships based on rate and equilibrium constants for the binding of these peptides to ordered target proteins, PDZ domains, demonstrate that native side-chain interactions form mainly after the rate-limiting barrier for binding and in a cooperative fashion. This finding suggests that these disordered peptides first form a weak encounter complex with non-native interactions. The data do not support the recent notion that the affinities of intrinsically disordered proteins toward their targets are generally governed by their association rate constants. Instead, we observed the opposite for peptide-PDZ interactions, namely, that changes in K-d correlate with changes in k(off).
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- Helander, Sara, et al.
(författare)
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Pre-Anchoring of Pin1 to Unphosphorylated c-Myc in a Fuzzy Complex Regulates c-Myc Activity
- 2015
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Ingår i: Structure. - : Cell Press. - 0969-2126 .- 1878-4186. ; 23:12, s. 2267-2279
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Tidskriftsartikel (refereegranskat)abstract
- Hierarchic phosphorylation and concomitant Pin1-mediated proline isomerization of the oncoprotein c-Myc controls its cellular stability and activity. However, the molecular basis for Pin1 recognition and catalysis of c-Myc and other multisite, disordered substrates in cell regulation and disease is unclear. By nuclear magnetic resonance, surface plasmon resonance, and molecular modeling, we show that Pin1 subdomains jointly pre-anchor unphosphorylated c-Myc1–88 in the Pin1 interdomain cleft in a disordered, or “fuzzy”, complex at the herein named Myc Box 0 (MB0) conserved region N-terminal to the highly conserved Myc Box I (MBI). Ser62 phosphorylation in MBI intensifies previously transient MBI-Pin1 interactions in c-Myc1–88 binding, and increasingly engages Pin1PPIase and its catalytic region with maintained MB0 interactions. In cellular assays, MB0 mutated c-Myc shows decreased Pin1 interaction, increased protein half-life, but lowered rates of Myc-driven transcription and cell proliferation. We propose that dynamic Pin1 recognition of MB0 contributes to the regulation of c-Myc activity in cells
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