| 1. |
- Fagerberg, Eric
(författare)
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Assessing the structural and dynamical properties of concentrated solutions of the disordered proteins Histatin 5 and its tandem repeat
- 2022
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Intrinsically disordered proteins are distinguished by a lack of distinct three-dimensional structure, existing instead as an ensemble of heterogenous structures. In this research, the effect of crowding on these proteins is investigated using a combined approach of experiment and computer simulation, mainly using coarse-grained simulation models to make simulation computationally feasible at the high concentration conditions crowding is displayed.Firstly, the saliva protein Histatin 5 (Hst5) is studied with SAXS, where a selection of coarse-grained models were evaluated using the SAXS data. It was determined that no model could provide adequate simulation-experiment agreement, but a best-performing model could be established. This model predicted moderate change in structure with crowding in the case of Histatin 5.It was postulated the moderate effect of crowding on Histatin 5 was due to its short sequence-length. Thus, the dimer of Hst5 was formed and subjected to investigation by SAXS and computer simulation for crowding effects. The dimer was more challenging to model with a coarse-grained model, and circular dichroism data suggested secondary structures to be present, which a coarse-grained model cannot capture. Atomistic modelling followed, which however did not perform better than the coarse-grained models, showing the importance of further developing these models to represent intrinsically disordered proteins.Atomistic modelling was also performed at high concentrations of Hst5 5, combined with quasi-elastic neutron spectroscopy to elucidate diffusion behaviour at crowded conditions. Diffusion decreased with increasing protein concentration, with temperature effects following Stokes-Einstein beha- viour and increses in salt content to decrease diffusion. Depending on assumptions on the relation between effective- and translational-diffusion, the atomistic model displayed semi-quantitative agreement with experiment.Using neutral polymeric crowders rather than self-crowding showed no impact on structure, as investigated by SAXS. Using DLS did as well not reveal any crowding impact, with the exception of Ficoll®, where Hst5 seemed to modulate Ficoll® self-crowding behaviour in terms of diffusion, decreasing the self-crowding effect. Several coarse-grained models showed similar non-existant effects on structure by crowding, with small deviations from experiment.Benchmarking three coarse-grained models indicate higher degree of finegraining and additional parameters does necessarily follow the intuitive notion of increasing performance, with the most advanced not having as good performance as the two simpler models in terms of predicting radius of gyration.
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| 2. |
- Fagerberg, Eric, et al.
(författare)
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Comparative Performance of Computer Simulation Models of Intrinsically Disordered Proteins at Different Levels of Coarse-Graining
- 2023
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Ingår i: Journal of Chemical Information and Modeling. - 1549-960X. ; 63:13, s. 4079-4087
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Tidskriftsartikel (refereegranskat)abstract
- Coarse-graining is commonly used to decrease the computational cost of simulations. However, coarse-grained models are also considered to have lower transferability, with lower accuracy for systems outside the original scope of parametrization. Here, we benchmark a bead-necklace model and a modified Martini 2 model, both coarse-grained models, for a set of intrinsically disordered proteins, with the different models having different degrees of coarse-graining. The SOP-IDP model has earlier been used for this set of proteins; thus, those results are included in this study to compare how models with different levels of coarse-graining compare. The sometimes naive expectation of the least coarse-grained model performing best does not hold true for the experimental pool of proteins used here. Instead, it showed the least good agreement, indicating that one should not necessarily trust the otherwise intuitive notion of a more advanced model inherently being better in model choice.
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| 3. |
- Fagerberg, Eric, et al.
(författare)
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Evaluating Models of Varying Complexity of Crowded Intrinsically Disordered Protein Solutions against SAXS
- 2019
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Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 15:12, s. 6968-6983
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Tidskriftsartikel (refereegranskat)abstract
- Intrinsically disordered proteins (IDPs) adopt heterogeneous conformational ensembles in solution. The properties of the conformational ensemble are dependent upon the solution conditions, including the presence of ions, temperature, and crowding, and often directly impact biological function. Many in vitro investigations focus on the properties of IDPs under dilute conditions, rather than the crowded environment found in vivo. Due to their heterogeneous nature, the study of IDPs under crowded conditions is challenging both experimentally and computationally. Despite this, such studies are worth pursuing due to the insight gained into biologically relevant phenomena. Here, we study the highly charged IDP Histatin 5 under self-crowded conditions in low and high salt conditions. A combination of small-angle X-ray scattering and different simulation models, spanning a range of computational complexity and detail, is used. Most models are found to have limited application when compared to results from experiments. The best performing model is the highly coarse-grained, bead-necklace model. This model shows that Histatin 5 has a conserved radius of gyration and a decreasing flexibility with increasing protein concentration. Due to its computational efficiency, we propose that it is a suitable model to study crowded IDP solutions, despite its simplicity.
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| 4. |
- Fagerberg, Eric, et al.
(författare)
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Self-Diffusive Properties of the Intrinsically Disordered Protein Histatin 5 and the Impact of Crowding Thereon : A Combined Neutron Spectroscopy and Molecular Dynamics Simulation Study
- 2021
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207.
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Tidskriftsartikel (refereegranskat)abstract
- Intrinsically disordered proteins (IDPs) are proteins that, in comparison with globular/structured proteins, lack a distinct tertiary structure. Here, we use the model IDP, Histatin 5, for studying its dynamical properties under self-crowding conditions with quasi-elastic neutron scattering in combination with full atomistic molecular dynamics (MD) simulations. The aim is to determine the effects of crowding on the center-of-mass diffusion as well as the internal diffusive behavior. The diffusion was found to decrease significantly, which we hypothesize can be attributed to some degree of aggregation at higher protein concentrations, (≥100 mg/mL), as indicated by recent small-angle X-ray scattering studies. Temperature effects are also considered and found to, largely, follow Stokes-Einstein behavior. Simple geometric considerations fail to accurately predict the rates of diffusion, while simulations show semiquantitative agreement with experiments, dependent on assumptions of the ratio between translational and rotational diffusion. A scaling law that previously was found to successfully describe the behavior of globular proteins was found to be inadequate for the IDP, Histatin 5. Analysis of the MD simulations show that the width of the distribution with respect to diffusion is not a simplistic mirroring of the distribution of radius of gyration, hence, displaying the particular features of IDPs that need to be accounted for.
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| 5. |
- Fagerberg, Eric, et al.
(författare)
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The Effects of Chain Length on the Structural Properties of Intrinsically Disordered Proteins in Concentrated Solutions
- 2021
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 124:52, s. 11843-11853
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Tidskriftsartikel (refereegranskat)abstract
- Intrinsically disordered proteins (IDP) are proteins that sample a heterogeneous ensemble of conformers in solution. An estimated 25-30% of all eukaryotic proteins belong to this class. In vivo, IDPs function under conditions that are highly crowded by other biological macromolecules. Previous research has highlighted that the presence of crowding agents can influence the conformational ensemble sampled by IDPs, resulting in either compaction or expansion. The effects of self-crowding of the disordered protein Histatin 5 has, in an earlier study, been found to have limited influence on the conformational ensemble. In this study, it is examined whether the short chain length of Histatin 5 can explain the limited effects of crowding observed, by introducing (Histatin 5)2, a tandem repeat of Histatin 5. By utilizing small-angle X-ray scattering, it is shown that the conformational ensemble is conserved at high protein concentrations, in resemblance with Histatin 5, although with a lowered protein concentration at which aggregation arises. Under dilute conditions, atomistic molecular dynamics and coarse-grained Monte Carlo simulations, as well as an established scaling law, predicted more extended conformations than indicated by experimental data, hence implying that (Histatin 5)2 does not behave as a self-avoiding random walk.
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| 6. |
- Lazar, Tamas, et al.
(författare)
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PED in 2021 : A major update of the protein ensemble database for intrinsically disordered proteins
- 2021
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Ingår i: Nucleic Acids Research. - : Oxford University Press (OUP). - 0305-1048 .- 1362-4962. ; 49:D1, s. 404-411
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Tidskriftsartikel (refereegranskat)abstract
- The Protein Ensemble Database (PED) (https://proteinensemble.org), which holds structural ensembles of intrinsically disordered proteins (IDPs), has been significantly updated and upgraded since its last release in 2016. The new version, PED 4.0, has been completely redesigned and reimplemented with cutting-edge technology and now holds about six times more data (162 versus 24 entries and 242 versus 60 structural ensembles) and a broader representation of state of the art ensemble generation methods than the previous version. The database has a completely renewed graphical interface with an interactive feature viewer for region-based annotations, and provides a series of descriptors of the qualitative and quantitative properties of the ensembles. High quality of the data is guaranteed by a new submission process, which combines both automatic and manual evaluation steps. A team of biocurators integrate structured metadata describing the ensemble generation methodology, experimental constraints and conditions. A new search engine allows the user to build advanced queries and search all entry fields including cross-references to IDP-related resources such as DisProt, MobiDB, BMRB and SASBDB. We expect that the renewed PED will be useful for researchers interested in the atomic-level understanding of IDP function, and promote the rational, structure-based design of IDP-targeting drugs.
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| 7. |
- Lenton, Samuel, et al.
(författare)
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From dilute to concentrated solutions of intrinsically disordered proteins : Interpretation and analysis of collected data
- 2023
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Ingår i: Small Angle Scattering Part B: Methods for Structural Interpretation. - : Elsevier. - 1557-7988 .- 0076-6879. - 9780323991810 ; 678, s. 299-330
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Bokkapitel (refereegranskat)abstract
- Intrinsically disordered proteins (IDPs) have a broad energy landscape and consequently sample many different conformations in solution. The innate flexibility of IDPs is exploited in their biological function, and in many instances allows a single IDP to regulate a range of processes in vivo. Due to their highly flexible nature, characterizing the structural properties of IDPs is not straightforward. Often solution-based methods such as Nuclear Magnetic Resonance (NMR), Förster Resonance Energy Transfer (FRET), and Small-Angle X-ray Scattering (SAXS) are used. SAXS is indeed a powerful technique to study the structural and conformational properties of IDPs in solution, and from the obtained SAXS spectra, information about the average size, shape, and extent of oligomerization can be determined. In this chapter, we will introduce model-free methods that can be used to interpret SAXS data and introduce methods that can be used to interpret SAXS data beyond analytical models, for example, by using atomistic and different levels of coarse-grained models in combination with molecular dynamics (MD) and Monte Carlo simulations.
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| 8. |
- Tivesten, Åsa, 1969, et al.
(författare)
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Low serum testosterone and high serum estradiol associate with lower extremity peripheral arterial disease in elderly men. The MrOS Study in Sweden
- 2007
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Ingår i: Journal of the American College of Cardiology. - : Elsevier BV. - 0735-1097 .- 1558-3597. ; 50:11, s. 1070-1076
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Tidskriftsartikel (refereegranskat)abstract
- Objectives: This study sought to determine whether serum levels of testosterone and estradiol associate with lower extremity peripheral arterial disease (PAD) in a large population-based cohort of elderly men. Background: Few studies have explored the relationship between serum sex steroids and lower extremity PAD in men. Methods: The Swedish arm of the MrOS (Osteoporotic Fractures in Men) study (n = 3,014; average age 75.4 years) assessed ankle-brachial index (ABI) and defined lower extremity PAD as ABI <0.90. Radioimmunoassay measured serum levels of total testosterone, estradiol, and sex hormone-binding globulin, and we calculated free testosterone and free estradiol levels from the mass action equations. Results: A linear regression model including age, current smoking, previous smoking, diabetes, hypertension, body mass index, free testosterone, and free estradiol showed that free testosterone independently and positively associates with ABI (p < 0.001), whereas free estradiol independently and negatively associates with ABI (p < 0.001). Logistic regression analyses showed that free testosterone in the lowest quartile (vs. quartiles 2 to 4; odds ratio [OR] 1.65, 95% confidence interval [CI] 1.22 to 2.23, p = 0.001) and free estradiol in the highest quartile (vs. quartiles 1 to 3; OR 1.45, 95% CI 1.09 to 1.94, p = 0.012) independently associate with lower extremity PAD. Conclusions: This cross-sectional study shows for the first time that low serum testosterone and high serum estradiol levels associate with lower extremity PAD in elderly men. Future prospective and interventional studies are needed to establish possible causal relationships between sex steroids and the development of lower extremity PAD in men.
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| 9. |
- Willeit, Peter, et al.
(författare)
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Inflammatory markers and extent and progression of early atherosclerosis : Meta-analysis of individual-participant-data from 20 prospective studies of the PROG-IMT collaboration
- 2016
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Ingår i: European Journal of Preventive Cardiology. - : Oxford University Press (OUP). - 2047-4873 .- 2047-4881. ; 23:2, s. 194-205
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Tidskriftsartikel (refereegranskat)abstract
- BackgroundLarge-scale epidemiological evidence on the role of inflammation in early atherosclerosis, assessed by carotid ultrasound, is lacking. We aimed to quantify cross-sectional and longitudinal associations of inflammatory markers with common-carotid-artery intima-media thickness (CCA-IMT) in the general population. MethodsInformation on high-sensitivity C-reactive protein, fibrinogen, leucocyte count and CCA-IMT was available in 20 prospective cohort studies of the PROG-IMT collaboration involving 49,097 participants free of pre-existing cardiovascular disease. Estimates of associations were calculated within each study and then combined using random-effects meta-analyses. ResultsMean baseline CCA-IMT amounted to 0.74mm (SD=0.18) and mean CCA-IMT progression over a mean of 3.9 years to 0.011mm/year (SD=0.039). Cross-sectional analyses showed positive linear associations between inflammatory markers and baseline CCA-IMT. After adjustment for traditional cardiovascular risk factors, mean differences in baseline CCA-IMT per one-SD higher inflammatory marker were: 0.0082mm for high-sensitivity C-reactive protein (p<0.001); 0.0072mm for fibrinogen (p<0.001); and 0.0025mm for leucocyte count (p=0.033). Inflammatory load', defined as the number of elevated inflammatory markers (i.e. in upper two quintiles), showed a positive linear association with baseline CCA-IMT (p<0.001). Longitudinal associations of baseline inflammatory markers and changes therein with CCA-IMT progression were null or at most weak. Participants with the highest inflammatory load' had a greater CCA-IMT progression (p=0.015). ConclusionInflammation was independently associated with CCA-IMT cross-sectionally. The lack of clear associations with CCA-IMT progression may be explained by imprecision in its assessment within a limited time period. Our findings for inflammatory load' suggest important combined effects of the three inflammatory markers on early atherosclerosis.
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