| 1. |
- Andersson, Bo, et al.
(författare)
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Recent developments in the Lund fragmentation model
- 2003
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Ingår i: Proceedings of the XXXII International Symposium on Multiparticle Dynamics. - 9812384030 ; , s. 7-10
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Konferensbidrag (refereegranskat)abstract
- A new fragmentation model for multigluon strings is presented
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| 2. |
- Andersson, Bo, et al.
(författare)
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The lambda-measure and the generalised dipoles in the Lund model
- 2002
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Ingår i: Nuclear Physics, Section B. - 0550-3213. ; 646:1-2, s. 102-126
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Tidskriftsartikel (refereegranskat)abstract
- We demonstrate that the multiple gluon emission phase space in the dipole cascade model has a strong linear correlation with the number of gluons emitted. The number of gluons per unit available phase space at a certain resolution scale is found to be remarkably independent of the cms energy and global event properties like thrust, and even changes in the ordering variable or resolution scale. We show that the distribution of sizes of gluon-gluon dipoles in a parton cascade has stability properties which are sufficient to account for those of the phase space variable. We observe that certain more abstract entities, defined in the context of hadronisation and related to the gluon emission phase space, share those properties of colour dipoles and name them generalised dipoles. We also present an analytical model to qualitatively describe our findings. (C) 2002 Elsevier Science B.V. All rights reserved.
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| 3. |
- Bille, Anna, et al.
(författare)
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Equilibrium simulation of trp-cage in the presence of protein crowders.
- 2015
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 143:17
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Tidskriftsartikel (refereegranskat)abstract
- While steric crowders tend to stabilize globular proteins, it has been found that protein crowders can have an either stabilizing or destabilizing effect, where a destabilization may arise from nonspecific attractive interactions between the test protein and the crowders. Here, we use Monte Carlo replica-exchange methods to explore the equilibrium behavior of the miniprotein trp-cage in the presence of protein crowders. Our results suggest that the surrounding crowders prevent trp-cage from adopting its global native fold, while giving rise to a stabilization of its main secondary-structure element, an α-helix. With the crowding agent used (bovine pancreatic trypsin inhibitor), the trp-cage-crowder interactions are found to be specific, involving a few key residues, most of which are prolines. The effects of these crowders are contrasted with those of hard-sphere crowders.
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| 4. |
- Bille, Anna, et al.
(författare)
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Peptide folding in the presence of interacting protein crowders
- 2016
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 144:17
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Tidskriftsartikel (refereegranskat)abstract
- Using Monte Carlo methods, we explore and compare the effects of two protein crowders, BPTI and GB1, on the folding thermodynamics of two peptides, the compact helical trp-cage and the β-hairpin-forming GB1m3. The thermally highly stable crowder proteins are modeled using a fixed backbone and rotatable side-chains, whereas the peptides are free to fold and unfold. In the simulations, the crowder proteins tend to distort the trp-cage fold, while having a stabilizing effect on GB1m3. The extent of the effects on a given peptide depends on the crowder type. Due to a sticky patch on its surface, BPTI causes larger changes than GB1 in the melting properties of the peptides. The observed effects on the peptides stem largely from attractive and specific interactions with the crowder surfaces, and differ from those seen in reference simulations with purely steric crowder particles.
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| 5. |
- Bille, Anna, et al.
(författare)
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Stability and Local Unfolding of SOD1 in the Presence of Protein Crowders
- 2019
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 123:9, s. 1920-1930
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Tidskriftsartikel (refereegranskat)abstract
- Using NMR and Monte Carlo (MC) methods, we investigate the stability and dynamics of superoxide dismutase 1 (SOD1) in homogeneous crowding environments, where either bovine pancreatic trypsin inhibitor (BPTI) or the B1 domain of streptococcal protein G (PGB1) serves as a crowding agent. By NMR, we show that both crowders, and especially BPTI, cause a drastic loss in the overall stability of SOD1 in its apo monomeric form. Additionally, we determine chemical shift perturbations indicating that SOD1 interacts with the crowder proteins in a residue-specific manner that further depends on the identity of the crowding protein. Furthermore, the specificity of SOD1-crowder interactions is reciprocal: chemical shift perturbations on BPTI and PGB1 identify regions that interact preferentially with SOD1. By MC simulations, we investigate the local unfolding of SOD1 in the absence and presence of the crowders. We find that the crowders primarily interact with the long flexible loops of the folded SOD1 monomer. The basic mechanisms by which the SOD1 β-barrel core unfolds remain unchanged when adding the crowders. In particular, both with and without the crowders, the second β-sheet of the barrel is more dynamic and unfolding-prone than the first. Notably, the MC simulations (exploring the early stages of SOD1 unfolding) and the NMR experiments (under equilibrium conditions) identify largely the same set of PGB1 and BPTI residues as prone to form SOD1 contacts. Thus, contacts stabilizing the unfolded state of SOD1 in many cases appear to form early in the unfolding reaction.
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| 6. |
- Favrin, Giorgio, et al.
(författare)
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Oligomerization of amyloid A beta(16-22) peptides using hydrogen bonds and hydrophobicity forces
- 2004
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Ingår i: Biophysical Journal. - : Elsevier BV. - 1542-0086 .- 0006-3495. ; 87:6, s. 3657-3664
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Tidskriftsartikel (refereegranskat)abstract
- The 16 - 22 amino-acid fragment of the beta-amyloid peptide associated with the Alzheimer's disease, Abeta, is capable of forming amyloid fibrils. Here we study the aggregation mechanism of Abeta(16-22) peptides by unbiased thermodynamic simulations at the atomic level for systems of one, three, and six Abeta(16-22) peptides. We find that the isolated Abeta(16-22) peptide is mainly a random coil in the sense that both the alpha-helix and beta-strand contents are low, whereas the three- and six-chain systems form aggregated structures with a high beta-sheet content. Furthermore, in agreement with experiments on Abeta(16-22) fibrils, we find that large parallel beta-sheets are unlikely to form. For the six-chain system, the aggregated structures can have many different shapes, but certain particularly stable shapes can be identified.
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| 7. |
- Irbäck, Anders, et al.
(författare)
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All-atom Monte Carlo simulations of protein folding and aggregation
- 2013
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Ingår i: Computational methods to study the structure and dynamics of biomolecules and biomolecular processes: from bioinformatics to molecular quantum mechanics. - Berlin, Heidelberg : Springer Berlin Heidelberg. - 2193-9357 .- 2193-9349. - 9783642285530 - 9783642285547 ; 1, s. 433-444
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Bokkapitel (refereegranskat)
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| 8. |
- Irbäck, Anders, et al.
(författare)
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An effective all-atom potential for proteins
- 2009
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Ingår i: Food Biophysics. - : Springer Science and Business Media LLC. - 1557-1866. ; 2:1, s. 2-2
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Tidskriftsartikel (refereegranskat)abstract
- We describe and test an implicit solvent all-atom potential for simulations of protein folding and aggregation. The potential is developed through studies of structural and thermodynamic properties of 17 peptides with diverse secondary structure. Results obtained using the final form of the potential are presented for all these peptides. The same model, with unchanged parameters, is furthermore applied to a heterodimeric coiled-coil system, a mixed alpha/beta protein and a three-helix-bundle protein, with very good results. The computational efficiency of the potential makes it possible to investigate the free-energy landscape of these 49-67-residue systems with high statistical accuracy, using only modest computational resources by today's standards.PACS Codes: 87.14.E-, 87.15.A-, 87.15.Cc.
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| 9. |
- Irbäck, Anders, et al.
(författare)
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Dissecting the mechanical unfolding of ubiquitin
- 2005
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Ingår i: Proceedings of the National Academy of Sciences. - : Proceedings of the National Academy of Sciences. - 1091-6490 .- 0027-8424. ; 102:38, s. 13427-13432
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Tidskriftsartikel (refereegranskat)abstract
- The unfolding behavior of ubiquitin under the influence of a stretching force recently was investigated experimentally by single-molecule constant-force methods. Many observed unfolding traces had a simple two-state character, whereas others showed clear evidence of intermediate states. Here, we use Monte Carlo simulations to investigate the force-induced unfolding of ubiquitin at the atomic level. In agreement with experimental data, we find that the unfolding process can occur either in a single step or through intermediate states. In addition to this randomness, we find that many quantities, such as the frequency of occurrence of intermediates, show a clear systematic dependence on the strength of the applied force. Despite this diversity, one common feature can be identified in the simulated unfolding events, which is the order in which the secondary-structure elements break. This order is the same in two and three-state events and at the different forces studied. The observed order remains to be verified experimentally but appears physically reasonable.
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| 10. |
- Irbäck, Anders, et al.
(författare)
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Effective all-atom potentials for proteins
- 2011
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Ingår i: Multiscale approaches to protein modeling. - New York, NY : Springer New York. - 9781441968883 - 9781441968890 ; , s. 111-126
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Bokkapitel (refereegranskat)
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