| 1. |
- Bucciarelli, Saskia, et al.
(författare)
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Dramatic influence of patchy attractions on short-time protein diffusion under crowded conditions
- 2016
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Ingår i: Science Advances. - : American Association for the Advancement of Science (AAAS). - 2375-2548. ; 2:12, s. 1601432-1601432
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Tidskriftsartikel (refereegranskat)abstract
- In the dense and crowded environment of the cell cytoplasm, an individual protein feels the presence of and interacts with all surrounding proteins. While we expect this to strongly influence the short-time diffusion coefficient Ds of proteins on length scales comparable to the nearest-neighbor distance, this quantity is difficult to assess experimentally. We demonstrate that quantitative information about Ds can be obtained from quasi-elastic neutron scattering experiments using the neutron spin echo technique. We choose two well-characterized and highly stable eye lens proteins, bovine α-crystallin and γB-crystallin, and measure their diffusion at concentrations comparable to those present in the eye lens. While diffusion slows down with increasing concentration for both proteins, we find marked variations that are directly linked to subtle differences in their interaction potentials. A comparison with computer simulations shows that anisotropic and patchy interactions play an essential role in determining the local short-time dynamics. Hence, our study clearly demonstrates the enormous effect that weak attractions can have on the short-time diffusion of proteins at concentrations comparable to those in the cellular cytosol.
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| 2. |
- Myung, Jin Suk, et al.
(författare)
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Weak Shape Anisotropy Leads to a Nonmonotonic Contribution to Crowding, Impacting Protein Dynamics under Physiologically Relevant Conditions
- 2018
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Ingår i: The Journal of Physical Chemistry Part B. - : American Chemical Society (ACS). - 1520-5207 .- 1520-6106. ; 122
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Tidskriftsartikel (refereegranskat)abstract
- The effect of a nonspherical particle shape on the dynamics in crowded solutions presents a significant challenge for a comprehensive understanding of interaction and structural relaxation in biological and soft matter. We report that small deviations from a spherical shape induce a nonmonotonic contribution to the crowding effect on the short-time cage diffusion compared with spherical systems, using molecular dynamics simulations with mesoscale hydrodynamics of a multiparticle collision dynamics fluid in semidilute systems with volume fractions smaller than 0.35. We show that the nonmonotonic effect due to anisotropy is caused by the combination of a reduced relative mobility over the entire concentration range and a looser and less homogeneous cage packing of nonspherical particles. Our finding stresses that nonsphericity induces new complexity, which cannot be accounted for in effective sphere models, and is of great interest in applications such as formulations as well as for the fundamental understanding of soft matter in general and crowding effects in living cells in particular.
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| 3. |
- Park, Jun Dong, et al.
(författare)
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A review on particle dynamics simulation techniques for colloidal dispersions : Methods and applications
- 2016
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Ingår i: Korean Journal of Chemical Engineering. - : Springer Science and Business Media LLC. - 0256-1115 .- 1975-7220. ; 33:11, s. 3069-3078
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Tidskriftsartikel (refereegranskat)abstract
- Colloidal dispersions have attracted much attention both from academia and industry due to industrial significance and complex dynamic properties. Accordingly, a variety of attempts have been made to understand the complicated physics of colloidal dispersions. Particle dynamics simulation has been playing an important role in exploring colloidal systems as a strong complement to experimental approaches from which it is hard to get exact microscopic information. Our aim is to provide a well-organized and up-to-date guide to particle dynamics simulation of colloidal dispersions. Among diverse particle dynamics simulation techniques, we focus on Brownian dynamics, Stokesian dynamics, multi-particle collision dynamics, and self-consistent particle simulation techniques. First, the concept of the simulation techniques will be described. Then, for each simulation technique, pros and cons are discussed with a broad range of applications, including concentrated hard sphere suspensions and biological systems. It is expected that this article helps to identify and motivate research challenges.
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| 4. |
- Son, Ora, et al.
(författare)
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ATHB12, an ABA-Inducible Homeodomain-Leucine Zipper (HD-Zip) Protein of Arabidopsis, Negatively Regulates the Growth of the Inflorescence Stem by Decreasing the Expression of a Gibberellin 20-Oxidase Gene
- 2010
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Ingår i: Plant and Cell Physiology. - : Oxford University Press (OUP). - 0032-0781 .- 1471-9053. ; 51:9, s. 1537-1547
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Tidskriftsartikel (refereegranskat)abstract
- Arabidopsis thaliana homeobox 12 (ATHB12) is rapidly induced by ABA and water stress. A T-DNA insertion mutant of ATHB12 with a reduced level of ATHB12 expression in stems had longer inflorescence stems and reduced sensitivity to ABA during germination. A high level of transcripts of gibberellin 20-oxidase 1 (GA20ox1), a key enzyme in the synthesis of gibberellins, was detected in athb12 stems, while transgenic lines overexpressing ATHB12 (A12OX) had a reduced level of GA20ox1 in stems. Consistent with these data, ABA treatment of wild-type plants resulted in decreased GA20ox1 expression whereas ABA treatment of the athb12 mutant gave rise to slightly decreased GA20ox1 expression. Retarded stem growth in 3-week-old A12OX plants was rescued by exogenous GA(9), but not by GA(12), and less GA(9) was detected in A12OX stems than in wild-type stems. These data imply that ATHB12 decreases GA20ox1 expression in stems. On the other hand, the stems of A12OX plants grew rapidly after the first 3 weeks, so that they were almost as high as wild-type plants at about 5 weeks after germination. We also found changes in the stems of transgenic plants overexpressing ATHB12, such as alterations of expression GA20ox and GA3ox genes, and of GA(4) levels, which appear to result from feedback regulation. Repression of GA20ox1 by ATHB12 was confirmed by transfection of leaf protoplasts. ABA-treated protoplasts also showed increased ATHB12 expression and reduced GA20ox1 expression. These findings all suggest that ATHB12 negatively regulates the expression of a GA 20-oxidase gene in inflorescence stems.
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