| 1. |
- A. Strumpfer, Johan, et al.
(författare)
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Stretching of Twitchin Kinase
- 2012
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Ingår i: Biophysical Journal. - St. Louis, MO, United States : Cell Press. - 0006-3495 .- 1542-0086. ; 102:3 Supplement 1, s. 361a-362a
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Tidskriftsartikel (refereegranskat)abstract
- The giant proteins from the titin family, that form cytoskeletal filaments, have emerged as key mechanotransducers in the sarcomere. These proteins contain a conserved kinase region, which is auto-inhibited by a C-terminal tail domain. The inhibitory tail domain occludes the active sites of the kinases, thus preventing ATP from binding. It was proposed that through application of a force, such as that arising during muscle contraction, the inhibitory tail becomes detached, lifting inhibition. The force-sensing ability of titin kinase was demonstrated in AFM experiments and simulations [Puchner, et al., 2008, PNAS:105, 13385], which showed indeed that mechanical forces can remove the autoinhibitory tail of titin kinase. We report here steered molecular dynamics simulations (SMD) of the very recently resolved crystal structure of twitchin kinase, containing the kinase region and flanking fibronectin and immuniglobulin domains, that show a variant mechanism. Despite the significant structural and sequence similarity to titin kinase, the autoinhibitory tail of twitchin kinase remains in place upon stretching, while the N-terminal lobe of the kinase unfolds. The SMD simulations also show that the detachment and stretching of the linker between fibronectin and kinase regions, and the partial extension of the autoinhibitory tail, are the primary force-response. We postulate that this stretched state, where all structural elements are still intact, may represent the physiologically active state.
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| 2. |
- Adler, Jeremy, et al.
(författare)
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Quantification of Colocalisation; Co-Occurrence, Correlation, Empty Voxels, Regions of Interest and Thresholding
- 2014
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Ingår i: Biophysical Journal. - : Elsevier BV. - 0006-3495 .- 1542-0086. ; 106:2, s. 602A-602A
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Measuring colocalisation is not straightforward with a plethora of coefficients that encapsulate different definitions. Measurements may also be implemented differently. Not only do measurements differ; interconversion is impossible making comparisons challenging. There is a need to cull coefficients and for clear definitions of what precisely is meant by colocalisation in individual studies. Colocalisation can be considered to have two components; co-occurrence which reports whether the fluorophores are found together and correlation which reports on the similarity in their patterns of intensity.
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| 3. |
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| 4. |
- Ahlinder, Linnea, et al.
(författare)
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Large Uptake of Titania and Iron Oxide Nanoparticles in the Nucleus of Lung Epithelial Cells as Measured by Raman Imaging and Multivariate Classification
- 2013
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Ingår i: Biophysical Journal. - : Elsevier BV. - 0006-3495 .- 1542-0086. ; 105:2, s. 310-319
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Tidskriftsartikel (refereegranskat)abstract
- It is a challenging task to characterize the biodistribution of nanoparticles in cells and tissue on a subcellular level. Conventional methods to study the interaction of nanoparticles with living cells rely on labeling techniques that either selectively stain the particles or selectively tag them with tracer molecules. In this work, Raman imaging, a label-free technique that requires no extensive sample preparation, was combined with multivariate classification to quantify the spatial distribution of oxide nanoparticles inside living lung epithelial cells (A549). Cells were exposed to TiO2 (titania) and/or alpha-FeO(OH) (goethite) nanoparticles at various incubation times (4 or 48 h). Using multivariate classification of hyperspectral Raman data with partial least-squares discriminant analysis, we show that a surprisingly large fraction of spectra, classified as belonging to the cell nucleus, show Raman bands associated with nanoparticles. Up to 40% of spectra from the cell nucleus show Raman bands associated with nanoparticles. Complementary transmission electron microscopy data for thin cell sections qualitatively support the conclusions.
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| 5. |
- Ainla, Alar, 1982, et al.
(författare)
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Lab on a Biomembrane
- 2014
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Ingår i: Biophysical Journal. - 0006-3495 .- 1542-0086. ; 106:2, s. 209A-209A
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
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| 6. |
- Alizadehheidari, Mohammadreza, et al.
(författare)
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Nanoconfined Circular DNA
- 2014
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Ingår i: Biophysical Journal. - : Elsevier BV. - 0006-3495 .- 1542-0086. ; 106:2, s. 274A-274A
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Nanofluidic channels have become a versatile tool to manipulate single DNA molecules. They allow investigation of confined single DNA molecules from a fundamental polymer physics perspective as well as for example in DNA barcoding techniques.
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| 7. |
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| 8. |
- Almqvist, Joachim E, 1980, et al.
(författare)
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Modeling the Effect of Kv1.5 Block on the Canine Action Potential
- 2010
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Ingår i: Biophysical Journal. - : Elsevier BV. - 0006-3495 .- 1542-0086. ; 99:9, s. 2726-2736
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Tidskriftsartikel (refereegranskat)abstract
- A wide range of ion channels have been considered as potential targets for pharmacological treatment of atrial fibrillation. The Kv1.5 channel, carrying the IKur current, has received special attention because it contributes to repolarization in the atria but is absent or weakly expressed in ventricular tissue. The dog serves as an important animal model for electrophysiological studies of the heart and mathematical models of the canine atrial action potential (CAAP) have been developed to study the interplay between ionic currents. To enable more-realistic studies on the effects of Kv1.5 blockers on the CAAP in silico, two continuous-time Markov models of the guarded receptor type were formulated for Kv1.5 and subsequently inserted into the Ramirez-Nattel-Courtemanche model of the CAAP. The main findings were: 1), time- and state-dependent Markov models of open-channel Kv1.5 block gave significantly different results compared to a time- and state-independent model with a downscaled conductance; 2), the outcome of Kv1.5 block on the macroscopic system variable APD90 was dependent on the precise mechanism of block; and 3), open-channel block produced a reverse use-dependent prolongation of APD90. This study suggests that more-complex ion-channel models are a prerequisite for quantitative modeling of drug effects.
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| 9. |
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| 10. |
- Andersson, Magnus, et al.
(författare)
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Transport Pathway in Cu+ P-Type ATPases
- 2014
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Ingår i: Biophysical Journal. - : Elsevier BV. - 0006-3495 .- 1542-0086. ; 106:2, s. 427A-427A
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
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| 11. |
- Ashrafzadeh, Parham, et al.
(författare)
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Actin Filaments Attachment to the Plasma Membrane Cause the Formation of Ordered Lipid Domains in Live Cells
- 2014
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Ingår i: Biophysical Journal. - : Elsevier BV. - 0006-3495 .- 1542-0086. ; 106:2, s. 706A-706A
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- The aim of this study was to investigate the relationship between ordered plasma membrane nanodomains and actin filaments using di-4-ANEPPDHQ and laurdan together with the reagents that affect actin filament dynamics in live Jurkat and primary T cells. The degree of lipid packing can be quantified using polarity sensitive membrane dyes such as laurdan and di-4-ANEPPDHQ. These two dyes display a red shift in their emission peaks for membranes in ld phase relative to lo phase. Laurdan is uncharged and can easily flip between two leaflets of the plasma membrane and we demonstrate that it reports equally on the two leaflets of the plasma membrane.
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| 12. |
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| 13. |
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| 14. |
- Barrozo, Alexandre H., et al.
(författare)
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Understanding Functional Evolution in the Alkaline Phosphatase Superfamily
- 2014
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Ingår i: Biophysical Journal. - : Elsevier BV. - 0006-3495 .- 1542-0086. ; 106:2, s. 675A-675A
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Over the past 40 years, it has been demonstrated that many enzymes are capable of promiscuous catalytic activities, facilitating the turnover of more than one chemically distinct substrate. This has been argued to play an important role in enzyme evolution, with highly promiscuous progenitor enzymes evolving under evolutionary pressure to modern day specialists, while still retaining some level of their former promiscuous activities1. This theory has been extensively tested by different experiments using in vitro evolution2. The alkaline phosphatase superfamily members provide a particularly attractive showcase for studying enzyme promiscuity, as they often show reciprocal promiscuity, in that the native reaction for one member is often a side-reaction for another3. While deceptively similar, their catalyzed reactions (cleavage of P-O and S-O bonds) proceed via distinct transition states and protonation requirements4,5. We present detailed computational studies of the promiscuous catalytic activity of three evolutionarily related members: the arylsulfatase from Pseudomonas aeruginosa6, and the phosphonate monoester hydrolases from Burkholderia caryophili7and Rhizobium leguminosarum8. By tracking their structural and electrostatic features, and comparing to other known members of the superfamily, we provide an atomic-level map for functional evolution within this superfamily.
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| 15. |
- Beckham, Gregg T., et al.
(författare)
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The O-Glycosylated Linker from the Trichoderma reesei Family 7 Cellulase Is a Flexible, Disordered Protein
- 2010
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Ingår i: Biophysical Journal. - : Elsevier BV. - 0006-3495 .- 1542-0086. ; 99:11, s. 3773-3781
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Tidskriftsartikel (refereegranskat)abstract
- Fungi and bacteria secrete glycoprotein cocktails to deconstruct cellulose Cellulose degrading enzymes (cellulases) are often modular with catalytic domains for cellulose hydrolysis and carbohydrate binding modules connected by linkers rich in serine and threonine with O-glycosylation Few studies have probed the role that the linker and O-glycans play in catalysis Since different expression and growth conditions produce different glycosylation patterns that affect enzyme activity the structure function relationships that glycosylation imparts to linkers are relevant for understanding cellulase mechanisms Here the linker of the Trichoderma reesei Family 7 cellobiohydrolase (Cel7A) is examined by simulation Our results suggest that the Cel7A linker is an intrinsically disordered protein with and without glycosylation Contrary to the predominant view the O-glycosylation does not change the stiffness of the linker as measured by the relative fluctuations in the end to end distance rather it provides a 16 A extension thus expanding the operating range of Cel7A We explain observations from previous biochemical experiments in the light of results obtained here and compare the Cel7A linker with linkers from other cellulases with sequence based tools to predict disorder This preliminary screen indicates that linkers from Family 7 enzymes from other genera and other cellulases within T reesei may not be as disordered warranting further study
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| 16. |
- Behrens, Manja, et al.
(författare)
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The Shapes of Z-alpha(1)-Antitrypsin Polymers in Solution Support the C-Terminal Domain-Swap Mechanism of Polymerization
- 2014
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Ingår i: Biophysical Journal. - : Elsevier BV. - 1542-0086 .- 0006-3495. ; 107:8, s. 1905-1912
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Tidskriftsartikel (refereegranskat)abstract
- Emphysema and liver cirrhosis can be caused by the Z mutation (Glu342Lys) in the serine protease inhibitor alpha 1-antitrypsin (alpha 1AT), which is found in more than 4% of the Northern European population. Homozygotes experience deficiency in the lung concomitantly with a massive accumulation of polymers within hepatocytes, causing their destruction. Recently, it was proposed that Z-alpha 1AT polymerizes by a C-terminal domain swap. In this study, small-angle x-ray scattering (SAXS) was used to characterize Z-alpha 1AT polymers in solution. The data show that the Z-alpha 1AT trimer, tetramer, and pentamer all form ring-like structures in strong support of a common domain-swap polymerization mechanism that can lead to self-terminating polymers.
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| 17. |
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| 18. |
- Bengtsson, Elina, et al.
(författare)
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Actomyosin Interactions and Different Structural States of Actin Filaments
- 2013
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Ingår i: Biophysical Journal. - : Biophysical Society. - 0006-3495 .- 1542-0086. ; 104:2 Suppl. 1, s. 480A-481A
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- The persistence length (LP) of a polymer is proportional to its flexural rigidity and quantifies the decay length of its tangent angle (for a polymer freely suspended in solution). Further, it has been suggested that the decay length for the sliding direction of heavy meromyosin (HMM) propelled actin filaments in the in vitro motility assay (IVMA) is quantitatively identical to Lp of the free leading filament end. On this assumption we measured LP under different conditions to address a hypothesis that the actin filament exists in different metastable conformations, each characterized by a different flexural rigidity. The following values for Lp (mean 5 95 % confidence limits) were obtained: 1. with phalloidin (Ph) in solution: 12.61 5 0.65 mm (N=809). 2. without Phin solution: 9.07 5 1.06 mm (N=811), 3. with Ph and HMM in solution (rigor):10.21 5 0.75 mm (N=429), 4. without Ph (from IVMA paths; 1 mM MgATP):10.0850.66 mm (N=309), 5. with Ph, IVMA (1 mM MgATP): 11.41 5 0.57 mm (N=243), 6. with Ph, IVMA, 0.05 mM MgATP: 6.30 5 0.27 mm (N=383) and 7. without Ph, IVMA, 0.02-0.05 mM MgATP: 5.33 5 0.37 mm (N=161). The re-sults are consistent with different actin filament states where one is stabilized by phalloidin and one is favored by HMM binding and the absence of Ph. Effects of HMM are consistent with a possible role of the structural state of actin filaments in effective actomyosin motility. The very low LP found for IVMA at low [MgATP] (6-7) may reflect the presence of an actin filament state populated at low average cross-bridge strains, possibly with MgADP at the active site. Alternatively, it may be due to sideways forces produced by increased number of HMM-actin interactions close to the leading filament end.
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| 19. |
- Bengtsson, Elina, et al.
(författare)
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Winding Actin Filament Paths Provide Mechanistic Insights Into Actomyosin Function
- 2012
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Ingår i: Biophysical Journal. - : Biophysical Society. - 0006-3495 .- 1542-0086. ; 102:3 Suppl. 1, s. 146A-146A
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- The statistics of heavy meromyosin (HMM) driven actin filament paths in vitro, and thermal fluctuations of actin filaments suspended in a pseudo 2D-space in solution, can be described by the cosine correlation equation (CCE): = exp(-s/[2*Lp]). Here, q0) and qs) represent tangent angles at distance 0 and s, respectively from one filament end (in solution) or from the starting point of the path. The quantity Lp is the persistence length (proportional to flexural rigidity) of the filament/path. In vitro motility assay (IVMA) studies (27-29oC) were performed along with studies of actin filaments suspended between two cover-slips in solution. Fits to the CCE gave LP = 16.5 5 1.7 mm (mean 5 95 % confidence interval) and 11.1 5 0.6 mm for phalloidin stabilized filaments in solution and propelled by HMM, respectively. In contrast, phalloidin free actin filaments (NHS-rhodamine labeled) exhibited similar LP in solution 10.1 52.1 mm and during HMM propulsion (9.8 5 0.9 mm). The filament paths were modeled using a Monte-Carlo approach updating angular changes in sliding direction at short time intervals (dt) assuming 1. lateral displacements due to cross-bridge forces and 2. thermal fluctuations of the leading filament end. The results suggest that > 3nm average lateral displacement during each actomyosin interaction would reduce LP by > 30 % compared to that of filaments without HMM. The findings are consistent with the following ideas: 1. Actin filaments exist in two different flexural rigidity states, one favored by myosin binding and the other by phalloidin stabilization, 2. Changes in actin filament flexural rigidity is not required for motion generation. 3. The myosin cross-bridges produce minimal lateral movements (< 3 nm) during the power-stroke.
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| 20. |
- Bernado, Pau, et al.
(författare)
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Structure and Dynamics of Ribosomal Protein L12: An Ensemble Model Based on SAXS and NMR Relaxation
- 2010
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Ingår i: Biophysical Journal. - : Elsevier BV. - 1542-0086 .- 0006-3495. ; 98:10, s. 2374-2382
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Tidskriftsartikel (refereegranskat)abstract
- Ribosomal protein L12 is a two-domain protein that forms dimers mediated by its N-terminal domains. A 20-residue linker separates the N- and C-terminal domains. This linker results in a three-lobe topology with significant flexibility, known to be critical for efficient translation. Here we present an ensemble model of spatial distributions and correlation times for the domain reorientations of L12 that reconciles experimental data from small-angle x-ray scattering and nuclear magnetic resonance. We generated an ensemble of L12 conformations in which the structure of each domain is fixed but the domain orientations are variable. The ensemble reproduces the small-angle x-ray scattering data and the optimized correlation times of its reorientational eigenmodes fit the N-15 relaxation data. The ensemble model reveals intrinsic conformational properties of L12 that help explain its function on the ribosome. The two C-terminal domains sample a large volume and extend further away from the ribosome anchor than expected for a random-chain linker, indicating that the flexible linker has residual order. Furthermore, the distances between each C-terminal domain and the anchor are anticorrelated, indicating that one of them is more retracted on average. We speculate that these properties promote the function of L12 to recruit translation factors and control their activity on the ribosome.
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| 21. |
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| 22. |
- Bhattacherjee, Arnab, et al.
(författare)
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Coupled Folding-Binding in a Hydrophobic/Polar Protein Model: Impact of Synergistic Folding and Disordered Flanks
- 2012
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Ingår i: Biophysical Journal. - : Elsevier BV. - 1542-0086 .- 0006-3495. ; 102:3, s. 569-578
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Tidskriftsartikel (refereegranskat)abstract
- Coupled folding-binding is central to the function of many intrinsically disordered proteins, yet not fully understood. With a continuous three-letter protein model, we explore the free-energy landscape of pairs of interacting sequences and how it is impacted by 1), variations in the binding mechanism; and 2), the addition of disordered flanks to the binding region. In particular, we focus on two sequences, one with 16 and one with 35 amino acids, which make a stable dimeric three-helix bundle at low temperatures. Three distinct binding mechanisms are realized by altering the stabilities of the individual monomers: docking, coupled folding-binding of a single α-helix, and synergistic folding and binding. Compared to docking, the free-energy barrier for binding is reduced when the single α-helix is allowed to fold upon binding, but only marginally. A greater reduction is found for synergistic folding, which in addition results in a binding transition state characterized by very few interchain contacts. Disordered flanking chain segments attached to the α-helix sequence can, despite a negligible impact on the dimer stability, lead to a downhill free-energy surface in which the barrier for binding is eliminated.
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| 23. |
- Björklund, Sebastian, et al.
(författare)
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Skin membrane electrical impedance properties under the influence of a varying water gradient
- 2013
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Ingår i: Biophysical Journal. - : Elsevier. - 0006-3495 .- 1542-0086. ; 104:12, s. 2639-2650
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Tidskriftsartikel (refereegranskat)abstract
- The stratum corneum (SC) is an effective permeability barrier. One strategy to increase drug delivery across skin is to increase the hydration. A detailed description of how hydration affects skin permeability requires characterization of both macroscopic and molecular properties and how they respond to hydration. We explore this issue by performing impedance experiments on excised skin membranes in the frequency range 1 Hz to 0.2 MHz under the influence of a varying gradient in water activity (aw). Hydration/dehydration induces reversible changes of membrane resistance and effective capacitance. On average, the membrane resistance is 14 times lower and the effective capacitance is 1.5 times higher when the outermost SC membrane is exposed to hydrating conditions (aw ¼ 0.992), as compared to the case of more dehydrating conditions (aw ¼ 0.826). Molecular insight into the hydration effects on the SC components is provided by natural-abundance 13C polarization transfer solidstate NMR and x-ray diffraction under similar hydration conditions. Hydration has a significant effect on the dynamics of the keratin filament terminals and increases the interchain spacing of the filaments. The SC lipids are organized into lamellar structures with ~ 12.6 nm spacing and hexagonal hydrocarbon chain packing with mainly all-trans configuration of the acyl chains, irrespective of hydration state. Subtle changes in the dynamics of the lipids due to mobilization and incorporation of cholesterol and long-chain lipid species into the fluid lipid fraction is suggested to occur upon hydration, which can explain the changes of the impedance response. The results presented here provide information that is useful in explaining the effect of hydration on skin permeability.
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| 24. |
- Björnham, Oscar, 1976-, et al.
(författare)
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Catch-Bond behavior of bacteria binding by slip bonds
- 2010
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Ingår i: Biophysical Journal. - : Elsevier BV. - 0006-3495 .- 1542-0086. ; 99:5, s. 1331-1341
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Tidskriftsartikel (refereegranskat)abstract
- It is shown that multipili-adhering bacteria expressing helix-like pili binding by slip bonds can show catch-bond behavior. When exposed to an external force, such bacteria can mediate adhesion to their hosts by either of two limiting means: sequential or simultaneous pili force exposure (referring to when the pili mediate force in a sequential or simultaneous manner, respectively). As the force is increased, the pili can transition from sequential to simultaneous pili force exposure. Since the latter mode of adhesion gives rise to a significantly longer bacterial adhesion lifetime than the former, this results in a prolongation of the lifetime, which shows up as a catch-bond behavior. The properties and conditions of this effect were theoretically investigated and assessed in some detail for dual-pili-adhering bacteria, by both analytical means and simulations. The results indicate that the adhesion lifetime of such bacteria can be prolonged by more than an order of magnitude. This implies that the adhesion properties of multibinding systems cannot be directly conveyed to the individual adhesion-receptor bonds.
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| 25. |
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| 26. |
- Brandt, Erik G., et al.
(författare)
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Interpretation of Fluctuation Spectra in Lipid Bilayer Simulations
- 2011
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Ingår i: Biophysical Journal. - : Elsevier BV. - 0006-3495 .- 1542-0086. ; 100:9, s. 2104-2111
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Tidskriftsartikel (refereegranskat)abstract
- Atomic resolution and coarse-grained simulations of dimyristoylphosphatidylcholine lipid bilayers were analyzed for fluctuations perpendicular to the bilayer using a completely Fourier-based method. We find that the fluctuation spectrum of motions perpendicular to the bilayer can be decomposed into just two parts: 1), a pure undulation spectrum proportional to q(-4) that dominates in the small-q regime; and 2), a molecular density structure factor contribution that dominates in the large-q regime. There is no need for a term proportional to q(-2) that has been postulated for protrusion fluctuations and that appeared to have been necessary to fit the spectrum for intermediate q. We suggest that earlier reports of such a term were due to the artifact of binning and smoothing in real space before obtaining the Fourier spectrum. The observability of an intermediate protrusion regime from the fluctuation spectrum is discussed based on measured and calculated material constants.
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| 27. |
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| 28. |
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| 29. |
- Braun, Anthony R., et al.
(författare)
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Determination of Electron Density Profiles and Area from Simulations of Undulating Membranes
- 2011
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Ingår i: Biophysical Journal. - : Elsevier BV. - 0006-3495 .- 1542-0086. ; 100:9, s. 2112-2120
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Tidskriftsartikel (refereegranskat)abstract
- The traditional method for extracting electron density and other transmembrane profiles from molecular dynamics simulations of lipid bilayers fails for large bilayer systems, because it assumes a flat reference surface that does not take into account long wavelength undulations. We have developed what we believe to be a novel set of methods to characterize these undulations and extract the underlying profiles in the large systems. Our approach first obtains an undulation reference surface for each frame in the simulation and subsequently isolates the long-wavelength undulations by filtering out the intrinsic short wavelength modes. We then describe two methods to obtain the appropriate profiles from the undulating reference surface. Most combinations of methods give similar results for the electron density profiles of our simulations of 1024 DMPC lipids. From simulations of smaller systems, we also characterize the finite size effect related to the boundary conditions of the simulation box. In addition, we have developed a set of methods that use the undulation reference surface to determine the true area per lipid which, due to undulations, is larger than the projected area commonly reported from simulations.
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| 30. |
- Brorsson, Ann-Christin, et al.
(författare)
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Intrinsic determinants of neurotoxic aggregate formation by the amyloid beta peptide
- 2010
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Ingår i: Biophysical Journal. - : Elsevier BV. - 0006-3495 .- 1542-0086. ; 98:8, s. 1677-84
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Tidskriftsartikel (refereegranskat)abstract
- The extent to which proteins aggregate into distinct structures ranging from prefibrillar oligomers to amyloid fibrils is key to the pathogenesis of many age-related degenerative diseases. We describe here for the Alzheimer's disease-related amyloid beta peptide (Abeta) an investigation of the sequence-based determinants of the balance between the formation of prefibrillar aggregates and amyloid fibrils. We show that by introducing single-point mutations, it is possible to convert the normally harmless Abeta40 peptide into a pathogenic species by increasing its relative propensity to form prefibrillar but not fibrillar aggregates, and, conversely, to abolish the pathogenicity of the highly neurotoxic E22G Abeta42 peptide by reducing its relative propensity to form prefibrillar species rather than mature fibrillar ones. This observation can be rationalized by the demonstration that whereas regions of the sequence of high aggregation propensity dominate the overall tendency to aggregate, regions with low intrinsic aggregation propensities exert significant control over the balance of the prefibrillar and fibrillar species formed, and therefore play a major role in determining the neurotoxicity of the Abeta peptide.
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| 31. |
- Brändén, Magnus, 1971, et al.
(författare)
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Refractive-Index-Based Screening of Membrane-Protein-Mediated Transfer across Biological Membranes
- 2010
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Ingår i: Biophysical Journal. - : Elsevier BV. - 0006-3495 .- 1542-0086. ; 99:1, s. 124-133
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Tidskriftsartikel (refereegranskat)abstract
- Numerous membrane-transport proteins are major drug targets, and therefore a key ingredient in pharmaceutical development is the availability of reliable, efficient tools for membrane transport characterization and inhibition. Here, we present the use of evanescent-wave sensing for screening of membrane-protein-mediated transport across lipid bilayer membranes. This method is based on a direct recording of the temporal variations in the refractive index that occur upon a transfer-dependent change in the solute concentration inside liposomes associated to a surface plasmon resonance (SPR) active sensor surface. The applicability of the method is demonstrated by a functional study of the aquaglyceroporin PfAQP from the malaria parasite Plasmodium falciparum. Assays of the temperature dependence of facilitated diffusion of sugar alcohols on a single set of PfAQP-reconstituted liposomes reveal that the activation energies for facilitated diffusion of xylitol and sorbitol are the same as that previously measured for glycerol transport in the aquaglyceroporin of Escherichia coli (5 kcal/mole). These findings indicate that the aquaglyceroporin selectivity filter does not discriminate sugar alcohols based on their length, and that the extra energy cost of dehydration of larger sugar alcohols, upon entering the pore, is compensated for by additional hydrogen-bond interactions within the aquaglyceroporin pore.
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| 32. |
- Börjesson, Sara, et al.
(författare)
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Electrostatic Tuning of Cellular Excitability
- 2010
-
Ingår i: Biophysical Journal. - : Elsevier BV. - 0006-3495 .- 1542-0086. ; 98:3, s. 396-403
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Tidskriftsartikel (refereegranskat)abstract
- Voltage-gated ion channels regulate the electric activity of excitable tissues, such as the heart and brain. Therefore, treatment for conditions of disturbed excitability is often based on drugs that target ion channels. In this study of a voltage-gated K channel, we propose what we believe to be a novel pharmacological mechanism for how to regulate channel activity. Charged lipophilic substances can tune channel opening, and consequently excitability, by an electrostatic interaction with the channels voltage sensors. The direction of the effect depends on the charge of the substance. This was shown by three compounds sharing an arachiclonyl backbone but bearing different charge: arachidonic acid, methyl arachidonate, and arachidonyl amine. Computer simulations of membrane excitability showed that small changes in the voltage dependence of Na and K channels have prominent impact on excitability and the tendency for repetitive firing. For instance, a shift in the voltage dependence of a K channel with -5 or +5 mV corresponds to a threefold increase or decrease in K channel density, respectively. We suggest that electrostatic tuning of ion channel activity constitutes a novel and powerful pharmacological approach with which to affect cellular excitability.
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| 33. |
- Cans, Ann-Sofie, 1971, et al.
(författare)
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A Secretory Artificial Cell for Exocytosis
- 2013
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Ingår i: Biophysical Journal. - : Elsevier BV. - 0006-3495 .- 1542-0086. ; 104:2 Suppl 1
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- The complexity of exocytosis has left the molecular details of the process unclear. We present a minimal, artificial secretory cell designed for amperometric studies of release of signalling molecules through the fusion pore of single vesicles. In replacement of SNARE-proteins, the cell model has been equipped with an analog composed of complimentary DNA constructs, one on the vesicle and one on the target membrane. The DNA constructs hybridize in a zipper-like fashion bringing about docking of the vesicles and following the addition of Ca2+, fusion of the vesicles is completed. Exocytotic events recorded from the artificial cell closely approximate exocytosis in live cells. The results together with simulations of vesicular release demonstrate that the lipid-based fusion pore initially retains stability and limits diffusion of the secreted molecules.
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| 34. |
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| 35. |
- Christiansen, Alexander, 1982-, et al.
(författare)
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Quantification of excluded volume effects on the folding landscape of Pseudomonas aeruginosa Apoazurin In Vitro
- 2013
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Ingår i: Biophysical Journal. - : Elsevier. - 0006-3495 .- 1542-0086. ; 105:7, s. 1689-1699
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Tidskriftsartikel (refereegranskat)abstract
- Proteins fold and function inside cells that are crowded with macromolecules. Here, we address the role of the resulting excluded volume effects by in vitro spectroscopic studies of Pseudomonas aeruginosa apoazurin stability (thermal and chemical perturbations) and folding kinetics (chemical perturbation) as a function of increasing levels of crowding agents dextran (sizes 20, 40, and 70 kDa) and Ficoll 70. We find that excluded volume theory derived by Minton quantitatively captures the experimental effects when crowding agents are modeled as arrays of rods. This finding demonstrates that synthetic crowding agents are useful for studies of excluded volume effects. Moreover, thermal and chemical perturbations result in free energy effects by the presence of crowding agents that are identical, which shows that the unfolded state is energetically the same regardless of method of unfolding. This also underscores the two-state approximation for apoazurin’s unfolding reaction and suggests that thermal and chemical unfolding experiments can be used in an interchangeable way. Finally, we observe increased folding speed and invariant unfolding speed for apoazurin in the presence of macromolecular crowding agents, a result that points to unfolded-state perturbations. Although the absolute magnitude of excluded volume effects on apoazurin is only on the order of 1–3 kJ/mol, differences of this scale may be biologically significant.
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| 42. |
- Elf, Johan
(författare)
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Direct Measurements of Transcription Factor Binding and Dissociation at Individual Chromosomal Operators
- 2014
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Ingår i: Biophysical Journal. - : Elsevier BV. - 0006-3495 .- 1542-0086. ; 106:2, s. 444A-444A
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- I will discuss some of our recent progress in studying transcription factor kinetics at the level of individual molecules in E. coli. I will in particular describe an assay for measuring the rate of dissociation for a LacI repressor from an individual chromosomal operator site. When combined with the corresponding association rate measurement, the assay allows us to test the commonly used assumption that TF kinetics can be considered to be at equilibrium and that the gene expression is proportional to the time the operator is free .
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| 43. |
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| 44. |
- Fabry, Ben, et al.
(författare)
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Focal adhesion kinase stabilizes the cytoskeleton.
- 2011
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Ingår i: Biophysical Journal. - : Elsevier BV. - 0006-3495 .- 1542-0086. ; 101:9, s. 2131-8
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Tidskriftsartikel (refereegranskat)abstract
- Focal adhesion kinase (FAK) is a central focal adhesion protein that promotes focal adhesion turnover, but the role of FAK for cell mechanical stability is unknown. We measured the mechanical properties of wild-type (FAKwt), FAK-deficient (FAK-/-), FAK-silenced (siFAK), and siControl mouse embryonic fibroblasts by magnetic tweezer, atomic force microscopy, traction microscopy, and nanoscale particle tracking microrheology. FAK-deficient cells showed lower cell stiffness, reduced adhesion strength, and increased cytoskeletal dynamics compared to wild-type cells. These observations imply a reduced stability of the cytoskeleton in FAK-deficient cells. We attribute the reduced cytoskeletal stability to rho-kinase activation in FAK-deficient cells that suppresses the formation of ordered stress fiber bundles, enhances cortical actin distribution, and reduces cell spreading. In agreement with this interpretation is that cell stiffness and cytoskeletal stability in FAK-/- cells is partially restored to wild-type level after rho-kinase inhibition with Y27632.
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| 45. |
- Fange, David, et al.
(författare)
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Thermodynamic Modeling of Variations in the Rate of RNA Chain Elongation of E-coli rrn Operons
- 2014
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Ingår i: Biophysical Journal. - : Elsevier BV. - 0006-3495 .- 1542-0086. ; 106:1, s. 55-64
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Tidskriftsartikel (refereegranskat)abstract
- Previous electron-microscopic imaging has shown high RNA polymerase occupation densities in the 16S and 23S encoding regions and low occupation densities in the noncoding leader, spacer, and trailer regions of the rRNA (rrn) operons in E. coli. This indicates slower transcript elongation within the coding regions and faster elongation within the noncoding regions of the operon. Inactivation of four of the seven rrn operons increases the transcript initiation frequency at the promoters of the three intact operons and reduces the time for RNA polymerase to traverse the operon. We have used the DNA sequence-dependent standard free energy variation of the transcription complex to model the experimentally observed changes in the elongation rate along the rrnB operon. We also model the stimulation of the average transcription rate over the whole operon by increasing rate of transcript initiation. Monte Carlo simulations, taking into account initiation of transcription, translocation, and backward and forward tracking of RNA polymerase, partially reproduce the observed transcript elongation rate variations along the rrn operon and fully account for the increased average rate in response to increased frequency of transcript initiation.
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| 46. |
- Flores, Samuel C.
(författare)
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Elucidating Ribosomal Translocation with Internal Coordinate Flexible Fitting
- 2014
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Ingår i: Biophysical Journal. - : Elsevier BV. - 0006-3495 .- 1542-0086. ; 106:2, s. 492A-493A
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Determining conformational changes of large macromolecules is challenging experimentally and computationally. The ribosome has been observed crystallographically in several states but many others have been seen only by low-resolution methods including cryo-electron microscopy. Meanwhile the crucial dynamics between states remain out of reach of experimental structure determination methods. Most existing computational approaches model complexes at all-atom resolution, at very high cost, or use approximations which lose some of the most interesting dynamical details. I have developed Internal Coordinate Flexible Fitting (ICFF), a multiscale method that uses full atomic forces and flexibility only in key regions of a model, capturing extensive conformational rearrangements at low cost. I use ICFF to turn low-resolution density maps, crystallographic structures, and biochemical information into the largest-scale all-atoms trajectory of ribosomal translocation modeled to date. ICFF is three orders of magnitude faster than the most comparable existing method. The results suggest an intriguing possible mechanism of translocation.
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| 47. |
- Fornander, Louise Helena, et al.
(författare)
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Using Nanofluidic Channels to Probe the Dynamics of Rad51-DNA Filaments
- 2014
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Ingår i: Biophysical Journal. - : Elsevier BV. - 0006-3495 .- 1542-0086. ; 106:2, s. 692A-693A
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Rad51 is a key protein involved in the strand exchange reaction, a reaction where genetic material is transferred between two homologous DNA strands. Strand exchange is initiated by Rad51 forming a helical filament around single-stranded DNA (ssDNA), and the strand exchange is thereafter executed with a homologous double-stranded DNA (dsDNA). The structure of Rad51-DNA filaments, and also the activity of the strand exchange reaction, is dependent on the presence of ATP and dications, where Ca2+ has been shown to promote a higher degree of strand exchange than Mg2+.
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| 48. |
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| 49. |
- Franco-Gonzalez, Juan F., et al.
(författare)
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Protein-Protein and Protein-Membrane Interactions Regarding the Erbb2/Trastuzumab-Fab Complexes. A Coarse-Grained Molecular Dynamics Description
- 2014
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Ingår i: Biophysical Journal. - : Elsevier BV. - 0006-3495 .- 1542-0086. ; 106:2, s. 666-667
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Tidskriftsartikel (refereegranskat)abstract
- ErbB2 is a member of epidermal growth factor receptor (EGFR) family and is overexpressed in many cancers. Specifically, Trastuzumab, which is a monoclonal antibody, is used against ErbB2, but its action mechanism is still unknown. ErbB2 can exist as both monomers and Homodimers, suggesting that Trastuzumab mechanims may be subtle. On the other hand, the membrane plays a role in the action mechanism of Trastuzumab but generates difficulties for structural studies. Coarse-Grained Molecular Dynamics has been used to study the influence of the Trastuzumab on the protein-protein and protein-membrane interactions of the full ErbB2 receptor. Our simulations start from conformations which both extracelullar and intracelullar domains are extended. The results show in both monomers and homodimers systems a folded conformation on the membrane: several experimental results, mainly obtained on ErbB1 support them. The protein-protein interaction on transmembrane and juxtamembrane domains are disrupted on the dimer and disordered on the monomer by the Trastuzumab effect, therefore, the dimerization-driven activation are unfavourable. We present a detailed description of the type of interactions governing the homodimerization and antobody complexation phenomena and the role that the membrane plays on that.
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| 50. |
- Frykholm, Karolin, et al.
(författare)
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Probing Physical Properties of a DNA-Protein Complex Using Nanofluidic Channels
- 2014
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Ingår i: Biophysical Journal. - : Elsevier BV. - 0006-3495 .- 1542-0086. ; 106:2, s. 428A-429A
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Nanofluidic channels have become an important tool to investigate single DNA molecules both from a fundamental polymer physics perspective as well as in e.g. optical mapping techniques. However, less effort has been made to study DNA-protein complexes. A main reason is that the extreme surface-to-volume ratio in the nanochannels causes most proteins to stick to the channel walls. We have recently overcome this problem by coating the channels with a lipid bilayer, thereby eliminating sticking.
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