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  • 1.
    Adler, Jeremy
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Cancer and Vascular Biology.
    Parmryd, Ingela
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Cell Biology.
    Quantification of Colocalisation; Co-Occurrence, Correlation, Empty Voxels, Regions of Interest and Thresholding2014In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 106, no 2, p. 602A-602AArticle in journal (Other academic)
    Abstract [en]

    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.

  • 2.
    Ahlinder, Linnea
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Solid State Physics.
    Ekstrand-Hammarstrom, Barbro
    Geladi, Paul
    Österlund, Lars
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Solid State Physics.
    Large Uptake of Titania and Iron Oxide Nanoparticles in the Nucleus of Lung Epithelial Cells as Measured by Raman Imaging and Multivariate Classification2013In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 105, no 2, p. 310-319Article in journal (Refereed)
    Abstract [en]

    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.

  • 3. Alizadehheidari, Mohammadreza
    et al.
    Werner, Erik
    Noble, Charleston
    Nyberg, Lena
    Fritzsche, Joachim
    Mehlig, Bernhard
    Tegenfeldt, Jonas
    Ambjoernsson, Tobias
    Persson, Fredrik
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
    Westerlund, Fredrik
    Nanoconfined Circular DNA2014In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 106, no 2, p. 274A-274AArticle in journal (Other academic)
    Abstract [en]

    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.

  • 4.
    Alizadehheidari, Mohammadreza
    et al.
    Chalmers, Biol & Biol Engn, S-41296 Gothenburg, Sweden..
    Werner, Erik
    Gothenburg Univ, Phys, Gothenburg, Sweden..
    Noble, Charleston
    Lund Univ, Phys, Lund, Sweden..
    Nyberg, Lena
    Chalmers, Biol & Biol Engn, S-41296 Gothenburg, Sweden..
    Fritzsche, Joachim
    Chalmers, Appl Phys, S-41296 Gothenburg, Sweden..
    Persson, Fredrik
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Mehlig, Bernhard
    Gothenburg Univ, Phys, Gothenburg, Sweden..
    Tegenfeldt, Jonas
    Lund Univ, Solid State Phys, Gothenburg, Sweden..
    Ambjornsson, Tobias
    Lund Univ, Phys, Lund, Sweden..
    Westerlund, Fredrik
    Chalmers, Biol & Biol Engn, S-41296 Gothenburg, Sweden..
    Unfolding of Nanoconfined Circular DNA2015In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 108, no 2, p. 231A-231AArticle in journal (Other academic)
  • 5.
    Almaqwashi, Ali A.
    et al.
    Northeastern Univ, Dept Phys, Boston, MA 02115 USA..
    Andersson, Johanna
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC. Chalmers, Dept Chem & Chem Engn, S-41296 Gothenburg, Sweden..
    Lincoln, Per
    Chalmers, Dept Chem & Chem Engn, S-41296 Gothenburg, Sweden..
    Rouzina, Ioulia
    Ohio State Univ, Dept Chem & Biochem, Columbus, OH 43210 USA..
    Westerlund, Fredrik
    Chalmers, Dept Biol & Biol Engn, S-41296 Gothenburg, Sweden..
    Williams, Mark C.
    Northeastern Univ, Dept Phys, Boston, MA 02115 USA..
    Dissecting the Dynamic Pathways of Stereoselective DNA Threading Intercalation2016In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 110, no 6, p. 1255-1263Article in journal (Refereed)
    Abstract [en]

    DNA intercalators that have high affinity and slow kinetics are developed for potential DNA-targeted therapeutics. Although many natural intercalators contain multiple chiral subunits, only intercalators with a single chiral unit have been quantitatively probed. Dumbbell-shaped DNA threading intercalators represent the next order of structural complexity relative to simple intercalators, and can provide significant insights into the stereoselectivity of DNA-ligand intercalation. We investigated DNA threading intercalation by binuclear ruthenium complex [mu-dppzip(phen)(4)Ru-2](4+) (Piz). Four Piz stereoisomers are defined by the chirality of the intercalating subunit (Ru(phen)(2)dppz) and the distal subunit (Ru(phen)(2)ip), respectively, each of which can be either right-handed (Delta) or left-handed (Lambda). We used optical tweezers to measure single DNA molecule elongation due to threading intercalation, revealing force-dependent DNA intercalation rates and equilibrium dissociation constants. The force spectroscopy analysis provided the zero-force DNA binding affinity, the equilibrium DNA-ligand elongation Delta x(eq), and the dynamic DNA structural deformations during ligand association x(on) and dissociation x(off). We found that Piz stereoisomers exhibit over 20-fold differences in DNA binding affinity, from a K-d of 27 +/- 3 nM for (Delta,Lambda)-Piz to a K-d of 622 +/- 55 nM for (Lambda,Delta)-Piz. The striking affinity decrease is correlated with increasing Delta x(eq) from 0.30 +/- 0.02 to 0.48 +/- 0.02 nm and x(on) from 0.25 +/- 0.01 to 0.46 +/- 0.02 nm, but limited x(off) changes. Notably, the affinity and threading kinetics is 10-fold enhanced for right-handed intercalating subunits, and 2- to 5-fold enhanced for left-handed distal subunits. These findings demonstrate sterically dispersed transition pathways and robust DNA structural recognition of chiral intercalators, which are critical for optimizing DNA binding affinity and kinetics.

  • 6.
    Almaqwashi, Ali A.
    et al.
    Northeastern Univ, Dept Phys, Boston, MA 02115 USA..
    Andersson, Johanna
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC. Chalmers, Dept Chem & Biol Engn, S-41296 Gothenburg, Sweden..
    Lincoln, Per
    Chalmers, Dept Chem & Biol Engn, S-41296 Gothenburg, Sweden..
    Rouzina, Ioulia
    Univ Minnesota, Dept Biochem Mol Biol & Biophys, Minneapolis, MN USA..
    Westerlund, Fredrik
    Chalmers, Dept Chem & Biol Engn, S-41296 Gothenburg, Sweden..
    Williams, Mark C.
    Northeastern Univ, Dept Phys, Boston, MA 02115 USA..
    Resolving the DNA Binding Mode of a Rotationally Flexible Binuclear Ruthenium Complex2015In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 108, no 2, p. 396A-396AArticle in journal (Other academic)
  • 7.
    Amselem, Elias
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Systems Biology.
    Marklund, Emil
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Systems Biology.
    Kipper, Kalle
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Johansson, Magnus
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Systems Biology.
    Deindl, Sebastian
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Systems Biology.
    Elf, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Systems Biology.
    Real- Time Single Protein Tracking with Polarization Readout using a Confocal Microscope2017In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 112, no 3, p. 295A-295AArticle in journal (Other academic)
  • 8.
    Andér, Martin
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structural Molecular Biology.
    Luzhkov, Victor B.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Åqvist, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structural Molecular Biology.
    Ligand binding to the voltage-gated Kv1.5 potassium channel in the open state - Docking and computer simulations of a homology model2008In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 94, no 3, p. 820-831Article in journal (Refereed)
    Abstract [en]

    The binding of blockers to the human voltage-gated Kv1.5 potassium ion channel is investigated using a three-step procedure consisting of homology modeling, automated docking, and binding free energy calculations from molecular dynamics simulations, in combination with the linear interaction energy method. A reliable homology model of Kv1.5 is constructed using the recently published crystal structure of the Kv1.2 channel as a template. This model is expected to be significantly more accurate than earlier ones based on less similar templates. Using the three-dimensional homology model, a series of blockers with known affinities are docked into the cavity of the ion channel and their free energies of binding are calculated. The predicted binding free energies are in very good agreement with experimental data and the binding is predicted to be mainly achieved through nonpolar interactions, whereas the relatively small differences in the polar contribution determine the specificity. Apart from confirming the importance of residues V505, I508, V512, and V516 for ligand binding in the cavity, the results also show that A509 and P513 contribute significantly to the nonpolar binding interactions. Furthermore, we find that pharmacophore models based only on optimized free ligand conformations may not necessarily capture the geometric features of ligands bound to the channel cavity. The calculations herein give a detailed structural and energetic picture of blocker binding to Kv1.5 and this model should thus be useful for further ligand design efforts.

  • 9.
    Ashrafzadeh, Parham
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Cell Biology.
    Dinic, Jelena
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Cell Biology.
    Parmryd, Ingela
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Cell Biology.
    Actin Filaments Attachment to the Plasma Membrane Cause the Formation of Ordered Lipid Domains in Live Cells2014In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 106, no 2, p. 706A-706AArticle in journal (Other academic)
    Abstract [en]

    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.

  • 10.
    Badell, Maria Valldeperas
    et al.
    Lund Univ, Phys Chem, Lund, Sweden.;Lund Univ, NanoLund, Lund, Sweden..
    Dabkowska, Aleksandra
    Lund Univ, Phys Chem, Lund, Sweden.;Lund Univ, NanoLund, Lund, Sweden..
    Naidjonoka, Polina
    Lund Univ, Phys Chem, Lund, Sweden..
    Welbourn, Rebecca
    Rutherford Appleton Lab, STFC, ISIS Neutron & Muon Source, Didcot, Oxon, England..
    Pålsson, Gunnar K.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Physics. Inst Laue Langevin, Grenoble, France..
    Barauskas, Justas
    Camurus AB, Lund, Sweden.;Malmo Univ, Biomed Sci, Malmo, Sweden..
    Nylander, Tommy
    Lund Univ, Phys Chem, Lund, Sweden.;Lund Univ, NanoLund, Lund, Sweden..
    Lipid Sponge-Phase Nanoparticles as Carriers for Enzymes2018In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 114, no 3, p. 15A-15AArticle in journal (Other academic)
  • 11.
    Barg, Sebastian
    et al.
    Department of Molecular and Cellular Physiology, Institute of Physiological Sciences, Lund University, Lund.
    Ma, Xiaosong
    Department of Molecular and Cellular Physiology, Institute of Physiological Sciences, Lund University, Lund.
    Eliasson, Lena
    Department of Molecular and Cellular Physiology, Institute of Physiological Sciences, Lund University, Lund.
    Galvanovskis, Juris
    Department of Molecular and Cellular Physiology, Institute of Physiological Sciences, Lund University, Lund.
    Göpel, Sven O
    Department of Molecular and Cellular Physiology, Institute of Physiological Sciences, Lund University, Lund.
    Obermüller, Stefanie
    Department of Molecular and Cellular Physiology, Institute of Physiological Sciences, Lund University, Lund.
    Platzer, Josef
    Institut für Biochemische Pharmakologie, Innsbruck.
    Renström, Erik
    Department of Molecular and Cellular Physiology, Institute of Physiological Sciences, Lund University, Lund.
    Trus, Michel
    Department of Biological Chemistry, The Hebrew University of Jerusalem.
    Atlas, Daphne
    Department of Biological Chemistry, The Hebrew University of Jerusalem.
    Striessnig, Jörg
    Institut für Biochemische Pharmakologie, Innsbruck.
    Rorsman, Patrik
    Department of Molecular and Cellular Physiology, Institute of Physiological Sciences, Lund University, Lund.
    Fast exocytosis with few Ca(2+) channels in insulin-secreting mouse pancreatic B cells2001In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 81, no 6, p. 3308-23Article in journal (Refereed)
    Abstract [en]

    The association of L-type Ca(2+) channels to the secretory granules and its functional significance to secretion was investigated in mouse pancreatic B cells. Nonstationary fluctuation analysis showed that the B cell is equipped with <500 alpha1(C) L-type Ca(2+) channels, corresponding to a Ca(2+) channel density of 0.9 channels per microm(2). Analysis of the kinetics of exocytosis during voltage-clamp depolarizations revealed an early component that reached a peak rate of 1.1 pFs(-1) (approximately 650 granules/s) 25 ms after onset of the pulse and is completed within approximately 100 ms. This component represents a subset of approximately 60 granules situated in the immediate vicinity of the L-type Ca(2+) channels, corresponding to approximately 10% of the readily releasable pool of granules. Experiments involving photorelease of caged Ca(2+) revealed that the rate of exocytosis was half-maximal at a cytoplasmic Ca(2+) concentration of 17 microM, and concentrations >25 microM are required to attain the rate of exocytosis observed during voltage-clamp depolarizations. The rapid component of exocytosis was not affected by inclusion of millimolar concentrations of the Ca(2+) buffer EGTA but abolished by addition of exogenous L(C753-893), the 140 amino acids of the cytoplasmic loop connecting the 2(nd) and 3(rd) transmembrane region of the alpha1(C) L-type Ca(2+) channel, which has been proposed to tether the Ca(2+) channels to the secretory granules. In keeping with the idea that secretion is determined by Ca(2+) influx through individual Ca(2+) channels, exocytosis triggered by brief (15 ms) depolarizations was enhanced 2.5-fold by the Ca(2+) channel agonist BayK8644 and 3.5-fold by elevating extracellular Ca(2+) from 2.6 to 10 mM. Recordings of single Ca(2+) channel activity revealed that patches predominantly contained no channels or many active channels. We propose that several Ca(2+) channels associate with a single granule thus forming a functional unit. This arrangement is important in a cell with few Ca(2+) channels as it ensures maximum usage of the Ca(2+) entering the cell while minimizing the influence of stochastic variations of the Ca(2+) channel activity.

  • 12.
    Barrozo, Alexandre H.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
    Harnessing Promiscuity Patterns to Map Evolution in the Alkaline Phosphatase Superfamily2013In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 104, no 2, p. 232A-232AArticle in journal (Other academic)
  • 13.
    Barrozo, Alexandre H.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
    Carvalho, Alexandra Pires
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
    Understanding Functional Evolution in the Alkaline Phosphatase Superfamily2014In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 106, no 2, p. 675A-675AArticle in journal (Other academic)
    Abstract [en]

    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.

  • 14. Basanez, G
    et al.
    RuizArguello, MB
    Alonso, A
    Goni, FM
    Karlsson, Göran
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical Chemistry.
    Edwards, Katarina
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical Chemistry.
    Morphological changes induced by phospholipase C and by sphingomyelinase on large unilamellar vesicles: a cryo-transmission electron microscopy study of liposome fusion.1997In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 72, no 6, p. 2630-2637Article in journal (Refereed)
    Abstract [en]

    Cryo-transmission electron microscopy has been applied to the study of the changes induced by phospholipase C on large unilamellar vesicles containing phosphatidylcholine, as well as to the action of sphingomyelinase on vesicles containing sphingomyelin. In both cases vesicle aggregation occurs as the earliest detectable phenomenon; later, each system behaves differently. Phospholipase C induces vesicle fusion through an intermediate consisting of aggregated and closely packed vesicles (the ''honeycomb structure'') that finally transforms into large spherical vesicles. The same honeycomb structure is also observed in the absence of enzyme when diacylglycerols are mixed with the other lipids in organic solution, before hydration. In this case the sample then evolves toward a cubic phase. The fact that the same honeycomb intermediate can lead to vesicle fusion (with enzyme-generated diacylglycerol) or to a cubic phase (when diacylglycerol is premixed with the lipids) is taken in support of the hypothesis according to which a highly curved lipid structure (''stalk'') would act as a structural intermediate in membrane fusion, Sphingomyelinase produces complete leakage of vesicle aqueous contents and an increase in size of about one-third of the vesicles. A mechanism of vesicle opening and reassembling is proposed in this case.

  • 15. Beugin, S
    et al.
    Edwards, Katarina
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical Chemistry.
    Karlsson, Göran
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical Chemistry.
    Ollivon, M
    Lesieur, S
    New sterically stabilized vesicles based on nonionic surfactant, cholesterol, and poly(ethylene glycol)-cholesterol conjugates.1998In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 74, no 6, p. 3198-3210Article in journal (Other academic)
    Abstract [en]

    Monomethoxypoly(ethylene glycol) cholesteryl carbonates (M-PEG-Chol) with polymer chain molecular weights of 1000 (M-PEG1000-Chol) and 2000 (M-PEG2000-Chol) have been newly synthesized and characterized. Their aggregation behavior in mixture with diglycerol hexadecyl ether (C(16)G(2)) and cholesterol has been examined by cryotransmission electron microscopy, high-performance gel exclusion chromatography, and quasielastic light scattering. Nonaggregated, stable, unilamellar vesicles were obtained at low polymer levels with optimal shape and size homogeneity at cholesteryl conjugate/ lipids ratios of 10 mol% M-PEG1000-Chol or 5 mol% M-PEG2000-Chol, corresponding to the theoretically predicted brush conformational state of the PEG chains. At 20 mol% M-PEG1000-Chol or 10 mol% M-PEG2000-Chol, the saturation threshold of the C(16)G(2)/cholesterol membrane in polymer is exceeded, and open disk-shaped aggregates are seen in coexistence with closed vesicles. Higher levels up to 30 mol% lead to the complete solubilization of the vesicles into disk-like structures of decreasing size with increasing PEG content. This study underlines the bivalent role of M-PEG-Chol derivatives: while behaving as solubilizing surfactants, they provide an efficient steric barrier, preventing the vesicles from aggregation and fusion over a period of at least 2 weeks.

  • 16.
    Caban, Kelvin
    et al.
    Columbia Univ, Dept Chem, New York, NY 10027 USA..
    Pavlov, Michael
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Biology.
    Kaledhonkar, Sandip
    Columbia Univ, Dept Biochem & Mol Biophys, New York, NY USA..
    Fu, Ziao
    Columbia Univ, Dept Biochem & Mol Biophys, New York, NY USA..
    Frank, Joachim
    Columbia Univ, Dept Biochem & Mol Biophys, New York, NY USA.;Columbia Univ, Dept Biol Sci, New York, NY 10027 USA..
    Ehrenberg, Måns
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Biology.
    Gonzalez, Ruben L., Jr.
    Columbia Univ, Dept Chem, New York, NY 10027 USA..
    The Structural Basis for Initiation Factor 2 Activation during Translation Initiation2018In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 114, no 3, p. 593A-593AArticle in journal (Other academic)
  • 17.
    Choi, Junhong
    et al.
    Stanford Univ, Appl Phys, Stanford, CA 94305 USA..
    Indrisiunaite, Gabriele
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Biology.
    DeMirci, Hasan
    SLAC Natl Accelerator Lab, Menlo Pk, CA USA..
    Ieong, Ka-Weng
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Biology.
    Wang, Jinfan
    Stanford Univ, Stanford, CA 94305 USA..
    Petrov, Alexey
    Stanford Univ, Stanford, CA 94305 USA..
    Prabhakar, Arjun
    Stanford Univ, Stanford, CA 94305 USA..
    Rechavi, Gideon
    Chaim Sheba Med Ctr, Canc Res Ctr, Tel Hashomer, Israel.;Tel Aviv Univ, Tel Aviv, Israel..
    Dominissini, Dan
    Tel Aviv Univ, Tel Aviv, Israel.;Chaim Sheba Med Ctr, Tel Hashomer, Israel..
    He, Chuan
    Univ Chicago, Chicago, IL 60637 USA..
    Ehrenberg, Måns
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Biology.
    Puglisi, Joseph D.
    Stanford Univ, Stanford, CA 94305 USA..
    How 2 '-O-Methylation in mRNA Disrupts tRNA Decoding during Translation Elongation2018In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 114, no 3, p. 592A-592AArticle in journal (Other academic)
  • 18. Copello, J A
    et al.
    Barg, S
    Onoue, H
    Fleischer, S
    Heterogeneity of Ca2+ gating of skeletal muscle and cardiac ryanodine receptors.1997In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 73, no 1, p. 141-56Article in journal (Refereed)
    Abstract [en]

    The single-channel activity of rabbit skeletal muscle ryanodine receptor (skeletal RyR) and dog cardiac RyR was studied as a function of cytosolic [Ca2+]. The studies reveal that for both skeletal and cardiac RyRs, heterogeneous populations of channels exist, rather than a uniform behavior. Skeletal muscle RyRs displayed two extremes of behavior: 1) low-activity RyRs (LA skeletal RyRs, approximately 35% of the channels) had very low open probability (Po < 0.1) at all [Ca2+] and remained closed in the presence of Mg2+ (2 mM) and ATP (1 mM); 2) high-activity RyRs (HA skeletal RyRs) had much higher activity and displayed further heterogeneity in their Po values at low [Ca2+] (< 50 nM), and in their patterns of activation by [Ca2+]. Hill coefficients for activation (nHa) varied from 0.8 to 5.2. Cardiac RyRs, in comparison, behaved more homogeneously. Most cardiac RyRs were closed at 100 nM [Ca2+] and activated in a cooperative manner (nHa ranged from 1.6 to 5.0), reaching a high Po (> 0.6) in the presence and absence of Mg2+ and ATP. Heart RyRs were much less sensitive (10x) to inhibition by [Ca2+] than skeletal RyRs. The differential heterogeneity of heart versus skeletal muscle RyRs may reflect the modulation required for calcium-induced calcium release versus depolarization-induced Ca2+ release.

  • 19.
    Czapla-Masztafiak, Joanna
    et al.
    Paul Scherrer Inst, Villigen, Switzerland.;Polish Acad Sci, Inst Nucl Phys, Krakow, Poland..
    Szlachetko, Jakub
    Paul Scherrer Inst, Villigen, Switzerland.;Jan Kochanowski Univ Humanities & Sci, Inst Phys, Kielce, Poland..
    Milne, Christopher J.
    Paul Scherrer Inst, Villigen, Switzerland..
    Lipiec, Ewelina
    Sa, Jacinto
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Physical Chemistry. Polish Acad Sci, Inst Phys Chem, Warsaw, Poland..
    Penfold, Thomas J.
    Newcastle Univ, Dept Chem, Bedson Bldg, Newcastle Upon Tyne NE1 7RU, Tyne & Wear, England..
    Huthwelker, Thomas
    Paul Scherrer Inst, Villigen, Switzerland..
    Borca, Camelia
    Paul Scherrer Inst, Villigen, Switzerland..
    Abela, Rafael
    Paul Scherrer Inst, Villigen, Switzerland..
    Kwiatek, Wojciech M.
    Polish Acad Sci, Inst Nucl Phys, Krakow, Poland..
    Investigating DNA Radiation Damage Using X-Ray Absorption Spectroscopy2016In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 110, no 6, p. 1304-1311Article in journal (Refereed)
    Abstract [en]

    The biological influence of radiation on living matter has been studied for years; however, several questions about the detailed mechanism of radiation damage formation remain largely unanswered. Among all biomolecules exposed to radiation, DNA plays an important role because any damage to its molecular structure can affect the whole cell and may lead to chromosomal rearrangements resulting in genomic instability or cell death. To identify and characterize damage induced in the DNA sugar-phosphate backbone, in this work we performed x-ray absorption spectroscopy at the P K-edge on DNA irradiated with either UVA light or protons. By combining the experimental results with theoretical calculations, we were able to establish the types and relative ratio of lesions produced by both UVA and protons around the phosphorus atoms in DNA.

  • 20.
    Dogan, Jakob
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Jemth, Per
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Only kinetics can prove conformational selection2014In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 107, no 8, p. 1997-1998Article in journal (Other academic)
  • 21.
    Duarte, Fernanda
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
    Kamerlin, Shina C. Lynn
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
    Rationalizing the Catalytic Activity of an Unusual Oxidoreductase (FucO)2013In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 104, no 2, p. 495A-495AArticle in journal (Other academic)
  • 22.
    Edwards, Katarina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Physical Chemistry I.
    Johnsson, M
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Physical Chemistry I.
    Karlsson, G
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Physical Chemistry I.
    Silvander, M
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Physical and Analytical Chemistry, Physical Chemistry I.
    Effect of polyethyleneglycol-phospholipids on aggregate structure in preparations of small unilamellar liposomes1997In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 73, no 1, p. 258-266Article in journal (Other academic)
    Abstract [en]

    Phospholipids with covalently attached poly(ethylene glycol) (PEG lipids) are commonly used for the preparation of long circulating liposomes. Although it is well known that lipid/PEG-lipid mixed micelles may form above a certain critical concentration of PEG-lipid, little is known about the effects of PEG-lipids on liposome structure and leakage at submicellar concentrations. In this study we have used cryogenic transmission electron microscopy to investigate the effect of PEG(2000)-PE on aggregate structure in preparations of liposomes with different membrane compositions. The results reveal a number of important aggregate structures not documented before. The micrographs show that enclosure of PEG-PE induces the formation of open bilayer discs at concentrations well below those where mixed micelles begin to form. The maximum concentration of PEG-lipid that may be incorporated without alteration of the liposome structure depends on the phospholipid chain length, whereas phospholipid saturation or the presence of cholesterol has little or no effect. The presence of cholesterol does, however, affect the shape of the mixed micelles formed at high concentrations of PEG-lipid. Threadlike micelles form in the absence of cholesterol but adapt a globular shape when cholesterol is present.

  • 23.
    Ehrenberg, Måns
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology.
    Pavlov, Michael Yu
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology.
    Optimal Strategy for Rapid Proteome Re-Arrangements in Bacterial Populations2013In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 104, no 2, p. 205A-206AArticle in journal (Other academic)
  • 24.
    Elf, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
    Direct Measurements of Transcription Factor Binding and Dissociation at Individual Chromosomal Operators2014In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 106, no 2, p. 444A-444AArticle in journal (Other academic)
    Abstract [en]

    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 .

  • 25. Fabry, Ben
    et al.
    Klemm, Anna H
    Kienle, Sandra
    Schäffer, Tilman E
    Goldmann, Wolfgang H
    Focal adhesion kinase stabilizes the cytoskeleton.2011In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 101, no 9, p. 2131-8Article in journal (Refereed)
    Abstract [en]

    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.

  • 26.
    Fange, David
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
    Mellenius, Harriet
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology.
    Dennis, Patrick P.
    Ehrenberg, Måns
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology.
    Thermodynamic Modeling of Variations in the Rate of RNA Chain Elongation of E-coli rrn Operons2014In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 106, no 1, p. 55-64Article in journal (Refereed)
    Abstract [en]

    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.

  • 27.
    Flores, Samuel C.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
    Elucidating Ribosomal Translocation with Internal Coordinate Flexible Fitting2014In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 106, no 2, p. 492A-493AArticle in journal (Other academic)
    Abstract [en]

    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.

  • 28. Fornander, Louise Helena
    et al.
    Persson, Fredrik
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
    Fritzsche, Joachim
    Araya, Joshua
    Nevin, Philip
    Beuning, Penny
    Modesti, Mauro
    Frykholm, Karolin
    Westerlund, Fredrik
    Using Nanofluidic Channels to Probe the Dynamics of Rad51-DNA Filaments2014In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 106, no 2, p. 692A-693AArticle in journal (Other academic)
    Abstract [en]

    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+.

  • 29. Freyhult, EK
    et al.
    Andersson, K
    Gustafsson, Mats G
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Signals and Systems Group.
    Structural modeling extends QSAR analysis of antibody-lysozome interactions to 3D-QSAR2003In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 84, no 4, p. 2265-2272Article in journal (Refereed)
  • 30. Frykholm, Karolin
    et al.
    Alizadehheidari, Mohammadreza
    Fritzsche, Joachim
    Wigenius, Jens
    Nevin, Philip
    Araya, Joshua
    Beuning, Penny
    Modesti, Mauro
    Persson, Fredrik
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
    Westerlund, Fredrik
    Probing Physical Properties of a DNA-Protein Complex Using Nanofluidic Channels2014In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 106, no 2, p. 428A-429AArticle in journal (Other academic)
    Abstract [en]

    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.

  • 31.
    Gandasi, Nikhil R.
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Cell Biology.
    Barg, Sebastian
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Cell Biology.
    Quantitative Imaging of the Exocytosis Machinery Assembly2015In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 108, no 2, p. 102A-102AArticle in journal (Other academic)
  • 32.
    Gomez-Llobregat, Jordi
    et al.
    Stockholm Univ, Dept Biochem & Biophys, Ctr Biomembrane Res, S-10691 Stockholm, Sweden..
    Elias-Wolff, Federico
    Stockholm Univ, Dept Biochem & Biophys, Ctr Biomembrane Res, S-10691 Stockholm, Sweden..
    Lindén, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Anisotropic Membrane Curvature Sensing by Amphipathic Peptides2016In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 110, no 1, p. 197-204Article in journal (Refereed)
    Abstract [en]

    Many proteins and peptides have an intrinsic capacity to sense and induce membrane curvature, and play crucial roles for organizing and remodeling cell membranes. However, the molecular driving forces behind these processes are not well understood. Here, we describe an approach to study curvature sensing by simulating the interactions of single molecules with a buckled lipid bilayer. We analyze three amphipathic antimicrobial peptides, a class of membrane-associated molecules that specifically target and destabilize bacterial membranes, and find qualitatively different sensing characteristics that would be difficult to resolve with other methods. Our findings provide evidence for direction-dependent curvature sensing mechanisms in amphipathic peptides and challenge existing theories of hydrophobic insertion. The buckling approach is generally applicable to a wide range of curvature-sensing molecules, and our results provide strong motivation to develop new experimental methods to track position and orientation of membrane proteins.

  • 33.
    Gomez-Llobregat, Jordi
    et al.
    Stockholm Univ, Biochem & Biophys, S-10691 Stockholm, Sweden..
    Lindén, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
    Anisotropic Membrane Curvature Sensing by Antibacterial Peptides2015In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 108, no 2, p. 550A-550AArticle in journal (Other academic)
  • 34.
    Hauryliuk, Vasili
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Biology.
    Hansson, Sebastian
    Laboratoire d’Enzymologie et Biochimie Structurales, CNRS, Gif-sur-Yvette, France.
    Ehrenberg, Måns
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Biology.
    Co-factor dependent conformational switching of GTPases2008In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Biophysical J, ISSN 0006-3495, Vol. 95, no 4, p. 1704-1715Article in journal (Refereed)
    Abstract [en]

    This theoretical work covers structural and biochemical aspects of nucleotide binding and GDP/GTP exchange of GTP hydrolases belonging to the family of small GTPases. Current models of GDP/GTP exchange regulation are often based on two specific assumptions. The first is that the conformation of a GTPase is switched by the exchange of the bound nucleotide from GDP to GTP or vice versa. The second is that GDP/GTP exchange is regulated by a guanine nucleotide exchange factor, which stabilizes a GTPase conformation with low nucleotide affinity. Since, however, recent biochemical and structural data seem to contradict this view, we present a generalized scheme for GTPase action. This novel ansatz accounts for those important cases when conformational switching in addition to guanine nucleotide exchange requires the presence of cofactors, and gives a more nuanced picture of how the nucleotide exchange is regulated. The scheme is also used to discuss some problems of interpretation that may arise when guanine nucleotide exchange mechanisms are inferred from experiments with analogs of GTP, like GDPNP, GDPCP, and GDP gamma S.

  • 35. He, Yuhui
    et al.
    Tsutsui, Makusu
    Scheicher, Ralph H.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Fan, Chun
    Taniguchi, Masateru
    Kawai, Tomoji
    Mechanism of How Salt-Gradient-Induced Charges Affect the Translocation of DNA Molecules through a Nanopore2013In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 105, no 3, p. 776-782Article in journal (Refereed)
    Abstract [en]

    Experiments using nanopores demonstrated that a salt gradient enhances the capture rate of DNA and reduces its transfocation speed. These two effects can help to enable electrical DNA sequencing with nanopores. Here, we provide a quantitative theoretical evaluation that shows the positive net charges, which accumulate around the pore entrance due to the salt gradient, are responsible for the two observed effects: they reinforce the electric capture field, resulting in promoted molecule capture rate; and they induce cationic electroosmotic flow through the nanopore, thus significantly retarding the motion of the anionic DNA through the nanopore. Our multiphysical simulation results show that, during the polymer trapping stage, the former effect plays the major role, thus resulting in promoted DNA capture rate, while during the nanopore-penetrating stage the latter effect dominates and consequently reduces the DNA translocation speed significantly. Quantitative agreement with experimental results has been reached by further taking nanopore wall surface charges into account.

  • 36.
    Herling, Therese W.
    et al.
    Univ Cambridge, Dept Chem, Lensfield Rd, Cambridge CB2 1EW, England..
    O'Connell, David J.
    Univ Coll Dublin, Sch Biomol & Biomed Sci, Dublin 2, Ireland..
    Bauer, Mikael C.
    Lund Univ, Dept Biochem & Struct Biol, Lund, Sweden..
    Persson, Jonas
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology, Clinical Immunology. Lund Univ, Dept Biochem & Struct Biol, Lund, Sweden..
    Weininger, Ulrich
    Lund Univ, Dept Biophys Chem, Lund, Sweden..
    Knowles, Tuomas P. J.
    Univ Cambridge, Dept Chem, Lensfield Rd, Cambridge CB2 1EW, England..
    Linse, Sara
    Lund Univ, Dept Biochem & Struct Biol, Lund, Sweden..
    A Microfluidic Platform for Real-Time Detection and Quantification of Protein-Ligand Interactions2016In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 110, no 9, p. 1957-1966Article in journal (Refereed)
    Abstract [en]

    The key steps in cellular signaling and regulatory pathways rely on reversible noncovalent protein-ligand binding, yet the equilibrium parameters for such events remain challenging to characterize and quantify in solution. Here, we demonstrate a microfluidic platform for the detection of protein-ligand interactions with an assay time on the second timescale and without the requirement for immobilization or the presence of a highly viscous matrix. Using this approach, we obtain absolute values for the electrophoretic mobilities characterizing solvated proteins and demonstrate quantitative comparison of results obtained under different solution conditions. We apply this strategy to characterize the interaction between calmodulin and creatine kinase, which we identify as a novel calmodulin target. Moreover, we explore the differential calcium ion dependence of calmodulin ligand-binding affinities, a system at the focal point of calcium-mediated cellular signaling pathways. We further explore the effect of calmodulin on creatine kinase activity and show that it is increased by the interaction between the two proteins. These findings demonstrate the potential of quantitative microfluidic techniques to characterize binding equilibria between biomolecules under native solution conditions.

  • 37. Horn, Richard
    et al.
    Roux, Benoit
    Åqvist, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
    Permeation Redux: Thermodynamics and Kinetics of Ion Movement through Potassium Channels2014In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 106, no 9, p. 1859-1863Article in journal (Refereed)
    Abstract [en]

    The fundamental biophysics underlying the selective movement of ions through ion channels was launched by George Eisenman in the 1960s, using glass electrodes. This minireview examines the insights from these early studies and the explosive progress made since then.

  • 38.
    Hub, Jochen S.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Aponte-Santamaria, Camilo
    Grubmueller, Helmut
    de Groot, Bert L.
    Voltage-Regulated Water Flux through Aquaporin Channels In Silico2010In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 99, no 12, p. L97-L99Article in journal (Refereed)
    Abstract [en]

    Aquaporins (AQPs) facilitate the passive flux of water across biological membranes in response to an osmotic pressure. A number of AQPs, for instance in plants and yeast, have been proposed to be regulated by phosphorylation, cation concentration, pH change, or membrane-mediated mechanical stress. Here we report an extensive set of molecular dynamics simulations of AQP1 and AQP4 subject to large membrane potentials in the range of +/- 1.5 V, suggesting that AQPs may in addition be regulated by an electrostatic potential. As the regulatory mechanism we identified the relative population of two different states of the conserved arginine in the aromatic/arginine constriction region. A positive membrane potential was found to stabilize the arginine in an up-state, which allows rapid water flux, whereas a negative potential favors a down-state, which reduces the single-channel water permeability.

  • 39.
    Jones, Daniel
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Systems Biology.
    Unoson, Cecilia
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Leroy, Prune
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Curic, Vladimir
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    Elf, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Systems Biology.
    Kinetics of dCas9 Target Search in Escherichia Coli2017In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 112, no 3, p. 314A-314AArticle in journal (Other academic)
  • 40.
    Karlsson, Elin
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Andersson, Eva
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Jones, Nykola C.
    Aarhus Univ, ISA, Dept Phys & Astron, Aarhus, Denmark.
    Hoffmann, Sören Vrönning
    Aarhus Univ, ISA, Dept Phys & Astron, Aarhus, Denmark.
    Jemth, Per
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Kjaergaard, Magnus
    Aarhus Univ, Dept Mol Biol & Genet, Aarhus, Denmark;Aarhus Univ, Aarhus Inst Adv Studies, Aarhus, Denmark.
    Coupled Binding and Helix Formation Monitored by Synchrotron-Radiation Circular Dichroism2019In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 117, no 4, p. 729-742Article in journal (Refereed)
    Abstract [en]

    Intrinsically disordered proteins organize interaction networks in the cell in many regulation and signaling processes. These proteins often gain structure upon binding to their target proteins in multistep reactions involving the formation of both secondary and tertiary structure. To understand the interactions of disordered proteins, we need to understand the mechanisms of these coupled folding and binding reactions. We studied helix formation in the binding of the molten globule-like nuclear coactivator binding domain and the disordered interaction domain from activator of thyroid hormone and retinoid receptors. We demonstrate that helix formation in a rapid binding reaction can be followed by stopped-flow synchrotron-radiation circular dichroism (CD) spectroscopy and describe the design of such a beamline. Fluorescence-monitored binding experiments of activator of thyroid hormone and retinoid receptors and nuclear coactivator binding domain display several kinetic phases, including one concentration-independent phase, which is consistent with an intermediate stabilized at high ionic strength. Time-resolved CD experiments show that almost all helicity is formed upon initial association of the proteins or separated from the encounter complex by only a small energy barrier. Through simulation of mechanistic models, we show that the intermediate observed at high ionic strength likely involves a structural rearrangement with minor overall changes in helicity. Our experiments provide a benchmark for simulations of coupled binding reactions and demonstrate the feasibility of using synchrotron-radiation CD for mechanistic studies of protein-protein interactions.

  • 41.
    Kasson, Peter
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular biophysics. Univ Virginia, Uppsala, Sweden..
    Simulations and Experiments Show a Mechanistic Role for Influenza Fusion Peptides in Membrane Bending and Fusion Stoichiometry2018In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 114, no 3, p. 605A-605AArticle in journal (Other academic)
  • 42.
    Koster, Anna K.
    et al.
    Stanford Univ.
    Wood, Chase
    Stanford Univ.
    Thomas-Tran, Rhiannon
    Stanford Univ.
    Chavan, Tanmay S.
    Stanford Univ.
    Almqvist, Jonas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Structure and Molecular Biology.
    Choi, Kee-Hyun
    Stanford Univ; Korea Inst Sci & Technol.
    Du Bois, Justin
    Stanford Univ.
    Maduke, Merritt
    Stanford Univ.
    Developing a Novel Class of CLC Chloride-Channel Inhibitors2017In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 112, no 3, p. 339A-339AArticle in journal (Other academic)
  • 43. Kouyoumdjian, Alexandre
    et al.
    Ortie, Erwan
    Tek, Alex
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
    Pluot, Aurelien
    Henon, Eric
    Chavent, Matthieu
    Baaden, Marc
    Game on, Science - How Video Game Technology may Help Biophysicists Tackle Visualization Challenges2014In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 106, no 2, p. 809A-809AArticle in journal (Other academic)
    Abstract [en]

    The video games industry develops ever more advanced technologies to improve rendering, image quality, ergonomics and user experience of their creations providing very simple to use tools to design new games. In biophysics, only a small number of experts with specialized know-how are able to design interactive visualization applications, typically static computer programs that cannot easily be modified. Are there lessons to be learned from video games? Could their technology help us explore new molecular graphics ideas and render graphics developments accessible to non-specialists?

  • 44.
    Krotee, Pascal
    et al.
    Univ Calif Los Angeles, HHMI, UCLA DOE Inst, Dept Biol Chem,Mol Biol Inst, Los Angeles, CA USA.;Univ Calif Los Angeles, HHMI, UCLA DOE Inst, Dept Biochem Mol,Mol Biol Inst, Los Angeles, CA USA..
    Rodriguez, Jose A.
    Univ Calif Los Angeles, HHMI, UCLA DOE Inst, Dept Biol Chem,Mol Biol Inst, Los Angeles, CA USA.;Univ Calif Los Angeles, HHMI, UCLA DOE Inst, Dept Biochem Mol,Mol Biol Inst, Los Angeles, CA USA..
    Sawaya, Michael R.
    Univ Calif Los Angeles, HHMI, UCLA DOE Inst, Dept Biol Chem,Mol Biol Inst, Los Angeles, CA USA.;Univ Calif Los Angeles, HHMI, UCLA DOE Inst, Dept Biochem Mol,Mol Biol Inst, Los Angeles, CA USA..
    Cascio, Duilio
    Univ Calif Los Angeles, HHMI, UCLA DOE Inst, Dept Biol Chem,Mol Biol Inst, Los Angeles, CA USA.;Univ Calif Los Angeles, HHMI, UCLA DOE Inst, Dept Biochem Mol,Mol Biol Inst, Los Angeles, CA USA..
    Reyes, Francis E.
    Howard Hughes Med Inst, Janelia Res Campus, Ashburn, VA USA..
    Shi, Dan
    Howard Hughes Med Inst, Janelia Res Campus, Ashburn, VA USA..
    Hattne, Johan
    Howard Hughes Med Inst, Janelia Res Campus, Ashburn, VA USA..
    Nannenga, Brent L.
    Howard Hughes Med Inst, Janelia Res Campus, Ashburn, VA USA..
    Oskarsson, Marie E.
    Uppsala Univ, Dept Med Cell Biol, Uppsala, Sweden..
    Jiang, Lin
    Univ Calif Los Angeles, Dept Neurol, Mol Bio Inst, Brain Res Inst,David Geffen Sch Med, Los Angeles, CA 90024 USA..
    Westermark, Gunilla T.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Cell Biology.
    Gonen, Tamir
    Howard Hughes Med Inst, Janelia Res Campus, Ashburn, VA USA..
    Eisenberg, David S.
    Univ Calif Los Angeles, HHMI, UCLA DOE Inst, Dept Biol Chem,Mol Biol Inst, Los Angeles, CA USA.;Univ Calif Los Angeles, HHMI, UCLA DOE Inst, Dept Biochem Mol,Mol Biol Inst, Los Angeles, CA USA..
    The Cryo-EM Method Micro-ED Structure Determination of Type II Diabetes-Related Protein Segments2017In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 112, no 3, p. 14A-14AArticle in journal (Other academic)
  • 45. Lange, Oliver F.
    et al.
    van der Spoel, David
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
    de Groot, Bert L.
    Scrutinizing Molecular Mechanics Force Fields on the Submicrosecond Timescale with NMR Data2010In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 99, no 2, p. 647-655Article in journal (Refereed)
    Abstract [en]

    Protein dynamics on the atomic level and on the microsecond timescale has recently become accessible from both computation and experiment. To validate molecular dynamics (MD) at the submicrosecond timescale against experiment we present microsecond MD simulations in 10 different force-field configurations for two globular proteins, ubiquitin and the gb3 domain of protein G, for which extensive NMR data is available. We find that the reproduction of the measured NMR data strongly depends on the chosen force field and electrostatics treatment. Generally, particle-mesh Ewald outperforms cut-off and reaction-field approaches. A comparison to measured J-couplings across hydrogen bonds suggests that there is room for improvement in the force-field description of hydrogen bonds in most modern force fields. Our results show that with current force fields, simulations beyond hundreds of nanoseconds run an increased risk of undergoing transitions to nonnative conformational states or will persist within states of high free energy for too long, thus skewing the obtained population frequencies. Only for the AMBER99sb force field have such transitions not been observed. Thus, our results have significance for the interpretation of data obtained with long MD simulations, for the selection of force fields for MD studies and for force-field development. We hope that this comprehensive benchmark based on NMR data applied to many popular MD force fields will serve as a useful resource to the MD community. Finally, we find that for gb3, the force-field AMBER99sb reaches comparable accuracy in back-calculated residual dipolar couplings and J-couplings across hydrogen bonds to ensembles obtained by refinement against NMR data.

  • 46.
    Lignell, Martin
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Photochemistry and Molecular Science, Chemical Physics.
    Becker, Hans-Christian
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Photochemistry and Molecular Science, Chemical Physics.
    Recognition and binding of a helix-loop-helix peptide to carbonic anhydrase occurs via partly folded intermediate structures2010In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 98, no 3, p. 425-433Article in journal (Refereed)
    Abstract [en]

    We have studied the association of a fluorescently labeled helix–loop–helix peptide scaffold carrying a benzensulfonamide ligand to carbonic anhydrase using steady state and time-resolved fluorescence spectroscopy. The helix–loop–helix peptide, developed for biosensing applications, is labeled with the fluorescent probe dansyl, which serves as a polarity-sensitive reporter of the binding event. Using maximum entropy analysis of the fluorescence lifetime of the dansyl at 1:1 stoichiometry reveals three characteristic fluorescence lifetime groups, which are interpreted as differently interacting peptide–protein structures. We characterize these as mostly bound but unfolded, bound and partly folded, and strongly bound and folded peptide–protein complexes. Furthermore, analysis of the fluorescence anisotropy decay resulted in three different dansyl rotational correlation times, namely 0.18, 1.2, and 23 ns. Using their amplitudes, we can correlate the lifetime groups with the corresponding fluorescence lifetime group. The 23 ns rotational correlation time, which appears with the same amplitude as a 17 ns fluorescence lifetime, shows that the dansyl fluophorophore follows the rotational diffusion of carbonic anhydrase when it is a part of the folded peptide–protein complex. A partly folded and partly hydrated interfacial structure is manifested by a 8 ns dansyl fluorescence lifetime and a 1.2 ns rotational correlation time. This structure, we believe, is similar to a molten-globule-like interfacial structure which allows faster segmental movements and a higher degree of solvent exposure of dansyl. Excitation of dansyl on the helix–loop–helix peptide through Förster energy transfer from one or several tryptophans in the carbonic anhydrase, shows that the helix–loop–helix scaffold binds to a tryptophan-rich domain of the carbonic anhydrase. We conclude that the binding of the peptide to carbonic anhydrase involves a transition from a disordered to ordered structure of the helix–loop–helix scaffold.

  • 47.
    Lignell, Martin
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Photochemistry and Molecular Science, Chemical Physics.
    Becker, Hans-Christian
    Sequential Equilibrium Unfolding of a Four-helix Bundle Peptide Shows that Urea and Guanidine have Different Effects on Tertiary and Secondary Structure. A CD and Time-resolved Fluorescence Spectroscopy StudyIn: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086Article in journal (Refereed)
    Abstract [en]

    In this paper we show, using time-resolved fluorescence and CD spectroscopy, that equilibrium unfolding of the homodimeric four-helix bundle peptide (KE2D15)2 occurs via different pathways depending on the denaturant. The initial effect of guanidine hydrochloride (GdHCl) and urea is similar insofar that the tertiary structure is slightly destabilized. This is accompanied by a slight increase in helicity, which we believe is due to stabilization of the backbone at the expense of hydrophobic core stability. With GdHCl we observe an almost immediate (≥2 M GdHCl) dissociation of the dimer into helical monomers, while the effect of urea is to stabilize the helices and induce a solvent- or urea-separated state that persists up to about 5 M urea. At high urea concentrations, the peptide exists in monomeric but helical form. The partial and full dissociation of the dimeric four-helix bundle is monitored through time-resolved fluorescence spectroscopy. Through the use of time-resolved fluorescence, we can assess the heterogeneity of the partly and fully denatured states even though the denaturation is carried out at equilibrium conditions. The width of the fluorescence lifetime distributions are analyzed in terms of conformational space of the peptide.

  • 48.
    Lignell, Martin
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Photochemistry and Molecular Science, Chemical Physics.
    Tegler, Lotta
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Biochemistry and Organic Chemistry.
    Becker, Hans-Christian
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Photochemistry and Molecular Science, Chemical Physics.
    Hydrated and Dehydrated Tertiary Interactions - Opening and Closing - of a Four-helix Bundle Peptide2009In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 97, no 2, p. 572-580Article in journal (Refereed)
    Abstract [en]

    The structural heterogeneity and thermal denaturation of a dansyl-labeled four-helix bundle homodimeric peptide has been studied with steady state and time-resolved fluorescence spectroscopy and with circular dichroism. At room temperature the fluorescence decay of the polarity-sensitive dansyl, located in the hydrophobic core region, can be described by a broad distribution of fluorescence lifetimes, reflecting the heterogeneous microenvironment. However, the lifetime distribution is nearly bimodal, which we ascribe to the presence of two major conformational subgroups. Since the fluorescence lifetime reflects the water content of the four-helix bundle conformations we can use the lifetime analysis to monitor the change of hydration state of the hydrophobic core of the four-helix bundle. Increasing the temperature from 9 °C to 23 °C leads to an increased population of molten-globule-like conformations with a less ordered helical backbone structure. The fluorescence emission maximum remains constant in this temperature interval, and the hydrophobic core is not strongly affected. Above 30 °C the structural dynamics involve transient openings of the four-helix bundle structure as evidenced by the emergence of a water-quenched component and less negative CD. Above 60 °C the homodimer starts to dissociate, as shown by the increasing loss of CD and narrow, short-lived fluorescence lifetime distributions.

  • 49.
    Lindén, Martin
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
    Elf, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology.
    Single Molecule Tracking in Living Cells: Multistep Reactions, Simulated Microscopy and New Analysis Methods2015In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 108, no 2, p. 360A-360AArticle in journal (Other academic)
  • 50.
    Lindén, Martin
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Systems Biology.
    Elf, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Systems Biology.
    Variational Algorithms for Analyzing Noisy Multistate Diffusion Trajectories2018In: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 115, no 2, p. 276-282Article in journal (Refereed)
    Abstract [en]

    Single-particle tracking offers a noninvasive high-resolution probe of biomolecular reactions inside living cells. However, efficient data analysis methods that correctly account for various noise sources are needed to realize the full quantitative potential of the method. We report algorithms for hidden Markov-based analysis of single-particle tracking data, which incorporate most sources of experimental noise, including heterogeneous localization errors and missing positions. Compared to previous implementations, the algorithms offer significant speedups, support for a wider range of inference methods, and a simple user interface. This will enable more advanced and exploratory quantitative analysis of single-particle tracking data.

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