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  • 1. Aman, K.
    et al.
    Lindahl, E.
    Edholm, Olle
    KTH, Tidigare Institutioner                               , Fysik.
    Hakansson, P.
    Westlund, P. O.
    Structure and dynamics of interfacial water in an L-alpha phase lipid bilayer from molecular dynamics simulations2003Ingår i: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 84, nr 1, s. 102-115Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Based on molecular dynamics simulations, an analysis of structure and dynamics is performed on interfacial water at a liquid crystalline dipalmitoylphosphatidycholine/water system. Water properties relevant for understanding NMR relaxation are emphasized. The first and second rank orientational order parameters of the water O-H bonds were calculated, where the second rank order parameter is in agreement with experimental determined quadrupolar splittings. Also, two different interfacial water regions (bound water regions) are revealed with respect to different signs of the second rank order parameter. The water reorientation correlation function reveals a mixture of fast and slow decaying parts. The fast (ps) part of the correlation function is due to local anisotropic water reorientation whereas the much slower part is due to more complicated processes including lateral diffusion along the interface and chemical exchange between free and bound water molecules. The 100-ns-long molecular dynamics simulation at constant pressure (1 atm) and at a temperature of 50degreesC of 64 lipid molecules and 64 x 23 water molecules lack a slow water reorientation correlation component in the ns time scale. The (H2O)-H-2 powder spectrum of the dipalmitoylphosphatidycholine/water system is narrow and consequently, the NMR relaxation time T-2 is too short compared to experimental results.

  • 2.
    Aman, Ken
    et al.
    Umeå University.
    Lindahl, Erik
    KTH, Tidigare Institutioner, Fysik.
    Edholm, Olle
    KTH, Tidigare Institutioner, Fysik.
    Håkansson, Pär
    Umeå University.
    Westlund, Per-Olof
    Umeå University.
    Structure and dynamics of interfacial water in an Lalpha phase lipid bilayer from molecular dynamics simulations.2003Ingår i: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 84, nr 1, s. 102-15Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Based on molecular dynamics simulations, an analysis of structure and dynamics is performed on interfacial water at a liquid crystalline dipalmitoylphosphatidycholine/water system. Water properties relevant for understanding NMR relaxation are emphasized. The first and second rank orientational order parameters of the water O-H bonds were calculated, where the second rank order parameter is in agreement with experimental determined quadrupolar splittings. Also, two different interfacial water regions (bound water regions) are revealed with respect to different signs of the second rank order parameter. The water reorientation correlation function reveals a mixture of fast and slow decaying parts. The fast (ps) part of the correlation function is due to local anisotropic water reorientation whereas the much slower part is due to more complicated processes including lateral diffusion along the interface and chemical exchange between free and bound water molecules. The 100-ns-long molecular dynamics simulation at constant pressure (1 atm) and at a temperature of 50 degrees C of 64 lipid molecules and 64 x 23 water molecules lack a slow water reorientation correlation component in the ns time scale. The (2)H(2)O powder spectrum of the dipalmitoylphosphatidycholine/water system is narrow and consequently, the NMR relaxation time T(2) is too short compared to experimental results.

  • 3.
    Andersson, Magnus
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik.
    Lindahl, Erik
    Stockholm Univ, Dept Biochem & Biophys, S-10691 Stockholm, Sweden..
    White, Stephen H.
    Univ Calif Irvine, Irvine, CA USA..
    Kaback, Ronald H.
    Univ Calif Los Angeles, Los Angeles, CA USA..
    The Molecular Basis for Substrate Specificity in Lactose Permease2015Ingår i: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 108, nr 2, s. 309A-309AArtikel i tidskrift (Övrigt vetenskapligt)
  • 4.
    Andersson, Magnus
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik, Beräkningsbiofysik. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Mattle, Daniel
    Sitsel, Oleg
    Nielsen, Anna Marie
    Lindahl, Erik
    KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik, Experimentell biomolekylär fysik. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    White, Stephen H.
    Nissen, Poul
    Gourdon, Pontus
    Transport Pathway in Cu+ P-Type ATPases2014Ingår i: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 106, nr 2, s. 427A-427AArtikel i tidskrift (Övrigt vetenskapligt)
  • 5. Beckham, Gregg T.
    et al.
    Bomble, Yannick J.
    Matthews, James F.
    Taylor, Courtney B.
    Resch, Michael G.
    Yarbrough, John M.
    Decker, Steve R.
    Bu, Lintao
    Zhao, Xiongce
    McCabe, Clare
    Wohlert, Jakob
    Bergenstråhle, Malin
    KTH, Skolan för kemivetenskap (CHE), Centra, Wallenberg Wood Science Center.
    Brady, John W.
    Adney, William S.
    Himmel, Michael E.
    Crowley, Michael F.
    The O-Glycosylated Linker from the Trichoderma reesei Family 7 Cellulase Is a Flexible, Disordered Protein2010Ingår i: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 99, nr 11, s. 3773-3781Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    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

  • 6. Benninger, R. K. P.
    et al.
    Önfelt, Björn
    Neil, M. A. A.
    Davis, D. M.
    French, P. M. W.
    Fluorescence imaging of two-photon linear dichroism: Cholesterol depletion disrupts molecular orientation in cell membranes2005Ingår i: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 88, nr 1, s. 609-622Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The plasma membrane of cells is an ordered environment, giving rise to anisotropic orientation and restricted motion of molecules and proteins residing in the membrane. At the same time as being an organized matrix of defined structure, the cell membrane is heterogeneous and dynamic. Here we present a method where we use fluorescence imaging of linear dichroism to measure the orientation of molecules relative to the cell membrane. By detecting linear dichroism as well as fluorescence anisotropy, the orientation parameters are separated from dynamic properties such as rotational diffusion and homo energy transfer ( energy migration). The sensitivity of the technique is enhanced by using two-photon excitation for higher photo-selection compared to single photon excitation. We show here that we can accurately image lipid organization in whole cell membranes and in delicate structures such as membrane nanotubes connecting two cells. The speed of our wide-field imaging system makes it possible to image changes in orientation and anisotropy occurring on a subsecond timescale. This is demonstrated by time-lapse studies showing that cholesterol depletion rapidly disrupts the orientation of a fluorophore located within the hydrophobic region of the cell membrane but not of a surface bound probe. This is consistent with cholesterol having an important role in stabilizing and ordering the lipid tails within the plasma membrane.

  • 7. Benninger, Richard K. P.
    et al.
    Vanherberghen, Bruno
    KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik, Cellens fysik.
    Young, Stephen
    Taner, Sabrina B.
    Culley, Fiona I.
    Schnyder, Tim
    Neil, Mark A. A.
    Wuestner, Daniel
    French, Paul M. W.
    Davis, Daniel M.
    Önfelt, Björn
    KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik, Cellens fysik.
    Live Cell Linear Dichroism Imaging Reveals Extensive Membrane Ruffling within the Docking Structure of Natural Killer Cell Immune Synapses2009Ingår i: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 96, nr 2, s. L13-L15Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We have applied fluorescence imaging of two-photon linear dichroism to measure the subresolution organization of the cell membrane during formation of the activating (cytolytic) natural killer (NK) cell immune synapse (IS). This approach revealed that the NK cell plasma membrane is convoluted into ruffles at the periphery, but not in the center of a mature cytolytic NK cell IS. Time-lapse imaging showed that the membrane ruffles formed at the initial point of contact between NK cells and target cells and then spread radialy across the intercellular contact as the size of the IS increased, becoming absent from the center of the mature synapse. Understanding the role of such extensive membrane ruff ling in the assembly of cytolytic synapses is an intriguing new goal.

  • 8. Blau, Christian
    Gromaps: A Gromacs-Based Toolset to Analyse Density Maps Derived from Molecular Dynamics Simulations2019Ingår i: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 116, nr 1, s. 4-11Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    We introduce a computational toolset, named GROmaρs, to obtain and compare time-averaged density maps from molecular dynamics simulations. GROmaρs efficiently computes density maps by fast multi-Gaussian spreading of atomic densities onto a three-dimensional grid. It complements existing map-based tools by enabling spatial inspection of atomic average localization during the simulations. Most importantly, it allows the comparison between computed and reference maps (e.g., experimental) through calculation of difference maps and local and time-resolved global correlation. These comparison operations proved useful to quantitatively contrast perturbed and control simulation data sets and to examine how much biomolecular systems resemble both synthetic and experimental density maps. This was especially advantageous for multimolecule systems in which standard comparisons like RMSDs are difficult to compute. In addition, GROmaρs incorporates absolute and relative spatial free-energy estimates to provide an energetic picture of atomistic localization. This is an open-source GROMACS-based toolset, thus allowing for static or dynamic selection of atoms or even coarse-grained beads for the density calculation. Furthermore, masking of regions was implemented to speed up calculations and to facilitate the comparison with experimental maps. Beyond map comparison, GROmaρs provides a straightforward method to detect solvent cavities and average charge distribution in biomolecular systems. We employed all these functionalities to inspect the localization of lipid and water molecules in aquaporin systems, the binding of cholesterol to the G protein coupled chemokine receptor type 4, and the identification of permeation pathways through the dermicidin antimicrobial channel. Based on these examples, we anticipate a high applicability of GROmaρs for the analysis of molecular dynamics simulations and their comparison with experimentally determined densities.

  • 9.
    Brandt, Erik G.
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik, Teoretisk biologisk fysik.
    Braun, Anthony R.
    Sachs, Jonathan N.
    Nagle, John F.
    Edholm, Olle
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik.
    Interpretation of Fluctuation Spectra in Lipid Bilayer Simulations2011Ingår i: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 100, nr 9, s. 2104-2111Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    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.

  • 10.
    Brandt, Erik G.
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik.
    Edholm, Olle
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik.
    Dynamic structure factors from lipid membrane molecular dynamics simulations2009Ingår i: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 96, nr 5, s. 1828-1838Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Dynamic structure factors for a lipid bilayer have been calculated from molecular dynamics simulations. From trajectories of a system containing 1024 lipids we obtain wave vectors down to 0.34 nm(-1), which enables us to directly resolve the Rayleigh and Brillouin lines of the spectrum. The results confirm the validity of a model based on generalized hydrodynamics, but also improves the line widths and the position of the Brillouin lines. The improved resolution shows that the Rayleigh line is narrower than in earlier studies, which corresponds to a smaller thermal diffusivity. From a detailed analysis of the power spectrum, we can, in fact, distinguish two dispersive contributions to the elastic scattering. These translate to two exponential relaxation processes in separate time domains. Further, by including a first correction to the wave-vector-dependent position of the Brillouin lines, the results agree favorably to generalized hydrodynamics even up to intermediate wave vectors, and also yields a 20% higher adiabatic sound velocity. The width of the Brillouin lines shows a linear, not quadratic, dependence to low wave vectors.

  • 11.
    Brandt, Erik G.
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik, Teoretisk biologisk fysik.
    Edholm, Olle
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik, Teoretisk biologisk fysik.
    Molecular Dynamics Simulations of In-Plane Density Fluctuations in Phospholipid Bilayers2010Ingår i: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 98, nr 3, s. 664A-664AArtikel i tidskrift (Övrigt vetenskapligt)
  • 12. Braun, Anthony R.
    et al.
    Brandt, Erik G.
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik, Teoretisk biologisk fysik.
    Edholm, Olle
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik.
    Nagle, John F.
    Sachs, Jonathan N.
    Determination of Electron Density Profiles and Area from Simulations of Undulating Membranes2011Ingår i: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 100, nr 9, s. 2112-2120Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    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.

  • 13. Conti, Luca
    et al.
    Renhorn, Jakob
    Gabrielsson, Anders
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik, Beräkningsbiofysik.
    Turesson, Fredrik
    Liin, Sara
    Lindahl, Erik
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik, Beräkningsbiofysik.
    Elinder, Fredrik
    A Reciprocal Voltage Sensor-To-Pore Coupling in C-Type Inactivation2016Ingår i: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 110, nr 3, s. 104A-104AArtikel i tidskrift (Övrigt vetenskapligt)
  • 14.
    Delemotte, Lucie
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Fysik, Beräkningsbiofysik.
    van Keulen, Siri
    Roethlisberger, Ursula
    Gianti, Eleonora
    Carnevale, Vincenzo
    Klein, Michael L.
    Does Proton Conduction in the Voltage-Gated Proton Channel hH(V)1 Involve Grotthus Hopping via Acidic Residues?2017Ingår i: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 112, nr 3, s. 163A-164AArtikel i tidskrift (Övrigt vetenskapligt)
  • 15. Doerr, Denis
    et al.
    Sandrin, Deborah
    Kalinin, Stanislav
    Kuehnemuth, Ralf
    Overmann, Sebastian
    Pfiffi, Daniela
    Schaper, Klaus
    Seidel, Claus A. M.
    Mueller, Thomas J. J.
    Chmyrov, Andriy
    Widengren, Jerker
    KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik, Experimentell biomolekylär fysik.
    Bier, Brigitte A.
    Maximizing the Fluorescence Signal and Photostability of Fluorophores by Quenching Dark-States2014Ingår i: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 106, nr 2, s. 196A-196AArtikel i tidskrift (Övrigt vetenskapligt)
  • 16. dos Remedios, Cristobal G.
    et al.
    Estigoy, Colleen
    Cameron, Darryl
    Ho, Joshua W. K.
    Herbert, Benjamin
    Padula, Matthew
    Pickford, Russel
    Guilhaus, Michael
    Odeberg, Jacob
    KTH, Skolan för bioteknologi (BIO), Proteomik (stängd 20130101).
    Ponten, Fredrik
    Proteomics of the Human Cardiac Intercalated Disc: A More Complex Multi-Functional Structure than was Previously Thought2010Ingår i: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 98, nr 3, s. 755A-756AArtikel i tidskrift (Övrigt vetenskapligt)
  • 17.
    Edholm, O
    KTH, Tidigare Institutioner (före 2005), Fysik.
    Dynamics of lipid bilayers from molecular dynamics simulations2005Ingår i: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 88, nr 1, s. 26A-26AArtikel i tidskrift (Övrigt vetenskapligt)
  • 18.
    Edholm, O
    KTH, Tidigare Institutioner (före 2005), Fysik.
    Simulations of lipid bilayers on mesoscopic scales: Issues, answers and challenges.2005Ingår i: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 88, nr 1, s. 32A-32AArtikel i tidskrift (Övrigt vetenskapligt)
  • 19.
    Edholm, Olle
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik, Teoretisk biologisk fysik.
    Nagle, J. F.
    Areas of molecules in membranes consisting of mixtures2005Ingår i: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 89, nr 3, s. 1827-1832Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The question has arisen in recent literature: how to partition the total area in simulations of membranes consisting of more than one kind of molecule into average areas for each kind of molecule. Several definitions have been proposed, each of which has arbitrary features. When applied to mixtures of cholesterol and DPPC, these definitions give different results. This note recalls that physical chemistry provides a canonical way to de. ne molecular area, in analogy to the definition of partial-specific volume. Results for partial-specific area are obtained from simulations of DPPC/cholesterol bilayers and compared to the results from the other recent definitions. The partial-specific-area formalism dramatically demonstrates the condensing effect of cholesterol and this leads to the introduction of a specific model that accounts for the area of mixtures of cholesterol and lipid over the entire range of cholesterol concentrations.

  • 20.
    Edholm, Olle
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik, Teoretisk biologisk fysik.
    Tjörnhammar, Richard
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik, Teoretisk biologisk fysik.
    Waheed, Qaiser
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik, Teoretisk biologisk fysik.
    Cholesterol/Phospholipid Bilayer Phase Diagrams from Coarse Grained Simulations2013Ingår i: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 104, nr 2, s. 590A-590AArtikel i tidskrift (Övrigt vetenskapligt)
  • 21.
    Farsi, Zohreh
    et al.
    Helmholtz Assoc, Max Delbruck Ctr Mol Med, Light Microscopy Platform, Berlin, Germany..
    Gowrisankaran, Sindhuja
    European Neurosci Inst, Gottingen, Germany..
    Krunic, Matija
    European Neurosci Inst, Gottingen, Germany..
    Rammner, Burkhard
    Sciloop, Hamburg, Germany..
    Woehler, Andrew
    Helmholtz Assoc, Max Delbruck Ctr Mol Med, Light Microscopy Platform, Berlin, Germany..
    Mim, Carsten
    KTH, Skolan för teknik och hälsa (STH).
    Jahn, Reinhard
    Max Planck Inst Biophys Chem, Neurobiol, Gottingen, Germany..
    Milosevic, Ira
    European Neurosci Inst, Synapt Vesicle Dynam, Gottingen, Germany..
    Clathrin Coat Controls Vesicle Acidification by Blocking Vacuolar ATPase Activity2018Ingår i: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 114, nr 3, s. 280A-280AArtikel i tidskrift (Övrigt vetenskapligt)
  • 22. Fridberger, A.
    et al.
    Widengren, Jerker
    KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik, Experimentell biomolekylär fysik.
    de Monvel, J. B.
    Measuring hearing organ vibration patterns with confocal microscopy and optical flow2004Ingår i: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 86, nr 1, s. 535-543Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    A new method for visualizing vibrating structures is described. The system provides a means to capture very fast repeating events by relatively minor modi. cations to a standard confocal microscope. An acousto-optic modulator was inserted in the beam path, generating brief pulses of laser light. Images were formed by summing consecutive frames until every pixel of the resulting image had been exposed to a laser pulse. Images were analyzed using a new method for optical flow computation; it was validated through introducing artificial displacements in confocal images. Displacements in the range of 0.8 to 4 pixels were measured with 5% error or better. The lower limit for reliable motion detection was 20% of the pixel size. These methods were used for investigating the motion pattern of the vibrating hearing organ. In contrast to standard theory, we show that the organ of Corti possesses several degrees of freedom during sound-evoked vibration. Outer hair cells showed motion indicative of deformation. After acoustic overstimulation, supporting cells contracted. This slowly developing structural change was visualized during simultaneous intense sound stimulation and its speed measured with the optical flow technique.

  • 23.
    Gabrielsson, Anders
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik, Beräkningsbiofysik. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Liin, Sara
    Elinder, Fredrik
    Lindahl, Erik
    Binding Structure & Dynamics for Toxins Modifying the Gating Mechanism of Kv Channels2014Ingår i: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 106, nr 2, s. 738A-738AArtikel i tidskrift (Övrigt vetenskapligt)
  • 24. Geissbuehler, Matthias
    et al.
    Spielmann, Thiemo
    KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik, Experimentell biomolekylär fysik.
    Formey, Aurlie
    Maerki, Iwan
    Leutenegger, Marcel
    Hinz, Boris
    Johnsson, Kai
    Van De Ville, Dimitri
    Lasser, Theo
    Triplet Imaging of Oxygen Consumption during the Contraction of a Single Smooth Muscle Cell (A7r5)2010Ingår i: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 98, nr 2, s. 339-349Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The measurement of tissue and cell oxygenation is important for understanding cell metabolism. We have addressed this problem with a novel optical technique, called triplet imaging, that exploits oxygen-induced triplet lifetime changes and is compatible with a variety of fluorophores. A modulated excitation of varying pulse widths allows the extraction of the lifetime of the essentially dark triplet state using a high-fluorescence signal intensity. This enables the monitoring of fast kinetics of oxygen concentration in living cells combined with high temporal and spatial resolution. First, the oxygen-dependent triplet-state quenching of tetramethylrhodamine is validated and then calibrated in an L-ascorbic acid titration experiment demonstrating the linear relation between triplet lifetime and oxygen concentration according to the Stern-Volmer equation. Second, the method is applied to a biological cell system, employing as reporter a cytosolic fusion protein of beta-galactosidase with SNAP-tag labeled with tetramethylrhodamine. Oxygen consumption in single smooth muscle cells A7r5 during an [Arg(8)]-vasopressin-induced contraction is measured. The results indicate a consumption leading to an intracellular oxygen concentration that decays monoexponentially with time. The proposed method has the potential to become a new tool for investigating oxygen metabolism at the single cell and the subcellular level.

  • 25. Gronberg, Christina
    et al.
    Sitsel, Oleg
    Lindahl, Erik
    Gourdon, Pontus
    Andersson, Magnus
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik. KTH, Centra, SeRC - Swedish e-Science Research Centre. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Membrane Anchoring and Ion-Entry Dynamics in P-type ATPase Copper Transport2016Ingår i: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 111, nr 11, s. 2417-2429Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Cu+-specific P-type ATPase membrane protein transporters regulate cellular copper levels. The lack of crystal structures in Cu+-binding states has limited our understanding of how ion entry and binding are achieved. Here, we characterize the molecular basis of Cu+ entry using molecular-dynamics simulations, structural modeling, and in vitro and in vivo functional assays. Protein structural rearrangements resulting in the exposure of positive charges to bulk solvent rather than to lipid phosphates indicate a direct molecular role of the putative docking platform in Cu+ delivery. Mutational analyses and simulations in the presence and absence of Cu+ predict that the ion-entry path involves two ion-binding sites: one transient Met148-Cys382 site and one intramembranous site formed by trigonal coordination to Cys384, Asn689, and Met717. The results reconcile earlier biochemical and x-ray absorption data and provide a molecular understanding of ion entry in Cu+-transporting P-type ATPases.

  • 26.
    Heinz, William F.
    et al.
    Johns Hopkins Sch Med, Physiol, Baltimore, MD USA.;Helianthus LLC, Sykesville, MD USA..
    Werbin, Jeffrey
    Johns Hopkins Sch Med, Physiol, Baltimore, MD USA.;RareCyte Inc, Seattle, WA USA..
    Hoh, Jan H
    KTH.
    Restricted Exchange Environment Chambers for Creating and Manipulating Diffusive Gradients in 2D Cell Culture2015Ingår i: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 108, nr 2, s. 458A-458AArtikel i tidskrift (Övrigt vetenskapligt)
  • 27.
    Hermanowska, Malgorzata
    et al.
    Univ Southern Denmark, Dept Phys & Chem, Odense M, Denmark.;Univ Southern Denmark, MEMPHYS, Odense M, Denmark..
    Bijelic, Goran
    KTH, Skolan för kemivetenskap (CHE).
    Ciobanasu, Corina
    Univ Bonn, Inst Phys & Theoret Chem, Bonn, Germany..
    Kubitscheck, Ulrich
    Univ Bonn, Inst Phys & Theoret Chem, Bonn, Germany..
    Claesson, Per M.
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH), Kemi, Yt- och korrosionsvetenskap.
    Klosgen, Beate M.
    Univ Southern Denmark, Dept Phys & Chem, Odense M, Denmark.;Univ Southern Denmark, MEMPHYS, Odense M, Denmark..
    Charges in phospholipid layers2009Ingår i: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 96, nr 3, s. 18A-18AArtikel i tidskrift (Övrigt vetenskapligt)
  • 28. Heusser, Stephanie A.
    et al.
    Howard, Rebecca J.
    Pouya, Iman
    KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Klement, Göran
    KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Borghese, Cecilia
    Harris, R. Adron
    Lindahl, Erik
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik, Beräkningsbiofysik. KTH, Centra, Science for Life Laboratory, SciLifeLab. Stockholms universitet.
    A Single Mutation in GLIC Reveals Both the Potentiating and the Inhibitory Nature of Propofol2016Ingår i: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 110, nr 3, s. 456A-456AArtikel i tidskrift (Övrigt vetenskapligt)
  • 29.
    Heusser, Stephanie A.
    et al.
    Stockholm Univ, Dept Biochem & Biophys, SciLifeLab, Stockholm, Sweden..
    Lycksell, Marie
    Stockholm Univ, Dept Biochem & Biophys, SciLifeLab, Stockholm, Sweden..
    Wang, Xueqing
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik. KTH, Centra, Science for Life Laboratory, SciLifeLab. Stockholm Univ, Dept Biochem & Biophys, SciLifeLab, Stockholm, Sweden.
    Howard, Rebecca J.
    Stockholm Univ, Dept Biochem & Biophys, SciLifeLab, Stockholm, Sweden..
    Lindahl, Erik
    KTH, Centra, Science for Life Laboratory, SciLifeLab. KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik. Stockholm Univ, Dept Biochem & Biophys, SciLifeLab, Stockholm, Sweden.
    Flexibility of a Transmembrane Helix Underlies Dramatic Reversal of Net Anesthetic Effects in a Pentameric Ligand-Gated Ion Channel2018Ingår i: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 114, nr 3, s. 488A-489AArtikel i tidskrift (Övrigt vetenskapligt)
  • 30.
    Heusser, Stephanie A.
    et al.
    SciLifeLab, Solna, Sweden.;Stockholm Univ, S-10691 Stockholm, Sweden..
    Yoluk, Ozge
    KTH, Centra, Science for Life Laboratory, SciLifeLab. KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Lindahl, Erik
    KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Exploring the Gating Pathway in an Eukaryotic Ligand-Gated Ion Channel2015Ingår i: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 108, nr 2, s. 433A-433AArtikel i tidskrift (Övrigt vetenskapligt)
  • 31. Hofsass, C.
    et al.
    Lindahl, E.
    Edholm, Olle
    KTH, Tidigare Institutioner                               , Fysik.
    Molecular dynamics simulations of phospholipid bilayers with cholesterol2003Ingår i: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 84, nr 4, s. 2192-2206Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    To investigate the microscopic interactions between cholesterol and lipids in biological membranes, we have performed a series of molecular dynamics simulations of large membranes with different levels of cholesterol content. The simulations extend to 10 ns, and were performed with hydrated dipalmitoylphosphatidylcholine (DPPC) bilayers. The bilayers contain 1024 lipids of which 0-40% were cholesterol and the rest DPPC. The effects of cholesterol on the structure and mesoscopic dynamics of the bilayer were monitored as a function of cholesterol concentration. The main effects observed are a significant ordering of the DPPC chains (as monitored by NMR type order parameters), a reduced fraction of gauche bonds, a reduced surface area per lipid, less undulations-corresponding to an increased bending modulus for the membrane, smaller area fluctuations, and a reduced lateral diffusion of DPPC-lipids as well as cholesterols.

  • 32.
    Hofsäss, Christofer
    et al.
    KTH, Tidigare Institutioner, Fysik.
    Lindahl, Erik
    KTH, Tidigare Institutioner, Fysik.
    Edholm, Olle
    KTH, Tidigare Institutioner, Fysik.
    Molecular dynamics simulations of phospholipid bilayers with cholesterol.2003Ingår i: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 84, nr 4, s. 2192-206Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    To investigate the microscopic interactions between cholesterol and lipids in biological membranes, we have performed a series of molecular dynamics simulations of large membranes with different levels of cholesterol content. The simulations extend to 10 ns, and were performed with hydrated dipalmitoylphosphatidylcholine (DPPC) bilayers. The bilayers contain 1024 lipids of which 0-40% were cholesterol and the rest DPPC. The effects of cholesterol on the structure and mesoscopic dynamics of the bilayer were monitored as a function of cholesterol concentration. The main effects observed are a significant ordering of the DPPC chains (as monitored by NMR type order parameters), a reduced fraction of gauche bonds, a reduced surface area per lipid, less undulations--corresponding to an increased bending modulus for the membrane, smaller area fluctuations, and a reduced lateral diffusion of DPPC-lipids as well as cholesterols.

  • 33.
    Hoh, Jan H.
    et al.
    KTH.
    Heinz, William F.
    Johns Hopkins Sch Med, Physiol, Baltimore, MD USA..
    Bacterial Chemotactic Tumble Angles Reduce Backtracking and Maximize Information Gathering2015Ingår i: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 108, nr 2, s. 601A-602AArtikel i tidskrift (Övrigt vetenskapligt)
  • 34.
    Howard, Rebecca J.
    et al.
    Stockholm Univ, Dept Biochem & Biophys, Sci Life Lab, Solna, Sweden..
    Fourati, Zaineb
    Inst Pasteur, Unit Struct Dynam Macromol, Paris, France..
    Heusser, Stephanie A.
    Stockholm Univ, Dept Biochem & Biophys, Sci Life Lab, Solna, Sweden..
    Hui, Haidai
    Inst Pasteur, Unit Struct Dynam Macromol, Paris, France..
    Ruza, Reinis R.
    Inst Pasteur, Unit Struct Dynam Macromol, Paris, France..
    Sauguet, Ludovic
    Inst Pasteur, Unit Struct Dynam Macromol, Paris, France..
    Lindahl, Erik
    KTH, Skolan för teknikvetenskap (SCI), Fysik, Beräkningsbiofysik. Stockholm Univ, Dept Biochem & Biophys, Sci Life Lab, Solna, Sweden.
    Delarue, Marc
    Inst Pasteur, Unit Struct Dynam Macromol, Paris, France..
    Structural Details of an Allosteric Mechanism for Bimodal Anesthetic Modulation of Pentameric Ligand-Gated Ion Channels2018Ingår i: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 114, nr 3, s. 204A-204AArtikel i tidskrift (Övrigt vetenskapligt)
  • 35. Howard, Rebecca J.
    et al.
    Heusser, Stephanie A.
    Yoluk, Ozge
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik.
    Snow, Oliver
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik. Stockholm Univ, Sweden.
    Klement, Göran
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik. Stockholm Univ, Sweden.
    Mola, Alex R.
    Ruel, Travers M. D.
    Lindahl, Erik
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik. Stockholm Univ, Sweden.
    Transmembrane Structural Determinants of Alcohol Binding and Modulation in a Model Ligand-Gated Ion Channel2017Ingår i: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 112, nr 3, s. 554A-554AArtikel i tidskrift (Refereegranskat)
  • 36. Howard, Rebecca J.
    et al.
    Murail, Samuel
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik, Beräkningsbiofysik.
    Ondricek, Kathryn E.
    Corringer, Pierre-Jean
    Lindahl, Erik
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik, Beräkningsbiofysik.
    Trudell, James R.
    Harris, R. Adron
    Structural Basis For Alcohol Modulation of Pentameric Ligand-Gated Ion Channels2012Ingår i: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 102, nr 3, s. 411A-411AArtikel i tidskrift (Övrigt vetenskapligt)
  • 37. Howard, Rebecca J.
    et al.
    Sauguet, Ludovic
    Brömstrup, Torben
    Swedish e-Science Resarch Centre.
    Murail, Samuel
    Lee, Ui S.
    Horani, Suzzane
    Trudell, James R.
    Corringer, Pierre-Jean
    Lindahl, Erik
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik, Beräkningsbiofysik.
    Delarue, Marc
    Harris, R. Adron
    Alcohol and Anesthetic Binding to Pentameric Ligand-Gated Ion Channels Revealed in a Prokaryotic Model System2013Ingår i: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 104, nr 2, s. 635A-636AArtikel i tidskrift (Övrigt vetenskapligt)
  • 38.
    Johansson, Anna C V
    et al.
    Stockholm University.
    Lindahl, Erik
    Stockholm University.
    Amino-acid solvation structure in transmembrane helices from molecular dynamics simulations.2006Ingår i: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 91, nr 12, s. 4450-63Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Understanding the solvation of amino acids in biomembranes is an important step to better explain membrane protein folding. Several experimental studies have shown that polar residues are both common and important in transmembrane segments, which means they have to be solvated in the hydrophobic membrane, at least until helices have aggregated to form integral proteins. In this work, we have used computer simulations to unravel these interactions on the atomic level, and classify intramembrane solvation properties of amino acids. Simulations have been performed for systematic mutations in poly-Leu helices, including not only each amino acid type, but also every z-position in a model helix. Interestingly, many polar or charged residues do not desolvate completely, but rather retain hydration by snorkeling or pulling in water/headgroups--even to the extent where many of them exist in a microscopic polar environment, with hydration levels corresponding well to experimental hydrophobicity scales. This suggests that even for polar/charged residues a large part of solvation cost is due to entropy, not enthalpy loss. Both hydration level and hydrogen bonding exhibit clear position-dependence. Basic side chains cause much less membrane distortion than acidic, since they are able to form hydrogen bonds with carbonyl groups instead of water or headgroups. This preference is supported by sequence statistics, where basic residues have increased relative occurrence at carbonyl z-coordinates. Snorkeling effects and N-/C-terminal orientation bias are directly observed, which significantly reduces the effective thickness of the hydrophobic core. Aromatic side chains intercalate efficiently with lipid chains (improving Trp/Tyr anchoring to the interface) and Ser/Thr residues are stabilized by hydroxyl groups sharing hydrogen bonds to backbone oxygens.

  • 39.
    Kasimova, Marina A.
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik, Biofysik.
    Lindahl, Erik
    KTH.
    Delemotte, Lucie
    KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik, Biofysik.
    Detection of Voltage-Sensing Residues in Membrane Proteins2018Ingår i: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 114, nr 3, s. 476A-476AArtikel i tidskrift (Övrigt vetenskapligt)
  • 40.
    Kasimova, Marina
    et al.
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik.
    Yazici, Aysenur
    Granata, Daniele
    Rohacs, Tibor
    Carnevale, Vincenzo
    Dynamic Solvation of Protein Cavities Underlies TRPV1 Gating2017Ingår i: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 112, nr 3, s. 466A-466AArtikel i tidskrift (Refereegranskat)
  • 41.
    Khorshidi, Mohammad A.
    et al.
    KTH, Skolan för bioteknologi (BIO), Proteomik och nanobioteknologi.
    Vanherberghen, Bruno
    KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik, Cellens fysik.
    Önfelt, Björn
    KTH, Skolan för teknikvetenskap (SCI), Tillämpad fysik, Cellens fysik.
    Natural Killer Cell-Mediated Tumor Surveillance: Correlation Between Killing Efficiency, Transient Migration Behavior and Morphology2012Ingår i: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 102, nr 3, s. 706A-706AArtikel i tidskrift (Övrigt vetenskapligt)
  • 42. Kimanius, Dari
    et al.
    White, Stephen
    Lindahl, Erik
    KTH, Skolan för teknikvetenskap (SCI), Fysik, Beräkningsbiofysik. Stockholm University, Sweden.
    Kaback, Ronald
    Andersson, Magnus
    KTH, Skolan för teknikvetenskap (SCI), Fysik, Beräkningsbiofysik.
    Uptake Dynamics in the LacY Membrane Protein Transporter2017Ingår i: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 112, nr 3, s. 128A-128AArtikel i tidskrift (Övrigt vetenskapligt)
  • 43. Klement, Goran
    et al.
    Pouya, Iman
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik, Beräkningsbiofysik. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Yoluk, Özge
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik, Beräkningsbiofysik. KTH, Centra, Science for Life Laboratory, SciLifeLab.
    Howard, Rebecca
    Lindahl, Erik
    Ligand-Gated Ion Channel Gating Kinetics and the Opening/Closing Mechanism are Sensitive to Mutations Altering the Hydrophobicity of the Ion Conduction Pore2014Ingår i: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 106, nr 2, s. 343A-343AArtikel i tidskrift (Övrigt vetenskapligt)
  • 44. Kumar, Ramakrishnan B.
    et al.
    Hebert, Hans
    KTH, Skolan för teknik och hälsa (STH), Strukturell bioteknik.
    Jegerschold, Caroline
    Deciphering the Interaction of FLAP and 5LO2013Ingår i: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 104, nr 2, s. 540A-540AArtikel i tidskrift (Övrigt vetenskapligt)
  • 45.
    Kumar, Ramakrishnan
    et al.
    Karolinska Inst, Dept Biosci & Nutr, Huddinge, Sweden.
    Hebert, Hans
    KTH, Skolan för kemi, bioteknologi och hälsa (CBH). Karolinska Inst, Dept Biosci & Nutr, Huddinge, Sweden.
    Jegerschöld, Caroline
    KTH, Skolan för teknik och hälsa (STH). Karolinska Inst, Dept Biosci & Nutr, Huddinge, Sweden.
    Elucidating the Interaction of 5-Lipoxygenase and FLAP2015Ingår i: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 108, nr 2, s. 499A-499AArtikel i tidskrift (Övrigt vetenskapligt)
  • 46. Laurent, Benoist
    et al.
    Murail, Samuel
    Brömstrup, Torben
    KTH.
    Lindahl, Erik
    KTH, Skolan för teknikvetenskap (SCI), Teoretisk fysik, Beräkningsbiofysik.
    Baaden, Marc
    Study of the Interaction between General Anesthetics and a Bacterial Homologue to the Human Nicotinic Receptor2013Ingår i: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 104, nr 2, s. 623A-623AArtikel i tidskrift (Övrigt vetenskapligt)
  • 47. Liin, Sara
    et al.
    Gabrielsson, Anders
    KTH, Centra, SeRC - Swedish e-Science Research Centre.
    Elinder, Fredrik
    Lindahl, Erik
    The Molecular Mechanism of the Dual Spider Toxin Effect on Voltage Gated K+ Channels2016Ingår i: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 110, nr 3, s. 107A-107AArtikel i tidskrift (Övrigt vetenskapligt)
  • 48.
    Liljeblad, Jonathan F. D.
    et al.
    KTH, Skolan för kemivetenskap (CHE), Kemi, Yt- och korrosionsvetenskap.
    Bulone, Vincent
    KTH, Skolan för bioteknologi (BIO), Glykovetenskap.
    Tyrode, Eric C.
    KTH, Skolan för kemivetenskap (CHE), Kemi, Yt- och korrosionsvetenskap.
    Johnson, Magnus C.
    KTH, Skolan för kemivetenskap (CHE), Kemi, Yt- och korrosionsvetenskap.
    Rutland, Mark W.
    KTH, Skolan för kemivetenskap (CHE), Kemi, Yt- och korrosionsvetenskap.
    Molecular Structure and Stability of Phospholipid Monolayers Probed by Vibrational Sum Frequency Spectroscopy (VSFS)2012Ingår i: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 102, nr 3, s. 591A-591AArtikel i tidskrift (Övrigt vetenskapligt)
  • 49.
    Liljeblad, Jonathan F.D.
    et al.
    KTH, Skolan för kemivetenskap (CHE), Kemi, Yt- och korrosionsvetenskap.
    Bulone, Vincent
    KTH, Skolan för bioteknologi (BIO), Glykovetenskap.
    Tyrode, Eric
    KTH, Skolan för kemivetenskap (CHE), Kemi, Yt- och korrosionsvetenskap.
    Rutland, Mark W.
    KTH, Skolan för kemivetenskap (CHE), Kemi, Yt- och korrosionsvetenskap. Institute for Surface Chemistry, Stockholm, Sweden.
    Johnson, Magnus C.
    KTH, Skolan för kemivetenskap (CHE), Kemi, Yt- och korrosionsvetenskap.
    Phospholipid Monolayers Probed by Vibrational Sum Frequency Spectroscopy: Instability of Unsaturated Phospholipids2010Ingår i: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 98, s. L50-L52Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    The surface specific technique vibrational sum frequency spectroscopy has been applied to in situ studies of the degradation of Langmuir monolayers of 1,2-diacyl-phosphocholines with various degrees of unsaturation in the aliphatic chains. To monitor the degradation of the phospholipids, the time-dependent change of the monolayer area at constant surface pressure and the sum frequency intensity of the vinyl CH stretch at the carbon-carbon double bonds were measured. The data show a rapid degradation of monolayers of phospholipids carrying unsaturated aliphatic chains compared to the stable lipids carrying fully saturated chains when exposed to the ambient laboratory air. In addition, the degradation of the phospholipids can be inhibited by purging the ambient air with nitrogen. This instability may be attributed to spontaneous degradation by oxidation mediated by various reactive species in the air. To further elucidate the process of lipid oxidation in biological membranes artificial Langmuir monolayers probed by a surface specific spectroscopic technique as in this study can serve as a model system for studying the degradation/oxidation of cell membrane constituents.

  • 50.
    Lindahl, E
    et al.
    KTH, Tidigare Institutioner, Fysik.
    Edholm, O
    KTH, Tidigare Institutioner, Fysik.
    Mesoscopic undulations and thickness fluctuations in lipid bilayers from molecular dynamics simulations.2000Ingår i: Biophysical Journal, ISSN 0006-3495, E-ISSN 1542-0086, Vol. 79, nr 1, s. 426-33Artikel i tidskrift (Refereegranskat)
    Abstract [en]

    Molecular dynamics simulations of fully hydrated Dipalmitoylphosphatidylcholine bilayers, extending temporal and spatial scales by almost one order of magnitude, are presented. The present work reaches system sizes of 1024 lipids and times 10-60 ns. The simulations uncover significant dynamics and fluctuations on scales of several nanoseconds, and enable direct observation and spectral decomposition of both undulatory and thickness fluctuation modes. Although the former modes are strongly damped, the latter exhibit signs of oscillatory behavior. From this, it has been possible to calculate mesoscopic continuum properties in good agreement with experimental values. A bending modulus of 4 x 10(-20) J, bilayer area compressibility of 250-300 mN/m, and mode relaxation times in the nanosecond range are obtained. The theory of undulatory motions is revised and further extended to cover thickness fluctuations. Finally, it is proposed that thickness fluctuations is the explanation to the observed system-size dependence of equilibrium-projected area per lipid.

123 1 - 50 av 102
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