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  • 1.
    Andersson, C. David
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Martinez, Nicolas
    Zeller, Dominik
    Allgardsson, Anders
    Koza, Michael M.
    Frick, Bernhard
    Ekström, Fredrik
    Peters, Judith
    Linusson, Anna
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Influence of Enantiomeric Inhibitors on the Dynamics of Acetylcholinesterase Measured by Elastic Incoherent Neutron Scattering2018Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 122, nr 36, s. 8516-8525Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The enzyme acetylcholinesterase (AChE) is essential in humans and animals because it catalyzes the breakdown of the nerve-signaling substance acetylcholine. Small molecules that inhibit the function of AChE are important for their use as drugs in the, for example, symptomatic treatment of Alzheimer's disease. New and improved inhibitors are warranted, mainly because of severe side effects of current drugs. In the present study, we have investigated if and how two enantiomeric inhibitors of AChE influence the overall dynamics of noncovalent complexes, using elastic incoherent neutron scattering. A fruitful combination of univariate models, including a newly developed non-Gaussian model for atomic fluctuations, and multivariate methods (principal component analysis and discriminant analysis) was crucial to analyze the fine details of the data. The study revealed a small but clear increase in the dynamics of the inhibited enzyme compared to that of the noninhibited enzyme and contributed to the fundamental knowledge of the mechanisms of AChE-inhibitor binding valuable for the future development of inhibitors.

  • 2.
    Andersson, Ove
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysik.
    Häussermann, Ulrich
    A Second Glass Transition in Pressure Collapsed Type II Clathrate Hydrates2018Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 122, nr 15, s. 4376-4384Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Type II clathrate hydrates (CHs) M·17 H2O, with M = tetrahydrofuran (THF) or 1,3-dioxolane, are known to collapse, or amorphize, on pressurization to ∼1.3 GPa in the temperature range 77–140 K. On heating at 1 GPa, these pressure-amorphized CH states show a weak, stretched sigmoid-shaped, heat-capacity increase because of a glass transition. Here we use thermal conductivity and heat capacity measurements to show that also type II CH with M = cyclobutanone (CB) collapses on isothermal pressurization and undergoes a similar, weak, glass transition upon heating at 1 GPa. Furthermore, we reveal for both THF CH and CB CH a second, much more pronounced, glass transition at temperatures above the thermally weak glass transition on heating in the 0.2–0.7 GPa range. This result suggests the general occurrence of two glass transitions in water-rich (94 mol %) pressure-collapsed CHs. Because of a large increase in dielectric permittivity concurrently as the weak heat capacity increase, the first glass transition must be due to kinetic unfreezing of water molecules. The thermal features of the second glass transition, measured on isobaric temperature cycling, are typical of a glass–liquid–glass transition, which suggests that pressure-amorphized CHs transform reversibly to liquids.

  • 3.
    Andersson, Ove
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysik.
    Nakazawa, Yasuhiro
    Transitions in pressure collapsed clathrate hydrates2015Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 119, nr 9, s. 3846-3853Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Type II clathrate hydrates (CHs), or ice clathrates, are inclusion compounds in which a hydrogen-bonded cage-like structure of H2O accommodates molecules of suitable size, known as guest molecules. CHs have similar local geometrical arrangements of the hydrogen-bonded water network as ice and both are known to collapse to amorphous states on isothermal pressurization at temperatures below about 140 K. Moreover, the collapsed CH states undergo a glass, or glass-like, transition at 140 K on heating at 1 GPa, which is identical to that of collapsed ice, or high density amorphous ice. Here we use thermal conductivity and dielectric measurements to study the transition behavior of two type II CHs with tetrahydrofuran and 1,3 dioxolane, respectively, as guest molecules. After their collapsed states have been heated to well above the glass transition at 1 GPa, we find transitions corresponding to the high to low density amorphous ice transition of ice with only slightly shifted temperature-pressure (T-p) coordinates compared to those of pure water. Thus, collapsed CHs show the same transition behaviors as cold water, which provide the basis for the model that explains the unusual temperature and pressure behaviors of waters properties in terms of two distinct types of liquid water. Collapsed CHs are, however, more stable than collapsed ice and can therefore be studied in a wider T-p interval. The results suggest sluggish homogenizing and phase separation processes, which affect the transition behaviors of collapsed CHs.

  • 4.
    Dzwilewski, Andrzej
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysik.
    Matyba, Piotr
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysik.
    Edman, Ludvig
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysik.
    Facile fabrication of efficient organic CMOS circuits2010Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 114, nr 1, s. 135-140Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Organic electronic circuits based on a combination of n- and p-type transistors (so-called CMOS circuits) are attractive, since they promise the realization of a manifold of versatile and low-cost electronic devices. Here, we report a novel photoinduced transformation method, which allows for a particularly straightforward fabrication of highly functional organic CMOS circuits. A solution-deposited single-layer film, comprising a mixture of the n-type semiconductor [6,6]-phenyl-C61-butyric acid methyl ester (PCBM) and the p-type semiconductor poly-3-hexylthiophene (P3HT) in a 3:1 mass ratio, was utilized as the common active material in an array of transistors. Selected film areas were exposed to laser light, with the result that the irradiated PCBM monomers were photochemically transformed into a low-solubility and high-mobility dimeric state. Thereafter, the entire film was developed via immersion into a developer solution, which selectively removed the nonexposed, and monomeric, PCBM component. The end result was that the transistors in the exposed film areas are n-type, as dimeric PCBM is the majority component in the active material, while the transistors in the nonexposed film areas are p-type, as P3HT is the sole remaining material. We demonstrate the merit of the method by utilizing the resulting combination of n-type and p-type transistors for the realization of CMOS inverters with a high gain of ∼35.

  • 5.
    Håkansson, Pär
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Isaksson, Mikael
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Westlund, Per-Olof
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Johansson, Lennart B-Å
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Extended Förster theory for determining intraprotein distances: 1. The K2-dynamics and fluorophore reorientation2004Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 108, nr 44, s. 17243-17250Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    A detailed analysis of the previously developed (J. Chem. Phys. 1996, 105, 10896) extended Förster theory (EFT) is presented for analyzing electronic energy migration within pairs of donors (D). Synthetic data that mimics experimental time-correlated single photon counting data were generated and re-analyzed. To cover a wide dynamic range and various orientational restrictions, the rates of reorientation, as well as the orientational configurations of the interacting D-groups were varied. In general DD distances are recovered within an error limit of 5%, while the errors in orientational configurations are usually larger. The Maier−Saupe and cone potentials were used to generate an immense variety of orientational trajectories. The results obtained exhibit no significant dependence on the choice of potential function used for generating EFT data. Present work demonstrates how to overcome the classical “κ2-problem” and the frequently applied approximation of κ2 = 2/3 in the data analyses. This study also outlines the procedure for analyzing fluorescence depolarization data obtained for proteins, which are specifically labeled with D-groups. The EFT presented here brings the analyses of DDEM data to the same level of molecular detail as in ESR- and NMR-spectroscopy.

  • 6.
    Kalinin, Stanislav
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Johansson, Lennart B-Å
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Energy migration and transfer rates are invariant to modeling the fluorescence relaxation by discrete and continuous distributions of lifetimes2004Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, ISSN 1520-6106, Vol. 108, nr 9, s. 3092-3097Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Fluorescent groups typically exhibit nonexponential photophysics when incorporated into biomolecular structures, e.g., proteins and lipid membranes. Models assuming discrete and continuous distributions of lifetimes can each accurately describe the observed relaxation. In the analyses of energy transfer and PDDEM (partial donor-donor energy migration) experiments, one frequently needs to model the nonexponential decays of noninteracting donor and acceptor groups. The present paper aims at exploring whether calculated transfer/migration rates depend on modeling the photophysics' decay by discrete or continuous distributions of lifetimes. Discrete or continuous distribution models of the decay, generated synthetically, were analyzed as well as true experimental data. Two proteins were studied. In one of the systems, we examined energy transfer from Trp (donor) to BODIPY (acceptor) in ribosomal protein S6, obtained from Thermus thermophilus. In the second system, we examined PDDEM between different BODIPY derivatives that were pairwise specifically incorporated in mutant forms of plasminogen activator inhibitor type 2. Interestingly, the rates of electronic energy migration/transfer and distances determined within pairs of interacting chromophores reveal small or negligible influence on using discrete or continuous distributions of lifetimes.

  • 7.
    Kalinin, Stanislav
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Molotkovsky, Julian G
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Johansson, Lennart B-Å
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Distance Measurements Using Partial Donor-Donor Energy Migration within Pairs of Fluorescent Groups in Lipid Bilayers.2003Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 107, nr 14, s. 3318-3324Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    For distance measurements the fluorescence relaxation was explored within pairwise interacting chemically identical, but photophysically different fluorescent groups. The recently developed theory (Kalinin, S. V.; et al. Spectrochim. Acta, Part A 2002, 58, 1087-1097) of partial donor-donor energy migration (PDDEM) was tested on lipid vesicles as a model system, which, for example, enables arrangement of a pH gradient between the inside and outside of the lipid bilayer. Time-correlated single-photon counting and steady-state fluorescence experiments were performed on mono- and bis-lipid derivatives of fluorescein solubilized in lipid bilayers. The PDDEM approach was successfully applied in the analyses of the different experiments. The distances extracted between the fluorescein groups of bis-fluorescein derivatives in lipid vesicles composed 1,2-dioleoyl-sn-glycero-3-phosphocholine and 1,2-dimyristoyl-sn-glycero-3-phosphocholine were found to be in reasonable agreement with independent measurements of the bilayer thickness.

  • 8. Krivchikov, Alexander I.
    et al.
    Andersson, Ove
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Institutionen för fysik.
    Thermal Conductivity of Triphenyl Phosphite's Liquid, Glassy, and Glacial States2016Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 120, nr 10, s. 2845-2853Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The thermal conductivity kappa and heat capacity per unit volume rho C-p of triphenyl phosphite (TPP) were measured under different pressure and temperature conditions, and with time during the sluggish liquid to glacial state transformation at temperatures about 15 K above the glass transition temperature. As the transformation slowly proceeds during several hours, rho C-p decreases monotonically from that of the liquid state to a value close to that of the vitrified state. Concurrently, kappa increases nonmonotonically with an intermediate local maximum followed by a minimum, before the final rise to a higher kappa. The properties of the ultimately formed glacial state depend on the thermal history, which implies that the state formed under these conditions is a heterogeneous mixture of nanocrystals and mainly amorphous-like solid, and that the relative amount and microstructure depend on the conditions of the transformation. The nonmonotonic changes in phonon propagation during the liquid to glacial transformation suggest microstructural changes which are consistent with a liquid-liquid transformation and sluggish growth of nanocrystals within amorphous-like solid domains. The isobaric thermal conductivity of the as-formed glacial state shows a reversible step increase, just prior to crystallization on heating, which deviates from the typical behavior of glasses, liquids, and crystals. An increase in pressure shifts the step to higher temperatures and suppresses crystallization, which reveals another reversible rise in kappa and C-p. These results show that increased molecular mobility in the glacial state increases and suggest reduced thermal resistance at boundaries or that the motions carry heat.

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  • 9.
    Nilsson, Lina
    et al.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Ådén, Jörgen
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Niemiec, Moritz S.
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Nam, Kwangho
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen. Computational Life Science Center (CLiC), Umeå University,.
    Wittung-Stafshede, Pernilla
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Small pH and Salt Variations Radically Alter the Thermal Stability of Metal-Binding Domains in the Copper Transporter, Wilson Disease Protein2013Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 117, nr 42, s. 13038-13050Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Although strictly regulated, pH and solute concentrations in cells may exhibit temporal and spatial fluctuations. Here we study the effect of such changes on the stability, structure, and dynamics in vitro and in silico of a two-domain construct (WD56) of the fifth and sixth metal-binding domains of the copper transport protein, ATP7B (Wilson disease protein). We find that the thermal stability of WD56 is increased by 40 °C when increasing the pH from 5.0 to 7.5. In contrast, addition of salt at pH 7.2 decreases WD56 stability by up to 30 °C. In agreement with domain-domain coupling, fractional copper loading increases the stability of both domains. HSQC chemical shift changes demonstrate that, upon lowering the pH from 7.2 to 6, both His in WD6 as well as the second Cys of the copper site in each domain become protonated. MD simulations reveal increased domain-domain fluctuations at pH 6 and in the presence of high salt concentration, as compared to at pH 7 and low salt concentration. Thus, the surface charge distribution at high pH contributes favorably to overall WD56 stability. By introducing more positive charges by lowering the pH, or by diminishing charge-charge interactions by salt, fluctuations among the domains are increased and thereby overall stability is reduced. Copper transfer activity also depends on pH: delivery of copper from chaperone Atox1 to WD56 is more efficient at pH 7.2 than at pH 6 by a factor of 30. It appears that WD56 is an example where the free energy landscapes for folding and function are linked via structural stability.

  • 10. Ovchinnikov, Victor
    et al.
    Nam, Kwangho
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Karplus, Martin
    A Simple and Accurate Method To Calculate Free Energy Profiles and Reaction Rates from Restrained Molecular Simulations of Diffusive Processes2016Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 120, nr 33, s. 8457-8472Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    A method is developed to obtain simultaneously free energy profiles and diffusion constants from restrained molecular simulations in diffusive systems. The method is based on low-order expansions of the free energy and diffusivity as functions of the reaction coordinate. These expansions lead to simple analytical relationships between simulation statistics and model parameters. The method is tested on 1D and 2D model systems; its accuracy is found to be comparable to or better than that of the existing alternatives, which are briefly discussed. An important aspect of the method is that the free energy is constructed by integrating its derivatives, which can be computed without need for overlapping sampling windows. The implementation of the method in any molecular simulation program that supports external umbrella potentials (e.g., CHARMM) requires modification of only a few lines of code. As a demonstration of its applicability to realistic biomolecular systems, the method is applied to model the alpha-helix <-> beta-sheet transition in a 16-residue peptide in implicit solvent, with the reaction coordinate provided by the string method. Possible modifications of the method are briefly discussed; they include generalization to multidimensional reaction coordinates [in the spirit of the model of Ermak and McCammon (Ermak, D. L.; McCammon, J. A. J. Chem. Phys. 1978, 69, 1352-1360)], a higher-order expansion of the free energy surface, applicability in nonequilibrium systems, and a simple test for Markovianity. In view of the small overhead of the method relative to standard umbrella sampling, we suggest its routine application in the cases where umbrella potential simulations are appropriate.

  • 11. Rodriguez-Granillo, Agustina
    et al.
    Crespo, Alejandro
    Estrin, Dario A
    Wittung-Stafshede, Pernilla
    Umeå universitet, Teknisk-naturvetenskapliga fakulteten, Kemiska institutionen.
    Copper-transfer mechanism from the human chaperone Atox1 to a metal-binding domain of Wilson disease protein2010Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 114, nr 10, s. 3698-3706Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The molecular details of how copper (Cu) is transferred from the human Cu chaperone Atox1 to metal-binding domains (MBDs) of P(1B)-type ATPases are still unclear. Here, we use a computational approach, employing quantum mechanics/molecular mechanics (QM/MM) methods, to shed light on the reaction mechanism [probable intermediates, Cu(I) coordination geometries, activation barriers, and energetics] of Cu(I) transfer from Atox1 to the fourth MBD of Wilson disease protein (WD4). Both Atox1 and WD4 have solvent-exposed metal-binding motifs with two Cys residues that coordinate Cu(I). After assessing the existence of all possible 2-, 3- and 4-coordinate Cu-intermediate species, one dominant reaction path emerged. First, without activation barrier, WD4's Cys1 binds Cu(I) in Atox1 to form a 3-coordinated intermediate. Next, with an activation barrier of about 9.5 kcal/mol, a second 3-coordinated intermediate forms that involves both of the Cys residues in WD4 and Cys1 of Atox1. This species can then form the product by decoordination of Atox1's Cys1 (barrier of about 8 kcal/mol). Overall, the Cu-transfer reaction from Atox1 to WD4 appears to be kinetically accessible but less energetically favorable (DeltaE = 7.7 kcal/mol). Our results provide unique insights into the molecular mechanism of protein-mediated Cu(I) transfer in the secretory pathway and are in agreement with existing experimental data.

  • 12.
    Xu, Weixin
    et al.
    East China Normal University, Shanghai, China.
    Zhang, Ce
    Umeå universitet, Medicinska fakulteten, Institutionen för medicinsk kemi och biofysik.
    Morozova-Roche, Ludmilla
    Umeå universitet, Medicinska fakulteten, Institutionen för medicinsk kemi och biofysik.
    Zhang, John Z H
    East China Normal University, Shanghai, China.
    Mu, Yuguang
    School of Biological Sciences, Nanyang Technological University, Singapore.
    pH-Dependent Conformational Ensemble and Polymorphism of Amyloid-beta Core Fragment2013Inngår i: Journal of Physical Chemistry B, ISSN 1520-6106, E-ISSN 1520-5207, Vol. 117, nr 28, s. 8392-9Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    Characterization of amyloid oligomeric species is important due to its possible responsibility for the toxicity of amyloid proteins, whereas it is difficult to detect by current spectroscopic techniques. The pH-dependent tetramerization and fibrillation of the central hydrophobic segment of Alzheimer amyloid β-peptide (Aβ(12-24)) were respectively explored by all-atom replica exchange molecular dynamics simulations and by fluorescence and atomic force microscopy measurements. Our combined study shows that more β-sheet structures in the early event of tetramerization is linked directly to the high propensity to form amyloid fibrils in the consequent fibrillation. Both tetramerization and fibrillation are strongly regulated by pH. At pH 5.0, Aβ(12-24) has two opposite terminal charges. The electrostatic attraction between the side-chains of His13/His14 and Glu22/Asp23 thus acts as a "pattern keeper", resulting in high propensity of amyloid formation. These results suggest that pH effects most likely by affecting the ionization properties of the Aβ(12-24) peptide. Specifically, the pH-dependent equilibrium conformational distribution of different aggregate species are well-investigated in detail. Our findings also give hints to other experimental findings that the kinetics and morphologies of Aβ fibril formation are strongly pH-dependent.

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