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Träfflista för sökning "WFRF:(Marrink Siewert Jan) "

Sökning: WFRF:(Marrink Siewert Jan)

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1.
  • Murtola, Teemu, et al. (författare)
  • Low density lipoprotein : structure, dynamics, and interactions of apoB-100 with lipids
  • 2011
  • Ingår i: Soft Matter. - : Royal Society of Chemistry (RSC). - 1744-683X .- 1744-6848. ; 7:18, s. 8135-8141
  • Tidskriftsartikel (refereegranskat)abstract
    • Low-density lipoprotein (LDL) transports cholesterol in the bloodstream and plays an important role in the development of cardiovascular diseases, in particular atherosclerosis. Despite its importance to health, the structure of LDL is not known in detail. This is worrying since the lack of LDL's structural information makes it more difficult to understand its function. In this work, we have combined experimental and theoretical data to construct LDL models comprised of the apoB-100 protein wrapped around a lipid droplet of about 20 nm in size. The models are considered by near-atomistic multi-microsecond simulations to unravel structural as well as dynamical properties of LDL, with particular attention paid to lipids and their interactions with the protein. We find that the distribution and the ordering of the lipids in the LDL particle are rather complex. The previously proposed 2- and 3- layer models turn out to be inadequate to describe the properties of the lipid droplet. At the surface of LDL, apoB-100 is found to interact favorably with cholesterol and its esters. The interactions of apoB-100 with core molecules, in particular cholesteryl esters, are rather frequent and arise from hydrophobic amino acids interacting with the ring of cholesteryl esters, and also in part from the rather loose packing of lipids at the surface of the lipoparticle. The loose packing may foster the function of transfer proteins, which transport lipids between lipoproteins. Finally, the comparison of the several apoB-100 models in our study suggests that the properties of lipids in LDL are rather insensitive to the conformation of apoB-100. Altogether, the findings pave the way for further studies of LDL to better understand the central steps in the emergence of atherosclerosis.
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2.
  • Smeets, Cleo J. L. M., et al. (författare)
  • Altered secondary structure of Dynorphin A associates with loss of opioid signalling and NMDA-mediated excitotoxicity in SCA23
  • 2016
  • Ingår i: Human Molecular Genetics. - : Oxford University Press (OUP). - 0964-6906 .- 1460-2083. ; 25:13, s. 2728-2737
  • Tidskriftsartikel (refereegranskat)abstract
    • Spinocerebellar ataxia type 23 (SCA23) is caused by missense mutations in prodynorphin, encoding the precursor protein for the opioid neuropeptides alpha-neoendorphin, Dynorphin (Dyn) A and Dyn B, leading to neurotoxic elevated mutant Dyn A levels. Dyn A acts on opioid receptors to reduce pain in the spinal cord, but its cerebellar function remains largely unknown. Increased concentration of or prolonged exposure to Dyn A is neurotoxic and these deleterious effects are very likely caused by an N-methyl-D-aspartate-mediated non-opioidmechanism as Dyn A peptides were shown to bind NMDA receptors and potentiate their glutamate-evoked currents. In the present study, we investigated the cellular mechanisms underlying SCA23-mutant Dyn A neurotoxicity. We show that SCA23 mutations in the Dyn A-coding region disrupted peptide secondary structure leading to a loss of the N-terminal alpha-helix associated with decreased kappa-opioid receptor affinity. Additionally, the altered secondary structure led to increased peptide stability of R6W and R9C Dyn A, as these peptides showed marked degradation resistance, which coincided with decreased peptide solubility. Notably, L5S Dyn A displayed increased degradation and no aggregation. R6W and wt Dyn A peptides were most toxic to primary cerebellar neurons. For R6W Dyn A, this is likely because of a switch from opioid to NMDA-receptor signalling, while for wt Dyn A, this switch was not observed. We propose that the pathology of SCA23 results from converging mechanisms of loss of opioid-mediated neuroprotection and NMDA-mediated excitotoxicity.
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3.
  • Wohlert, Jakob, 1976- (författare)
  • Atomistic computer simulations of lipid bilayers
  • 2006
  • Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
    • Computer simulation has become an important tool for the study of biomolecular systems. This thesis deals with molecular dynamics simulations of one-component lipid bilayers, which may serve as models for biological membranes. The main scientific contributions are: • It is possible to analyze the electrostatic contribution to the surface tension at a lipid-water interface in terms of dipole-dipole interactions between lipid headgroup shielded by a dielectric medium (water). The interaction can be divided into two parts. The in-plane components of the dipoles give rise to a positive, i.e. contractive contribution to the surface tension, albeit rather short ranged due to them being fluctuating dipoles. The normal components give rise to a negative, i.e. expansive contribution that will dominate the interaction at large distances. • Simulated membrane areas are extremely sensitive to details, especially the treatment of long-range electrostatic interactions. When cut-offs are used for the electrostatics, the exact definition of charge groups play an important role. Furthermore, using Ewald summation for the long-range interactions seems to have an overall stabilizing effect, and the area becomes less sensitive to other factors, such as system size and hydration. • Using atomistic simulations it is possible to study formation and evolution of a hydrophilic trans-membrane pore in detail. Free energy of pore nucleation and expansion can be calculated using potentials of mean constraint force. The resulting free energy profile shows no local maximum between the intact and pre-pore states, contrary to what is suggested by experiments. • The present force field reproduces even the slowest dynamics in the lipid chains, as reflected in NMR relaxation rates. Furthermore, since the simulated system was relatively small, the experimentally observed variation of relaxation rates with Larmor frequency cannot be explained by large scale collective dynamics, or it would not have shown up in the simulation. • Lipid lateral diffusion can be studied in detail on all relevant time scales by molecular dynamics. Using simple assumptions, the different diffusion coefficients measured on short and long times respectively can be connected in an analytic expression that fit calculated mean square displacements on timescales ranging from picoseconds to hundreds of nanoseconds.
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