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  • 1
    UID:
    (DE-627)1577144406
    Format: 14
    ISSN: 2045-2322
    Content: Regulation of aquaporins is a key process of living organisms to counteract sudden osmotic changes. Aqy1, which is a water transporting aquaporin of the yeast Pichia pastoris, is suggested to be gated by chemo-mechanical stimuli as a protective regulatory-response against rapid freezing. Here, we tested the influence of temperature by determining the X-ray structure of Aqy1 at room temperature (RT) at 1.3 Å resolution, and by exploring the structural dynamics of Aqy1 during freezing through molecular dynamics simulations. At ambient temperature and in a lipid bilayer, Aqy1 adopts a closed conformation that is globally better described by the RT than by the low-temperature (LT) crystal structure. Locally, for the blocking-residue Tyr31 and the water molecules inside the pore, both LT and RT data sets are consistent with the positions observed in the simulations at room-temperature. Moreover, as the temperature was lowered, Tyr31 adopted a conformation that more effectively blocked the channel, and its motion was accompanied by a temperature-driven rearrangement of the water molecules inside the channel. We therefore speculate that temperature drives Aqy1 from a loosely- to a tightly-blocked state. This analysis provides high-resolution structural evidence of the influence of temperature on membrane-transport channels.
    Note: Gesehen am 02.07.2018 , An author correction to this article was published on 05 December 2017 , This error has now been corrected in the HTML and PDF versions of the article
    In: Scientific reports, [London] : Macmillan Publishers Limited, part of Springer Nature, 2011, 7(2017) Artikel-Nummer 4016, 14 Seiten, 2045-2322
    In: volume:7
    In: year:2017
    In: extent:14
    Language: English
    URL: Volltext  (kostenfrei)
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  • 2
    UID:
    (DE-627)715455540
    Format: Ill., graph. Darst
    Note: Göttingen, Univ., Diss., 2011
    Additional Edition: Online-Ausg. Aponte-Santamaria, Camilo Andrés Understanding the molecular machinery of aquaporins through molecular dynamics simulations 2011
    Language: English
    Keywords: Hochschulschrift
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  • 3
    UID:
    (DE-627)715456407
    Format: Online-Ressource (PDF-Datei: 130 S., 19.366 KB) , Ill., graph. Darst
    Content: Aquaporins are protein channels responsible for the permeation of water and other small solutes through biological membranes in response to osmotic pressure. The goal of the present thesis is to expand our understanding on the molecular machinery of aquaporins by employing molecular dynamics simulations and related computational techniques. First, we provide a solute permeation mechanism for the solute permeation through the Plasmodium falciparum aquaglyceroporin that is a promising antimalarial drug target. In this mechanism, hydrophobic regions in the middle of the channel are the main water rate limiting barriers. In addition, the replacement of water-arginine interactions by solute-arginine interactions and the matching of the solute at the most constricted region of the channel are the main determinants underlying selectivity for the permeation of solutes like glycerol and urea ...
    Note: Göttingen, Univ., Diss., 2011
    Additional Edition: Druckausg. Aponte-Santamaria, Camilo Andrés Understanding the molecular machinery of aquaporins through molecular dynamics simulations 2011
    Language: English
    Keywords: Hochschulschrift
    URL: Volltext  (kostenfrei)
    URL: Volltext  (kostenfrei)
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  • 4
    UID:
    (DE-627)1577143434
    Format: 9
    ISSN: 1542-0086
    Content: The large multimeric glycoprotein von Willebrand Factor (VWF) plays a pivotal adhesive role during primary hemostasis. VWF is cleaved by the protease ADAMTS13 as a down-regulatory mechanism to prevent excessive VWF-mediated platelet aggregation. For each VWF monomer, the ADAMTS13 cleavage site is located deeply buried inside the VWF A2 domain. External forces in vivo or denaturants in vitro trigger the unfolding of this domain, thereby leaving the cleavage site solvent-exposed and ready for cleavage. Mutations in the VWF A2 domain, facilitating the cleavage process, cause a distinct form of von Willebrand disease (VWD), VWD type 2A. In particular, the VWD type 2A Gly1629Glu mutation drastically accelerates the proteolytic cleavage activity, even in the absence of forces or denaturants. However, the effect of this mutation has not yet been quantified, in terms of kinetics or thermodynamics, nor has the underlying molecular mechanism been revealed. In this study, we addressed these questions by using fluorescence correlation spectroscopy, molecular dynamics simulations, and free energy calculations. The measured enzyme kinetics revealed a 20-fold increase in the cleavage rate for the Gly1629Glu mutant compared with the wild-type VWF. Cleavage was found cooperative with a cooperativity coefficient n = 2.3, suggesting that the mutant VWF gives access to multiple cleavage sites of the VWF multimer at the same time. According to our simulations and free energy calculations, the Gly1629Glu mutation causes structural perturbation in the A2 domain and thereby destabilizes the domain by ∼10 kJ/mol, promoting its unfolding. Taken together, the enhanced proteolytic activity of Gly1629Glu can be readily explained by an increased availability of the ADAMTS13 cleavage site through A2-domain-fold thermodynamic destabilization. Our study puts forward the Gly1629Glu mutant as a very efficient enzyme substrate for ADAMTS13 activity assays.
    Note: Available online 10 January 2017 , Gesehen am 02.07.2018
    In: Biophysical journal, Cambridge, Mass. : Cell Press, 1960, 112(2017), 1, Seite 57-65, 1542-0086
    In: volume:112
    In: year:2017
    In: number:1
    In: pages:57-65
    In: extent:9
    Language: English
    URL: Volltext  (kostenfrei)
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  • 5
    UID:
    (DE-627)1666499587
    Format: 8
    ISSN: 1542-0086
    Content: 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.
    Note: Available online 1 December 2018 , Gesehen am 31.05.2019
    In: Biophysical journal, Cambridge, Mass. : Cell Press, 1960, 116(2019), 1, Seite 4-11, 1542-0086
    In: volume:116
    In: year:2019
    In: number:1
    In: pages:4-11
    In: extent:8
    Language: English
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  • 6
    UID:
    (DE-627)1741222168
    Format: 12
    ISSN: 1362-4962
    Content: Abstract. Neutrophils release their intracellular content, DNA included, into the bloodstream to form neutrophil extracellular traps (NETs) that confine and kil
    Note: Gesehen am 26.11.2020 , A corrigendum to this article was published on 22 October 2020
    In: Nucleic acids research, Oxford : Oxford Univ. Press, 1974, 48(2020), 13, Seite 7333-7344, 1362-4962
    In: volume:48
    In: year:2020
    In: number:13
    In: pages:7333-7344
    In: extent:12
    Language: English
    URL: Volltext  (lizenzpflichtig)
    URL: Volltext  (lizenzpflichtig)
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  • 7
    UID:
    (DE-627)1582372217
    Format: 10
    ISSN: 2045-2322
    Content: Disulfide bonds are key stabilizing and yet potentially labile cross-links in proteins. While spontaneous disulfide rearrangement through thiol-disulfide exchange is increasingly recognized to play an important physiological role, its molecular determinants are still largely unknown. Here, we used a novel hybrid Monte Carlo and Molecular Dynamics scheme to elucidate the molecular principles of thiol-disulfide exchange in proteins, for a mutated immunoglobulin domain as a model system. Unexpectedly, using simple proximity as the criterion for thiol-disulfide exchange, our method correctly predicts the experimentally observed regiospecificity and selectivity of the cysteine-rich protein. While redox reactivity has been examined primarily on the level of transition states and activation barriers, our results argue for accessibility of the disulfide by the attacking thiol given the highly dynamic and sterically demanding protein as a major bottleneck of thiol-disulfide exchange. This scenario may be similarly at play in other proteins with or without an evolutionarily designed active site.
    Note: Gesehen am 29.10.2018
    In: Scientific reports, [London] : Macmillan Publishers Limited, part of Springer Nature, 2011, 7(2017), Artikel-ID 9858, 2045-2322
    In: volume:7
    In: year:2017
    In: elocationid:9858
    In: extent:10
    Language: English
    URL: Volltext  (kostenfrei)
    URL: Volltext  (kostenfrei)
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  • 8
    UID:
    (DE-627)1582469369
    Format: 8
    ISSN: 1095-8657
    Content: The von Willebrand factor (VWF) is a glycoprotein in the blood that plays a central role in hemostasis. Among other functions, VWF is responsible for platelet adhesion at sites of injury via its A1 domain. Its adjacent VWF domain A2 exposes a cleavage site under shear to degrade long VWF fibers in order to prevent thrombosis. Recently, it has been shown that VWF A1/A2 interactions inhibit the binding of platelets to VWF domain A1 in a force-dependent manner prior to A2 cleavage. However, whether and how this interaction also takes place in longer VWF fragments as well as the strength of this interaction in the light of typical elongation forces imposed by the shear flow of blood remained elusive. Here, we addressed these questions by using single molecule force spectroscopy (SMFS), Brownian dynamics (BD), and molecular dynamics (MD) simulations. Our SMFS measurements demonstrate that the A2 domain has the ability to bind not only to single A1 domains but also to VWF A1A2 fragments. SMFS experiments of a mutant [A2] domain, containing a disulfide bond which stabilizes the domain against unfolding, enhanced A1 binding. This observation suggests that the mutant adopts a more stable conformation for binding to A1. We found intermolecular A1/A2 interactions to be preferred over intramolecular A1/A2 interactions. Our data are also consistent with the existence of two cooperatively acting binding sites for A2 in the A1 domain. Our SMFS measurements revealed a slip-bond behavior for the A1/A2 interaction and their lifetimes were estimated for forces acting on VWF multimers at physiological shear rates using BD simulations. Complementary fitting of AFM rupture forces in the MD simulation range adequately reproduced the force response of the A1/A2 complex spanning a wide range of loading rates. In conclusion, we here characterized the auto-inhibitory mechanism of the intramolecular A1/A2 bond as a shear dependent safeguard of VWF, which prevents the interaction of VWF with platelets.
    Note: Published online: 23 April 2016 , Gesehen am 31.10.2018
    In: Journal of structural biology, San Diego, Calif. : Elsevier, 1990, 197(2017), 1, Seite 57-64, 1095-8657
    In: volume:197
    In: year:2017
    In: number:1
    In: pages:57-64
    In: extent:8
    Language: English
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  • 9
    UID:
    (DE-627)1662428073
    Format: 7
    ISSN: 1520-5207
    Content: Mechanical perturbations are ubiquitous in living cells, and many biological functions are dependent on the mechanical response of lipid membranes. Recent force-spectroscopy studies have captured the stepwise fracture of stacks of bilayers, avoiding substrate effects. However, the effect of stacking bilayers, as well as the exact molecular mechanism of the fracture process, is unknown. Here, we use atomistic and coarse-grained force-clamp molecular dynamics simulation to assess the effects of mechanical indentation on stacked and single bilayers. Our simulations show that the rupture process obeys the laws of force-activated barrier crossing, and stacking multiple membranes stabilizes them. The rupture times follow a log-normal distribution which allows the interpretation of membrane rupture as a pore-growth process. Indenter hydrophobicity determines the type of pore formation, the preferred dwelling region, and the resistance of the bilayer against rupture. Our results provide a better understanding of the nanomechanics underlying the plastic rupture of lipid membranes.
    Note: Gesehen am 27.03.2019
    In: The journal of physical chemistry. B, Biophysics, biomaterials, liquids, and soft matter, Washington, DC : Americal Chemical Society, 1997, 122(2018), 28, Seite 7073-7079, 1520-5207
    In: volume:122
    In: year:2018
    In: number:28
    In: pages:7073-7079
    In: extent:7
    Language: English
    URL: Volltext  (kostenfrei)
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  • 10
    UID:
    (DE-627)1577137868
    Format: 4
    ISSN: 1520-5126
    Content: Membrane tension plays various critical roles in the cell. We here asked how fast and how far localized pulses of mechanical stress dynamically propagate through biological lipid bilayers. In both coarse-grained and all-atom molecular dynamics simulations of a dipalmitoylphosphatidylcholine lipid bilayer, we observed nanometer-wide stress pulses, propagating very efficiently longitudinally at a velocity of approximately 1.4 ± 0.5 nm/ps (km/s), in close agreement with the expected speed of sound from experiments. Remarkably, the predicted characteristic attenuation time of the pulses was in the order of tens of picoseconds, implying longitudinal stress propagation over length scales up to several tens of nanometers before damping. Furthermore, the computed dispersion relation leading to such damping was consistent with proposed continuum viscoelastic models of propagation. We suggest this mode of stress propagation as a potential ultrafast mechanism of signaling that may quickly couple mechanosensitive elements in crowded biological membranes.
    Note: Published online 30 August 2017 , Gesehen am 02.07.2018
    In: American Chemical Society, Journal of the American Chemical Society, Washington, DC : ACS Publications, 1879, 139(2017), 39, Seite 13588-13591, 1520-5126
    In: volume:139
    In: year:2017
    In: number:39
    In: pages:13588-13591
    In: extent:4
    Language: English
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