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  • 1
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    Dynamic properties of force fields (2015)
    American Institute of Physics (AIP)
    Details
    Publication Date: 2015-02-25
    Description: Molecular-dynamics simulations are increasingly used to study dynamic properties of biological systems. With this development, the ability of force fields to successfully predict relaxation timescales and the associated conformational exchange processes moves into focus. We assess to what extent the dynamic properties of model peptides (Ac-A-NHMe, Ac-V-NHMe, AVAVA, A 10 ) differ when simulated with different force fields (AMBER ff99SB-ILDN, AMBER ff03, OPLS-AA/L, CHARMM27, and GROMOS43a1). The dynamic properties are extracted using Markov state models. For single-residue models (Ac-A-NHMe, Ac-V-NHMe), the slow conformational exchange processes are similar in all force fields, but the associated relaxation timescales differ by up to an order of magnitude. For the peptide systems, not only the relaxation timescales, but also the conformational exchange processes differ considerably across force fields. This finding calls the significance of dynamic interpretations of molecular-dynamics simulations into question.
    Electronic ISSN: 1931-9223
    Topics: Chemistry and Pharmacology , Physics
    Published by American Institute of Physics (AIP)
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  • 2
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    Crystal structure of nucleotide-free dynamin (2011)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2011-09-20
    Description: Dynamin is a mechanochemical GTPase that oligomerizes around the neck of clathrin-coated pits and catalyses vesicle scission in a GTP-hydrolysis-dependent manner. The molecular details of oligomerization and the mechanism of the mechanochemical coupling are currently unknown. Here we present the crystal structure of human dynamin 1 in the nucleotide-free state with a four-domain architecture comprising the GTPase domain, the bundle signalling element, the stalk and the pleckstrin homology domain. Dynamin 1 oligomerized in the crystals via the stalks, which assemble in a criss-cross fashion. The stalks further interact via conserved surfaces with the pleckstrin homology domain and the bundle signalling element of the neighbouring dynamin molecule. This intricate domain interaction rationalizes a number of disease-related mutations in dynamin 2 and suggests a structural model for the mechanochemical coupling that reconciles previous models of dynamin function.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Faelber, Katja -- Posor, York -- Gao, Song -- Held, Martin -- Roske, Yvette -- Schulze, Dennis -- Haucke, Volker -- Noe, Frank -- Daumke, Oliver -- England -- Nature. 2011 Sep 18;477(7366):556-60. doi: 10.1038/nature10369.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Crystallography, Max-Delbruck-Centrum for Molecular Medicine, Robert-Rossle-Strasse 10, 13125 Berlin, Germany. katja.faelber@mdc-berlin.de〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21927000" target="_blank"〉PubMed〈/a〉
    Keywords: Crystallography, X-Ray ; Dynamin I/*chemistry/metabolism ; Dynamin II/genetics/metabolism ; GTP Phosphohydrolases/chemistry/metabolism ; Guanosine Triphosphate/metabolism ; HeLa Cells ; Humans ; Hydrolysis ; Models, Molecular ; Molecular Dynamics Simulation ; *Nucleotides ; Protein Binding ; Protein Structure, Tertiary ; Signal Transduction ; Transferrin/metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 3
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    Crystal structure of the dynamin tetramer (2015)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2015-08-25
    Description: The mechanochemical protein dynamin is the prototype of the dynamin superfamily of large GTPases, which shape and remodel membranes in diverse cellular processes. Dynamin forms predominantly tetramers in the cytosol, which oligomerize at the neck of clathrin-coated vesicles to mediate constriction and subsequent scission of the membrane. Previous studies have described the architecture of dynamin dimers, but the molecular determinants for dynamin assembly and its regulation have remained unclear. Here we present the crystal structure of the human dynamin tetramer in the nucleotide-free state. Combining structural data with mutational studies, oligomerization measurements and Markov state models of molecular dynamics simulations, we suggest a mechanism by which oligomerization of dynamin is linked to the release of intramolecular autoinhibitory interactions. We elucidate how mutations that interfere with tetramer formation and autoinhibition can lead to the congenital muscle disorders Charcot-Marie-Tooth neuropathy and centronuclear myopathy, respectively. Notably, the bent shape of the tetramer explains how dynamin assembles into a right-handed helical oligomer of defined diameter, which has direct implications for its function in membrane constriction.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Reubold, Thomas F -- Faelber, Katja -- Plattner, Nuria -- Posor, York -- Ketel, Katharina -- Curth, Ute -- Schlegel, Jeanette -- Anand, Roopsee -- Manstein, Dietmar J -- Noe, Frank -- Haucke, Volker -- Daumke, Oliver -- Eschenburg, Susanne -- England -- Nature. 2015 Sep 17;525(7569):404-8. doi: 10.1038/nature14880. Epub 2015 Aug 24.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institut fur Biophysikalische Chemie, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, 30625 Hannover, Germany. ; Max-Delbruck-Centrum fur Molekulare Medizin, Kristallographie, Robert-Rossle-Strasse 10, 13125 Berlin, Germany. ; Institut fur Mathematik, Freie Universitat Berlin, Arnimallee 6, 14195 Berlin, Germany. ; Leibniz-Institut fur Molekulare Pharmakologie, Robert-Rossle-Strasse 10, 13125 Berlin, Germany. ; Forschungseinrichtung Strukturanalyse, Medizinische Hochschule Hannover, Carl-Neuberg-Str. 1, 30625 Hannover, Germany. ; Institut fur Chemie und Biochemie, Freie Universitat Berlin, Takustrasse 6, 14195 Berlin, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26302298" target="_blank"〉PubMed〈/a〉
    Keywords: Charcot-Marie-Tooth Disease ; Crystallography, X-Ray ; Dynamins/*antagonists & inhibitors/*chemistry/genetics/metabolism ; Humans ; Markov Chains ; Models, Molecular ; Molecular Dynamics Simulation ; Mutant Proteins/antagonists & inhibitors/chemistry/genetics/metabolism ; Mutation/genetics ; Myopathies, Structural, Congenital ; Nucleotides ; *Protein Multimerization/genetics ; Structure-Activity Relationship
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 4
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    Spatiotemporal control of endocytosis by phosphatidylinositol-3,4-bisphosphate (2013)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2013-07-05
    Description: Phosphoinositides serve crucial roles in cell physiology, ranging from cell signalling to membrane traffic. Among the seven eukaryotic phosphoinositides the best studied species is phosphatidylinositol-4,5-bisphosphate (PI(4,5)P2), which is concentrated at the plasma membrane where, among other functions, it is required for the nucleation of endocytic clathrin-coated pits. No phosphatidylinositol other than PI(4,5)P2 has been implicated in clathrin-mediated endocytosis, whereas the subsequent endosomal stages of the endocytic pathway are dominated by phosphatidylinositol-3-phosphates(PI(3)P). How phosphatidylinositol conversion from PI(4,5)P2-positive endocytic intermediates to PI(3)P-containing endosomes is achieved is unclear. Here we show that formation of phosphatidylinositol-3,4-bisphosphate (PI(3,4)P2) by class II phosphatidylinositol-3-kinase C2alpha (PI(3)K C2alpha) spatiotemporally controls clathrin-mediated endocytosis. Depletion of PI(3,4)P2 or PI(3)K C2alpha impairs the maturation of late-stage clathrin-coated pits before fission. Timed formation of PI(3,4)P2 by PI(3)K C2alpha is required for selective enrichment of the BAR domain protein SNX9 at late-stage endocytic intermediates. These findings provide a mechanistic framework for the role of PI(3,4)P2 in endocytosis and unravel a novel discrete function of PI(3,4)P2 in a central cell physiological process.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Posor, York -- Eichhorn-Gruenig, Marielle -- Puchkov, Dmytro -- Schoneberg, Johannes -- Ullrich, Alexander -- Lampe, Andre -- Muller, Rainer -- Zarbakhsh, Sirus -- Gulluni, Federico -- Hirsch, Emilio -- Krauss, Michael -- Schultz, Carsten -- Schmoranzer, Jan -- Noe, Frank -- Haucke, Volker -- England -- Nature. 2013 Jul 11;499(7457):233-7. doi: 10.1038/nature12360. Epub 2013 Jul 3.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Leibniz Institut fur Molekulare Pharmakologie & Freie Universitat Berlin, Robert-Roessle-Strasse 10, 13125 Berlin, Germany.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23823722" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Animals ; COS Cells ; Cercopithecus aethiops ; Class II Phosphatidylinositol 3-Kinases/metabolism ; Clathrin-Coated Vesicles/metabolism ; *Endocytosis ; HEK293 Cells ; HeLa Cells ; Humans ; Molecular Sequence Data ; Phosphatidylinositol Phosphates/*metabolism ; Phosphoric Monoester Hydrolases/metabolism ; Sorting Nexins/metabolism ; Time Factors
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 5
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    Dynamic properties of force fields (2015)
    American Institute of Physics (AIP)
    Details
    Publication Date: 2015-02-25
    Description: Molecular-dynamics simulations are increasingly used to study dynamic properties of biological systems. With this development, the ability of force fields to successfully predict relaxation timescales and the associated conformational exchange processes moves into focus. We assess to what extent the dynamic properties of model peptides (Ac-A-NHMe, Ac-V-NHMe, AVAVA, A 10 ) differ when simulated with different force fields (AMBER ff99SB-ILDN, AMBER ff03, OPLS-AA/L, CHARMM27, and GROMOS43a1). The dynamic properties are extracted using Markov state models. For single-residue models (Ac-A-NHMe, Ac-V-NHMe), the slow conformational exchange processes are similar in all force fields, but the associated relaxation timescales differ by up to an order of magnitude. For the peptide systems, not only the relaxation timescales, but also the conformational exchange processes differ considerably across force fields. This finding calls the significance of dynamic interpretations of molecular-dynamics simulations into question.
    Print ISSN: 0021-9606
    Electronic ISSN: 1089-7690
    Topics: Chemistry and Pharmacology , Physics
    Published by American Institute of Physics (AIP)
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  • 6
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    Exclusion of Saccharomyces kudriavzevii from a wine model system mediated by Saccharomyces cerevisiae (2011)
    Wiley
    Details
    Publication Date: 2011-03-06
    Print ISSN: 0749-503X
    Electronic ISSN: 1097-0061
    Topics: Biology
    Published by Wiley
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  • 7
    Electronic Resource
    Electronic Resource
    α-Amino-β-(pyrazolyl-N) Propionic Acid: a New Amino-Acid from Citrullus vulgaris (Water Melon) (1959)
    [s.l.] : Nature Publishing Group
    Nature 184.1959, 4688, B.A.69-, (2 S.) 
    Details
    ISSN: 1476-4687
    Source: Nature Archives 1869 - 2009
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Notes: [Auszug] This amino-acid is unique in that it is the first example of a natural product which contains a pyrazole ring. Furthermore, in contrast to the other heterocyclic ring-containing amino-acids, histidine and tryptophan, the side-chain of $PA is attached to the pyrazole ring through a carbon to ...
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1038/184069a0
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  • 8
    Electronic Resource
    Electronic Resource
    Organometallic and coordination chemistry on phosphazenes. III. Synthesis, characterization, and electrochemical behavior of transition metal-cinnamonitrile cyclophosphazene derivatives (1996)
    Springer
    Journal of inorganic and organometallic polymers and materials 6 (1996), S. 145-170 
    Details
    ISSN: 1572-8870
    Keywords: Phosphazenes ; coordination chemistry ; synthesis ; electrochemical behavior ; transition metal ; cinnamonitrile cyclophosphazene
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract Hexakist 4-formylphenoxy cyclophosphazene (1) reacts with six equivalents of cyanomethylenetriphenylphosphorane to give hexakist 4-cinnamonitrile cyclotriphosphazene bearing 12 functional groups tsix nitriles and six olefins' able to coordinate up to 12 metals. In this way a series of polynuclear phosphazene metal derivatives (8–12) was prepared with different transition metals and in different oxidation states. Pt(0), Pt(II) and Rh(I). The analogous cinnamonitrile derivatives (3–7) were prepared and used as models for the characterization of corresponding phosphazene compounds. The redox properties of the complexes3–5 and8–10 as well as of the free cinnamonitrile2 and the free substituted cyclophosphazene1 have been investigated by cyclic voltammetry (CV) and controlled potential electrolysis (CPE) in aprotic media (THF, CH2Cl2, or NCMe 0.2M [NBu4][BF4]), at Pt electrodes. Cathodic processes have been detected only when the unsaturated C=C bond of the cinnamonitrile group is uncoordinated: hence, for compounds1. 4. and9. they are irreversible occur at potentialsE p red ca. −1.3 to ca. −1.9V vs SCE which are less cathodic than that exhibited by the free cinnamonitrile (2:E p red ca. −2.0 V vs SCE), and are believed to be centered at the electron-acceptor emptyπ * (C=C) orbital of each of the cinnamonitrile groups present in the molecule. Anodic processes are displayed only by complexes3. 5. 8. and10 with at least one Pt(0) site: they are irreversible, conceivably centered at such a metal center, and occur at potentials (E p bv ca. 0.7 1.2 V vs SCE) which are dependent on the electronic effects of the ligands, in particular the strong electron-withdrawing ability of the cyclophosphazene group. Complex10 undergoes dissociation in NCMe to form9 and possibly solvated [Pt(PPh3)2] species which adsorb at the electrode surface. No evidence for any redox process centered at the phosphazene ring has been found.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01057745
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  • 9
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    Kinetic characterization of the critical step in HIV-1 protease maturation (2012)
    National Academy of Sciences
    Details
    Publication Date: 2012-11-26
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 10
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    Collective hydrogen-bond rearrangement dynamics in liquid water (2018)
    American Institute of Physics
    Details
    Publication Date: 2018-12-28
    Print ISSN: 0021-9606
    Electronic ISSN: 1089-7690
    Topics: Chemistry and Pharmacology , Physics
    Published by American Institute of Physics
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