Research Area A - Publications 2016

Proteins, DOI: 10.1002/prot.25196
Proteins, online article

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The ATTRACT coarse-grained docking approach in combination with various types of atomistic, flexible refinement methods has been applied to predict protein-protein and peptide-protein complexes in CAPRI rounds 28–36. For a large fraction of CAPRI targets (12 out of 18), at least one model of acceptable or better quality was generated, corresponding to a success ...

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PNAS, doi: 10.1073/pnas.1605873113
PNAS, online article

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An essential early step in the assembly of human spliceosomes onto pre-mRNA involves the recognition of regulatory RNA cis elements in the 3′ splice site by the U2 auxiliary factor (U2AF). The large (U2AF65) and small (U2AF35) subunits of the U2AF heterodimer contact the polypyrimidine tract (Py-tract) and the AG-dinucleotide, respectively. The tandem RNA ...

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Structure, Volume 24, Issue 11, p1936–1946, DOI: http://dx.doi.org/10.1016/j.str.2016.08.015
Structure, online article

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HIV-1 integrase (IN) catalyzes viral DNA integration into the host genome and facilitates multifunctional steps including virus particle maturation. Competency of IN to form multimeric assemblies is functionally critical, presenting an approach for anti-HIV strategies. Multimerization of IN depends on interactions between the distinct subunit domains and among ...

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J. Chem. Phys. 145, 124103, http://dx.doi.org/10.1063/1.4962260
J. Chem. Phys., online article

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We present a (sub)linear-scaling algorithm to determine indirect nuclear spin–spin coupling constants at the Hartree–Fock and Kohn–Sham density functional levels of theory. Employing efficient integral algorithms and sparse algebra routines, an overall (sub)linear scaling behavior can be obtained for systems with a non-vanishing HOMO-LUMO gap. Calculations on ...

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J. Chem. Theory Comput., 12 (10), pp 5170–5178, DOI: 10.1021/acs.jctc.6b00359
J. Chem. Theory Comput., online article

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A theoretical study on the NMR shifts of the hydrogen bond network around the chromophore, para-coumaric acid (pCA), of photoactive yellow protein (PYP) is presented. Previous discrepancies between theoretical and experimental studies are resolved by our findings of a previously unknown rapid conformational exchange near the active site of PYP. This exchange ...

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Science, Vol. 353, Issue 6304, DOI: 10.1126/science.aaf5508
Science, online article

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INTRODUCTION: In DNA double helices, hydrogen bonds connect the base pairs across the two strands, and stacking bonds act along the helical axis between neighboring base pairs. Our understanding of DNA and the way it is processed in biology would profit from improved knowledge about the elementary bonds in DNA. Detailed knowledge of the time scales for breaking ...

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J. Am. Chem. Soc., 138 (37), pp 12219–12227, DOI: 10.1021/jacs.6b05981
J. Am. Chem. Soc., online article

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Controlling the internal motions of molecules by outside stimuli is a decisive task for the generation of responsive and complex molecular behavior and functionality. Light-induced structural changes of photoswitches are of special high interest due to the ease of signal application and high repeatability. Typically photoswitches use one reaction coordinate in ...

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Structure, Volume 24, Issue 8, p1387–1397, http://dx.doi.org/10.1016/j.str.2016.06.007
Structure, online article

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Modeling driven by small-angle X-ray scattering (SAXS) combines low-resolution data with computational modeling to predict the structure of biomolecular assemblies. A new protocol, ATTRACT-SAXS, has been developed and tested on a large protein-protein docking benchmark with simulated SAXS data. For 88% of cases, high-quality solutions were generated using SAXS ...

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PNAS, vol. 113, no. 27, 7533–7538, doi: 10.1073/pnas.1600614113
PNAS, online article

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Spontaneous folding of a polypeptide chain into a knotted structure remains one of the most puzzling and fascinating features of protein folding. The folding of knotted proteins is on the timescale of minutes and thus hard to reproduce with atomistic simulations that have been able to reproduce features of ultrafast folding in great detail. Furthermore, it is ...

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Biochimica et Biophysica Acta (BBA), Volume 1860, Issue 9, Pages 2031–2036, doi:10.1016/j.bbagen.2016.06.021
Biochimica et Biophysica Acta (BBA), online article

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We investigated the properties of six Escherichia coli adhesion inhibitors under static and under flow conditions. On mannan-covered model substrates and under static conditions, all inhibitors were able to almost completely abolish lectin-mediated E. coli adhesion. On a monolayer of living human microvascular endothelial cells (HMEC-1), the inhibitors reduced ...

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Nanoscale, 2016, 8, 13352-13367, DOI: 10.1039/C5NR08419A
Nanoscale, online article

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In this work we investigate the interaction between endothelial cells and nanoparticles emitted by catalytic converters. Although catalyst-derived particles are recognized as growing burden added to environmental pollution, very little is known about their health impact. We use platinum-decorated ceria nanoparticles as model compounds for the actual emitted ...

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JCB, vol. 213, no. 3, 305-314, doi: 10.1083/jcb.201601089
JCB, online article

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Sorting and export of transmembrane cargoes and lysosomal hydrolases at the trans-Golgi network (TGN) are well understood. However, elucidation of the mechanism by which secretory cargoes are segregated for their release into the extracellular space remains a challenge. We have previously demonstrated that, in a reaction that requires Ca2+, the soluble ...

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ChemPhysChem, Volume 17, Issue 6, Pages 829–835, DOI : 10.1002/cphc.201500809

ChemPhysChem, online article

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We present a method to artificially induce network formation of membrane glycoproteins and show the precise tuning of their interconnection on living cells. For this, membrane glycans are first metabolically labeled with azido sugars and then tagged with biotin by copper-free click chemistry. Finally, these biotin-tagged membrane proteins are interconnected with ...

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Biomacromolecules, 17 (4), pp 1330–1338, DOI: 10.1021/acs.biomac.5b01726
Biomacromolecules, online article

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Repetitive protein-based polymers are important for many applications in biotechnology and biomaterials development. Here we describe the sequential additive ligation of highly repetitive DNA sequences, their assembly into genes encoding protein–polymers with precisely tunable lengths and compositions, and their end-specific post-translational modification with ...

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Nanoscale, 2016, 8, 8101-8110, DOI: 10.1039/C5NR08163G

Nanoscale, online article

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Effective and controlled drug delivery systems with on-demand release and targeting abilities have received enormous attention for biomedical applications. Here, we describe a novel enzyme-based cap system for mesoporous silica nanoparticles (MSNs) that is directly combined with a targeting ligand via bio-orthogonal click chemistry. The capping system is based on ...

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Journal of Structural Biology, DOI: http://dx.doi.org/10.1016/j.jsb.2016.02.011
Journal of Structural Biology, online article

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Single-molecule force spectroscopy sheds light onto the free energy landscapes governing protein folding and molecular recognition. Since only a single molecule or single molecular complex is probed at any given point in time, the technique is capable of identifying low-probability conformations within a large ensemble of possibilities. It furthermore allows ...

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PNAS, vol. 113, no. 5, 1232–1237, doi: 10.1073/pnas.1518827113
PNAS, online article

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Folding of small proteins often occurs in a two-state manner and is well understood both experimentally and theoretically. However, many proteins are much larger and often populate misfolded states, complicating their folding process significantly. Here we study the complete folding and assembly process of the 1,418 amino acid, dimeric chaperone Hsp90 using ...

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Journal of Molecular Biology, Volume 428, Issue 6, Pages 1315–1332, http://dx.doi.org/10.1016/j.jmb.2016.01.015
Journal of Molecular Biology, online article

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The aggregation of mostly antibody light chain variable (VL) domains into amyloid fibrils in various tissues is the main cause of death in systemic amyloid light chain amyloidosis. Point mutations within the domain are important to shift the VL into the fibrillar pathway, but why and how only some site-specific mutations achieve this still remains elusive. We ...

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J. Chem. Phys., 144, 031101, http://dx.doi.org/10.1063/1.4939841
J. Chem. Phys., online article

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An atomic-orbital (AO) reformulation of the random-phase approximation (RPA) correlation energy is presented allowing to reduce the steep computational scaling to linear, so that large systems can be studied on simple desktop computers with fully numerically controlled accuracy. Our AO-RPA formulation introduces a contracted double-Laplace transform and employs ...

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