Research Area A - Publications 2014

PLOS, 2014, DOI: 10.1371/journal.pone.0115049, published on 29.12.2014
PLOS, online article
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Quantitative proteome research is greatly promoted by high-resolution parallel format assays. A characterization of protein complexes based on binding forces offers an unparalleled dynamic range and allows for the effective discrimination of non-specific interactions. Here we present a DNA-based Molecular Force Assay to quantify protein-protein interactions, ...

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J. Chem. Theory Comput., 2014, DOI: 10.1021/ct5007295, 11 (1), pp 37–44 published on 22.12.2014
J. Chem. Theory Comput., online article
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Spin component-scaled and scaled opposite-spin second-order Møller–Plesset perturbation approaches (SCS-MP2 and SOS-MP2) are introduced for calculating NMR chemical shifts in analogy to the well-established scaled approaches for MP2 energies. Gauge-including atomic orbitals (GIAO) are employed throughout this work. The GIAO-SCS-MP2 and GIAO-SOS-MP2 methods ...

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Proteins, 2014, DOI: 10.1002/prot.24728, Volume 83, Issue 2, pages 248–258 published on 18.12.2014
Proteins: Structure, Function, and Bioinformatics, online article
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Protein-protein interactions are abundant in the cell but to date structural data for a large number of complexes is lacking. Computational docking methods can complement experiments by providing structural models of complexes based on structures of the individual partners. A major caveat for docking success is accounting for protein flexibility. Especially, ...

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Angewandte Chemie International Edition, 2014, DOI: 10.1002/anie.201409803, Volume 54, Issue 6, pages 1946–1949, published on 17.12.2014
Angewandte Chemie International Edition, online article
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We report the development of dendritic siRNA nanostructures that are able to penetrate even difficult to transfect cells such as neurons with the help of a special receptor ligand. The nanoparticles elicit strong siRNA responses, despite the dendritic structure. An siRNA dendrimer directed against the crucial rabies virus (RABV) nucleoprotein (N protein) and ...

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PNAS, 2014, doi: 10.1073/pnas.1414073111, vol. 111, no. 50, 17881–17886 published on 16.12.2014
PNAS, online article
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The heat shock protein 90 (Hsp90) is a dimeric molecular chaperone essential in numerous cellular processes. Its three domains (N, M, and C) are connected via linkers that allow the rearrangement of domains during Hsp90’s chaperone cycle. A unique linker, called charged linker (CL), connects the N- and M-domain of Hsp90. We used an integrated approach, combining ...

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Chem. Commun., 2014, DOI: 10.1039/C4CC07663J, 50, 15623-15626, published on 24.10.2014
Chem. Commun., online article
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UV excitation of the DNA single strand (dT)18 leads to electronically excited states that are potential gateways to DNA photolesions. Using time-resolved infrared spectroscopy we characterized a species with a lifetime of [similar]100 ps and identified it as a charge separated excited state between two thymine bases..  

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Chemistry - A European Journa, 2014, DOI: 10.1002/chem.201403661, Volume 20, Issue 43, pages 13984–13992, published on 20.10.2014

Chemistry - A European Journal, online article

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Hemithioindigo (HTI) photoswitches have a tremendous potential for biological and supramolecular applications due to their absorptions in the visible-light region in conjunction with ultrafast photoisomerization and high thermal bistability. Rational tailoring of the photophysical properties for a specific application is the key to exploit the full potential of ...

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Angewandte Chemie International Edition, 2014, DOI: 10.1002/anie.201406286, Volume 53, Issue 42, pages 11366–11369 published on 13.10.2014
Angewandte Chemie International Edition, online article
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Excited-state dynamics are essential to understanding the formation of DNA lesions induced by UV light. By using femtosecond IR spectroscopy, it was possible to determine the lifetimes of the excited states of all four bases in the double-stranded environment of natural DNA. After UV excitation of the DNA duplex, we detected a concerted decay of base pairs ...

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Chem. Rev., 2014, DOI: 10.1021/cr400326k, 114 (1), pp 660–667 published on 03.09.2014
Chem. Rev., online article
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INTRODUCTION: Natively folded proteins generally have a significant number of hydrophobic residues that cluster together to form a hydrophobic core. However, during the vectorial synthesis on the ribosome and subsequent folding, these hydrophobic residues are exposed. Because folding occurs in a highly crowded environment, exposed residues can lead to undesired ...

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J. Org. Chem., 2014, DOI: 10.1021/jo501206k, 79 (20), pp 9812–9817 published on 28.08.2014

J. Org. Chem., online article

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A short total synthesis of the published structure of racemic trichodermatide A is reported. Our synthesis involves a Knoevenagel condensation/Michael addition sequence, followed by the formation of tricyclic hexahydroxanthene-dione and a diastereoselective bis-hydroxylation. The final product, the structure of which was confirmed by X-ray crystallography, has ...

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Biophysical Journal, 2014, http://dx.doi.org/10.1016/j.bpj.2013.05.059, Volume 105, 848–861 published on 20.08.2014
Biophysical Journal, online article
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Fluorescence fluctuation imaging is a powerful means to investigate dynamics, interactions, and stoichiometry of proteins inside living cells. Pulsed interleaved excitation (PIE) is the method of nanosecond alternating excitation with time-resolved detection and allows accurate, independent, and quasi-simultaneous determination of fluorescence intensities and ...

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THE JOURNAL OF CHEMICAL PHYSICS, 2014, http://dx.doi.org/10.1063/1.4891797, 141, 051106 published on 06.08.2014

THE JOURNAL OF CHEMICAL PHYSICS, online article

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We present a low-prefactor, cubically scaling scaled-opposite-spin second-order Møller-Plesset perturbation theory (SOS-MP2) method which is highly suitable for massively parallel architectures like graphics processing units (GPU). The scaling is reduced from O(N5) to O(N3) by a reformulation of the MP2-expression in the atomic orbital basis via Laplace ...

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The Journal of Biological Chemistry, 2014, doi: 10.1074/jbc.M114.582247, 289, 26829-26846, published on 05.08.2014
The Journal of Biological Chemistry, online article
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Variable (V) domains of antibodies are essential for antigen recognition by our adaptive immune system. However, some variants of the light chain V domains (VL) form pathogenic amyloid fibrils in patients. It is so far unclear which residues play a key role in governing these processes. Here, we show that the conserved residue 2 of VL domains is crucial for ...

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Angewandte Chemie International Edition, 2014, DOI: 10.1002/anie.201403334, Volume 53, Issue 38, pages 10044–10048 published on 25.07.2014

Angewandte Chemie International Edition, online article

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Living organisms protect the genome against external influences by recognizing and repairing damaged DNA. A common source of gene mutation is the oxidized guanine, which undergoes base excision repair through cleavage of the glycosidic bond between the ribose and the nucleobase of the lesion. We unravel the repair mechanism utilized by bacterial glycosylase, ...

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PLOS ONE, 2014, DOI: 10.1371/journal.pone.0101834, Volume 9, Issue 7, e101834 published on 08.07.2014
PLOS ONE, online aticle
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In the central nervous system, lipid-protein interactions are pivotal for myelin maintenance, as these interactions regulate protein transport to the myelin membrane as well as the molecular organization within the sheath. To improve our understanding of the fundamental properties of myelin, we focused here on the lateral membrane organization and dynamics of ...

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THE JOURNAL OF CHEMICAL PHYSICS, 2014, http://dx.doi.org/10.1063/1.4881144, 140, 224112 published on 13.06.2014

THE JOURNAL OF CHEMICAL PHYSICS, online article

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Our recently developed QQR-type integral screening is introduced in our Cholesky-decomposed pseudo-densities Møller-Plesset perturbation theory of second order (CDD-MP2) method. We use the resolution-of-the-identity (RI) approximation in combination with efficient integral transformations employing sparse matrix multiplications. The RI-CDD-MP2 method shows an ...

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Chemical Physics Letters, 2014, DOI: 10.1016/j.cplett.2014.03.085, Volume 601,Pages 103–109 published on 09.05.2014

Chemical Physics Letters, online article

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The primary dynamics of reaction centers from Rhodobacter sphaeroides at room temperature are studied at low excitation intensities and low excitation rates. Analysis based on singular value decomposition yields three time constants in the picosecond range (ca. 1.2 ps, 3.5 ps and 220 ps). The spectral and temporal signatures are fully consistent with the ...

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Journal of Controlled Release, 2014, http://dx.doi.org/10.1016/j.jconrel.2014.02.015, Volume 180, Pages 42–50 published on 28.04.2014
Journal of Controlled Release, online article
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Native chemical ligation (NCL) was established for the conversion of sequence-defined oligomers of different topologies into targeted and PEG shielded pDNA and siRNA carriers. From an existing library of non-targeted oligoethanamino amides, six oligomers containing N-terminal cysteines were selected as cationic cores, to which monodisperse polyethylene glycol ...

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Nucl. Acids Res., 2014, doi: 10.1093/nar/gku273, Vol. 42, No. 10 6219–6231 published on 17.04.2014
Nucleic Acids Research, online article
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During transcription initiation, the promoter DNA is recognized and bent by the basal transcription factor TATA-binding protein (TBP). Subsequent association of transcription factor B (TFB) with the TBP–DNA complex is followed by the recruitment of the ribonucleic acid polymerase resulting in the formation of the pre-initiation complex. TBP and TFB/TF(II)B are ...

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PNAS, 2014, doi: 10.1073/pnas.1319448111, vol. 111 no. 15, 5568–5573, published on 15.04.2014
PNAS, online article
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Proline switches, controlled by cis–trans isomerization, have emerged as a particularly effective regulatory mechanism in a wide range of biological processes. In this study, we use single-molecule mechanical measurements to develop a full kinetic and energetic description of a highly conserved proline switch in the force-sensing domain 20 of human filamin and ...

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Chemical Physics Letters, 2014, DOI: 10.1021/jz500364g, 5 (9), pp 1616–1622 published on 15.04.2014

Chemical Physics Letters, online article

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The decay of triplet states and the formation of cyclobutane pyrimidine dimers (CPDs) after UV excitation of the all-thymine oligomer (dT)18 and the locked dinucleotide TLpTL were studied by nanosecond IR spectroscopy. IR marker bands characteristic for the CPD lesion and the triplet state were observed from 1 ns (time resolution of the setup) onward. The ...

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J. Med. Chem, 2014, DOI: 10.1021/jm401874n, 57 (8), pp 3314–3323 published on 03.04.2014
J. Med. Chem, online article
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Despite the promising potentials of σ2 receptors in cancer therapy and diagnosis, there are still ambiguities related to the nature and physiological role of the σ2 protein. With the aim of providing potent and reliable tools to be used in σ2 receptor research, we developed a novel series of fluorescent σ2 ligands on the basis of our previous work, where ...

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PNAS, 2014, doi: 10.1073/pnas.1323700111, Vol.111 no. 12, 4369-4374 published on 10.03.2014

PNAS, online article

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Base stacking in DNA is related to long-living excited states whose molecular nature is still under debate. To elucidate the molecular background we study well-defined oligonucleotides with natural bases, which allow selective UV excitation of one single base in the strand. IR probing in the picosecond regime enables us to dissect the contribution of different ...

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ChemPhysChem, 2014, DOI: 10.1002/cphc.201300954, Volume 15, Issue 3, pages 420–423, published on 24.02.2014

ChemPhysChem; online article

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Methylated cytidine plays an important role as an epigenetic signal in gene regulation. Its oxidation products are assumed to be involved in active demethylation processes but also in damaging DNA. Here, we report the photochemical production of the 5-methyl-2′-deoxycytidine radical cation via a two-photon ionization process. The radical cation is detected by ...

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J. Chem. Theory Comput., 2014, DOI: 10.1021/ct400780f, 10 (2), pp 572–578 published on 23.01.2014

J. Chem. Theory Comput., online article

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An extensive study of error distributions for calculating hydrogen and carbon NMR chemical shifts at Hartree–Fock (HF), density functional theory (DFT), and Møller–Plesset second-order perturbation theory (MP2) levels is presented. Our investigation employs accurate CCSD(T)/cc-pVQZ calculations for providing reference data for 48 hydrogen and 40 carbon nuclei ...

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Angewandte Chemie, 2014, DOI: 10.1002/ange.201307016, Volume 126, Issue 2, pages 602–605 published on 07.01.2014

Angewandte Chemie, online article

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Die photochemischen Eigenschaften des Indigo, eines weit verbreiteten industriellen Produkts, haben von Anfang an das Interesse von Wissenschaftlern geweckt. Die Photostabilität von Indigo war Gegenstand intensiver Forschungen. In neuerer Zeit wurde vorgeschlagen, dass nach Photoanregung ein intramolekularer Protonentransfer auftritt, der gefolgt von einem ...

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