Institute for Physical and Theoretical Chemistry

Bergen auf Rügen, Germany

Institute for Physical and Theoretical Chemistry

Bergen auf Rügen, Germany
SEARCH FILTERS
Time filter
Source Type

Lee S.,University of Warwick | Sundaram S.,University of Warwick | Sundaram S.,Allahabad University | Armitage L.,University of Leeds | And 5 more authors.
ACS Chemical Biology | Year: 2014

Structure-activity profiles for the phytohormone auxin have been collected for over 70 years, and a number of synthetic auxins are used in agriculture. Auxin classification schemes and binding models followed from understanding auxin structures. However, all of the data came from whole plant bioassays, meaning the output was the integral of many different processes. The discovery of Transport Inhibitor-Response 1 (TIR1) and the Auxin F-Box (AFB) proteins as sites of auxin perception and the role of auxin as molecular glue in the assembly of co-receptor complexes has allowed the development of a definitive quantitative structure-activity relationship for TIR1 and AFB5. Factorial analysis of binding activities offered two uncorrelated factors associated with binding efficiency and binding selectivity. The six maximum-likelihood estimators of Efficiency are changes in the overlap matrixes, inferring that Efficiency is related to the volume of the electronic system. Using the subset of compounds that bound strongly, chemometric analyses based on quantum chemical calculations and similarity and self-similarity indices yielded three classes of Specificity that relate to differential binding. Specificity may not be defined by any one specific atom or position and is influenced by coulomb matrixes, suggesting that it is driven by electrostatic forces. These analyses give the first receptor-specific classification of auxins and indicate that AFB5 is the preferred site for a number of auxinic herbicides by allowing interactions with analogues having van der Waals surfaces larger than that of indole-3-acetic acid. The quality factors are also examined in terms of long-standing models for the mechanism of auxin binding. © 2013 American Chemical Society.


News Article | December 9, 2016
Site: www.eurekalert.org

Scientists at the University of Bonn have succeeded in observing an important cell protein at work. To do this, they used a method that allows to measure structural changes within complex molecules. The further developed procedure makes it possible to elucidate such processes in the cell, i.e. in the natural environment. The researchers are also providing a tool kit, which allows a wide range of molecules to be measured. Their study has now been published in the journal "Angewandte Chemie International Edition". If we want to open a Christmas season walnut, we usually use a nutcracker. In the simplest case, this consists of two arms, which move against each other around a joint and can thus exert pressure on the shell. Very simple, actually - to understand how this kind of nutcracker works, it is sufficient for us to see it in action just once. However, it is much more difficult to understand how cellular molecules work. They also alter their spatial structure as they work - similar to the nutcracker, where the arms open or close. These conformational changes tell experts a great deal about the way in which the molecule fulfills its job. Unfortunately, it is very difficult to measure these kind of movements because they occur on a very small length scale. This applies even more so if one wants to investigate the structural changes in the natural cellular environment, where countless simultaneous processes make it very hard to isolate any specific information from the general noise. The working group from the Institute for Physical and Theoretical Chemistry at the University of Bonn has now succeeded in doing this. To this end, the scientists further developed a method that has been used for many years to measure distances within large molecules. "However, this normally only works in a test tube," explains the head of the study, Prof. Olav Schiemann. "In contrast, our technique can also be used in cells." The researchers used what is known as electron paramagnetic resonance spectroscopy (EPR) for their measurements. The molecule to be measured is usually given a magnetic marker at two different sites. Through radiation with microwaves, the polarity of one of these mini magnets is reversed. The magnetic field emitted by it is thus changed, which in turn influences the second mini magnet. This influence is greater the closer both markers are to each other. "We now measure how strongly the second magnet reacts to the reverse polarity of the first," explains Schiemann. "From this, we can ascertain the distance between both markers." If - metaphorically speaking - both arms of the nutcracker are marked in this way, their movement against each other can be understood. In principle, the technique is not new. "However, we have succeeded in producing a new kind of label with which we can mark a wide range of biomolecules in a site-specific way", explains Schiemann's staff member Jean Jacques Jassoy. Usually, these labels consist of radicals - which are chemical compounds that carry a single free electron. The electron acts as a magnet during the measurement. The problem here: single electrons are highly reactive - they try to form pairs of electrons as quickly as possible. The chemists at the University of Bonn thus used a very stable radical in their work - a so called trityl group. They created various derivatives of this trityl radical. Each of these magnetic markers is designed to target specific sites within biomolecules and thus enables several approaches for the structural analysis of different biomolecules. In their study, the researchers used this methodological advance to investigate a protein from the cytochrome P450 group. These proteins occur in almost all living beings and fulfill important tasks, for instance during oxidation processes in the cell. "With our method, we were able to precisely measure the distance between two areas of the cytochrome to a fraction of a millionth of a millimeter," emphasizes Schiemann´s staff member Andreas Berndhäuser. The procedure is suitable for making biomolecule conformational changes visible in the cell. At the same time, it also generally facilitates the clarification of molecular structures. Schiemann: "We are thus providing researchers with a new tool kit that could help answer many biochemical questions." Publication: J. Jacques Jassoy, Andreas Berndhäuser, Fraser Duthie, Sebastian P. Kühn, Gregor Hagelueken, Olav Schiemann: Versatile Trityl Spin Labels for Nanometer Distance Measurements on Biomolecules in vitro and within cells; Angewandte Chemie International Edition; DOI: 10.1002/anie.201609085


Latteyer F.,Institute for Physical and Theoretical Chemistry | Peisert H.,Institute for Physical and Theoretical Chemistry | Aygul U.,Institute for Physical and Theoretical Chemistry | Biswas I.,Institute for Physical and Theoretical Chemistry | And 4 more authors.
Journal of Physical Chemistry C | Year: 2011

The molecular orientation and homogeneity of gallium(III) and aluminum(III) chlorine phthalocyanine (GaClPc and AlClPc) are studied on flat (gold single crystal, Au(100)) and rough surfaces (indium tin oxide, ITO) by Raman spectroscopy in combination with X-ray absorption spectroscopy (XAS) in detail. In the case of Raman spectroscopy, Euler angles are used to describe the geometry while Raman imaging provides insight into homogeneity. For XAS, synchrotron radiation is applied to study the angle dependence of the excitation structure. On Au(100) the molecules are highly ordered and tend to align parallel to the surface (lying) with a layer by layer growth mode. Contrarily, on technically relevant substrates, as in the case of ITO, less ordered films due to the roughness of the surface nature are present. The results are discussed in relation to the substrate's nature and the influence of dipole moments. © 2011 American Chemical Society.


Veith R.,Institute for Physical and Theoretical Chemistry | Sorkalla T.,University of Bonn | Baumgart E.,Institute for Physical and Theoretical Chemistry | Anzt J.,Institute for Physical and Theoretical Chemistry | And 4 more authors.
Biophysical Journal | Year: 2010

A detailed conception of intranuclear messenger ribonucleoprotein particle (mRNP) dynamics is required for the understanding of mRNP processing and gene expression outcome. We used complementary state-of-the-art fluorescence techniques to quantify native mRNP mobility at the single particle level in living salivary gland cell nuclei. Molecular beacons and fluorescent oligonucleotides were used to specifically label BR2.1 mRNPs by an in vivo fluorescence in situ hybridization approach. We characterized two major mobility components of the BR2.1 mRNPs. These components with diffusion coefficients of 0.3 ± 0.02 μm2/s and 0.73 ± 0.03 μm2/s were observed independently of the staining method and measurement technique used. The mobility analysis of inert tracer molecules revealed that the gland cell nuclei contain large molecular nonchromatin structures, which hinder the mobility of large molecules and particles. The mRNPs are not only hindered by these mobility barriers, but in addition also interact presumably with these structures, what further reduces their mobility and effectively leads to the occurrence of the two diffusion coefficients. In addition, we provide evidence that the remarkably high mobility of the large, 50 nm-sized BR2.1 mRNPs was due to the absence of retarding chromatin. © 2010 by the Biophysical Society.


Thevarpadam J.,Goethe University Frankfurt | Bessi I.,Institute for Organic Chemistry and Chemical Biology | Binas O.,Institute for Organic Chemistry and Chemical Biology | Goncalves D.P.N.,Goethe University Frankfurt | And 6 more authors.
Angewandte Chemie - International Edition | Year: 2016

The ability of three different bifunctional azobenzene linkers to enable the photoreversible formation of a defined intermolecular two-tetrad G-quadruplex upon UV/Vis irradiation was investigated. Circular dichroism and NMR spectroscopic data showed the formation of G-quadruplexes with K+ ions at room temperature in all three cases with the corresponding azobenzene linker in an E conformation. However, only the para-para-substituted azobenzene derivative enables photoswitching between a nonpolymorphic, stacked, tetramolecular G-quadruplex and an unstructured state after E-Z isomerization. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA.


Latteyer F.,Institute for Physical and Theoretical Chemistry | Savu S.,Institute for Physical and Theoretical Chemistry | Peisert H.,Institute for Physical and Theoretical Chemistry | Chasso T.,Institute for Physical and Theoretical Chemistry
Journal of Raman Spectroscopy | Year: 2012

This work presents an investigation of films prepared by doctor blade casting, the formation of self-assembled microstructures of a liquid crystalline phthalocyanine with highly oriented molecules. Raman Spectroscopy in combination with atomic force microscopy is applied to study the structures within the films. By keeping the substrate at room temperature or at 353 K during coating, different geometric structures namely rods and islands form. Rod-like structures are growing in coating direction, whereas directional growth of the islands is not observed. The distribution of the rod lengths varies widely, whereas the width appears more uniform. Annealing of the samples shows a different behavior of the two textures. Islands tend to melt, and rods smooth their structural form, which is extracted from Raman imaging in combination with atomic force microscopy. Additionally, Raman imaging gives insight into laterally different relative crystallinity. These observations are discussed in the context of the molecular orientation as probed by polarized Raman spectroscopy. These polarized Raman spectra indicate azimuthal alignment of the molecules within the rods (edge on alignment). This alignment occurs along and also perpendicular to the growth direction. In contrast to the alignment in the rods, the molecules inside the islands occurring at higher temperature do not show preferential molecular orientation. After annealing, no preferential molecular orientation is observed in rods because of the loss of anisotropy, too. Copyright © 2012 John Wiley & Sons, Ltd.


Acuna G.,Institute for Physical and Theoretical Chemistry | Grohmann D.,Institute for Physical and Theoretical Chemistry | Tinnefeld P.,Institute for Physical and Theoretical Chemistry
FEBS Letters | Year: 2014

Single-molecule fluorescence spectroscopy has become an important research tool in the life sciences but a number of limitations hinder the widespread use as a standard technique. The limited dynamic concentration range is one of the major hurdles. Recent developments in the nanophotonic field promise to alleviate these restrictions to an extent that even low affinity biomolecular interactions can be studied. After motivating the need for nanophotonics we introduce the basic concepts of nanophotonic devices such as zero mode waveguides and nanoantennas. We highlight current applications and the future potential of nanophotonic approaches when combined with biological systems and single-molecule spectroscopy. © 2014 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.


PubMed | Institute for Physical and Theoretical Chemistry, Goethe University Frankfurt and Institute for Organic Chemistry and Chemical Biology
Type: Journal Article | Journal: Angewandte Chemie (International ed. in English) | Year: 2016

The ability of three different bifunctional azobenzene linkers to enable the photoreversible formation of a defined intermolecular two-tetrad G-quadruplex upon UV/Vis irradiation was investigated. Circular dichroism and NMR spectroscopic data showed the formation of G-quadruplexes with K(+) ions at room temperature in all three cases with the corresponding azobenzene linker in an Econformation. However, only the para-para-substituted azobenzene derivative enables photoswitching between a nonpolymorphic, stacked, tetramolecular G-quadruplex and an unstructured state after E-Zisomerization.


PubMed | Institute for Physical and Theoretical Chemistry
Type: Journal Article | Journal: FEBS letters | Year: 2014

Single-molecule fluorescence spectroscopy has become an important research tool in the life sciences but a number of limitations hinder the widespread use as a standard technique. The limited dynamic concentration range is one of the major hurdles. Recent developments in the nanophotonic field promise to alleviate these restrictions to an extent that even low affinity biomolecular interactions can be studied. After motivating the need for nanophotonics we introduce the basic concepts of nanophotonic devices such as zero mode waveguides and nanoantennas. We highlight current applications and the future potential of nanophotonic approaches when combined with biological systems and single-molecule spectroscopy.


News Article | December 9, 2016
Site: phys.org

To open a Christmas season walnut, we usually use a nutcracker. The simplest of them consists of two arms that move against each other around a joint and can thus exert pressure on the shell. Cellular molecules also alter their spatial structure as they work – similar to the nutcracker, which has arms that open or close. These conformational changes tell experts a great deal about the way in which the molecule fulfills its job. Unfortunately, it is very difficult to measure these kind of movements because they occur on a very small length scale. This complicates the observation of structural changes in the natural cellular environment, where countless simultaneous processes make it very hard to isolate any specific information from the general noise. The working group from the Institute for Physical and Theoretical Chemistry at the University of Bonn has now succeeded in doing this. To this end, the scientists further developed a method that has been used for many years to measure distances within large molecules. "However, this normally only works in a test tube," explains the head of the study, Prof. Olav Schiemann. "In contrast, our technique can also be used in cells." The researchers used what is known as electron paramagnetic resonance spectroscopy (EPR) for their measurements. The molecule to be measured is usually given a magnetic marker at two different sites. Through radiation with microwaves, the polarity of one of these mini magnets is reversed. The magnetic field emitted by it is thus changed, which in turn influences the second mini magnet. This influence is greater the closer both markers are to each other. "We now measure how strongly the second magnet reacts to the reverse polarity of the first," explains Schiemann. "From this, we can ascertain the distance between both markers." If – metaphorically speaking – both arms of the nutcracker are marked in this way, their movement against each other can be understood. In principle, the technique is not new. "However, we have succeeded in producing a new kind of label with which we can mark a wide range of biomolecules in a site-specific way", explains Schiemann's staff member Jean Jacques Jassoy. Usually, these labels consist of radicals – which are chemical compounds that carry a single free electron. The electron acts as a magnet during the measurement. The problem here: single electrons are highly reactive – they try to form pairs of electrons as quickly as possible. The chemists at the University of Bonn thus used a very stable radical in their work – a so called trityl group. They created various derivatives of this trityl radical. Each of these magnetic markers is designed to target specific sites within biomolecules and thus enables several approaches for the structural analysis of different biomolecules. In their study, the researchers used this methodological advance to investigate a protein from the cytochrome P450 group. These proteins occur in almost all living beings and fulfill important tasks, for instance during oxidation processes in the cell. "With our method, we were able to precisely measure the distance between two areas of the cytochrome to a fraction of a millionth of a millimeter," emphasizes Schiemann´s staff member Andreas Berndhäuser. The procedure is suitable for making biomolecule conformational changes visible in the cell. At the same time, it also generally facilitates the clarification of molecular structures. Schiemann: "We are thus providing researchers with a new tool kit that could help answer many biochemical questions." More information: J. Jacques Jassoy et al. Versatile Trityl Spin Labels for Nanometer Distance Measurements on Biomolecules In Vitro and within Cells, Angewandte Chemie International Edition (2016). DOI: 10.1002/anie.201609085

Loading Institute for Physical and Theoretical Chemistry collaborators
Loading Institute for Physical and Theoretical Chemistry collaborators