2010

Photophysics of New Photostable Rylene Derivatives: Applications in Single-Molecule Studies and Membrane Labelling

Chem Phys Chem, 2010, doi:10.1002/cphc.201000666, published on 13.12.2010
Chem. Phys. Chem., online article
Three new photostable rylene dyes for applications in single molecule studies and membrane labelling have been synthesized and their photophysical properties were characterized. These dyes differ in the number of polyethylene glycol (PEG) chains attached to the core structure which is either a perylene derivate or a terrylene derivate. One perylene and one terrylene dye is modified with two PEG chains, and another terrylene derivate has four PEG chains. The results show that the terrylene dye with four PEG chains (4-PEG-TDI) forms soluble nonfluorescing H-aggregates in water, so that the absorption bands are blue-shifted with respect to those of the fluorescing monomeric form. The presence of a surfactant such as Pluronic P123 leads to the disruption of the aggregates due to the formation of monomers in micelles and a strong increase in fluorescence. Application for labelling cell membranes can be considered for this dye since it adsorbs in a similar way as monomer to a lipid bilayer. Furthermore a single-molecule study of all three rylene dyes in polymeric films of PMMA showed excellent photostability with respect to photobleaching, far above the photostability of other common water-soluble dyes, such as Oxazine-1, Atto647N, Cy5, Alexa647 and Rhodamin6G. Especially 4-PEG-TDI seems to be a promising dye for membrane labelling with its high photostability.

Davies_ChemPhysChem_2010_500



Molecular Driving Forces for Z/E Isomerization Mediated by Heteroatoms: The Example Hemithioindigo

J. Phys. Chem. A,, DOI: 10.1021/jp107899g, 114 (50), pp 13016–13030 published on 02.12.2010
J. Phys. Chem. A, online article
A combined experimental and theoretical investigation of photoinduced Z/E isomerizations is presented. Unsubstituted Hemithioindigo is selected as a representative minimal model to unravel the reaction mechanis in the presence of heteroatoms on an atomic level. Time-resolved spectroscopy reveals multiexponential reaction dynamics on the few picoseconds time scale, which are interpreted by quantum chemical calculations at the CASSCF/CASPT2 level of theory. Detailed insight into the processes governing the ultrafast decay from the first excited state, mediated by a number of conical intersections, is provided. Charge separation and charge balance recovery on the reaction pathway play the leading role and are controlled by the electron-donating or -withdrawing character of the heteroatoms. The electronic and geometric structures of the individual minimum energy conical intersections governing the reaction are rationalized, and an extended energetically low lying conical intersection seam is extracted. Comparison to the experimental results permits linking the observed time constants to molecular intermediates and pathways. An explanation is provided for the pronounced differences of Z / E and the E / Z photoreactions upon excitation to the first excited singlet state.

 

Zinth_JPhysChemA_114_13016_2010_500



Reporters in the nanoworld: diffusion of single molecules in mesoporous materials

Chemical Society Reviews, 2010, 39, 4731 - 40 published on 16.11.2010
Chemical Society Reviews, online article
Mesoporous materials have a high potential for a number of different applications in Materials Science such as in molecular sieving, as masks for the formation of nanometre-sized metallic wires, as novel drug-delivery systems or as advanced host systems for catalysis. For many of these applications a thorough understanding of the interaction of guest molecules within the host matrix is required. In this tutorial review, we cover recent single-molecule experiments that allow the investigation of host–guest dynamics with unprecedented detail. We will show how molecules diffusing in samples with (almost) perfect domain ordering still show a large heterogeneity in their mobility and interaction with the host. With the presented methodology it is now possible to dramatically improve our understanding of host–guest interactions and in return develop new nano-structured mesoporous materials with properties optimised for a certain application.

brauchle_michaelis_chemsocrev_2010_500



Controlling the Structure of Proteins at Surfaces

JACS, 2010, doi:10.1021/ja107212z, published on 16.11.2010
JACS, online article
With the help of single molecule force spectroscopy and molecular dynamics simulations, we determine the surface-induced structure of a single engineered spider silk protein. An amyloid like structure is induced in the vicinity of a surface with high surface energy and can be prohibited in the presence of a hydrophobic surface. The derived molecular energy landscapes highlight the role of single silk protein structure for the macroscopic toughness of spider silk.

Geisler_JACS_2010_500



Perylene-Labeled Silica Nanoparticles: Synthesis and Characterization of Three Novel Silica Nanoparticle Species for Live-Cell Imaging

Small, 2010, 6, 21, 2427 - 35 published on 05.11.2010
Small, online article
The increasing exposure of humans to nanoscaled particles requires well-defined systems that enable the investigation of the toxicity of nanoparticles on the cellular level. To facilitate this, surface-labeled silica nanoparticles, nanoparticles with a labeled core and a silica shell, and a labeled nanoparticle network—all designed for live-cell imaging—are synthesized. The nanoparticles are functionalized with perylene derivatives. For this purpose, two different perylene species containing one or two reactive silica functionalities are prepared. The nanoparticles are studied by transmission electron microscopy, widefield and confocal fluorescence microscopy, as well as by fluorescence spectroscopy in combination with fluorescence anisotropy, in order to characterize the size and morphology of the nanoparticles and to prove the success and homogeneity of the labeling. Using spinning-disc confocal measurements, silica nanoparticles are demonstrated to be taken up by HeLa cells, and they are clearly detectable inside the cytoplasm of the cells.

brauchle_small_nov2010_500



Bio-inspired novel design principles for artificial molecular motors

Current Opinion in Biotechnology, 2010, doi:10.1016/j.copbio.2010.06.003, published on 01.10.2010
Current Opinion in Biotechnology, online article
Since we have learned that biological organisms like ourselves are driven by tiny biological molecular motors we try to design and produce artificial molecular motors. However, despite the huge efforts since decades, man-made artificial molecular motors are still far from biological molecular motors or macroscopic motors with regard to performance, especially with respect to energy efficiency. This review highlights recent progress towards artificial molecular motors and discusses how their design and development can be guided by the design concepts of biological molecular motors or macroscopic motors.

Hugel_Lumme_CurrOp_2010_500



Dynamics of heat shock protein 90 C-terminal dimerization is an important part of its conformational cycle

PNAS, 2010, doi: 10.1073/pnas.1000916107, published on 24.08.2010
PNAS, online article
The molecular chaperone heat shock protein 90 (Hsp90) is an important and abundant protein in eukaryotic cells, essential for the activation of a large set of signal transduction and regulatory proteins. During the functional cycle, the Hsp90 dimer performs large conformational rearrangements. The transient N-terminal dimerization of Hsp90 has been extensively investigated, under the assumption that the C-terminal interface is stably dimerized. Using a fluorescence-based single molecule assay and Hsp90 dimers caged in lipid vesicles, we were able to separately observe and kinetically analyze N- and C-terminal dimerizations. Surprisingly, the C-terminal dimer opens and closes with fast kinetics. The occupancy of the unexpected C-terminal open conformation can be modulated by nucleotides bound to the N-terminal domain and by N-terminal deletion mutations, clearly showing a communication between the two terminal domains. Moreover our findings suggest that the C- and N-terminal dimerizations are anticorrelated. This changes our view on the conformational cycle of Hsp90 and shows the interaction of two dimerization domains.

hugel_buchner_pnas_2010_500



Role of Endosomal Escape for Disulfide-Based Drug Delivery from Colloidal Mesoporous Silica Evaluated by Live-Cell Imaging

NANO Letters, 2010, doi:10.1021/nl102180s, published on 02.08.2010
NANO Letters, online article
Redox-driven intracellular disulfide-cleavage is a promising strategy to achieve stimuli-responsive and controlled drug release. We synthesized colloidal mesoporous silica (CMS) nanoparticles with ATTO633-labeled cysteine linked to the inner particle core via disulfide-bridges and characterized their cysteine release behavior after internalization into HuH7 cells by high-resolution fluorescence microscopy. Our study revealed that endosomal escape is a bottleneck for disulfide-linkage based drug release. Photochemical opening of the endosome leads to successful delivery of fluorescently labeled cysteine to the cytosol.

Sauer_Nanoletters_2010_500



Structural and Mechanical Hierarchies in the Alpha Crystallin Domain Dimer of the Hyperthermophilic Small Heat Shock Protein Hsp16.5

Journal of Molecular Biology, 2010, doi:10.1016/j.jmb.2010.05.065, Volume 400, Issue 5, Pages 1046-1056 published on 30.07.2010
Journal of Molecular Biology, online article
In biological systems, proteins rarely act as isolated monomers. Association to dimers or higher oligomers is a commonly observed phenomenon. As an example, small heat shock proteins form spherical homo-oligomers of mostly 24 subunits, with the dimeric αlpha-crystallin domain as the basic structural unit. The structural hierarchy of this complex is key to its function as a molecular chaperone. In this article, we analyze the folding and association of the basic building block, the αlpha-crystallin domain dimer, from the hyperthermophilic archaeon Methanocaldococcus jannaschii Hsp16.5 in detail. Equilibrium denaturation experiments reveal that the αlpha-crystallin domain dimer is highly stable against chemical denaturation. In these experiments, protein dissociation and unfolding appear to follow an “all-ornone” mechanism with no intermediate monomeric species populated. When the mechanical stability was determined by single-molecule force spectroscopy, we found that the αlpha-crystallin domain dimer resists high forces when pulled at its termini. In contrast to bulk denaturation, stable monomeric unfolding intermediates could be directly observed in the mechanical unfolding traces after the αlpha-crystallin domain dimer had been dissociated by force. Our results imply that for this hyperthermophilic member of the small heat shock protein family, assembly of the spherical 24mer starts from folded monomers, which readily associate to the dimeric structure required for assembly of the higher oligomer.

 

175 Bertz Chen JMB 2010_500

 



Chaperonin-Catalyzed Rescue of Kinetically Trapped States in Protein Folding

Cell, 2010, doi:10.1016/j.cell.2010.05.027, Volume 142, Issue 1, 112-122 published on 09.07.2010
Cell, online article
GroEL and GroES form a chaperonin nano-cage for single protein molecules to fold in isolation. The folding properties that render a protein chaperonin dependent are not yet understood. Here, we address this question using a double mutant of the maltosebinding protein DM-MBP as a substrate. Upon spontaneous refolding, DM-MBP populates a kinetically trapped intermediate that is collapsed but structurally disordered. Introducing two long-range disulfide bonds into DM-MBP reduces the entropic folding barrier of this intermediate and strongly accelerates native state formation. Strikingly, steric confinement of the protein in the chaperonin cage mimics the kinetic effect of constraining disulfides on folding, in a manner mediated by negative charge clusters in the cage wall. These findings suggest that chaperonin dependence correlates with the tendency of proteins to populate entropically stabilized folding intermediates. The capacity to rescue proteins from such folding traps may explain the uniquely essential role of chaperonin cages within the cellular chaperone network.

Lamb_Hartl_Chakraborty_2010_Cell_142_112-22_500



DNA photodamage: Study of cyclobutane pyrimidine dimer fornlation il1 a locked thymine dinucleotide

Spectroscopy, 2010, 10.3233/SPE-2010-0437, Volume 24, Number 3-4, 2010 Pages 309-316 published on 02.07.2010
Spectroscopy, online article
The cyclobutane pyrimidine dimer (CPD) formed between two adjacent thymine bases is the most abundant DNA photolesion induced by UV radiation. The quantum yield of this reaction is on the order of ~1% in DNA. This small quantum yield hampers the study of damage formation in naturally occurring DNA. Investigations with increased accuracy become possible for a locked nucleotide model compound TLpTL which exhibits a quantum yield of about 10% for CPD formation. Time resolved IR spectroscopy on TLpTL and two other DNA model compounds (TpT and (dT)18) reveals that: (i) The absorption changes after ~1 ps are due to CPD photodamage. (ii) The quantum efficiency of CPD formation on the few picosecond time scale equals the quantum efficiency reported in stationary experiments. CPD photodamage formation in the investigated DNA constructs is thus predominantly formed from the primarily photoexcited singlet ππ* state, whereas the triplet channel does not play an essential role.

Zinth_Spectroscopy24_2010_500



Tautomerization of 2-nitroso-N-arylanilines by coordination as N,N′-chelate ligands to rhenium(I) complexes and the anticancer activity of newly synthesized oximine rhenium(I) complexes against human melanoma and leukemia cells in vitro

Journal of Inorganic Biochemistry, 2010, doi:10.1016/j.jinorgbio.2010.03.014, published on 01.07.2010
Journal of Inorganic Biochemistry, online article
The synthesis, structural characterization and biological activity of eight ortho-quinone(N-aryl)-oximine rhenium(i) complexes are described. The reaction of the halogenido complexes (CO)5ReX (X=Cl (4), Br (5)) with 2-nitroso-N-arylanilines {(C6H3ClNO)NH(C6H4R)} (R = p-Cl, p-Me, o-Cl, H) (3a–d) in tetrahydrofurane (THF) yields the complexes fac-(CO)3XRe{(C6H3ClNO)NH(C6H4R)} (6a–d, 7a–d) with the tautomerized ligand acting as a N,N′-chelate. The substitution of two carbonyl ligands leads to the formation of a nearly planar 5-membered metallacycle. During coordination the amino-proton is shifted to the oxygen of the nitroso group which can be observed in solution for 6 and 7 by 1H NMR spectroscopy and in solid state by crystal structure analysis. After purification, all compounds have been fully characterized by their 1H and 13C NMR, IR, UV/visible (UV/Vis) and mass spectra. The X-ray structure analyses revealed a distorted octahedral coordination of the CO, X and N,N′-chelating ligands for all Re(i) complexes. Biological activity of four oximine rhenium(i) complexes was assessed in vitro in two highly aggressive cancer cell lines: human metastatic melanoma A375 and human chronic myelogenous leukemia K562. Chlorido complexes (6a and 6c) were more efficient than bromido compounds (7d and 7b) in inducing apoptotic cell death of both types of cancer cells. Melanoma cells were more susceptible to tested rhenium(i) complexes than leukemia cells. None of the ligands (3a–d) showed any significant anticancer activity.

Wirth_JInorganicBiochemistry_2010_500



Pulling a Single Polymer Molecule off a Substrate Reveals the Binding Thermodynamics of Cosolutes

Angewandte Chemie Int. Ed., 2010, doi:10.1002/anie.200907098, published on 28.06.2010
Angewandte Chemie Int. Ed., online article
Cosolutes, such as ions, ligands, or small biomolecules, can cause a protein to fold into its biologically functional native form, to associate, to adhere or desorb from an interface, or even change its mechanical properties.[1–5] At the same time, the interaction of cosolutes with macromolecules, such as proteins, lipids and DNA, are themselves modified by changes in the environment, in particular by binding to surfaces, for example the cell membrane or the surface of histones and microtubules.[6,7] We combine single molecule atomic force microscopy with thermodynamic modeling and thereby extract the binding parameters of cosolutes onto a macro- molecule in solution as well as in its surface adsorbed state. Specifically, we obtain values for the adsorption site lengths (inverse maximal line densities) and the association constants. The considerable effect of substrates on cosolute binding is demonstrated with glucose as cosolute, poly(allylamine) as polymer, and surgical stainless steel or oxidized diamond as substrates.

Geisler_Angewandte_Eng_2010_500



Colchicine-Loaded Lipid Bilayer-Coated 50 nm Mesoporous Nanoparticles Efficiently Induce Microtubule Depolymerization upon Cell Uptake

Nano Letters, 2010, 10 (7) (DOI: 10.1021/nl100991w), 2484 published on 01.06.2010
Nano Letters, online article
We report on a one-step assembly route where supported lipid bilayers (SLB) are deposited on functionalized colloidal mesoporous silica (CMS) nanoparticles, resulting in a core−shell hybrid system (SLB@CMS). The supported membrane acts as an intact barrier against the escape of encapsulated dye molecules. These stable SLB@CMS particles loaded with the anticancer drug colchicine are readily taken up by cells and lead to the depolymerization of microtubules with remarkably enhanced efficiency as compared to the same dose of drug in solution.

braeuchle_nanoletters_2010_500



CIPSM-Professor Jens Michaelis receives the 2010 Nernst-Haber-Bodenstein Prize

2010, published on 19.05.2010
 
CIPSM researcher Jens Michaelis was awarded with the 2010 Nernst-Haber-Bodenstein Prize. The German Bunsen Society for Physical Chemistry awards the Nernst-Haber-Bodenstein Prize in remembrance of Max Bodenstein, Fritz Haber and Walter Nernst. Congratualtions Jens!

 

michaels_nersthaberbodenstein_prize_500



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Regulation of a heterodimeric kinesin-2 through an unprocessive motor domain that is turned processive by its partner

PNAS, 2010, doi/10.1073/pnas.1005177107, published on 17.05.2010
www.pnas.org, online article
Speedy couriers in the cell. Every single one of our cells contains so-called motor proteins that transport important substances from one location to another. However, very little is known about how exactly these transport processes occur. Biophysicists at CIPSM have now succeeded in explaining fundamental functions of a particularly interesting motor protein. Motorized transport proteins are one of the keys to the development of higher organisms. It is they that enable the cell to transport important substances directly and quickly to a specific location in the cell. As bacteria cannot do this, they are not able to form larger cells or even large organisms with many cells. Particularly important are fast transport proteins in the primary cilia, the cell’s antennas, with which they channel information from the surroundings into the cell.

 

rief_pnas_10_500



Novel detection scheme for application in pump–repump–probe spectroscopy

Optics Communications, 2010, 283, 1050-4 published on 01.05.2010
Optics Communications, online article
A novel detection scheme for pump–repump–probe spectroscopy is presented, where the use of modulation and referencing allows to record the efficiency of a photochemical reaction as a function of the pump–repump delay in a single measurement. This new technique is applied to investigate the ringopening reaction of an indolylfulgide after pre-excitation. Here the reaction efficiency doubles, when the excitation pulse is very close to the pre-excitation pulse, and the improvement of the efficiency decays with increasing pump–repump delay on the time scale of about 5 ps.

zinth_oc_10_500



Relaxation time prediction for a light switchable peptide by molecular dynamics

Phys. Chem. Chem. Phys., 2010, DOI: 10.1039/B921803C, 12, 6204-6218 published on 14.04.2010
Phys. Chem. Chem. Phys., online article
We study a monocyclic peptide called cAPB, whose conformations are light switchable due to the covalent integration of an azobenzene dye. Molecular dynamics (MD) simulations using the CHARMM22 force field and its CMAP extension serve us to sample the two distinct conformational ensembles of cAPB, which belong to the cis and trans isomers of the dye, at room temperature. For gaining sufficient statistics we apply a novel replica exchange technique. We find that the well-known NMR distance restraints are much better described by CMAP than by CHARMM22. In cAPB, the ultrafast cis/trans photoisomerization of the dye elicits a relaxation dynamics of the peptide backbone. Experimentally, we probe this relaxation at picosecond time resolution by IR spectroscopy in the amide I range up to 3 ns after the UV/vis pump flash. We interpret the spectroscopically identified decay kinetics using ensembles of non-equilibrium MD simulations, which provide kinetic data on conformational transitions well matching the observed kinetics. Whereas spectroscopy solely indicates that the relaxation toward the equilibrium trans ensemble is by no means complete after 3 ns, the 20 ns MD simulations of the process predict, independently of the applied force field, that the final relaxation into the trans-ensemble proceeds on a time scale of 23 ns. Overall our explicit solvent simulations cover more than 6 μs.

Zinth_PhysChemChemPhys_12_6204_ 2010_500



Increasing the efficiency of the ring-opening reaction of photochromic indolylfulgides by optical pre-excitation

Chemical Physics Letters, 2010, 489, 175 - 80 published on 09.04.2010
Chemical Physics Letters, online article
For three indolylfulgides the quantum efficiency of the ring-opening reaction upon pre-excitation is investigated in a multipulse experiment. The quantum efficiency grows by factor of up to 3.4, when the pre-excitation pulse immediately precedes the excitation process. The change in quantum efficiency after pre-excitation is discussed as a function of reaction time, steady-state quantum efficiency and energetic barriers in the excited electronic state. The observed differences can be explained by the molecular properties of the investigated indolylfulgides

zinth_cpl_10_500



The Conformational Dynamics of the Mitochondrial Hsp70 Chaperone

Molecular Cell, 2010, doi:10.1016/j.molcel.2010.03.010, Volume 38, Issue 1, 89-100 published on 09.04.2010
Molecular Cell, online article
Heat shock proteins 70 (Hsp70) represent a ubiquitous and conserved family of molecular chaperones involved in a plethora of cellular processes. The dynamics of their ATP hydrolysis-driven and cochaperone- regulated conformational cycle are poorly understood. We used fluorescence spectroscopy to analyze, in real time and at single-molecule resolution, the effects of nucleotides and cochaperones on the conformation of Ssc1, a mitochondrial member of the family. We report that the conformation of its ADP state is unexpectedly heterogeneous, in contrast to a uniform ATP state. Substrates are actively involved in determining the conformation of Ssc1. The J protein Mdj1 does not interact transiently with the chaperone, as generally believed, but rather is released slowly upon ATP hydrolysis. Analysis of the major bacterial Hsp70 revealed important differences between highly homologous members of the family, possibly explaining tuning of Hsp70 chaperones to meet specific functions in different organisms and cellular compartments.

 

Lamb_Mapa_2010_Molecular Cell_38_89-100_500



Aging of Hydrogenated and Oxidized Diamond

Advanced Materials, 2010, doi:10.1002/adma.200902198, published on 19.01.2010
Adv. Mater., online article
Single-molecule force spectroscopy experiments demonstrate that hydrogenation and oxidation of polycrystalline diamond effectively control molecular adhesion (see figure). Aging changes these properties and originates from the rapid formation of a thin and resistant contamination layer, as well as degradation of the artificial surface termination on longer time scales. This aging also affects the wettability, morphology, and the electrical properties of the surfaces.

Geisler_AdvMat_2010_500



Exploring the Conformation-Regulated Function of Titin Kinase by Mechanical Pump and Probe Experiments with Single Molecules

Angewandte Chemie, 2010, 49 Issue 6, 1147-50 published on 13.01.2010
Angewandte Chemie, online article
Protein function such as catalytic activity or molecular recognition is tightly coupled to the conformation and dynamics. Since protein conformations may be controlled by forces, diverse active and passive mechanisms have evolved that allow biological systems to respond to mechanical signals. However, forces act in a predetermined direction on these biomolecules and are so minute that the investigation of the underlying mechanisms is difficult to achieve in ensemble experiments and has to be performed on the level of individual molecules. Atomic force microscopy (AFM) based[1] single-molecule force spectroscopy (SMFS)[2] has evolved into a powerful tool for the investigation of such biomolecules in their natural parameter space of force and extension. In addition, it provides the necessary resolution in the submolecular nanometer and pico-Newton range to control or detect intermolecular conformational changes and their related functions[3,4] and to investigate protein folding and unfolding.

gaub_angewchem_10_500






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LMUexcellent
TU München
MPG
Helmholz Muenchen
MPI of Neurobiology
MPI of Biochemistry