Applying Principal-Components Analysis to Single DNA Molecules in a Thermophoretic Trap

Tobias Thalheim, Marco Braun, and Frank Cichos

Peter Debye Institute for Soft Matter Physics, Leipzig University, Linnéstr. 5, 04013 Leipzig

We report on single DNA molecules in liquids trapped over several minutes applying a feedback-driven dynamic temperature field. The thermophoretically induced drift velocities, which make the trapping of single nano-objects possible, are generated by spatially and temporally varying the temperature at a plasmonic nano-structure. The randomization of the positions and conformations by Brownian motion is prevented with the help of feedback-controlled switching of local temperature fields. A model-free statistical tool called principal-components analysis as introduced by Cohen & Moerner [1] is employed to assess the distortion of the DNA’s conformation and conformation dynamics.

[1] A. E. Cohen, and W. E. Moerner, PNAS 104 (31), 12622-12627 (2007). (link)

Enhanced-Sampling Simulations of Amyloids

N. Bernhardt, W. Xi, and Ulrich H.E. Hansmann

Dept. of Chemistry & Biochemistry, University of Oklahoma, Norman, OK 73019, USA

The primary toxic agents in Alzheimer’s disease appear to be small soluble oligomers formed either on-pathway or off-pathway to the assembly of the insoluble fibrils that are one hallmark of the illness. Hence, it is important to understand how the equilibrium between the polymorphous fibrils and oligomers is shifted by mutations, changing environmental conditions, or in the presence of prion-like amyloid strains. These processes are difficult to probe in experiments, and detailed experimental structures exist only for the amyloid fibrils. Most of these fibrils are built from Aβ1-40 peptides that form U-shaped β-hairpins. For the more toxic Aβ1-42 one observes in addition a S-shaped triple-β-stranded motif that cannot be formed by Aβ1-40 peptides. We argue that the higher toxicity of this species is related to the ability of Aβ1-42 to form this motif. In order to test this hypothesis we show that the S-shaped Aβ1-42 peptides assemble into oligomer and fibril structures that cannot be build by U-shaped chains. Stability of these aggregates and inter-conversion between them is studied by regular and enhanced molecular dynamics techniques. These simulations allow us to propose a mechanism for formation and propagation of Aβ1-42 amyloids.

[1] N.A. Bernhardt, W. Xi, W. Wang and U.H.E. Hansmann, J. Chem. Theor. Comp. 12, 5656 (2016). (link)
[2] W. Xi, W.Wang, G.L. Abbott and U.H.E. Hansmann, J. Phys. Chem. B, 120, 4548 (2016). (link)
[3] H. Zhang, W. Xi, U.H.E. Hansmann and Y. Wei, J. Chem. Theor. Comp., (DOI: 10.1021/acs.jctc.7b00383). (link)
[4] W. Xi and U.H.E. Hansmann, Scientific Report, 7, 6588 (2017) (link)

Serine substitution in Amyloid-β – a possible link between β-Methylamino-L-alanine and Alzheimer’s disease?

A. Korn1, M. Krüger2, S. Roßner3, D. Huster1

1Institute of Medical Physics and Biophysics, University of Leipzig, D-04107 Leipzig, Germany.
2Institute of Anatomy, University of Leipzig, D-04103 Leipzig, Germany
3Paul-Flechsig-Institut für Hirnforschung, Liebigstraße 19 D-04103 Leipzig, Germany

β-Methylamino-L-alanine (BMAA) was found as a possible reason for increased ALS-PDC (amyotrophic lateral sclerosis–parkinsonism/dementia complex) [1]. It is a non- proteinogenic amino acid produced by cyanobacteria that can be enriched via the food chain in plants, seafood, higher animals, and humans [2]. This is a critical factor because cyanobacteria are known for their excessive blooms not only in marine ecosystems but also in lakes that are used as fresh water source for millions of people supplying BMAA to human nutrition [3].
Although BMAA is known as a neurotoxin for several decades, its mode of action is still topic of controversial discussions. One of the more commonly accepted pathologic pathways is its function as a neurotransmitter mimetic where it can overstimulate glutamate receptors, deplete glutathione, increase free radical concentration and subsequently leads to neuronal damage [4]. Besides this, BMAA can also be misincorporated in proteins. Recent findings showed that serine tRNA synthetase accepts BMAA as substrate which may finally lead to a serine-BMAA substitution [5].
Assuming that BMAA can substitute Ser8 or Ser26 of Amyloid-β, the question arises if this may alter Amyloid-β fibrillation and structure leading to a higher risk for neurodegenerative pathogenesis.

[1] J. Pablo, S.A. Banack, PA Cox, T.E. Johnson, S. Papapetropoulos, W.G. Bradley, A. Buck, D.C. Mash, Acta Neurologica Scandinavica, 120, 216 (2009) (link)
[2] C.L. Garcia-Rodenas, M. Affolter, G. Vinyes-Pares, C.A. De Castro, L.G, Karagounis, Y.M. Zhang, P.Y Wang, S.K Thakkar, Nutrients, 8, 606, (2016) (link)
[3] M. Monteiro, M. Costa, C. Moreira, V.M. Vasconcelos, M.S. Baptista, Journal of Applied Phycology, 29, 879 (2017) (link)
[4] F. D’Mello, N. Braidy, H. Marcal, G. Guillemin, F. Rossi, M. Chinian, D. Laurent, C. Teo, B.A. Neilan, Neurotoxicity Research, 31, 245 (2017) (link)

Deformation and nano-void formation of β-phase isotactic polypropylene during uniaxial stretching

T. Kawai and S. Kuroda

Graduate School of Science and Engineering, Gunma University, Ota, Gunma 373-0057, Japan

Pseudo-hexagonal β-form is known to transform into thermodynamically stable monoclinic α -form during elongation. It is also reported that the nano-sized void is formed during deformation. Since the crystal deformation/void formation mechanism of β-iPP is not fully understood, we aim in this study to clarify the deformation behavior of β-iPP in both terms of crystal transformation (angstrom scale) and the void formation (nanometer scale). The film of β-iPP was prepared by melt crystallization of PP with 0.2% DCNDCA as a nucleating agent (kβ = 0.94). The samples were drawn uniaxially at 100ºC with fixed strain rate of 0.66 min-1. Synchrotron radiation WAXD/SAXS measurements were performed at BL40B2 in SPring-8, Japan. Deformation of β -iPP proceeded as follows; (i) at the yielding point of ε = 0.1 β-form started to decrease followed by increase in amorphous fraction. (ii) at ε = 0.4, α-form crystal with the chain orientation parallel to the stretching direction was formed. Importantly, as soon as α -form crystallized, formation of nano-sized void was initiated. Above findings strongly suggest that the β -form transforms to amorphous and/or mesomorphic state before recrystallization into α-form crystal. A detailed analysis on void structure by means of SAXS streak scattering is also to be discussed based on lamellar deformation during elongation.

Spatial Orientation and Order of Molecular Subunits in Films of Organic Semiconductors

A. M. Anton and F. Kremer

Peter Debye Institute for Soft Matter Physics, Leipzig University, Linnéstr. 5, 04013 Leipzig

Conjugated donor/acceptor copolymers have obtained significant attention due to their soft matter properties combined with semiconducting characteristics, which allows for their operation in organic field effect transistors or solar cells, for instance [1]. Because the devices’ macroscopic properties arise from the materials’ molecular organization, a detailed understanding of the microscopic structure is essential for targeted developments. In order to shed light on the spatial orientation and order in thin films of P(NDI2OD-T2) the technique of Infrared Transition Moment Orientational Analysis (IR-TMOA) is employed. Therefore, the absorbance of structure-specific bands depending on the inclination of the sample and on the polarization of the IR light is evaluated [2,3]. This enables to determine the tensor of absorption separately for the respective molecular moieties as well as to deduce the orientation of atomistic planes defined through the polymer subunits, relative to the substrate and hence relative to each other. We found that the solvent used for spin coating (chlorobenzene or a chloronaphthalene:xylene mixture) determines the alignment of the T2 part (either face on or edge on), whereas the NDI unit is not affected. On the other hand, the inclination of the NDI plane is well retained for diverse sample thicknesses in between nano- and micrometers.

[1] A. C. Arias, J. D. MacKenzie, I. McCulloch, J. Rivnay, A. Salleo, Chem. Rev. 110, 3 (2010). (link)
[2] A. M. Anton, R. Steyrleuthner, W. Kossack, D. Neher, F. Kremer, JACS 137, 6034 (2008). (link)
[3] A. M. Anton, R. Steyrleuthner, W. Kossack, D. Neher, F. Kremer, Macromolecules 49, 1798 (2016). (link)

Structure and Morphology Orientation of Comb-like Polymers with Rigid Backbones

V. Danke1,2, G. Gupta1,2, and M. Beiner1,2

1Fraunhofer-Institut für Mikrostruktur von Werkstoffen und Systemen IMWS, Walter-Hülse-Straße 1, 06120, Halle, Germany
2Institut für Chemie, Martin Luther Universität Halle-Wittenberg, 06120, Halle, Germany

Comb-like polymers with rigid backbones and flexible side chains are an important class of functional materials with applications in various fields like organic semiconductors and light weight components in high performance composite materials. A common feature of such polymers is the formation of layered structures with typical spacing in the 1-3 nm range wherein the side chains (long methylene sequences) aggregate to form alkyl nanodomains [1]. Crystallographic analysis in poly (1,4-phenylene-2,5-n-didecyloxy terephthalate) (PPDOT) and poly (2,5-didecyloxy-1,4-phenylene vinylene) (DOPPV) each having 10 alkyl carbons per side chain shows that PPDOT exhibits an orthorhombic unit cell, whereas the DOPPV is characterized by a monoclinic unit cell. The interplay between backbone and side chain packing within the alkyl nanodomain leading to different crystallographic states is discussed. Investigations on molecular orientation in extruded fibers of poly (1,4-phenylene-2,5-n-dialkyloxy terephthalate)s (PPAOT) and poly (2,5-dialkyloxy-1,4-phenylene vinylene)s (AOPPV) show that the backbones in case of PPAOT align along the shear direction whereas in AOPPV they align preferentially perpendicular to the shear direction [2]. Potential reasons for the differences in the preferred orientations for PPAOT and AOPPV are considered.

[1] About different packing states of alkyl groups in comb-like polymers with rigid backbones. T. Babur, G. Gupta and M. Beiner, Soft Matter, 2016, 12, 8093-8097 (link)
[2] Interrelations Between Side Chain and Main Chain Packing in Different Crystal Modifications of Alkoxylated Polyesters. G. Gupta, V. Danke, T. Babur, and M. Beiner. J. Phys. Chem. B, 2017, 121, 4583-45. (link)

Influence of Propylene-based Elastomer on Stress-whitening for Impact copolymer

Ying Lu2, Yingying Sun1, Lan Li1 and Yongfeng Men2

1ExxonMobil Asia Pacific Research & Development Co., Ltd, 1099 Zixing Road, Minhang District, 200241 Shanghai, P.R. China
2State Key Laboratory of Polymer Physics and Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Renmin Street 5625, 130022 Changchun, P.R. China

Two pure impact copolymer polypropylenes (ICP), one pure homo-polypropylene (HPP) and their compounds with different type and fraction of VistamaxxTM propylene-based elastomer (“Vistamaxx”) were used to investigate the stress whitening activated in the impact processes via ultra-small angle X-ray scattering technique. A characteristic macroscopic whitening of deformed materials was showed due to the formation of voids or cavities with a typical size up to the wavelength of visible light, that is, some hundreds of nanometers. The stress whitening presented in ICP is confirmed to be caused by the interfaces existed between ethylene-propylene (EP) rubber and polypropylene (PP) matrix, such kind stress whitening is apparently unlike the one initiated in the crystal phase of HPP. In this study, Vistamaxx with high crystallinity can adjust the compatibility of EP rubber and PP matrix which results in a reduction of interfaces, thus, a phenomenon of reduced stress whitening can be observed in blends of ICP with Vistamaxx. However, the enhancement of stress whitening can be found in blends of ICP with Vistamaxx which occupied low crystallinity. Such behaviors can be assigned to the poor compatibility between Vistamaxx and PP matrix.

Early oligomers and the process of oligomerization of the amyloid peptides Aβ40 and Aβ42

Jana Rüdel, Maria Ott

Institute of Physics, Martin-Luther-University Halle-Wittenberg

Similar to synthetic polymers like polyamides, amyloidogenic proteins as well as short peptide sequences display the inherent ability to form long and very stable fibers called fibrils. Along the pathway from a single peptide to the mature fibrils, various transient and long-lived intermediate states are formed spanning the whole range between small and mostly unstructured oligomers to well-ordered, β-sheet rich protofibrils. As early oligomeric states were found to be neurotoxic, they are a presumptive key to understand the development of neurodegenerative diseases [1].
In order to reveal the leading mechanisms of amyloid aggregation, we studied the appearance and development of early oligomeric states of the Aβ40- and the Aβ42-peptides using a combined approach of single-molecule fluorescence spectroscopy and imaging techniques, such as TEM and AFM. Additionally, thermodynamic stabilities of the detected amyloid aggregates were studied by the use of ultrafast-scanning calorimetry.
We could reveal and characterize soluble oligomers of the Aβ40- and the Aβ42-peptide and found distinct differences in terms of size distribution as well as the process of oligomerization. While the fibrillation of Aβ42-peptides includes small and large oligomers, the assembly of Aβ40-peptide display only small oligomers and an overall slower kinetic of fibril formation. We will discuss our results by the use of thermodynamic models of self-assembly.

[1] F. Bemporad and F. Chiti, Protein misfolded oligomers: Experimental approaches, mechanism of formation, and structure-toxicity relationships, Chem. Biol. 19 (2012), 315 (link)

Large area three-dimensional polarization control in P(VDF-TrFE) polymer films on graphite

R. Roth1, M. Koch2, J. Schaab2, M. Lilienblum2, T. Thurn-Albrecht1, and K. Dörr1

1Institute of Physics, Martin Luther University Halle-Wittenberg, 06099 Halle, Germany
2Department of Materials, ETH Zürich, Vladimir-Prelog-Weg 1-5/10,
8093 Zürich, Switzerland

Ferroelectric polymers are attractive candidates for functional layers in electronic devices like non-volatile memories, piezo- and magnetoelectric sensors, and capacitor-based high speed energy storage devices. Unfortunately, such thin films often reveal low di- and piezoelectric responses due to reduced crystalline and electrical dipole order, leading to compensation effects and low effective electric performance. One of the best characterized and often applied ferroelectric polymers is poly(vinylidene fluoride-co-trifluoroethylene) (P(VDF-TrFE)). We will present results on micron-sized domains with three dimensional ferroelectric polarization alignment in P(VDF-TrFE) films on graphite. The ferroelectric domains have been achieved by a combined procedure of electrical poling and mechanical annealing with an atomic force microscopy tip. They show strongly increased lateral and vertical piezoresponse compared to the as-prepared film and can be deliberately written and switched.

Effects of Hofmeister Ion Series on Stability of a Salt Bridge

S. Pylaeva, H. Elgabarty, and D. Sebastiani

Theoretical Chemistry, Institute of Chemistry, Martin Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120, Halle, Germany

Salt bridges are important components of protein structure stability. They can be defined as an interaction of two aminoacid side chains of opposite charge [1]. Such Coulomb attraction interaction is sensitive to presence of other charged species in the vicinity. Concentration of charged species – free ions can be significant in a crowded environment of a living cell. Additionally Hofmeister ion series have been shown to have a significant impact on structure and dynamics of water and solvated proteins [2, 3].

We have investigated effects of Hofmeister ion series on an arginine – aspartic acid salt bridge by means of computer simulations [4]. Changes in thermodynamic properties of a salt bridge and dynamic properties of their solvation shells will be discussed in a poster.

[1] J.E. Donald, D.W. Kulp, W.F. DeGrado, Proteins, 79(3), 898 (2011). (link)
[2] C. Allolio, N. Salas-Illanes, Y.S. Desmukh, M.R. Hansen, D. Sebastiani, JPCB 117(34), 9939 (2013) (link)
[3] M.D. Smith, L. Cruz, JPCB 117, 6614 (2013) (link)
[4] M. Fyta, R. Netz, JCP 136, 124103 (2012). (link)