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.

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

NMR investigations of amyloid formation

M. Baumann1, M. Gopalswamy1, J. Adler2, B. Voigt1, D. Huster2,
and J. Balbach1

1Institute of Physics, Biophysics, University Halle-Wittenberg, Germany
2Institute for Medical Physics and Biophysics, University Leipzig, Germany

Amyloids are well ordered protein aggregates involved in many functional and pathogenic processes of life. Various structural models of the molecular architecture of amyloids have been derived in the last decade mainly driven by advances in solid state NMR. This talk will summarize our NMR efforts to study not only structural features of mature fibrils but the amyloid formation mechanism. Two systems will be covered: the Alzheimer peptide Aβ(1-40) and variants as well as the human parathyroid hormone PTH(1-84). For Aβ(1-40) we show that backbone hydrogen bonds are the main driving force for fibril structure formation overwriting side chain effect and buffer conditions [1,2]. Additionally, we show that morphological properties of fibril seeds do not necessarily propagate towards the growing fibril [3]. Several molecular observations during the formation of PTH(1-84) fibrils will be presented [4] to classify them as functional amyloids and possible storage form of the hormone.Amyloids are well ordered protein aggregates involved in many functional and pathogenic processes of life. Various structural models of the molecular architecture of amyloids have been derived in the last decade mainly driven by advances in solid state NMR. This talk will summarize our NMR efforts to study not only structural features of mature fibrils but the amyloid formation mechanism. Two systems will be covered: the Alzheimer peptide Aβ(1-40) and variants as well as the human parathyroid hormone PTH(1-84). For Aβ(1-40) we show that backbone hydrogen bonds are the main driving force for fibril structure formation overwriting side chain effect and buffer conditions [1,2]. Additionally, we show that morphological properties of fibril seeds do not necessarily propagate towards the growing fibril [3]. Several molecular observations during the formation of PTH(1-84) fibrils will be presented [4] to classify them as functional amyloids and possible storage form of the hormone.

References
[1] M. Garvey, M. Baumann, M. Wulff, M. Fändrich, J. Balbach et al., Amyloid 23, 76 (2016). (link)
[2] J. Adler, M. Baumann, B. Voigt, H. A. Scheidt, D. Bhowmik, T. Haupl, B. Abel, P. K. Madhu, J. Balbach, S. Maiti, and D. Huster, ChemPhysChem 17, 2744 (2016). (link)
[3] M. Wulff, M. Baumann, J. Balbach, M. Fändrich et al., Angew. Chemie Int. Ed. 55, 5081 (2016). (link)
[4] M. Gopalswamy, A. Kumar, J. Adler, M. Baumann, M. Henze, S. T. Kumar, M. Fändrich, H. A. Scheidt, D. Huster, and J. Balbach, Biochim. Biophys. Acta 1854, 249 (2015). (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.

References
[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)

Interface-induced crystallization via prefreezing: A first order prewetting transition

Ann-Kristin Flieger, M. Schulz, and T. Thurn-Albrecht

Experimental Polymer Physics, Institute of Physics, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany

Interface-induced crystallization of a liquid on a solid substrate can either occur via heterogeneous nucleation or via prefreezing. Whereas heterogeneous nucleation takes place at finite supercooling below the melting temperature Tm, in prefreezing a crystalline layer is formed at the surface of a solid substrate already above Tm. Wetting theory predicts a jump in thickness at the formation and a divergence upon approaching coexistence. However, the thickness of the prefreezing layer has not been experimentally measured so far.

We studied ultrathin films of polycaprolactone (PCL) during the crystallization on graphite. With in-situ AFM-measurements we observe prefreezing instead of heterogeneous nucleation. The corresponding crystalline layer is formed at a temperature above the bulk melting temperature. Similar observations were already made for polyethylene on graphite [1]. In that case however, a direct measurement of the thickness of the prefreezing layer was not possible. Here, we show directly the finite thickness of the prefreezing layer for PCL. It forms with a thickness of a few nanometers which further increases during cooling. This observation demonstrates the transition is of first order, as expected for a prewetting transition.

The results prove that prefreezing can be described by common wetting theory. The studied system PCL-graphite is of importance for applications since graphitic materials are widely used as fillers for PCL.

References
[1] A.-K. Löhmann, T. Henze, and T. Thurn-Albrecht, PNAS 49, 17368-17372 (2014). (link)

Crystallization in melts of semi-flexible hard polymer chains: An interplay of entropies and dimensions

T. Shakirov, W. Paul

Institut für Physik, Martin Luther Universität Halle-Wittenberg, 06099 Halle 

Stochastic Approximation Monte Carlo simulations [1] are employed to obtain the complete thermodynamic equilibrium information for a melt of short, semi-flexible polymer chains with purely repulsive intermolecular interactions. Thermodynamics is obtained based on the density of states of our simple coarse-grained model, which varies by up to 5000 orders of magnitude. We show that our polymer melt undergoes a first-order crystallization transition upon increasing the chain stiffness at fixed density [2]. The lyotropic three-dimensional orientational ordering transition drives the crystallization and is accompanied by a two-dimensional hexagonal ordering transition in the plane perpendicular to the chains. While the three-dimensional ordering can be understood in terms of Onsager theory, the two-dimensional transition is similar to the liquid-hexatic transition of hard disks. Due to the domination of lateral two-dimensional translational entropy over the one-dimensional translational entropy connected with columnar displacements, the chains form a lamellar phase. The tilt of the chain axis with respect to the lamella surface makes this a rotator II phase.

References
[1] B. Werlich, T. Shakirov, M. P. Taylor, W. Paul, Comput. Phys. Commun. 186, 65, (2015) (link)
[2] T. Shakirov, W. Paul, preprint

The Functional Role of Nanocrystals in Native and Artificial Spider Silk

A. M. Anton and F. Kremer

Peter Debye Institute for Soft Matter Physics, University of Leipzig, Linnéstr. 5, 04103 Leipzig

Spider dragline silk exhibits remarkable characteristics such as exceptional toughness arising from high tensile strength combined with great elasticity. Its mechanical properties are based on a refined architecture on the molecular scale: Proteins with highly repetitive core motifs aggregate into nanometer-sized crystals, rich non alanine in β-sheet secondary structure, surrounded by an amorphous, glycine rich matrix. During spinning the less ordered parts are elongated, which orients both substructures and gives rise to an inherent non-equilibrium state. Thus, external stress is directly transferred to the crystallites, as demonstrated by FTIR experiments in combination with uniaxial stress [1] or hydrostatic pressure [2].Spider dragline silk exhibits remarkable characteristics such as exceptional toughness arising from high tensile strength combined with great elasticity. Its mechanical properties are based on a refined architecture on the molecular scale: Proteins with highly repetitive core motifs aggregate into nanometer-sized crystals, rich non alanine in β sheet secondary structure, surrounded by an amorphous, glycine rich matrix. During spinning the less ordered parts are elongated, which orients both substructures and gives rise to an inherent non-equilibrium state. Thus, external stress is directly transferred to the crystallites, as demonstrated by FTIR experiments in combination with uniaxial stress [1] or hydrostatic pressure [2].Even though the protein structure has been thoroughly studied, until recently it was not possible to artificially re-create this exceptional (morphological and functional) architecture. We show that wet spinning of a novel biomimetic protein results in fibers with a similar nanostructure as the natural template. However, only post spinning strain induces a microscopic non-equilibrium that gives rise to a similar mechanism of energy dissipation as in natural spider silk and comparable macroscopic toughness [3,4].

References
[1] P. Papadopoulos, J. Sölter, and F. Kremer, Eur. Phys. J. E 24, 193 (2007). (link)
[2] A. M. Anton, C. Kuntscher, F. Kremer et al., Macromolecules 46, 4919 (2013). (link)
[3] A. Heidebrecht, T. Scheibel et al., Adv. Mater. 27, 2189 (2015). (link)
[4] A. M. Anton, M. Beiner, T. Scheibel, F. Kremer et al, manuscript submitted

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.

References
[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.

References
[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)

Crystallization of Supramolecular Polymers Linked by Multiple Hydrogen Bonds

Pengju Pan, Jianna Bao, Xiaohua Chang, Ruoxing Chang, Guorong Shan, Yongzhong Bao

State Key Laboratory of Chemical Engineering, College of Chemical and Biological Engineering, Zhejiang University, 38 Zheda Road, Hangzhou 310027, P. R. China.

Supramolecular polymers (SMPs) have different crystallization behavior from conventional polymers. Crystallization of SMPs occurs in a “confined” and “dynamic” manner. Because of the reversible and stimuli-responsive natures of non-covalent bonds in SMPs, crystalline structure and crystallization kinetics of SMPs depend strongly on crystallization conditions (e.g., crystallization temperature, Tc). This offers a feasible way to tune the physical properties and functions of SMPs in processing. We first selected the 2-ureido-4[1H]-pyrimidione (UPy)-bonded poly(L-lactic acid) (PLLA) as a model SMP and investigated the crystallization kinetics, polymorphic crystalline structure, and phase transition of supramolecular PLLAs (SM-PLLAs). Crystallization rate and crystallinity of SM-PLLAs were strongly depressed as compared to the non-functionalized PLLA precursors. Crystalline structure of SM-PLLAs was sensitive to Tc. A low Tc (80~100 °C) facilitated the formation of metastable β crystals of PLLA in SM-PLLAs. The β crystals formed in SM-PLLAs transformed into the more stable α crystals in the following heating process. We further studied the stereocomplex crystallization between UPy-functionalized PLLA and poly(D-lactic acid) (PDLA). It was found that the stereocomplexation ability of PLLA and PDLA was highly improved after UPy end functionalization; this was ascribed to the enhanced interchain interaction.

References
[1] Chang, R. X., Pan, P. J., et al. Macromolecules 2015, 48, 7872. (link)
[2] Bao, J. N., Pan, P. J., et al. Polym. Chem. 2016, 7, 4891. (link)
[3] Bao, J. N.; Pan, P. J., et al. Cryst. Growth Des. 2016, 16, 1502. (link)