Sample records for kratkie soobshcheniya oiyai

  1. Stretching semiflexible polymer chains: Evidence for the importance of excluded volume effects from Monte Carlo simulation

    NASA Astrophysics Data System (ADS)

    Hsu, Hsiao-Ping; Binder, Kurt


    Semiflexible macromolecules in dilute solution under very good solvent conditions are modeled by self-avoiding walks on the simple cubic lattice (d = 3 dimensions) and square lattice (d = 2 dimensions), varying chain stiffness by an energy penalty ɛb for chain bending. In the absence of excluded volume interactions, the persistence length ℓp of the polymers would then simply be ℓ _p=ℓ _b(2d-2)^{-1}q_b^{-1} with qb = exp (-ɛb/kBT), the bond length ℓb being the lattice spacing, and kBT is the thermal energy. Using Monte Carlo simulations applying the pruned-enriched Rosenbluth method (PERM), both qb and the chain length N are varied over a wide range (0.005 ⩽ qb ⩽ 1, N ⩽ 50 000), and also a stretching force f is applied to one chain end (fixing the other end at the origin). In the absence of this force, in d = 2 a single crossover from rod-like behavior (for contour lengths less than ℓp) to swollen coils occurs, invalidating the Kratky-Porod model, while in d = 3 a double crossover occurs, from rods to Gaussian coils (as implied by the Kratky-Porod model) and then to coils that are swollen due to the excluded volume interaction. If the stretching force is applied, excluded volume interactions matter for the force versus extension relation irrespective of chain stiffness in d = 2, while theories based on the Kratky-Porod model are found to work in d = 3 for stiff chains in an intermediate regime of chain extensions. While for qb ≪ 1 in this model a persistence length can be estimated from the initial decay of bond-orientational correlations, it is argued that this is not possible for more complex wormlike chains (e.g., bottle-brush polymers). Consequences for the proper interpretation of experiments are briefly discussed.

  2. Understanding the stiffness of macromolecules: From linear chains to bottle-brushes

    NASA Astrophysics Data System (ADS)

    Binder, K.; Hsu, H.-P.; Paul, W.


    The intrinsic local stiffness of a polymer is characterized by its persistence length. However, its traditional definition in terms of the exponential decay of bond orientational correlations along the chain backbone is accurate only for Gaussian phantom-chain-like polymers. Also care is needed to clarify the conditions when the Kratky-Porod wormlike chain model is applicable. These problems are elucidated by Monte Carlo simulations of simple lattice models for polymers in both d = 2 and d = 3 dimensions. While the asymptotic decay of the bond orientational correlations for real polymers always is of power law form, the Kratky-Porod model is found to be applicable for rather stiff (but not too long) thin polymers in d = 3 (but not in d = 2). However, it does not describe thick chains, e.g., bottle-brush polymers, where stiffness is due to grafted flexible side-chains, and the persistence length grows proportional to the effective thickness of the bottle-brush. A scaling description of bottle-brushes is validated by simulations using the bond fluctuation model.

  3. Single chain structure in thin polymer films: corrections to Flory's and Silberberg's hypotheses

    NASA Astrophysics Data System (ADS)

    Cavallo, A.; Müller, M.; Wittmer, J. P.; Johner, A.; Binder, K.


    Conformational properties of polymer melts confined between two hard structureless walls are investigated by Monte Carlo simulation of the bond fluctuation model. Parallel and perpendicular components of chain extension, bond-bond correlation function and structure factor are computed and compared with recent theoretical approaches attempting to go beyond Flory's and Silberberg's hypotheses. We demonstrate that for ultrathin films where the thickness, H, is smaller than the excluded volume screening length (blob size), ξ, the chain size parallel to the walls diverges logarithmically, R2/2Napb2+clog(N) with c~1/H. The corresponding bond-bond correlation function decreases like a power law, C(s) = d/sω with s being the curvilinear distance between bonds and ω = 1. Upon increasing the film thickness, H, we find—in contrast to Flory's hypothesis—the bulk exponent ω = 3/2 and, more importantly, a decreasing d(H) that gives direct evidence for an enhanced self-interaction of chain segments reflected at the walls. Systematic deviations from the Kratky plateau as a function of H are found for the single chain form factor parallel to the walls in agreement with the non-monotonic behaviour predicted by theory. This structure in the Kratky plateau might give rise to an erroneous estimation of the chain extension from scattering experiments. For large H the deviations are linear with the wavevector, q, but are very weak. In contrast, for ultrathin films, H<ξ, very strong corrections (albeit logarithmic in q) are found suggesting a possible experimental verification of our results.

  4. Scattering function of semiflexible polymer chains under good solvent conditions

    NASA Astrophysics Data System (ADS)

    Hsu, Hsiao-Ping; Paul, Wolfgang; Binder, Kurt


    Using the pruned-enriched Rosenbluth Monte Carlo algorithm, the scattering functions of semiflexible macromolecules in dilute solution under good solvent conditions are estimated both in d = 2 and d = 3 dimensions, considering also the effect of stretching forces. Using self-avoiding walks of up to N = 25 600 steps on the square and simple cubic lattices, variable chain stiffness is modeled by introducing an energy penalty ɛb for chain bending; varying qb = exp (-ɛb/kBT) from qb = 1 (completely flexible chains) to qb = 0.005, the persistence length can be varied over two orders of magnitude. For unstretched semiflexible chains, we test the applicability of the Kratky-Porod worm-like chain model to describe the scattering function and discuss methods for extracting persistence length estimates from scattering. While in d = 2 the direct crossover from rod-like chains to self-avoiding walks invalidates the Kratky-Porod description, it holds in d = 3 for stiff chains if the number of Kuhn segments nK does not exceed a limiting value n^*_K (which depends on the persistence length). For stretched chains, the Pincus blob size enters as a further characteristic length scale. The anisotropy of the scattering is well described by the modified Debye function, if the actual observed chain extension ⟨X⟩ (end-to-end distance in the direction of the force) as well as the corresponding longitudinal and transverse linear dimensions ⟨X2⟩ - ⟨X⟩2, < R_{g,bot }^2 > are used.

  5. Size and structure of antigen-antibody complexes. Electron microscopy and light scattering studies.

    PubMed Central

    Murphy, R M; Slayter, H; Schurtenberger, P; Chamberlin, R A; Colton, C K; Yarmush, M L


    Size parameters of model antigen-antibody (Ag-Ab) complexes formed by the interaction of bovine serum albumin (BSA) and pairs of monoclonal anti-BSA antibodies (mAb) were evaluated by quasielastic light scattering, classical light scattering, and electron microscopy (EM). Mean values for the hydrodynamic radius, radius of gyration, and molecular weight were determined by light scattering. Detailed information regarding the molecular weight distribution and the presence of cycles or open chains was obtained with EM. Average molecular weights were calculated from the EM data, and the Porod-Kratky wormlike chain theory was used to model the conformational behavior of the Ag-mAb complexes. Ag-mAb complexes prepared from three different mAb pairs displayed significantly different properties as assessed by each of the techniques employed. Observations and size parameter calculations from EM photomicrographs were consistent with the results from light scattering. The differences observed between the mab pairs would not have been predicted by idealized thermodynamic models. These results suggest that the geometric constraints imposed by the individual epitope environment and/or the relative epitope location are important in determining the average size of complexes and the ratio of linear to cyclic complexes. Images FIGURE 3 FIGURE 3 FIGURE 5 FIGURE 7 PMID:3416033

  6. Synthesis, solution and crystal structure of the coenzyme B(12) analogue Co(β)-2'-fluoro-2',5'-dideoxyadenosylcobalamin.


    Hunger, Miriam; Wurst, Klaus; Kräutler, Bernhard


    Crystal structure analyses have helped to decipher the mode of binding of coenzyme B12 (AdoCbl) in the active site of AdoCbl-dependent enzymes. However, the question of how such enzymes perform their radical reactions is still incompletely answered. A pioneering study by Gruber and Kratky of AdoCbl-dependent glutamate mutase (GLM) laid out a path for the movement of the catalytically active 5'-deoxyadenosyl radical, in which H-bonds between the protein and the 2'- and 3'-OH groups of the protein bound AdoCbl would play a decisive role. Studies with correspondingly modified coenzyme B12-analogues are of interest to gain insights into cofactor binding and enzyme mechanism. Here we report the preparation of Coβ-2'-fluoro-2',5'-dideoxyadenosylcobalamin (2'FAdoCbl), which lacks the 2'-OH group critical for the interaction in enzymes. 2'FAdoCbl was prepared by alkylation of cob(I)alamin, obtained from the electrochemical reduction of aquocobalamin. Spectroscopic data and a single crystal X-ray analysis of 2'FAdoCbl established its structure, which was very similar to that one of coenzyme B12. 2'FAdoCbl is a (19)F NMR active mimic of coenzyme B12 that may help to gain insights into binding interactions of coenzyme B12 with AdoCbl-dependent enzymes, proteins of B12 transport and of AdoCbl-biosynthesis, as well as with B12-riboswitches.

  7. Kinetics of copper growth on graphene revealed by time-resolved small-angle x-ray scattering

    NASA Astrophysics Data System (ADS)

    Hodas, M.; Siffalovic, P.; Jergel, M.; Pelletta, M.; Halahovets, Y.; Vegso, K.; Kotlar, M.; Majkova, E.


    Metal growth on graphene has many applications. Transition metals are known to favor three-dimensional (3D) cluster growth on graphene. Copper is of particular interest for cost-effective surface-supported catalysis applications and as a contact material in electronics. This paper presents an in situ real-time study of Cu growth kinetics on graphene covering all stages preceding formation of a continuous film performed by laboratory-based grazing-incidence small-angle x-ray scattering (GISAXS) technique. In particular, nucleation and 3D cluster growth, coalescence, and percolation stages were identified. The cluster nucleation saturates after reaching a density of 1012c m-2 at ≈1 monolayer thickness. A Kratky plot and a paracrystal model with cumulative structural disorder were necessary to evaluate properly cluster growth and coalescence, respectively. The power law scaling constants 0.27 ±0.05 and 0.81 ±0.02 of the temporal evolution of Cu cluster size suggest the growth of isolated clusters and dynamic cluster coalescence keeping the cluster shape, respectively. Coalescence and percolation thresholds occur at Cu thicknesses of 2 ±0.4 and 8.8 ±0.7 nm , respectively. This paper demonstrates the potential of laboratory-based in situ GISAXS as a vital diagnostic tool for tailoring a large variety of Cu nanostructures on graphene based on an in situ Cu growth monitoring which is applicable in a broad range of deposition times.

  8. Nonlinear Behavior of Gelatin Networks Reveals a Hierarchical Structure.


    Yang, Zhi; Hemar, Yacine; Hilliou, Loic; Gilbert, Elliot P; McGillivray, Duncan J; Williams, Martin A K; Chaieb, Sahraoui


    We investigate the strain hardening behavior of various gelatin networks-namely physical gelatin gel, chemically cross-linked gelatin gel, and a hybrid gel made of a combination of the former two-under large shear deformations using the pre-stress, strain ramp, and large amplitude oscillations shear protocols. Further, the internal structures of physical gelatin gels and chemically cross-linked gelatin gels were characterized by small angle neutron scattering (SANS) to enable their internal structures to be correlated with their nonlinear rheology. The Kratky plots of SANS data demonstrate the presence of small cross-linked aggregates within the chemically cross-linked network whereas, in the physical gelatin gels, a relatively homogeneous structure is observed. Through model fitting to the scattering data, we were able to obtain structural parameters, such as the correlation length (ξ), the cross-sectional polymer chain radius (R(c)) and the fractal dimension (d(f)) of the gel networks. The fractal dimension d(f) obtained from the SANS data of the physical and chemically cross-linked gels is 1.31 and 1.53, respectively. These values are in excellent agreement with the ones obtained from a generalized nonlinear elastic theory that has been used to fit the stress-strain curves. The chemical cross-linking that generates coils and aggregates hinders the free stretching of the triple helix bundles in the physical gels.

  9. Bilayer thickness in unilamellar phosphatidylcholine vesicles: small-angle neutron scattering using contrast variation

    NASA Astrophysics Data System (ADS)

    Kučerka, N.; Uhríková, D.; Teixeira, J.; Balgavý, P.


    The thickness of the lipid bilayer in extruded unilamellar vesicles prepared from synthetic 1,2-diacyl-sn-glycero-3-phosphorylcholines with monounsaturated acyl chains (diCn:1PC, n=14-22) was studied at 30°C in the small-angle neutron scattering (SANS) experiment. Several contrasts of the neutron scattering length density between the aqueous phase and phospholipid bilayer of vesicles were used. The experimental data were evaluated using the small-angle form of the Kratky-Porod approximation ln[I(q)q2] vs. q2 of the SANS intensity I(q) in the appropriate range of scattering vector values q to obtain the bilayer radius of gyration Rg and its extrapolated value at infinite scattering contrast Rginf. The bilayer thickness parameter evaluated from a linear approximation of dependence of gyration radius on the inverse contrast was then obtained without using any bilayer structure model. The dependence of the thickness parameter dg≅120.5Rginf on the number n of acyl chain carbons was found to be linear with a slope of 1.8+/-0.2Å per one acyl chain carbon. This slope can be used in bilayer-protein interaction studies.

  10. Characterizing flexible and intrinsically unstructured biological macromolecules by SAS using the Porod-Debye law.


    Rambo, Robert P; Tainer, John A


    Unstructured proteins, RNA or DNA components provide functionally important flexibility that is key to many macromolecular assemblies throughout cell biology. As objective, quantitative experimental measures of flexibility and disorder in solution are limited, small angle scattering (SAS), and in particular small angle X-ray scattering (SAXS), provides a critical technology to assess macromolecular flexibility as well as shape and assembly. Here, we consider the Porod-Debye law as a powerful tool for detecting biopolymer flexibility in SAS experiments. We show that the Porod-Debye region fundamentally describes the nature of the scattering intensity decay by capturing the information needed for distinguishing between folded and flexible particles. Particularly for comparative SAS experiments, application of the law, as described here, can distinguish between discrete conformational changes and localized flexibility relevant to molecular recognition and interaction networks. This approach aids insightful analyses of fully and partly flexible macromolecules that is more robust and conclusive than traditional Kratky analyses. Furthermore, we demonstrate for prototypic SAXS data that the ability to calculate particle density by the Porod-Debye criteria, as shown here, provides an objective quality assurance parameter that may prove of general use for SAXS modeling and validation.

  11. Rouse-Bueche Theory and The Calculation of The Monomeric Friction Coefficient in a Filled System

    NASA Astrophysics Data System (ADS)

    Martinetti, Luca; Macosko, Christopher; Bates, Frank

    According to flexible chain theories of viscoelasticity, all relaxation and retardation times of a polymer melt (hence, any dynamic property such as the diffusion coefficient) depend on the monomeric friction coefficient, ζ0, i.e. the average drag force per monomer per unit velocity encountered by a Gaussian submolecule moving through its free-draining surroundings. Direct experimental access to ζ0 relies on the availability of a suitable polymer dynamics model. Thus far, no method has been suggested that is applicable to filled systems, such as filled rubbers or microphase-segregated A-B-A thermoplastic elastomers at temperatures where one of the blocks is glassy. Building upon the procedure proposed by Ferry for entangled and unfilled polymer melts, the Rouse-Bueche theory is applied to an undiluted triblock copolymer to extract ζ0 from the linear viscoelastic behavior in the rubber-glass transition region, and to estimate the size of Gaussian submolecules. At iso-free volume conditions, the so-obtained matrix monomeric friction factor is consistent with the corresponding value for the homopolymer melt. In addition, the characteristic Rouse dimensions are in good agreement with independent estimates based on the Kratky-Porod worm-like chain model. These results seem to validate the proposed approach for estimating ζ0 in a filled system. Although preliminary tested on a thermoplastic elastomer of the A-B-A type, the method may be extended and applied to filled homopolymers as well.

  12. Self-assembly of biaxial discorectangular lead carbonate nanosheets into stacked ribbons studied by SAXS and HAADF-STEM tomographic tilt series.


    Zhang, J; Vad, T; Heidelmann, M; Weirich, T E; Sager, W F C


    The self-assembling behaviour of 2.6 nm thin PbCO3 nanoplatelets with discorectangular shape and uniform width and thickness occurring after their formation in nonionic water-in-oil microemulsions has been investigated using synchrotron small angle X-ray scattering (SAXS) and (scanning) transmission electron microscopy ((S)TEM). The presence of attractive depletion forces originating from the ubiquitous microemulsion droplets triggers a new type of superstructure at low particle concentration. Instead of the universally observed formation of face-to-face assembled lamellar mesostructures, the nanosheets self-organise into extended ribbon structures, whereby each on top lying sheet is displaced by a constant shift in the length and width directions leading to a so far unprecedented staggered zigzag-type stack assembly with restricted height. This type of stacking gives rise to a complex interference pattern in the isotropic small angle scattering of the stacked ribbon assemblies (SRAs) in reverse micellar solution. Different to the, for lamellar-structured nanosheets typical, diffraction peaks at multiples of the wave vector corresponding to one particular repeat distance, the scattering peaks measured in this study are asymmetric, displaying a shoulder on their low wave vector side. The asymmetric shape of the observed face-to-face correlation peaks indicates that the SRAs do not extend in one direction only. Their scattering behaviour is analysed by expanding the Kratky-Porod structure factor for stacking plates into three dimensions. High-angle annular dark-field (HAADF)-STEM tilt series have complementary been acquired to retrieve three-dimensional structural information on the SRAs in the dry state and to confirm the model used for the refinement of the SAXS data.

  13. Lattice Monte Carlo simulations of polymer melts

    NASA Astrophysics Data System (ADS)

    Hsu, Hsiao-Ping


    We use Monte Carlo simulations to study polymer melts consisting of fully flexible and moderately stiff chains in the bond fluctuation model at a volume fraction 0.5. In order to reduce the local density fluctuations, we test a pre-packing process for the preparation of the initial configurations of the polymer melts, before the excluded volume interaction is switched on completely. This process leads to a significantly faster decrease of the number of overlapping monomers on the lattice. This is useful for simulating very large systems, where the statistical properties of the model with a marginally incomplete elimination of excluded volume violations are the same as those of the model with strictly excluded volume. We find that the internal mean square end-to-end distance for moderately stiff chains in a melt can be very well described by a freely rotating chain model with a precise estimate of the bond-bond orientational correlation between two successive bond vectors in equilibrium. The plot of the probability distributions of the reduced end-to-end distance of chains of different stiffness also shows that the data collapse is excellent and described very well by the Gaussian distribution for ideal chains. However, while our results confirm the systematic deviations between Gaussian statistics for the chain structure factor Sc(q) [minimum in the Kratky-plot] found by Wittmer et al. [EPL 77, 56003 (2007)] for fully flexible chains in a melt, we show that for the available chain length these deviations are no longer visible, when the chain stiffness is included. The mean square bond length and the compressibility estimated from collective structure factors depend slightly on the stiffness of the chains.

  14. Calponin-Like Chd64 Is Partly Disordered

    PubMed Central

    Jakób, Michał; Szpotkowski, Kamil; Wojtas, Magdalena; Rymarczyk, Grzegorz; Ożyhar, Andrzej


    20-hydroxyecdysone (20E) and juvenile hormone (JH) signaling pathways interact to regulate insect development. Recently, two proteins, a calponin-like Chd64 and immunophilin FKBP39 have been found to play a pivotal role in the cross-talk between 20E and JH, although the molecular basis of interaction remains unknown. The aim of this work was to identify the structural features that would provide understanding of the role of Chd64 in multiple and dynamic complex that cross-links the signaling pathways. Here, we demonstrate the results of in silico and in vitro analyses of the structural organization of Chd64 from Drosophila melanogaster and its homologue from Tribolium castaneum. Computational analysis predicted the existence of disordered regions on the termini of both proteins, while the central region appeared to be globular, probably corresponding to the calponin homology (CH) domain. In vitro analyses of the hydrodynamic properties of the proteins from analytical size-exclusion chromatography and analytical ultracentrifugation revealed that DmChd64 and TcChd64 had an asymmetrical, elongated shape, which was further confirmed by small angle X-ray scattering (SAXS). The Kratky plot indicated disorderness in both Chd64 proteins, which could possibly be on the protein termini and which would give rise to specific hydrodynamic properties. Disordered tails are often involved in diverse interactions. Therefore, it is highly possible that there are intrinsically disordered regions (IDRs) on both termini of the Chd64 proteins that serve as platforms for multiple interaction with various partners and constitute the foundation for their regulatory function. PMID:24805353

  15. Rigid and semi rigid polyurethane resins: A structural investigation using DMA, SAXS and Le Bail method

    NASA Astrophysics Data System (ADS)

    Trovati, Graziella; Sanches, Edgar A.; de Souza, Sérgio M.; dos Santos, Amanda L.; Neto, Salvador C.; Mascarenhas, Yvonne P.; Chierice, Gilberto O.


    Two different types of polyurethane (PU) resins were synthesized with pre-polymer/polyol (-NCO/-OH) mass proportions of 1:1 (Rigid PU) and 1:1.5 (Semi rigid PU). Based on the results from Dynamic Mechanical Analysis (DMA), rigid PU showed a higher Storage Modulus (E‧) which may be related to the macromolecules crosslinking process. In contrast, the greater Loss Modulus (E″) in semi rigid PU was related to the greater ability to dissipate energy, suggesting that the change in polyol/pre-polymer ratio promotes structural changes in PU resins. Le Bail method was performed with a triclinic crystal structure (for rigid PU, a = 4.9117 (2) Å, b = 8.1103 (2) Å, c = 19.7224 (2) Å, α = 116.2831 (2)°, β = 125.4058 (2)° and γ = 83.6960 (2)°). Average crystallite size was found in the range of 26 (1) Å for rigid PU and somewhat smaller around 20 (1) Å for semi rigid PU. The Guinier radii of gyration (Rg) and the maximum particle sizes (Dmax) were calculated based on Small Angle X-ray Scattering (SAXS) curves. Two different values for Radii of gyration (Rg) were calculated, one obtained from Guinier’s plot using the program Microcal Origin 7.5 (RgORIGIN) and other from the pair-distance distribution function (p(r)) calculation, using the GNOM (RgGNOM) program package The possible highest values of (RgORIGIN) were obtained from Guinier’s curves. For rigid and semi rigid PU resins, the (RgORIGIN) values were, respectively, (320 ± 1) and (260 ± 1) Å. The average radii of gyration (RgGNOM) were obtained from the calculated pair-distance distribution function (p(r)). For rigid and semi rigid PU resins, the RgGNOM values were, respectively, (95 ± 1) Å and (86 ± 1) Å. Dmax values were obtained from the p(r) and ranged from (330 ± 3) Å to (260 ± 3) Å for rigid and semi rigid PU, respectively. Kratky curves showed that less organized systems were produced when the polyol amount was increased.

  16. Small angle X-ray scattering analysis of Cu(2+)-induced oligomers of the Alzheimer's amyloid β peptide.


    Ryan, Timothy M; Kirby, Nigel; Mertens, Haydyn D T; Roberts, Blaine; Barnham, Kevin J; Cappai, Roberto; Pham, Chi Le Lan; Masters, Colin L; Curtain, Cyril C


    Research into causes of Alzheimer's disease and its treatment has produced a tantalising array of hypotheses about the role of transition metal dyshomeostasis, many of them on the interaction of these metals with the neurotoxic amyloid-β peptide (Aβ). Here, we have used small angle X-ray scattering (SAXS) to study the effect of the molar ratio, Cu(2+)/Aβ, on the early three-dimensional structures of the Aβ1-40 and Cu(2+)/Aβ1-42 peptides in solution. We found that at molar ratios of 0.5 copper to peptide Aβ1-40 aggregated, while Aβ1-42 adopted a relatively monodisperse cylindrical shape, and at a ratio of 1.5 copper to peptide Aβ1-40 adopted a monodisperse cylindrical shape, while Aβ1-42 adopted the shape of an ellipsoid of rotation. We also found, via in-line rapid mixing SAXS analysis, that both peptides in the absence of copper were monodisperse at very short timeframes (<2 s). Kratky plots of these scattering profiles indicated that immediately after mixing both were intrinsically disordered. Ensemble optimisation modelling reflected this, indicating a wide range of structural conformers. These data reflect the ensembles from which the Cu(2+)-promoted oligomers were derived. Our results are discussed in the light of other studies that have shown that the Cu(2+)/Aβ has a marked effect on fibril and oligomer formation by this peptide, with a higher ratio favouring the formation of cytotoxic non-amyloid oligomers. Our results are relatively consistent with previous two-dimensional studies of the conformations of these Cu(2+)-induced entities, made on a much longer time-scale than SAXS, by transmission electron microscopy and atomic force microscopy, which showed that a range of oligomeric species are formed. We propose that SAXS carried out on a modern synchrotron beamline enables studies on initial events in disordered protein folding on physiologically-relevant time-scales, and will likely provide great insight into the initiating processes of the A

  17. Semiflexible macromolecules in quasi-one-dimensional confinement: Discrete versus continuous bond angles

    NASA Astrophysics Data System (ADS)

    Huang, Aiqun; Hsu, Hsiao-Ping; Bhattacharya, Aniket; Binder, Kurt


    The conformations of semiflexible polymers in two dimensions confined in a strip of width D are studied by computer simulations, investigating two different models for the mechanism by which chain stiffness is realized. One model (studied by molecular dynamics) is a bead-spring model in the continuum, where stiffness is controlled by a bond angle potential allowing for arbitrary bond angles. The other model (studied by Monte Carlo) is a self-avoiding walk chain on the square lattice, where only discrete bond angles (0° and ±90°) are possible, and the bond angle potential then controls the density of kinks along the chain contour. The first model is a crude description of DNA-like biopolymers, while the second model (roughly) describes synthetic polymers like alkane chains. It is first demonstrated that in the bulk the crossover from rods to self-avoiding walks for both models is very similar, when one studies average chain linear dimensions, transverse fluctuations, etc., despite their differences in local conformations. However, in quasi-one-dimensional confinement two significant differences between both models occur: (i) The persistence length (extracted from the average cosine of the bond angle) gets renormalized for the lattice model when D gets less than the bulk persistence length, while in the continuum model it stays unchanged. (ii) The monomer density near the repulsive walls for semiflexible polymers is compatible with a power law predicted for the Kratky-Porod model in the case of the bead-spring model, while for the lattice case it tends to a nonzero constant across the strip. However, for the density of chain ends, such a constant behavior seems to occur for both models, unlike the power law observed for flexible polymers. In the regime where the bulk persistence length ℓp is comparable to D, hairpin conformations are detected, and the chain linear dimensions are discussed in terms of a crossover from the Daoud/De Gennes "string of blobs

  18. Low resolution structure of the human alpha4 protein (IgBP1) and studies on the stability of alpha4 and of its yeast ortholog Tap42.


    Smetana, Juliana Helena Costa; Oliveira, Cristiano Luiz Pinto; Jablonka, Willy; Aguiar Pertinhez, Thelma; Carneiro, Flavia Raquel Gonçalves; Montero-Lomeli, Monica; Torriani, Iris; Zanchin, Nilson Ivo Tonin


    The yeast Tap42 and mammalian alpha4 proteins belong to a highly conserved family of regulators of the type 2A phosphatases, which participate in the rapamycin-sensitive signaling pathway, connecting nutrient availability to cell growth. The mechanism of regulation involves binding of Tap42 to Sit4 and PPH21/22 in yeast and binding of alpha4 to the catalytic subunits of type 2A-related phosphatases PP2A, PP4 and PP6 in mammals. Both recombinant proteins undergo partial proteolysis, generating stable N-terminal fragments. The full-length proteins and alpha4 C-terminal deletion mutants at amino acids 222 (alpha4Delta222), 236 (alpha4Delta236) and 254 (alpha4Delta254) were expressed in E. coli. alpha4Delta254 undergoes proteolysis, producing a fragment similar to the one generated by full-length alpha4, whereas alpha4Delta222 and alpha4Delta236 are highly stable proteins. alpha4 and Tap42 show alpha-helical circular dichroism spectra, as do their respective N-terminal proteolysis resistant products. The cloned truncated proteins alpha4Delta222 and alpha4Delta236, however, possess a higher content of alpha-helix, indicating that the C-terminal region is less structured, which is consistent with its higher sensitivity to proteolysis. In spite of their higher secondary structure content, alpha4Delta222 and alpha4Delta236 showed thermal unfolding kinetics similar to the full-length alpha4. Based on small angle X-ray scattering (SAXS), the calculated radius of gyration for alpha4 and Tap42 were 41.2 +/- 0.8 A and 42.8 +/- 0.7 A and their maximum dimension approximately 142 A and approximately 147 A, respectively. The radii of gyration for alpha4Delta222 and alpha4Delta236 were 21.6 +/- 0.3 A and 25.7 +/- 0.2 A, respectively. Kratky plots show that all studied proteins show variable degree of compactness. Calculation of model structures based on SAXS data showed that alpha4Delta222 and alpha4Delta236 proteins have globular conformation, whereas alpha4 and Tap42 exhibit