Bibliography of Soviet Laser Developments, Number 72, July - August 1984.
1985-11-01
1609. 957. Bogdanov, D.D.; Ivanov, G.N.; Kolesov, I.V.; Orlova, O.A.; Rodin, A.M.; Timakov, V.A.; Ter-Akop’yan, G.M. (OIYaI) * The LIDIA -M highly...Rodin, A.M.; Timakov, V.A.; Ter-Akop’yan, G.M.; Chelnokov, L.P. (OIYaI). The LIDIA -M automated system for controlling and measuring mass spectra in a
Bibliography of Soviet Laser Developments, Number 55. September-October 1981.
1983-01-01
processes in molecules in an infrared laser field. Itogi nauki i tekhniki. VINITI. Fizika ;itoma i molekuly. Optika . 4 Magnitnyy rezonans, no. 2, Part...zavedeniy. Radiofizika JMO (JMKOA) Jemna mechanika a optika KE (KVEKA) Kvantovaya elektronika KhVE (KHVKA) Khimiya vysokikb energiy aL (KNLTA) Knizhnaya...letopis’ KSpF (KRSFA) Kratkiye soobshcheniya pa fizike **NM (IVNMA) Akademiya nauk SSSR. Izvestiya. Neorganicheskiye materialy O 01 (OPSPA) Optika i
NASA Astrophysics Data System (ADS)
Hsu, Hsiao-Ping; Binder, Kurt
2012-01-01
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.
Understanding the stiffness of macromolecules: From linear chains to bottle-brushes
NASA Astrophysics Data System (ADS)
Binder, K.; Hsu, H.-P.; Paul, W.
2016-10-01
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.
About the Experimental Determination of the Persistence Length of Wormlike Chains of Polystyrene
NASA Astrophysics Data System (ADS)
Brûlet, A.; Boué, F.; Cotton, J. P.
1996-06-01
This article describes a fitting method allowing to determine the persistence length of a wormlike Kratky-Porod chain. The form factor of a flexible polymer chain is measured by means of a scattering technique. Its theoretical expression is composed of the exact calculations of des Cloiseaux for an infinite chain and of the approximated function of Sharp and Bloomfield valid for a finite chain. Two examples of the determination of b illustrate this method : one describes a polyion in a semi dilute solution without salt, the other a polystyrene chain in its melt. Cet article décrit une méthode permettant d'obtenir la longueur de persistance b d'une chaîne de Kratky Porod. La méthode consiste à ajuster les données, mesurées par diffusion de rayonnement, avec un facteur de forme. Celui-ci provient de la fusion du calcul exact de des Cloizeaux pour une chaîne infinie et de l'approximation de Sharp et Bloomfield pour une chaîne finie. Elle est appliquée, avec succès, à la détermination de b pour un polyion en solution semi-diluée sans sel et pour une chaîne de polystyrène dans son fondu.
Gómez-Murcia, Victoria; Torrecillas, Alejandro; deGodos, Ana M; Corbalán-García, Senena; Gómez-Fernández, Juan C
2016-06-01
Here we present some of our data about the interaction of idebenone and idebenol with dipalmitoyl-phosphatidylcholine (DPPC). In particular, we include data of small angle X-ray diffraction (SAXD) and wide angle X-ray diffraction experiments, obtention of electronic profiles of the membranes, (2)H-NMR and (31)P-NMR, as part of the research article: "Both idebenone and idebenol are localized near the lipid-water interface of the membrane and increase its fluidity" (Gomez-Murcia et al., 2016) [1]. These data were obtained from model membranes that included different proportions of idebenone and idebenol, at temperatures both above and below of the gel to fluid phase. The X-ray experiments were carried out by using a modified Kratky compact camera (MBraun-Graz-Optical Systems, Graz Austria), incorporating two coupled linear position sensitive detectors. The NMR data were collected from a a Bruker Avance 600 instrument.
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.
2005-05-01
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.
Scattering function of semiflexible polymer chains under good solvent conditions
NASA Astrophysics Data System (ADS)
Hsu, Hsiao-Ping; Paul, Wolfgang; Binder, Kurt
2012-11-01
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.
Rambo, Robert P; Tainer, John A
2011-08-01
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.
A picture of dilute solution behavior of polymers through polyelectrolyte simulation
NASA Astrophysics Data System (ADS)
Yamakawa, Hiromi; Yoshizaki, Takenao; Ida, Daichi
2013-11-01
A Monte Carlo (MC) study is made of the persistence length q and the binary cluster integral β (or the excluded-volume strength B) for polyelectrolytes by the use of the discrete Kratky-Porod wormlike chain with hard-core-effective Debye-Hückel electrostatic pair potentials. The quantity q is determined from the initial decay rate of the bond correlation function after preliminary confirmation of the validity of this procedure using the chain with Lennard-Jones pair potentials. The quantity B is determined from the mean-square radius of gyration along with q by the use of the quasi-two-parameter (QTP) excluded-volume theory. They are evaluated for two model cases of polyelectrolytes, sodium hyaluronate as an example of semiflexible polymers and poly(sodium 4-styrenesulfonate) as a typical example of flexible polymers, both in aqueous sodium chloride. The behavior of MC data so obtained for q and B as functions of added salt concentration c is examined in detail, comparing them with the Odijk-Skolnick-Fixman theory of q and the Fixman-Skolnick (FS) theory of B and also with literature experimental data. In particular, the MC values of B are in almost complete agreement with the FS theory for large c, although the latter still overestimates B somewhat for small c. The values of B themselves and also the validity of the QTP theory in general are discussed in comparison with the case of nonionic polymers.
A picture of dilute solution behavior of polymers through polyelectrolyte simulation.
Yamakawa, Hiromi; Yoshizaki, Takenao; Ida, Daichi
2013-11-28
A Monte Carlo (MC) study is made of the persistence length q and the binary cluster integral β (or the excluded-volume strength B) for polyelectrolytes by the use of the discrete Kratky-Porod wormlike chain with hard-core-effective Debye-Hückel electrostatic pair potentials. The quantity q is determined from the initial decay rate of the bond correlation function after preliminary confirmation of the validity of this procedure using the chain with Lennard-Jones pair potentials. The quantity B is determined from the mean-square radius of gyration along with q by the use of the quasi-two-parameter (QTP) excluded-volume theory. They are evaluated for two model cases of polyelectrolytes, sodium hyaluronate as an example of semiflexible polymers and poly(sodium 4-styrenesulfonate) as a typical example of flexible polymers, both in aqueous sodium chloride. The behavior of MC data so obtained for q and B as functions of added salt concentration c is examined in detail, comparing them with the Odijk-Skolnick-Fixman theory of q and the Fixman-Skolnick (FS) theory of B and also with literature experimental data. In particular, the MC values of B are in almost complete agreement with the FS theory for large c, although the latter still overestimates B somewhat for small c. The values of B themselves and also the validity of the QTP theory in general are discussed in comparison with the case of nonionic polymers.
Statistical and Mechanical Properties of Semiflexible Polymers in an External Field
NASA Astrophysics Data System (ADS)
Liu, Ya; Chakraborty, Bulbul
2006-03-01
Semiflexible polymers such as the double-stranded DNA, are well described by the worm-like chain model originally proposed by Kratky and Porod (Rec. Trav. Chim. 68, 1106, (1949)). Recent work has focused on understanding statistical properties such as their end-to-end distribution function (J.Chem.Phys 121, 6064 (2004), PRE 71, 031803 (2005)) and their mechanical properties in response to a stretching force or the electric field (PRE 72, 041918 (2005)). The problem becomes very complicated unless the long-chain or rod-like-chain approximations for the persistence length are made. Self-avoidance effects are always neglected even for long chain in two dimensions and for confined polymers where these effects could become important. We make use of the Bond Fluctuation Algorithm (Macromolecules 21, 2819(1988)) to study the behavior of semiflexible polymers for all persistence lengths and investigate the relationship of their shape to the persistence length, the chain length and the external field. We will compare our results for the extension of a polymer under a constant stretching with analytical results in weak and strong force limit (PRE 72, 041918 (2005)). This work has been supported by NSF-DMR 0403997.
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.
2017-01-01
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.
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
2016-02-08
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.
NASA Astrophysics Data System (ADS)
Kučerka, N.; Uhríková, D.; Teixeira, J.; Balgavý, P.
2004-07-01
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.
Translational diffusion coefficient of cycloamylose in aqueous sodium hydroxide.
Nakata, Yasushi; Amitani, Keiji; Norisuye, Takashi; Kitamura, Shinichi
2003-08-01
Seven cyclic (1 --> 4)-alpha-D-glucan (cycloamylose) samples ranging in weight-average molecular weight from 5 x 10(3) to 1.8 x 10(4) and gamma-cyclodextrin have been studied by sedimentation equilibrium in dimethylsulfoxide (at 25 degrees C) and by dynamic light scattering in 0.5 N aqueous sodium hydroxide (at 25 degrees C), a good solvent for linear amylose. The measured translational diffusion coefficients D in the aqueous NaOH agree fairly closely with previous Monte Carlo results for cyclic (1 --> 4)-alpha-D-glucan chains with excluded volume, when correction is made for the effects of bead diameter and fluctuating hydrodynamic interaction (HI) on the Kirkwood theory on which the computation of D was based. These D data are also explained almost quantitatively by Yamakawa and Fujii's expression for the associated KP ring (based on the Kratky-Porod wormlike chain) with the molecular parameters for linear amylose if the fluctuating HI and excluded-volume effects are taken into account. It is concluded that the translational diffusion behavior of cycloamylose in the aqueous NaOH is consistent with the conformational characteristics derived from the conformational energy of maltose and dilute-solution data for linear amylose. Copyright 2003 Wiley Periodicals, Inc. Biopolymers 69: 508-516, 2003
Conformational statistics of bent semiflexible polymers
NASA Astrophysics Data System (ADS)
Zhou, Yu; Chirikjian, Gregory S.
2003-09-01
This paper extends previous methods for obtaining the probability distribution function of end-to-end distance for semiflexible polymers, and presents a general formalism that can generate conformational statistics of any continuum filament model of semiflexible chains with internal bends and twists. In particular, our focus is distribution functions for chains composed of straight or helical segments connected with discrete bends or twists. Prior polymer theories are not able to fully account for the effects of these internal shape discontinuities. We use the operational properties of the noncommutative Fourier transform for the group of rigid-body motions in three-dimensional space. This general method applies to various stiffness models of semiflexible chainlike macromolecules. Examples are given which apply the stiffness parameters defined in the Kratky-Porod model, Yamakawa helical wormlike chain model, and revised Marko-Siggia double-helix model to chains with intrinsic bends or twists in their undeformed (minimal energy) state. We demonstrate how the location and magnitude of internal bends in the chain affect the distribution of end-to-end distances for each of these models. This capability allows one to study the entropic effects of intrinsic shape changes (e.g., bend angle) in various models, and may lead to coarse-grained continuum mechanical models of processes that occur during transcription regulation.
Conformational Statistics of Semi-Flexible Macromolecular Chains with Internal Joints
Zhou, Yu
2010-01-01
Fluctuations in the bending angles at internal irregularities of DNA and RNA (such as symmetric loops, bulges, and nicks/gaps) have been observed from various experiments. However, little effort has been made to computationally predict and explain the statistical behavior of semi-flexible chains with internal defects. In this paper, we describe the general structure of these macromolecular chains as inextensible elastic chains with one or more internal joints which have limited ranges of rotation, and propose a method to compute the probability density functions of the end-to-end pose of these macromolecular chains. Our method takes advantage of the operational properties of the non-commutative Fourier transform for the group of rigid-body motions in three-dimensional space, SE(3). Two representative types of joints, the hinge for planar rotation and the ball joint for spatial rotation, are discussed in detail. The proposed method applies to various stiffness models of semi-flexible chain-like macromolecules. Examples are calculated using the Kratky-Porod model with specified stiffness, angular fluctuation, and joint locations. Entropic effects associated with internal angular fluctuations of semi-flexible macromolecular chains with internal joints can be computed using this formulation. Our method also provides a potential tool to detect the existence of internal irregularities. PMID:21243113
Size and structure of antigen-antibody complexes. Electron microscopy and light scattering studies.
Murphy, R M; Slayter, H; Schurtenberger, P; Chamberlin, R A; Colton, C K; Yarmush, M L
1988-01-01
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
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.
Seki, Yasutaka; Shimbo, Yudai; Nonaka, Takamasa; Soda, Kunitsugu
2011-07-12
A new method for generating polypeptide-chain conformations has been developed for studying structural characteristics of unfolded proteins. It enables us to generate a large number of conformations very rapidly by avoiding atomic collisions efficiently with the use of main-chain dihedral-angle distributions derived from a crystal-structure database of proteins. In addition, combining main-chain dihedral-angle distributions for the amino acid residues incorporated in different secondary structures, we can obtain diverse conformational ensembles with different structural features. Structural characteristics of proteins denatured in high-concentration denaturant solution were analyzed by comparing predictions from this method with results from solution X-ray scattering (SXS) measurement. Analysis of the dependence of the mean square radius (Rsq) of protein on the number of residues and the shape of its Kratky profile has confirmed that the highly denaturing solvent serves as a good solvent in accordance with previous reports. It was also found that, in order for a conformational ensemble to reproduce experimental data, the percentage in which main-chain dihedral angles are found in the α region must be in the range of 20-40%. It agrees with studies on the (3)JHNα coupling constant using the multidimensional NMR method. These results confirm that our method for generating diverse conformations of polypeptide chains is very useful to the conformational analysis of unfolded protein, because it enables us to analyze comprehensively both of the local structural features obtained from NMR and the global ones obtained from SXS.
Johs, Alexander; Harwood, Ian M; Parks, Jerry M; Nauss, Rachel; Smith, Jeremy C; Liang, Liyuan; Miller, Susan M
2011-01-01
The enzyme mercuric ion reductase, MerA, is the central component of bacterial mercury resistance encoded by the mer operon. Many MerA proteins possess a metallochaperone-like N-terminal domain, NmerA, that can transfer Hg2+ to the catalytic core (Core) for reduction to Hg0. These domains are tethered to the homodimeric Core by ~30-residue linkers that are subject to proteolysis, which has limited structural and functional characterization of the interactions of these domains. Here, we report purification of homogeneous full-length MerA using a fusion protein construct and combine small-angle X-ray and neutron scattering with molecular dynamics simulation to characterize the structure of constructs that mimic the system before and during handoff of Hg2+ from NmerA to the Core. The radii of gyration, distance distribution functions and Kratky plots derived from the small-angle X-ray scattering data are consistent with full-length MerA adopting elongated conformations resulting from flexibility in the linkers to the NmerA domains. The scattering profiles are best reproduced using an ensemble of linker conformations. This flexible attachment of NmerA may facilitate fast and efficient removal of Hg2+ from diverse protein substrates. Using a specific mutant of MerA allowed determination of the position and relative orientation of NmerA to the Core during Hg2+ handoff. The small buried surface area at the site of interaction suggests molecular recognition may be of less importance for the integrity of metal ion transfers between tethered domains than for transfers between separate proteins in metal trafficking pathways.
The methanol-induced transition and the expanded helical conformation in hen lysozyme.
Kamatari, Y. O.; Konno, T.; Kataoka, M.; Akasaka, K.
1998-01-01
Methanol-induced conformational transitions of hen egg white lysozyme were investigated with a combined use of far- and near-UV CD and NMR spectroscopies, ANS binding and small-angle X-ray scattering. Addition of methanol induced no global change in the native conformation itself, but induced a transition from the native state to the denatured state which was highly cooperative, as shown by the coincidence of transition curves monitored by the far- and near-UV CD spectroscopy, by isodichroic points in the far- and near-UV CD spectra and by the concomitant disappearance of individual 1H NMR signals of the native state. The ANS binding experiments could detect no intermediate conformer similar to the molten globule state in the process of the methanol denaturation. However, at high concentration of methanol, e.g., 60% (v/v) methanol/water, a highly helical state (H) was realized. The H state had a helical content much higher than the native state, monitored by far-UV CD spectroscopy, and had no specific tertiary structure, monitored both by near-UV CD and NMR spectroscopy. The radius of gyration in the H state, 24.9 angstroms, was significantly larger than that in the native state (15.7 angstroms). The Kratky plot for the H state did not show a clear peak and was quite similar to that for the urea-denatured state, indicating a complete lack of globularity. Thus we conclude that the H state has a considerably expanded, flexible broken rod-like conformation which is clearly distinguishable from the "molten globule" state. The stability of both N and H states depends on pH and methanol concentration. Thus a phase diagram involving N and H was constructed. PMID:9541400
Hunger, Miriam; Wurst, Klaus; Kräutler, Bernhard
2015-07-01
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. Copyright © 2015 Elsevier Inc. All rights reserved.
Lattice Monte Carlo simulations of polymer melts
NASA Astrophysics Data System (ADS)
Hsu, Hsiao-Ping
2014-12-01
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.
The compact and expanded denatured conformations of apomyoglobin in the methanol-water solvent.
Kamatari, Y. O.; Ohji, S.; Konno, T.; Seki, Y.; Soda, K.; Kataoka, M.; Akasaka, K.
1999-01-01
We have performed a detailed study of methanol-induced conformational transitions of horse heart apomyoglobin (apoMb) to investigate the existence of the compact and expanded denatured states. A combination of far- and near-ultraviolet circular dichroism, NMR spectroscopy, and small-angle X-ray scattering (SAXS) was used, allowing a phase diagram to be constructed as a function of pH and the methanol concentration. The phase diagram contains four conformational states, the native (N), acid-denatured (U(A)), compact denatured (I(M)), and expanded helical denatured (H) states, and indicates that the compact denatured state (I(M)) is stable under relatively mild denaturing conditions, whereas the expanded denatured states (U(A) and H) are realized under extreme conditions of pH (strong electric repulsion) or alcohol concentration (weak hydrophobic interaction). The results of this study, together with many previous studies in the literature, indicate the general existence of the compact denatured states not only in the salt-pH plane but also in the alcohol-pH plane. Furthermore, to determine the general feature of the H conformation we used several proteins including ubiquitin, ribonuclease A, alpha-lactalbumin, beta-lactoglobulin, and Streptomyces subtilisin inhibitor (SSI) in addition to apoMb. SAXS studies of these proteins in 60% methanol showed that the H states of these all proteins have expanded and nonglobular conformations. The qualitative agreement of the experimental data with computer-simulated Kratky profiles also supports this structural feature of the H state. PMID:10211833
Zhang, J; Vad, T; Heidelmann, M; Weirich, T E; Sager, W F C
2014-12-21
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.
Calponin-Like Chd64 Is Partly Disordered
Jakób, Michał; Szpotkowski, Kamil; Wojtas, Magdalena; Rymarczyk, Grzegorz; Ożyhar, Andrzej
2014-01-01
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
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.
2014-10-01
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.
NASA Astrophysics Data System (ADS)
Huang, Aiqun; Hsu, Hsiao-Ping; Bhattacharya, Aniket; Binder, Kurt
2015-12-01
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
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
2015-03-01
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
Problems at the Nexus of Geometry and Soft Matter: Rings, Ribbons and Shells
NASA Astrophysics Data System (ADS)
Yong, Ee Hou
There has been an increasing appreciation of the role in which elasticity plays in soft matter. The understanding of many shapes and conformations of complex systems during equilibrium or non-equilibrium processes, ranging from the macroscopic to the microscopic, can be explained to a large extend by the theory of elasticity. We are motivated by older studies on how topology and shape couple in different novel systems and in this thesis, we present novel systems and tools for gaining fundamental insights into the wonderful world of geometry and soft matter. We first look at how defects, topology and geometry come together in the physics of thin membranes. Topological constraint plays a fundamental role on the morphology of crumpling membranes of genus zero and suggest how different fundamental shapes, such as platonic solids, can arise through a crumpling process. We present a way of classifying disclinations using a generalized "Casper-Klug" coordination number. We show that there exist symmetry breaking during the crumpling process, which can be described using Landau theory and that thin membranes preserve the memory of their defects. Next we consider the problem of the shapes of Bacillus spores and show how one can understand the folding patterns seen in bacterial coats by looking at the simplified problem of two concentric rings connected via springs. We show that when the two rings loses contact, rucks spontaneous formed leading to the complex folding patterns. We also develop a simple system of an extensible elastic on a spring support to study bifurcation in system that has adhesion. We explain the bifurcation diagram and show how it differs from the classical results. Lastly, we investigate the statistical mechanics of the Sadowsky ribbon in a similar spirit to the famous Kratky-Porod model. We present a detail theoretical and numerical calculations of the Sadowsky ribbon under the effect of external force and torsion. This model may be able to explain new
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
2006-04-01
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