Sample records for macromolecular structure solution

  1. Macromolecular powder diffraction : structure solution via molecular.

    SciTech Connect

    Doebbler, J.; Von Dreele, R.; X-Ray Science Division

    2009-01-01

    Macromolecular powder diffraction is a burgeoning technique for protein structure solution - ideally suited for cases where no suitable single crystals are available. Over the past seven years, pioneering work by Von Dreele et al. [1,2] and Margiolaki et al. [3,4] has demonstrated the viability of this approach for several protein structures. Among these initial powder studies, molecular replacement solutions of insulin and turkey lysozyme into alternate space groups were accomplished. Pressing the technique further, Margiolaki et al. [5] executed the first molecular replacement of an unknown protein structure: the SH3 domain of ponsin, using data from a multianalyzer diffractometer. To demonstrate that cross-species molecular replacement using image plate data is also possible, we present the solution of hen egg white lysozyme using the 60% identical human lysozyme (PDB code: 1LZ1) as the search model. Due to the high incidence of overlaps in powder patterns, especially in more complex structures, we have used extracted intensities from five data sets taken at different salt concentrations in a multi-pattern Pawley refinement. The use of image plates severely increases the overlap problem due to lower detector resolution, but radiation damage effects are minimized with shorter exposure times and the fact that the entire pattern is obtained in a single exposure. This image plate solution establishes the robustness of powder molecular replacement resulting from different data collection techniques.

  2. Long-range correlations, geometrical structure, and transport properties of macromolecular solutions. The equivalence of configurational statistics and geometrodynamics of large molecules.

    PubMed

    Mezzasalma, Stefano A

    2007-12-01

    A special theory of Brownian relativity was previously proposed to describe the universal picture arising in ideal polymer solutions. In brief, it redefines a Gaussian macromolecule in a 4-dimensional diffusive spacetime, establishing a (weak) Lorentz-Poincaré invariance between liquid and polymer Einstein's laws for Brownian movement. Here, aimed at inquiring into the effect of correlations, we deepen the extension of the special theory to a general formulation. The previous statistical equivalence, for dynamic trajectories of liquid molecules and static configurations of macromolecules, and rather obvious in uncorrelated systems, is enlarged by a more general principle of equivalence, for configurational statistics and geometrodynamics. Accordingly, the three geodesic motion, continuity, and field equations could be rewritten, and a number of scaling behaviors were recovered in a spacetime endowed with general static isotropic metric (i.e., for equilibrium polymer solutions). We also dealt with universality in the volume fraction and, unexpectedly, found that a hyperscaling relation of the form, (average size) x (diffusivity) x (viscosity)1/2 ~f(N0, phi0) is fulfilled in several regimes, both in the chain monomer number (N) and polymer volume fraction (phi). Entangled macromolecular dynamics was treated as a geodesic light deflection, entaglements acting in close analogy to the field generated by a spherically symmetric mass source, where length fluctuations of the chain primitive path behave as azimuth fluctuations of its shape. Finally, the general transformation rule for translational and diffusive frames gives a coordinate gauge invariance, suggesting a widened Lorentz-Poincaré symmetry for Brownian statistics. We expect this approach to find effective applications to solutions of arbitrarily large molecules displaying a variety of structures, where the effect of geometry is more explicit and significant in itself (e.g., surfactants, lipids, proteins). PMID:17975938

  3. Solution-Phase Processes of Macromolecular Crystallization

    NASA Technical Reports Server (NTRS)

    Pusey, Marc L.; Minamitani, Elizabeth Forsythe

    2004-01-01

    We have proposed, for the tetragonal form of chicken egg lysozyme, that solution phase assembly processes are needed to form the growth units for crystal nucleation and growth. The starting point for the self-association process is the monomeric protein, and the final crystallographic symmetry is defined by the initial dimerization interactions of the monomers and subsequent n-mers formed, which in turn are a function of the crystallization conditions. It has been suggested that multimeric proteins generally incorporate the underlying multimers symmetry into the final crystallographic symmetry. We posed the question of what happens to a protein that is known to grow as an n-mer when it is placed in solution conditions where it is monomeric. The trypsin-treated, or cut, form of the protein canavalin (CCAN) has been shown to nucleate and grow crystals as a trimer from neutral to slightly acidic solutions. Under these conditions the solution is composed almost wholly of trimers. The insoluble protein can be readily dissolved by weakly basic solution, which results in a solution that is monomeric. There are three possible outcomes to an attempt at crystallization of the protein under monomeric (high pH) conditions: 1) we will obtain the same crystals as under trimer conditions, but at different protein concentrations governed by the self association equilibria; 2) we will obtain crystals having a different symmetry, based upon a monomeric growth unit; 3) we will not obtain crystals. Obtaining the first result would be indicative that the solution-phase self-association process is critical to the crystal nucleation and growth process. The second result would be less clear, as it may also reflect a pH-dependent shift in the trimer-trimer molecular interactions. The third result, particularly for experiments in the transition pH's between trimeric and monomeric CCAN, would indicate that the monomer does not crystallize, and that solution phase self association is not part of the crystal nucleation and growth path. Results are presented for crystallization experiments of CCAN over the pH 6.8 to 9.6 range.

  4. Size evolution of highly amphiphilic macromolecular solution assemblies via a distinct bimodal pathway

    PubMed Central

    Kelley, Elizabeth G.; Murphy, Ryan P.; Seppala, Jonathan E.; Smart, Thomas P.; Hann, Sarah D.

    2014-01-01

    The solution self-assembly of macromolecular amphiphiles offers an efficient, bottom-up strategy for producing well--defined nanocarriers, with applications ranging from drug delivery to nanoreactors. Typically, the generation of uniform nanocarrier architecturesis controlled by processing methods that rely upon cosolvent mixtures. These preparation strategies hinge on the assumption that macromolecular solution nanostructures are kinetically stable following transfer from an organic/aqueous cosolvent into aqueous solution. Herein we demonstrate that unequivocal step-change shifts in micelle populations occur over several weeks following transfer into a highly selective solvent. The unexpected micelle growth evolves through a distinct bimodal distribution separated by multiple fusion events and critically depends on solution agitation. Notably, these results underscore fundamental similarities between assembly processes in amphiphilic polymer, small molecule, and protein systems. Moreover, the non-equilibrium micelle size increase can have a major impact on the assumed stability of solution assemblies, for which performance is dictated by nanocarrier size and structure. PMID:24710204

  5. Macromolecular structure and self-assembly.

    PubMed

    Henderson, R

    1998-01-01

    The output from the molecular biology revolution has grown steadily and logarithmically from the first protein sequence, insulin (Ryle AP et al 1955 Biochem J 60:541-556), the first three-dimensional atomic structure of a macromolecule, myoglobin (Kendrew JC et al 1960 Nature 185:422-427), the first DNA gene sequence, phi X174 gene J (Sanger F et al 1977 Nature 265:687-695) and the first genome sequence for a free-living organism, Haemophilus influenzae (Fleischmann RD et al 1995 Science 269:496-512) to the current situation where the output rate is close to one new gene sequence every few minutes, several new three-dimensional structures a day and a new (bacterial) genome completed every few months. Those working in this field must readjust their horizons to this changing situation every year or two. In the area of three-dimensional structure of macromolecules and macromolecular assemblies, the methods of X-ray crystallography, nuclear magnetic resonance and electron microscopy have combined to produce powerful insights into how these molecular machines work. In this paper, I present three examples of molecular machines whose structure tells us a lot about how they work. These are the light-driven proton pump bacteriorhodopsin, the ATP synthetase molecule which contains a tiny motor and generator, and the flagellar rotary motor which provides the thrust to power physical movement of the bacterial cell. The structure itself in three-dimensional detail is thus often seen to provide the most important single insight into how things work, reducing biology to chemistry and physics. The reductionist approach in this field seems to be limited only by the accuracy by which it is possible to describe inter- and intra-molecular interactions in terms of hydrogen bonds, van der Waals interactions and electrostatic forces. At present, there is no fundamental limit in sight. PMID:9653714

  6. Crystallography & NMR System: A New Software Suite for Macromolecular Structure Determination

    Microsoft Academic Search

    AXEL T. BRUNGER; PAUL D. ADAMS; G. MARIUS CLORE; WARREN L. DELANO; PIET GROS; RALF W. GROSSE; JIAN-SHENG JIANG; MICHAEL NILGES; NAVRAJ S. PANNU; RANDY J. READ; LUKE M. RICE; THOMAS SIMONSON; GREGORY L. WARREN; John Kuszewski

    1998-01-01

    A new software suite, called Crystallography & NMR System (CNS), has been developed for macromolecular structure determination by X-ray crystallography or solution nuclear magnetic resonance (NMR) spectro- scopy. In contrast to existing structure-determination programs the architecture of CNS is highly flexible, allowing for extension to other structure-determination methods, such as electron microscopy and solid-state NMR spectroscopy. CNS has a hierarchical

  7. Electro-optical analysis of macromolecular structure and dynamics.

    PubMed

    Porschke, Dietmar

    2012-01-01

    Electro-optical effects are induced by external electric field pulses applied to solutions or suspensions and are recorded by various optical techniques. These effects are very useful for the characterization of macromolecular structures and their dynamics in solution. One of the field-induced effects is alignment of molecular dipoles, which can be detected at a very high sensitivity by measurements of the dichroism or the birefringence. Stationary values of these optical parameters recorded at different electric field strengths can be used to characterize dipole moments and to determine the orientation of chromophores with respect to the dipole vector. The transients reflect rotational diffusion, providing a particularly accurate measure of size and shape. The internal flexibility is also reflected in these transients. Another type of field-induced effect is chemical relaxation, which can be detected selectively and is very useful for the characterization of reactions, like ligand binding and conformation changes. The techniques based on electric field effects are unique in the sense that problems can be solved, which are difficult or even impossible to be sorted out by other techniques. PMID:22573451

  8. Automated structure solution with the PHENIX suite

    Microsoft Academic Search

    Thomas C Terwilliger; Peter H Zwart; Pavel V Afonine; Ralf W Grosse

    2008-01-01

    Significant time and effort are often required to solve and complete a macromolecular crystal structure. The development of automated computational methods for the analysis, solution, and completion of crystallographic structures has the potential to produce minimally biased models in a short time without the need for manual intervention. The PHENIX software suite is a highly automated system for macromolecular structure

  9. Automated Structure Solution with the PHENIX Suite

    Microsoft Academic Search

    Peter H. Zwart; Pavel Afonine; Ralf W. Grosse-Kunstleve; Li-Wei Hung; Tom R. Ioerger; A. J. McCoy; Eric McKee; Nigel Moriarty; Randy J. Read; James C. Sacchettini; Nicholas K. Sauter; L. C. Storoni; Tomas C. Terwilliger; Paul D. Adams

    2008-01-01

    Significant time and effort are often required to solve and complete a macromolecular crystal structure. The development of automated computational methods for the analysis, solution and completion of crystallographic structures has the potential to produce minimally biased models in a short time without the need for manual intervention. The PHENIX software suite is a highly automated system for macromolecular structure

  10. Refinement of macromolecular structures against neutron data with SHELXL2013

    PubMed Central

    Gruene, Tim; Hahn, Hinrich W.; Luebben, Anna V.; Meilleur, Flora; Sheldrick, George M.

    2014-01-01

    Some of the improvements in SHELX2013 make SHELXL convenient to use for refinement of macromolecular structures against neutron data without the support of X-ray data. The new NEUT instruction adjusts the behaviour of the SFAC instruction as well as the default bond lengths of the AFIX instructions. This work presents a protocol on how to use SHELXL for refinement of protein structures against neutron data. It includes restraints extending the Engh & Huber [Acta Cryst. (1991), A47, 392–400] restraints to H atoms and discusses several of the features of SHELXL that make the program particularly useful for the investigation of H atoms with neutron diffraction. SHELXL2013 is already adequate for the refinement of small molecules against neutron data, but there is still room for improvement, like the introduction of chain IDs for the refinement of macromolecular structures. PMID:24587788

  11. Modeling Symmetric Macromolecular Structures in Rosetta3

    PubMed Central

    DiMaio, Frank; Leaver-Fay, Andrew; Bradley, Phil; Baker, David; André, Ingemar

    2011-01-01

    Symmetric protein assemblies play important roles in many biochemical processes. However, the large size of such systems is challenging for traditional structure modeling methods. This paper describes the implementation of a general framework for modeling arbitrary symmetric systems in Rosetta3. We describe the various types of symmetries relevant to the study of protein structure that may be modeled using Rosetta's symmetric framework. We then describe how this symmetric framework is efficiently implemented within Rosetta, which restricts the conformational search space by sampling only symmetric degrees of freedom, and explicitly simulates only a subset of the interacting monomers. Finally, we describe structure prediction and design applications that utilize the Rosetta3 symmetric modeling capabilities, and provide a guide to running simulations on symmetric systems. PMID:21731614

  12. Effects of Macromolecular Crowding on the Structure of a Protein Complex

    SciTech Connect

    Rajapaksha Mudalige, Ajith Rathnaweera [ORNL; Stanley, Christopher B [ORNL; Todd, Brian [ORNL

    2015-01-01

    Macromolecular crowding can alter the structure and function of biological macromolecules. We used small angle scattering (SAS) to measure the change in size of a protein complex, superoxide dismutase (SOD), induced by macromolecular crowding. Crowding was induced using 400 MW polyethylene glycol (PEG), triethylene glycol (TEG), methyl- -glucoside ( -MG) and trimethylamine N-oxide (TMAO). Parallel small angle neutron scattering (SANS) and small angle x-ray scattering (SAXS) allowed us to unambiguously attribute apparent changes in radius of gyration to changes in the structure of SOD. For a 40% PEG solution, we find that the volume of SOD was reduced by 9%. Considering the osmotic pressure due to PEG, this deformation corresponds to a highly compressible structure. SAXS done in the presence of TEG suggests that for further deformation beyond a 9% decrease in volume the resistance to deformation may increase dramatically.

  13. A specification for defining and annotating regions of macromolecular structures

    SciTech Connect

    Brenner, S.E. [MRC Laboratory of Molecular Biology, Cambridge (United Kingdom); Hubbard, T.J.P. [Cambridge Centre for Protein Engineering, Cambridge (United Kingdom)

    1995-12-31

    We present a program- and machine-independent standard for annotating macromolecular structures. Data encoded by this specification may be used for communicating information about structures and for exchanging it between different computer systems. The format consists of a set of ASNA objects which are mechanically straightforward to parse, but are also easy for humans to create and understand. It differs from all other related standards in that it specifies how a molecule should be displayed without requiring a custom format for the coordinate data.

  14. Macromolecular Structure Database. Final Progress Report

    SciTech Connect

    Gilliland, Gary L.

    2003-09-23

    The central activity of the PDB continues to be the collection, archiving and distribution of high quality structural data to the scientific community on a timely basis. In support of these activities NIST has continued its roles in developing the physical archive, in developing data uniformity, in dealing with NMR issues and in the distribution of PDB data through CD-ROMs. The physical archive holdings have been organized, inventoried, and a database has been created to facilitate their use. Data from individual PDB entries have been annotated to produce uniform values improving tremendously the accuracy of results of queries. Working with the NMR community we have established data items specific for NMR that will be included in new entries and facilitate data deposition. The PDB CD-ROM production has continued on a quarterly basis, and new products are being distributed.

  15. E-MSD: the European Bioinformatics Institute Macromolecular Structure Database

    PubMed Central

    Boutselakis, H.; Dimitropoulos, D.; Fillon, J.; Golovin, A.; Henrick, K.; Hussain, A.; Ionides, J.; John, M.; Keller, P. A.; Krissinel, E.; McNeil, P.; Naim, A.; Newman, R.; Oldfield, T.; Pineda, J.; Rachedi, A.; Copeland, J.; Sitnov, A.; Sobhany, S.; Suarez-Uruena, A.; Swaminathan, J.; Tagari, M.; Tate, J.; Tromm, S.; Velankar, S.; Vranken, W.

    2003-01-01

    The E-MSD macromolecular structure relational database (http://www.ebi.ac.uk/msd) is designed to be a single access point for protein and nucleic acid structures and related information. The database is derived from Protein Data Bank (PDB) entries. Relational database technologies are used in a comprehensive cleaning procedure to ensure data uniformity across the whole archive. The search database contains an extensive set of derived properties, goodness-of-fit indicators, and links to other EBI databases including InterPro, GO, and SWISS-PROT, together with links to SCOP, CATH, PFAM and PROSITE. A generic search interface is available, coupled with a fast secondary structure domain search tool. PMID:12520052

  16. Macromolecular structure analysis and effective liquefaction pretreatment. Final report

    SciTech Connect

    Suuberg, E.M.; Yun, Y.; Lilly, W.D.; Leung, K.; Gates, T.; Otake, Y.; Deevi, S.C.

    1994-07-01

    This project was concerned with characterizing the changes in coal macromolecular structure, that are of significance for liquefaction pretreatments of coal. The macromolecular structure of the insoluble portion of coal is difficult to characterize. Techniques that do so indirectly (based upon, for example, NMR and FTIR characterizations of atomic linkages) are not particularly sensitive for this purpose. Techniques that characterize the elastic structure (such as solvent swelling) are much more sensitive to subtle changes in the network structure. It is for this reason that we focused upon these techniques. The overall objective involved identifying pretreatments that reduce the crosslinking (physical or chemical) of the network structure, and thus lead to materials that can be handled to a greater extent by traditional liquid-phase processing techniques. These techniques tend to be inherently more efficient at producing desirable products. This report is divided into seven chapters. Chapter II summarizes the main experimental approaches used throughout the project, and summarizes the main findings on the Argonne Premium coal samples. Chapter III considers synergistic effects of solvent pairs. It is divided into two subsections. The first is concerned with mixtures of CS{sub 2} with electron donor solvents. The second subsection is concerned with aromatic hydrocarbon - alcohol or hydrocarbon - alcohol mixtures, as might be of interest for preliquefaction delivery of catalysts into bituminous coals. Chapter IV deals with questions of how oxidation might influence the results that are obtained. Chapter V briefly details what conclusions may be drawn concerning the elastic behavior of coals, and the effects of thermal treatments on this behavior. Chapter VI is concerned with theories to describe the action of solvents that are capable of dissociating non-covalent crosslinks. Finally, Chapter VII discusses the practical implications of the study.

  17. Automated identification of elemental ions in macromolecular crystal structures.

    PubMed

    Echols, Nathaniel; Morshed, Nader; Afonine, Pavel V; McCoy, Airlie J; Miller, Mitchell D; Read, Randy J; Richardson, Jane S; Terwilliger, Thomas C; Adams, Paul D

    2014-04-01

    Many macromolecular model-building and refinement programs can automatically place solvent atoms in electron density at moderate-to-high resolution. This process frequently builds water molecules in place of elemental ions, the identification of which must be performed manually. The solvent-picking algorithms in phenix.refine have been extended to build common ions based on an analysis of the chemical environment as well as physical properties such as occupancy, B factor and anomalous scattering. The method is most effective for heavier elements such as calcium and zinc, for which a majority of sites can be placed with few false positives in a diverse test set of structures. At atomic resolution, it is observed that it can also be possible to identify tightly bound sodium and magnesium ions. A number of challenges that contribute to the difficulty of completely automating the process of structure completion are discussed. PMID:24699654

  18. Macromolecular microcrystallography

    Microsoft Academic Search

    Gwyndaf Evans; Danny Axford; David Waterman; Robin L. Owen

    2011-01-01

    Over a decade has passed since pioneering diffraction experiments on macromolecular microcrystals were performed at the European Synchrotron Radiation Facility. Since then the measurement of high-quality diffraction data for the purpose of structure determination has been transformed from a specialized experiment into routine practice at dedicated microfocus macromolecular crystallography beamlines at synchrotron facilities. In this article, we review the evolution

  19. Macromolecular crowding can account for RNase-sensitive constraint of bacterial nucleoid structure

    SciTech Connect

    Foley, Patricia L. [School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853-5201 (United States)] [School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853-5201 (United States); Wilson, David B. [Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853-5201 (United States)] [Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853-5201 (United States); Shuler, Michael L., E-mail: mls50@cornell.edu [School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853-5201 (United States); Department of Biomedical Engineering, Cornell University, Ithaca, NY 14853-5201 (United States)

    2010-04-23

    The shape and compaction of the bacterial nucleoid may affect the accessibility of genetic material to the transcriptional machinery in natural and synthetic systems. To investigate this phenomenon, the nature and contribution of RNA and protein to the compaction of nucleoids that had been gently released from Escherichia coli cells were investigated using fluorescent and transmission electron microscopy. We propose that the removal of RNA from the bacterial nucleoid affects nucleoid compaction by altering the branching density and molecular weight of the nucleoid. We show that a common detergent in nucleoid preparations, Brij 58, plays a previously unrecognized role as a macromolecular crowding agent. RNA-free nucleoids adopt a compact structure similar in size to exponential-phase nucleoids when the concentration of Brij 58 is increased, consistent with our hypothesis. We present evidence that control and protein-free nucleoids behave similarly in solutions containing a macromolecular crowding agent. These results show that the contribution to DNA compaction by nucleoid-associated proteins is small when compared to macromolecular crowding effects.

  20. Timely deposition of macromolecular structures is necessary for peer review

    SciTech Connect

    Joosten, Robbie P. [Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam (Netherlands); Soueidan, Hayssam; Wessels, Lodewyk F. A. [Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam (Netherlands); Perrakis, Anastassis, E-mail: a.perrakis@nki.nl [Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam (Netherlands)

    2013-12-01

    Deposition of crystallographic structures should be concurrent with or prior to manuscript submission for peer review, enabling validation and increasing reliability of the PDB. Most of the macromolecular structures in the Protein Data Bank (PDB), which are used daily by thousands of educators and scientists alike, are determined by X-ray crystallography. It was examined whether the crystallographic models and data were deposited to the PDB at the same time as the publications that describe them were submitted for peer review. This condition is necessary to ensure pre-publication validation and the quality of the PDB public archive. It was found that a significant proportion of PDB entries were submitted to the PDB after peer review of the corresponding publication started, and many were only submitted after peer review had ended. It is argued that clear description of journal policies and effective policing is important for pre-publication validation, which is key in ensuring the quality of the PDB and of peer-reviewed literature.

  1. Macromolecular ab initio phasing enforcing secondary and tertiary structure

    PubMed Central

    Millán, Claudia; Sammito, Massimo; Usón, Isabel

    2015-01-01

    Ab initio phasing of macromolecular structures, from the native intensities alone with no experimental phase information or previous particular structural knowledge, has been the object of a long quest, limited by two main barriers: structure size and resolution of the data. Current approaches to extend the scope of ab initio phasing include use of the Patterson function, density modification and data extrapolation. The authors’ approach relies on the combination of locating model fragments such as polyalanine ?-helices with the program PHASER and density modification with the program SHELXE. Given the difficulties in discriminating correct small substructures, many putative groups of fragments have to be tested in parallel; thus calculations are performed in a grid or supercomputer. The method has been named after the Italian painter Arcimboldo, who used to compose portraits out of fruit and vegetables. With ARCIMBOLDO, most collections of fragments remain a ‘still-life’, but some are correct enough for density modification and main-chain tracing to reveal the protein’s true portrait. Beyond ?-helices, other fragments can be exploited in an analogous way: libraries of helices with modelled side chains, ?-strands, predictable fragments such as DNA-binding folds or fragments selected from distant homologues up to libraries of small local folds that are used to enforce nonspecific tertiary structure; thus restoring the ab initio nature of the method. Using these methods, a number of unknown macromolecules with a few thousand atoms and resolutions around 2?Å have been solved. In the 2014 release, use of the program has been simplified. The software mediates the use of massive computing to automate the grid access required in difficult cases but may also run on a single multicore workstation (http://chango.ibmb.csic.es/ARCIMBOLDO_LITE) to solve straightforward cases. PMID:25610631

  2. Macromolecular coal structure as revealed by novel diffusion tests

    SciTech Connect

    Peppas, N.A.; Olivares, J.; Drummond, R.; Lustig, S.

    1990-01-01

    The main goal of the present work was the elucidation of the mechanistic characteristics of dynamic transport of various penetrants (solvents) in thin sections of coals by examining their penetrant uptake, front swelling and stress development. An important objective of this work was the study of coal network structure in different thermodynamically compatible penetrants and the analysis of dynamic swelling in terms of present anomalous transport theories. Interferometry/polariscopy, surface image analysis and related techniques were used to quantify the stresses and solvent concentration profiles in these sections. Dynamic and equilibrium swelling behavior were correlated using the polar interaction contributions of the solvent solubility parameters. The penetrant front position was followed in thin coal sections as a function of time. The initial front velocity was calculated for various coals and penetrants. Our penetrant studies with thin coal section from the same coal sample but with different thickness show that within the range of 150 {mu}m to 1500{mu}m the transport mechanism of dimethyl formamide in the macromolecular coal network is non-Fickian. In fact, for the thickest samples the transport mechanism is predominately Case-II whereas in the thinner samples penetrant uptake may be diffusion-controlled. Studies in various penetrants such as acetone, cyclohexane, methanol, methyl ethyl ketone, toluene and methylene chloride indicated that penetrant transport is a non-Fickian phenomenon. Stresses and cracks were observed for transport of methylene chloride. 73 refs., 88 figs., 15 tabs.

  3. Scale invariance of the density fluctuations in films and macromolecular aggregates in poly(styrene) solutions

    NASA Astrophysics Data System (ADS)

    Novikov, D. V.; Krasovski?, A. N.; Osmolovskaya, N. A.; Efremov, V. I.

    2007-02-01

    The specific features of the transformation of a polymer solution into a solid state (film) of an amorphous polymer are investigated using electron microscopy. The correspondence between the characteristics of fractal macromolecular aggregates in a solution and the parameters of the spatial distribution of density fluctuations at the surface of the film is established using a linear atactic poly(styrene) as an example. The correspondence exists under the condition that the packing density of coils does not exceed a critical value at the liquid-solid phase transition point and the polymer concentration in the solution provides the formation of a continuous network of entangled macromolecules.

  4. Effects of Macromolecular Crowding on the Structure of a Protein Complex: A Small-Angle Scattering Study of Superoxide Dismutase

    PubMed Central

    Rajapaksha, Ajith; Stanley, Christopher B.; Todd, Brian A.

    2015-01-01

    Macromolecular crowding can alter the structure and function of biological macromolecules. We used small-angle scattering to measure the effects of macromolecular crowding on the size of a protein complex, SOD (superoxide dismutase). Crowding was induced using 400 MW PEG (polyethylene glycol),TEG (triethylene glycol), ?-MG (methyl-?-glucoside), and TMAO (trimethylamine n-oxide). Parallel small-angle neutron scattering and small-angle x-ray scattering allowed us to unambiguously attribute apparent changes in radius of gyration to changes in the structure of SOD. For a 40% PEG solution, we find that the volume of SOD was reduced by 9%. Considering the osmotic pressure due to PEG, this deformation corresponds to a highly compressible structure. Small-angle x-ray scattering done in the presence of TEG suggests that for further deformation—beyond a 9% decrease in volume—the resistance to deformation may increase dramatically. PMID:25692601

  5. Microelectrophoretic study of calcium oxalate monohydrate in macromolecular solutions

    NASA Technical Reports Server (NTRS)

    Curreri, P. A.; Onoda, G. Y., Jr.; Finlayson, B.

    1987-01-01

    Electrophoretic mobilities were measured for calcium oxalate monohydrate (COM) in solutions containing macromolecules. Two mucopolysaccharides (sodium heparin and chondroitin sulfate) and two proteins (positively charged lysozyme and negatively charged bovine serum albumin) were studied as adsorbates. The effects of pH, calcium oxalate surface charge (varied by calcium or oxalate ion activity), and citrate concentration were investigated. All four macromolecules showed evidence for adsorption. The macromolecule concentrations needed for reversing the surface charge indicated that the mucopolysaccharides have greater affinity for the COM surface than the proteins. Citrate ions at high concentrations appear to compete effectively with the negative protein for surface sites but show no evidence for competing with the positively charged protein.

  6. The electrokinetic behavior of calcium oxalate monohydrate in macromolecular solutions

    NASA Technical Reports Server (NTRS)

    Curreri, P. A.; Onoda, G. Y., Jr.; Finlayson, B.

    1988-01-01

    Electrophoretic mobilities were measured for calcium oxalate monohydrate (COM) in solutions containing macromolecules. Two mucopolysaccharides (sodium heparin and chrondroitin sulfate) and two proteins (positively charged lysozyme and negatively charged bovine serum albumin) were studied as adsorbates. The effects of pH, calcium oxalate surface charge (varied by calcium or oxalate ion activity), and citrate concentration were investigated. All four macromolecules showed evidence for chemical adsorption. The macromolecule concentrations needed for reversing the surface charge indicated that the mucopopolysacchrides have greater affinity for the COM surface than the proteins. The amount of proteins that can chemically adsorb appears to be limited to approximately one monomolecular layer. When the surface charge is high, an insufficient number of proteins can chemically adsorb to neutralize or reverse the surface charge. The remaining surface charge is balanced by proteins held near the surface by longer range electrostatic forces only. Citrate ions at high concentrations appear to compete effectively with the negative protein for surface sites but show no evidence for competing with the positively charged protein.

  7. Macromolecular properties and polymeric structure of canine tracheal mucins.

    PubMed Central

    Shankar, V; Virmani, A K; Naziruddin, B; Sachdev, G P

    1991-01-01

    Two high-Mr mucus glycoproteins (mucins), CTM-A and CTM-B, were highly purified from canine tracheal pouch secretions, and their macromolecular properties as well as polymeric structure were investigated. On SDS/composite-gel electrophoresis, a diffuse band was observed for each mucin. Polyacrylamide-gel electrophoresis using 6% gels also showed the absence of low-Mr contaminants in the mucins. Comparison of chemical and amino acid compositions revealed significant differences between the two mucins. Using a static-laser-light-scattering technique, CTM-A and CTM-B were found to have weight-average Mr values of about 11.0 x 10(6) and 1.4 x 10(6) respectively. Both mucins showed concentration-dependent aggregation in buffer containing 6 M-guanidine hydrochloride. Under similar experimental conditions, reduced-alkylated CTM-A had an Mr of 5.48 x 10(6) and showed no concentration-dependent aggregation. Hydrophobic properties of the mucins, investigated by the fluorescent probe technique using mansylphenylalanine as the probe, showed the presence of a large number of low-affinity (KD approx. 10(5) M) binding sites. These sites appeared to be located on the non-glycosylated regions of the protein core, since Pronase digestion of the mucins almost completely eliminated probe binding. Reduction of disulphide bonds of CTM-A and CTM-B did not significantly alter the probe-binding properties. Also, addition of increasing NaCl concentrations (0.03-1.0 M) to the buffer caused only a small change in the hydrophobic properties of native and reduced-alkylated mucins. CTM-A was deglycosylated, without notable in the hydrophobic properties of native and reduced-alkylated mucins. CTM-A was deglycosylated, without notable degradation, using a combination of chemical and enzymic methods. On SDS/PAGE the protein core was estimated to have an Mr of approx. 60,000. On the basis of the protein and carbohydrate contents of the major mucin CTM-A, the mucin monomer was calculated to have an Mr of approx. 140,000. The high Mr (11 x 10(6] observed by physical methods is therefore due to self-association of the mucin monomer subunits. Images Fig. 3. Fig. 8. PMID:2049078

  8. Recent developments in phasing and structure refinement for macromolecular crystallography

    PubMed Central

    Adams, Paul D.; Afonine, Pavel V.; Grosse-Kunstleve, Ralf W.; Read, Randy J.; Richardson, Jane S.; Richardson, David C.; Terwilliger, Thomas C.

    2009-01-01

    Summary Central to crystallographic structure solution is obtaining accurate phases in order to build a molecular model, ultimately followed by refinement of that model to optimize its fit to the experimental diffraction data and prior chemical knowledge. Recent advances in phasing and model refinement and validation algorithms make it possible to arrive at better electron density maps and more accurate models. PMID:19700309

  9. The Neurobiologist's Guide to Structural Biology: A Primer on Why Macromolecular Structure Matters and How to Evaluate Structural Data

    PubMed Central

    Minor, Daniel L.

    2010-01-01

    Structural biology now plays a prominent role in addressing questions central to understanding how excitable cells function. Although interest in the insights gained from the definition and dissection of macromolecular anatomy is high, many neurobiologists remain unfamiliar with the methods employed. This primer aims to help neurobiologists understand approaches for probing macromolecular structure and where the limits and challenges remain. Using examples of macromolecules with neurobiological importance, the review covers X-ray crystallography, electron microscopy (EM), small-angle X-ray scattering (SAXS), and nuclear magnetic resonance (NMR) and biophysical methods with which these approaches are often paired: isothermal titration calorimetry (ITC), equilibrium analytical ultracentifugation, and molecular dynamics (MD). PMID:17521566

  10. Dynamic simulation of concentrated macromolecular solutions with screened long-range hydrodynamic interactions: Algorithm and limitations

    PubMed Central

    Ando, Tadashi; Chow, Edmond; Skolnick, Jeffrey

    2013-01-01

    Hydrodynamic interactions exert a critical effect on the dynamics of macromolecules. As the concentration of macromolecules increases, by analogy to the behavior of semidilute polymer solutions or the flow in porous media, one might expect hydrodynamic screening to occur. Hydrodynamic screening would have implications both for the understanding of macromolecular dynamics as well as practical implications for the simulation of concentrated macromolecular solutions, e.g., in cells. Stokesian dynamics (SD) is one of the most accurate methods for simulating the motions of N particles suspended in a viscous fluid at low Reynolds number, in that it considers both far-field and near-field hydrodynamic interactions. This algorithm traditionally involves an O(N3) operation to compute Brownian forces at each time step, although asymptotically faster but more complex SD methods are now available. Motivated by the idea of hydrodynamic screening, the far-field part of the hydrodynamic matrix in SD may be approximated by a diagonal matrix, which is equivalent to assuming that long range hydrodynamic interactions are completely screened. This approximation allows sparse matrix methods to be used, which can reduce the apparent computational scaling to O(N). Previously there were several simulation studies using this approximation for monodisperse suspensions. Here, we employ newly designed preconditioned iterative methods for both the computation of Brownian forces and the solution of linear systems, and consider the validity of this approximation in polydisperse suspensions. We evaluate the accuracy of the diagonal approximation method using an intracellular-like suspension. The diffusivities of particles obtained with this approximation are close to those with the original method. However, this approximation underestimates intermolecular correlated motions, which is a trade-off between accuracy and computing efficiency. The new method makes it possible to perform large-scale and long-time simulation with an approximate accounting of hydrodynamic interactions. PMID:24089734

  11. Probing the Interplay of Size, Shape, and Solution Environment in Macromolecular Diffusion Using a Simple Refraction Experiment

    ERIC Educational Resources Information Center

    Mankidy, Bijith D.; Coutinho, Cecil A.; Gupta, Vinay K.

    2010-01-01

    The diffusion coefficient of polymers is a critical parameter in biomedicine, catalysis, chemical separations, nanotechnology, and other industrial applications. Here, measurement of macromolecular diffusion in solutions is described using a visually instructive, undergraduate-level optical refraction experiment based on Weiner's method. To…

  12. Protein crystallography for aspiring crystallographers or how to avoid pitfalls and traps in macromolecular structure determination

    PubMed Central

    Wlodawer, Alexander; Minor, Wladek; Dauter, Zbigniew; Jaskolski, Mariusz

    2014-01-01

    The number of macromolecular structures deposited in the Protein Data Bank now approaches 100 000, with the vast majority of them determined by crystallographic methods. Thousands of papers describing such structures have been published in the scientific literature, and 20 Nobel Prizes in chemistry or medicine have been awarded for discoveries based on macromolecular crystallography. New hardware and software tools have made crystallography appear to be an almost routine (but still far from being analytical) technique and many structures are now being determined by scientists with very limited experience in the practical aspects of the field. However, this apparent ease is sometimes illusory and proper procedures need to be followed to maintain high standards of structure quality. In addition, many noncrystallographers may have problems with the critical evaluation and interpretation of structural results published in the scientific literature. The present review provides an outline of the technical aspects of crystallography for less experienced practitioners, as well as information that might be useful for users of macromolecular structures, aiming to show them how to interpret (but not overinterpret) the information present in the coordinate files and in their description. A discussion of the extent of information that can be gleaned from the atomic coordinates of structures solved at different resolution is provided, as well as problems and pitfalls encountered in structure determination and interpretation. PMID:24034303

  13. A MACROMOLECULAR REPEATING UNIT OF MITOCHONDRIAL STRUCTURE AND FUNCTION

    PubMed Central

    Fernández-Morán, H.; Oda, T.; Blair, P. V.; Green, D. E.

    1964-01-01

    A repeating particle associated with the cristae and the inner membrane of the external envelope has been recognized and characterized in beef heart mitochondria by correlated electron microscopic and biochemical studies. Many thousands (ca. 104 to 105) of these particles, disposed in regular arrays, are present in a single mitochondrion. The repeating particle, called the elementary particle (EP), consists of three parts: (1) a spherical or polyhedral head piece (80 to 100 A in diameter); (2) a cylindrical stalk (about 50 A long and 30 to 40 A wide); and (3) a base piece (40 x 110 A). The base pieces of the elementary particles form an integral part of the outer dense layers of the cristae. The elementary particles can be seen in electron micrographs of mitochondria in situ, of isolated mitochondria, and of submitochondrial particles with a complete electron transfer chain. Negative staining with phosphotungstate is only one of several techniques that can be used for reproducible demonstration of the repeating particles and underlying subunit organization of mitochondrial membranes. A particulate unit containing a complete electron transfer chain can be isolated from beef heart mitochondria. The isolated unit approximates in size that of the elementary particle in situ. The molecular weight of the particle in situ is calculated to be 1.3 x 106. Evidence is presented for identifying the isolated unit with the elementary particle visualized in situ. The elementary particle of the mitochondrion is believed to be a prototype of a class of functional particles or macromolecular assemblies of similar size found in association with membranes generally. PMID:14195622

  14. Accurate macromolecular structures using minimal measurements from X-ray free-electron lasers.

    PubMed

    Hattne, Johan; Echols, Nathaniel; Tran, Rosalie; Kern, Jan; Gildea, Richard J; Brewster, Aaron S; Alonso-Mori, Roberto; Glöckner, Carina; Hellmich, Julia; Laksmono, Hartawan; Sierra, Raymond G; Lassalle-Kaiser, Benedikt; Lampe, Alyssa; Han, Guangye; Gul, Sheraz; DiFiore, Dörte; Milathianaki, Despina; Fry, Alan R; Miahnahri, Alan; White, William E; Schafer, Donald W; Seibert, M Marvin; Koglin, Jason E; Sokaras, Dimosthenis; Weng, Tsu-Chien; Sellberg, Jonas; Latimer, Matthew J; Glatzel, Pieter; Zwart, Petrus H; Grosse-Kunstleve, Ralf W; Bogan, Michael J; Messerschmidt, Marc; Williams, Garth J; Boutet, Sébastien; Messinger, Johannes; Zouni, Athina; Yano, Junko; Bergmann, Uwe; Yachandra, Vittal K; Adams, Paul D; Sauter, Nicholas K

    2014-05-01

    X-ray free-electron laser (XFEL) sources enable the use of crystallography to solve three-dimensional macromolecular structures under native conditions and without radiation damage. Results to date, however, have been limited by the challenge of deriving accurate Bragg intensities from a heterogeneous population of microcrystals, while at the same time modeling the X-ray spectrum and detector geometry. Here we present a computational approach designed to extract meaningful high-resolution signals from fewer diffraction measurements. PMID:24633409

  15. FRONTIER MICROFOCUSING MACROMOLECULAR CRYSTALLOGRAPHY BEAMLINE (FMX)

    E-print Network

    Ohta, Shigemi

    FRONTIER MICROFOCUSING MACROMOLECULAR CRYSTALLOGRAPHY BEAMLINE (FMX) ADDITIONAL INFORMATION to find best diffracting regions and mitigate impact of radiation damage. Serial crystallography: Multi macromolecular crystallography (MX) · Elucidation of structure and function of macromolecular complexes from

  16. Macromolecular Crystallography for Synthetic Abiological Molecules: Combining xMDFF and PHENIX for Structure Determination of Cyanostar Macrocycles

    PubMed Central

    Singharoy, Abhishek; Venkatakrishnan, Balasubramanian; Liu, Yun; Mayne, Christopher G.; Lee, Semin; Chen, Chun-Hsing; Zlotnick, Adam; Schulten, Klaus; Flood, Amar H.

    2015-01-01

    Crystal structure determination has long provided insight into structure and bonding of small molecules. When those same small molecules are designed to come together in multi-molecular assemblies, such as in coordination cages, supramolecular architectures and organic-based frameworks, their crystallographic characteristics closely resemble biological macromolecules. This resemblance suggests that bio-macromolecular refinement approaches be used for structure determination of abiological molecular complexes that arise in an aggregate state. Following this suggestion we investigated the crystal structure of a pentagonal macrocycle, cyanostar, by means of biological structure analysis methods and compared results to traditional small molecule methods. Cyanostar presents difficulties seen in supramolecular crystallography including whole molecule disorder and highly flexible solvent molecules sitting in macrocyclic and intermolecule void spaces. We used the force-field assisted refinement method, molecular dynamics flexible fitting algorithm for X-ray crystallography (xMDFF), along with tools from the macromolecular structure determination suite PHENIX. We found that a standard implementation of PHENIX, namely one without xMDFF, either fails to produce a solution by molecular replacement alone or produces an inaccurate structure when using generic geometry restraints, even at a very high diffraction data resolution of 0.84 Å. The problems disappear when taking advantage of xMDFF, which applies an optimized force field to re-align molecular models during phasing by providing accurate restraints. The structure determination for this model system shows excellent agreement with the small-molecule methods. Therefore, the joint xMDFF-PHENIX refinement protocol provides a new strategy that uses macromolecule methods for structure determination of small molecules and their assemblies. PMID:26121416

  17. D Macromolecular Structure Analyses: Applications in Plant Proteins

    NASA Astrophysics Data System (ADS)

    Dede, Filiz; Dinler, Gizem; Sayers, Zehra

    Attempts to relate the function to the structural features of biological macromolecules have intensified through the use of synchrotron radiation (SR) based techniques. Small Angle X-ray Scattering (SXAS) is a technique that has become readily accessible through several bamlines on SR sources all over the world. SAXS is used for obtaining low resolution structural information and is particularly useful for macromolecules that do not easily crystallize or alternatively when time-resolved structural information is required. In this paper use of SAXS for determination of structural parameters of a wheat metallothionein as a fusion protein with glutathione-stransferase (GST) is presented together with low resolution models. Results are discussed in the framework of functional roles of wheat metallothionein.

  18. Perdeuteration: improved visualization of solvent structure in neutron macromolecular crystallography.

    PubMed

    Fisher, S J; Blakeley, M P; Howard, E I; Petit-Haertlein, I; Haertlein, M; Mitschler, A; Cousido-Siah, A; Salvay, A G; Popov, A; Muller-Dieckmann, C; Petrova, T; Podjarny, A

    2014-12-01

    The 1.8?Å resolution neutron structure of deuterated type III antifreeze protein in which the methyl groups of leucine and valine residues are selectively protonated is presented. Comparison between this and the 1.85?Å resolution neutron structure of perdeuterated type III antifreeze protein indicates that perdeuteration improves the visibility of solvent molecules located in close vicinity to hydrophobic residues, as cancellation effects between H atoms of the methyl groups and nearby heavy-water molecules (D2O) are avoided. PMID:25478844

  19. Macromolecular structural changes in bituminous coals during extraction and solubilization

    NASA Astrophysics Data System (ADS)

    Peppas, N. A.; Hill-Lievense, M. E.; Hooker, D. T., II; Lucht, L. M.

    Seven coal samples ranging from a lignite with 69.95% carbon to an anthracite with 94.17% carbon on a dry mineral matter-free (dmmf) basis were extracted with pyridine at its reflux temperature for two weeks. The coal matrices obtained were subjected to two degradation techniques, the Sternberg reductive alkylation technique and the Miyake alkylation technique. Gel permeation chromatographic analysis of pyridine-extracted liquids of the alkylated coal showed average molecular weights smaller than those of the original coal extracts. Electron impact mass spectrometry was used to obtain the mass spectra of these alkylated coal samples. Based on investigation of the recurring pattern of the peaks of the mass spectra of these products it was concluded that a cluster size of 126 to 130 is characteristic of the crosslinked structure of the coal studied. In addition, several chemical compounds in the range of m/e 78-191 were identified.

  20. Recovering a Representative Conformational Ensemble from Underdetermined Macromolecular Structural Data

    PubMed Central

    Berlin, Konstantin; Castañeda, Carlos A.; Schneidman-Duhovny, Dina; Sali, Andrej; Nava-Tudela, Alfredo; Fushman, David

    2013-01-01

    Structural analysis of proteins and nucleic acids is complicated by their inherent flexibility, conferred, for example, by linkers between their contiguous domains. Therefore, the macromolecule needs to be represented by an ensemble of conformations instead of a single conformation. Determining this ensemble is challenging because the experimental data are a convoluted average of contributions from multiple conformations. As the number of the ensemble degrees of freedom generally greatly exceeds the number of independent observables, directly deconvolving experimental data into a representative ensemble is an ill-posed problem. Recent developments in sparse approximations and compressive sensing have demonstrated that useful information can be recovered from underdetermined (ill-posed) systems of linear equations by using sparsity regularization. Inspired by these advances, we designed Sparse Ensemble Selection (SES) method for recovering multiple conformations from a limited number of observations. SES is more general and accurate than previously published minimum-ensemble methods, and we use it to obtain representative conformational ensembles of Lys48-linked di-ubiquitin, characterized by the residual dipolar coupling data measured at several pH conditions. These representative ensembles are validated against NMR chemical shift perturbation data and compared to maximum-entropy results. The SES method reproduced and quantified the previously observed pH dependence of the major conformation of Lys48-linked di-ubiquitin, and revealed lesser-populated conformations that are pre-organized for binding known di-ubiquitin receptors, thus providing insights into possible mechanisms of receptor recognition by polyubiquitin. SES is applicable to any experimental observables that can be expressed as a weighted linear combination of data for individual states. PMID:24093873

  1. Structure, assembly and dynamics of macromolecular complexes by single particle cryo-electron microscopy

    PubMed Central

    2013-01-01

    Background Proteins in their majority act rarely as single entities. Multisubunit macromolecular complexes are the actors in most of the cellular processes. These nanomachines are hold together by weak protein-protein interactions and undergo functionally important conformational changes. TFIID is such a multiprotein complex acting in eukaryotic transcription initiation. This complex is first to be recruited to the promoter of the genes and triggers the formation of the transcription preinitiation complex involving RNA polymerase II which leads to gene transcription. The exact role of TFIID in this process is not yet understood. Methods Last generation electron microscopes, improved data collection and new image analysis tools made it possible to obtain structural information of biological molecules at atomic resolution. Cryo-electron microscopy of vitrified samples visualizes proteins in a fully hydrated, close to native state. Molecular images are recorded at liquid nitrogen temperature in low electron dose conditions to reduce radiation damage. Digital image analysis of these noisy images aims at improving the signal-to-noise ratio, at separating distinct molecular views and at reconstructing a three-dimensional model of the biological particle. Results Using these methods we showed the early events of an activated transcription initiation process. We explored the interaction of the TFIID coactivator with the yeast Rap1 activator, the transcription factor TFIIA and the promoter DNA. We demonstrated that TFIID serves as an assembly platform for transient protein-protein interactions, which are essential for transcription initiation. Conclusions Recent developments in electron microscopy have provided new insights into the structural organization and the dynamic reorganization of large macromolecular complexes. Examples of near-atomic resolutions exist but the molecular flexibility of macromolecular complexes remains the limiting factor in most case. Electron microscopy has the potential to provide both structural and dynamic information of biological assemblies in order to understand the molecular mechanisms of their functions. PMID:24565374

  2. Accurate macromolecular structures using minimal measurements from X-ray free-electron lasers

    PubMed Central

    Hattne, Johan; Echols, Nathaniel; Tran, Rosalie; Kern, Jan; Gildea, Richard J.; Brewster, Aaron S.; Alonso-Mori, Roberto; Glöckner, Carina; Hellmich, Julia; Laksmono, Hartawan; Sierra, Raymond G.; Lassalle-Kaiser, Benedikt; Lampe, Alyssa; Han, Guangye; Gul, Sheraz; DiFiore, Dörte; Milathianaki, Despina; Fry, Alan R.; Miahnahri, Alan; White, William E.; Schafer, Donald W.; Seibert, M. Marvin; Koglin, Jason E.; Sokaras, Dimosthenis; Weng, Tsu-Chien; Sellberg, Jonas; Latimer, Matthew J.; Glatzel, Pieter; Zwart, Petrus H.; Grosse-Kunstleve, Ralf W.; Bogan, Michael J.; Messerschmidt, Marc; Williams, Garth J.; Boutet, Sébastien; Messinger, Johannes; Zouni, Athina; Yano, Junko; Bergmann, Uwe; Yachandra, Vittal K.; Adams, Paul D.; Sauter, Nicholas K.

    2014-01-01

    X-ray free-electron laser (XFEL) sources enable the use of crystallography to solve three-dimensional macromolecular structures under native conditions and free from radiation damage. Results to date, however, have been limited by the challenge of deriving accurate Bragg intensities from a heterogeneous population of microcrystals, while at the same time modeling the X-ray spectrum and detector geometry. Here we present a computational approach designed to extract statistically significant high-resolution signals from fewer diffraction measurements. PMID:24633409

  3. Macromolecular X-ray structure determination using weak, single-wavelength anomalous data.

    PubMed

    Bunkóczi, Gábor; McCoy, Airlie J; Echols, Nathaniel; Grosse-Kunstleve, Ralf W; Adams, Paul D; Holton, James M; Read, Randy J; Terwilliger, Thomas C

    2015-02-01

    We describe a likelihood-based method for determining the substructure of anomalously scattering atoms in macromolecular crystals that allows successful structure determination by single-wavelength anomalous diffraction (SAD) X-ray analysis with weak anomalous signal. With the use of partial models and electron density maps in searches for anomalously scattering atoms, testing of alternative values of parameters and parallelized automated model-building, this method has the potential to extend the applicability of the SAD method in challenging cases. PMID:25532136

  4. FRONTIER MACROMOLECULAR CRYSTALLOGRAPHY (FMX)

    E-print Network

    Ohta, Shigemi

    FRONTIER MACROMOLECULAR CRYSTALLOGRAPHY (FMX) SCIENTIFIC SCOPE BEAMLINE CHARACTERISTICS Micro. SCIENTIFIC APPLICATIONS TECHNIQUES: · Single and multi-axis MX · Serial crystallography · Micro crystallography (FMX) is an undulator beamline at sector 17-ID for structural biology investigations with micro

  5. Flexible torsion-angle noncrystallographic symmetry restraints for improved macromolecular structure refinement

    PubMed Central

    Headd, Jeffrey J.; Echols, Nathaniel; Afonine, Pavel V.; Moriarty, Nigel W.; Gildea, Richard J.; Adams, Paul D.

    2014-01-01

    One of the great challenges in refining macromolecular crystal structures is a low data-to-parameter ratio. Historically, knowledge from chemistry has been used to help to improve this ratio. When a macromolecule crystallizes with more than one copy in the asymmetric unit, the noncrystallographic symmetry relationships can be exploited to provide additional restraints when refining the working model. However, although globally similar, NCS-related chains often have local differences. To allow for local differences between NCS-related molecules, flexible torsion-based NCS restraints have been introduced, coupled with intelligent rotamer handling for protein chains, and are available in phenix.refine for refinement of models at all resolutions. PMID:24816103

  6. Biological Macromolecular Structures Data from the RCSB Protein Data Bank (RCSB PDB)

    DOE Data Explorer

    The Research Collaboratory for Structural Bioinformatics (RCSB) is a non-profit consortium that works to improve understanding of the function of biological systems through the study of the 3-D structure of biological macromolecules. The RCSB PDB is one of three sites serving as deposition, data processing, and distribution sites of the Protein Data Bank Archive. Each site provides its own view of the primary data, thus providing a variety of tools and resources for the global community. RCSB is also the official keeper for the PDB archive, with sole access authority to the PDB archive directory structure and contents. The RCSB PDB Information Portal for Biological Macromolecular Structures offers online tools for search and retrieval, for visualizing structures, for depositing, validating, or downloading data, news and highlights, a discussion forum, and links to other areas of related research. The PDB archive is a repository of atomic coordinates and other information describing proteins and other important biological macromolecules. Structural biologists use methods such as X-ray crystallography, NMR spectroscopy, and cryo-electron microscopy to determine the location of each atom relative to each other in the molecule. They then deposit this information, which is then annotated and publicly released into the archive by the wwPDB. Results can be viewed as 3-D images or models.

  7. Instrumentation on Multi-Scaled Scattering of Bio-Macromolecular Solutions

    PubMed Central

    Chu, Benjamin; Fang, Dufei; Mao, Yimin

    2015-01-01

    The design, construction and initial tests on a combined laser light scattering and synchrotron X-ray scattering instrument can cover studies of length scales from atomic sizes in Angstroms to microns and dynamics from microseconds to seconds are presented. In addition to static light scattering (SLS), dynamic light scattering (DLS), small angle X-ray scattering (SAXS) and wide angle X-ray diffraction (WAXD), the light scattering instrument is being developed to carry out studies in mildly turbid solutions, in the presence of multiple scattering. Three-dimensional photon cross correlation function (3D-PCCF) measurements have been introduced to couple with synchrotron X-ray scattering to study the structure, size and dynamics of macromolecules in solution. PMID:25946340

  8. Macromolecular structural dynamics visualized by pulsed dose control in 4D electron microscopy

    PubMed Central

    Kwon, Oh-Hoon; Ortalan, Volkan; Zewail, Ahmed H.

    2011-01-01

    Macromolecular conformation dynamics, which span a wide range of time scales, are fundamental to the understanding of properties and functions of their structures. Here, we report direct imaging of structural dynamics of helical macromolecules over the time scales of conformational dynamics (ns to subsecond) by means of four-dimensional (4D) electron microscopy in the single-pulse and stroboscopic modes. With temporally controlled electron dosage, both diffraction and real-space images are obtained without irreversible radiation damage. In this way, the order-disorder transition is revealed for the organic chain polymer. Through a series of equilibrium-temperature and temperature-jump dependencies, it is shown that the metastable structures and entropy of conformations can be mapped in the nonequilibrium region of a “funnel-like” free-energy landscape. The T-jump is introduced through a substrate (a “hot plate” type arrangement) because only the substrate is made to absorb the pulsed energy. These results illustrate the promise of ultrafast 4D imaging for other applications in the study of polymer physics as well as in the visualization of biological phenomena. PMID:21444766

  9. The structural biology center at the APS: an integrated user facility for macromolecular crystallography

    SciTech Connect

    Rosenbaum, G.; Westbrook, E. M. [Structural Biology Center, Argonne National Laboratory, Advanced Photon Source, 9700 S. Cass Ave., Argonne, Illinois 60439 (United States)

    1997-07-01

    The Structural Biology Center (SBC) has developed and operates a sector (undulator and bending magnet) of the APS as a user facility for macromolecular crystallography. Crystallographically determined structures of proteins, nucleic acids and their complexes with proteins, viruses, and complexes between macromolecules and small ligands have become of central importance in molecular and cellular biology. Major design goals were to make the extremely high brilliance of the APS available for brilliance limited studies, and to achieve a high throughput of less demanding studies, as well as optimization for MAS-phasing. Crystal samples will include extremely small crystals, crystals with large unit cells (viruses, ribosomes, etc.) and ensembles of closely similar crystal structures for drug design, protein engineering, etc. Data are recorded on a 3000x3000 pixel CCD-area detector (optionally on image plates). The x-ray optics of both beamlines has been designed to produce a highly demagnified image of the source in order to match the focal size with the sizes of the sample and the resolution element of the detector. Vertical focusing is achieved by a flat, cylindrically bent mirror. Horizontal focusing is achieved by sagitally bending the second crystal of the double crystal monochromator. Monochromatic fluxes of 1.3*10{sup 13} ph/s into focal sizes of 0.08 mm (horizontal)x0.04 mm (vertical) FWHM (flux density 3.5*10{sup 15} ph/s/mm{sup 2}) have been recorded.

  10. Free kick instead of cross-validation in maximum-likelihood refinement of macromolecular crystal structures.

    PubMed

    Pražnikar, Jure; Turk, Dušan

    2014-12-01

    The refinement of a molecular model is a computational procedure by which the atomic model is fitted to the diffraction data. The commonly used target in the refinement of macromolecular structures is the maximum-likelihood (ML) function, which relies on the assessment of model errors. The current ML functions rely on cross-validation. They utilize phase-error estimates that are calculated from a small fraction of diffraction data, called the test set, that are not used to fit the model. An approach has been developed that uses the work set to calculate the phase-error estimates in the ML refinement from simulating the model errors via the random displacement of atomic coordinates. It is called ML free-kick refinement as it uses the ML formulation of the target function and is based on the idea of freeing the model from the model bias imposed by the chemical energy restraints used in refinement. This approach for the calculation of error estimates is superior to the cross-validation approach: it reduces the phase error and increases the accuracy of molecular models, is more robust, provides clearer maps and may use a smaller portion of data for the test set for the calculation of Rfree or may leave it out completely. PMID:25478831

  11. The structural biology center at the APS: an integrated user facility for macromolecular crystallography

    SciTech Connect

    Rosenbaum, G.; Westbrook, E.M. [Structural Biology Center, Argonne National Laboratory, Advanced Photon Source, 9700 S. Cass Ave., Argonne, Illinois60439 (United States)

    1997-07-01

    The Structural Biology Center (SBC) has developed and operates a sector (undulator and bending magnet) of the APS as a user facility for macromolecular crystallography. Crystallographically determined structures of proteins, nucleic acids and their complexes with proteins, viruses, and complexes between macromolecules and small ligands have become of central importance in molecular and cellular biology. Major design goals were to make the extremely high brilliance of the APS available for brilliance limited studies, and to achieve a high throughput of less demanding studies, as well as optimization for MAS-phasing. Crystal samples will include extremely small crystals, crystals with large unit cells (viruses, ribosomes, etc.) and ensembles of closely similar crystal structures for drug design, protein engineering, etc. Data are recorded on a 3000{times}3000 pixel CCD-area detector (optionally on image plates). The x-ray optics of both beamlines has been designed to produce a highly demagnified image of the source in order to match the focal size with the sizes of the sample and the resolution element of the detector. Vertical focusing is achieved by a flat, cylindrically bent mirror. Horizontal focusing is achieved by sagitally bending the second crystal of the double crystal monochromator. Monochromatic fluxes of 1.3{sup {asterisk}}10{sup 13} ph/s into focal sizes of 0.08 mm (horizontal){times}0.04 mm (vertical) FWHM (flux density 3.5{sup {asterisk}}10{sup 15} ph/s/mm{sup 2}) have been recorded.{copyright} {ital 1997 American Institute of Physics.}

  12. Free kick instead of cross-validation in maximum-likelihood refinement of macromolecular crystal structures

    SciTech Connect

    Pražnikar, Jure [Institute Jožef Stefan, Jamova 39, 1000 Ljubljana (Slovenia); University of Primorska, (Slovenia); Turk, Dušan, E-mail: dusan.turk@ijs.si [Institute Jožef Stefan, Jamova 39, 1000 Ljubljana (Slovenia); Center of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, (Slovenia)

    2014-12-01

    The maximum-likelihood free-kick target, which calculates model error estimates from the work set and a randomly displaced model, proved superior in the accuracy and consistency of refinement of crystal structures compared with the maximum-likelihood cross-validation target, which calculates error estimates from the test set and the unperturbed model. The refinement of a molecular model is a computational procedure by which the atomic model is fitted to the diffraction data. The commonly used target in the refinement of macromolecular structures is the maximum-likelihood (ML) function, which relies on the assessment of model errors. The current ML functions rely on cross-validation. They utilize phase-error estimates that are calculated from a small fraction of diffraction data, called the test set, that are not used to fit the model. An approach has been developed that uses the work set to calculate the phase-error estimates in the ML refinement from simulating the model errors via the random displacement of atomic coordinates. It is called ML free-kick refinement as it uses the ML formulation of the target function and is based on the idea of freeing the model from the model bias imposed by the chemical energy restraints used in refinement. This approach for the calculation of error estimates is superior to the cross-validation approach: it reduces the phase error and increases the accuracy of molecular models, is more robust, provides clearer maps and may use a smaller portion of data for the test set for the calculation of R{sub free} or may leave it out completely.

  13. Protein crystallography for non-crystallographers, or how to get the best (but not more) from published macromolecular structures

    PubMed Central

    Wlodawer, Alexander; Minor, Wladek; Dauter, Zbigniew; Jaskolski, Mariusz

    2015-01-01

    The number of macromolecular structures deposited in the Protein Data Bank now exceeds 45 000, with the vast majority determined using crystallographic methods. Thousands of studies describing such structures have been published in the scientific literature, and 14 Nobel prizes in chemistry or medicine have been awarded to protein crystallographers. As important as these structures are for understanding the processes that take place in living organisms and also for practical applications such as drug design, many non-crystallographers still have problems with critical evaluation of the structural literature data. This review attempts to provide a brief outline of technical aspects of crystallography and to explain the meaning of some parameters that should be evaluated by users of macromolecular structures in order to interpret, but not over-interpret, the information present in the coordinate files and in their description. A discussion of the extent of the information that can be gleaned from the coordinates of structures solved at different resolution, as well as problems and pitfalls encountered in structure determination and interpretation are also covered. PMID:18034855

  14. Flux improvement by Dean vortices: ultrafiltration of colloidal suspensions and macromolecular solutions

    Microsoft Academic Search

    P Moulin; P Manno; J. C Rouch; C Serra; M. J Clifton; P Aptel

    1999-01-01

    Coiled and straight hollow-fibre modules have been built and tested; the permeate flux obtained in ultrafiltration with these two geometries is compared for two feeds: a colloidal bentonite suspension and a dextran solution. In the case of colloidal suspensions, the secondary flows induced by the coiled geometry allow fouling to be reduced and the permeate flux is multiplied by a

  15. Super-resolution in solution X-ray scattering and its applications to structural systems biology.

    PubMed

    Rambo, Robert P; Tainer, John A

    2013-01-01

    Small-angle X-ray scattering (SAXS) is a robust technique for the comprehensive structural characterizations of biological macromolecular complexes in solution. Here, we present a coherent synthesis of SAXS theory and experiment with a focus on analytical tools for accurate, objective, and high-throughput investigations. Perceived SAXS limitations are considered in light of its origins, and we present current methods that extend SAXS data analysis to the super-resolution regime. In particular, we discuss hybrid structural methods, illustrating the role of SAXS in structure refinement with NMR and ensemble refinement with single-molecule FRET. High-throughput genomics and proteomics are far outpacing macromolecular structure determinations, creating information gaps between the plethora of newly identified genes, known structures, and the structure-function relationship in the underlying biological networks. SAXS can bridge these information gaps by providing a reliable, high-throughput structural characterization of macromolecular complexes under physiological conditions. PMID:23495971

  16. Automated measurement of the static light scattering of macromolecular solutions over a broad range of concentration

    PubMed Central

    Fernández, Cristina; Minton, Allen P.

    2008-01-01

    A method and apparatus for automated measurement of the concentration dependence of static light scattering of protein solutions over a broad range of concentration is described. The gradient of protein concentration is created by successive dilutions of an initially concentrated solution contained within the scattering measurement cell, which is maintained at constant total volume. The method is validated by measurement of the concentration dependence of light scattering of bovine serum albumin, ovalbumin, and ovomucoid at concentrations up to 130 g/L. The experimentally obtained concentration dependence of scattering obtained from all three proteins is quantitatively consistent with the assumption that no significant self-association occurs over the measured range of concentration. PMID:18627764

  17. Tubular microporous alumina structure for demulsifying vegetable oil\\/water emulsions and concentrating macromolecular suspensions

    Microsoft Academic Search

    Sérgio R. Fontes; Viviane M. Silva Queiroz; Elson Longo; Marcus V. Antunes

    2005-01-01

    A microstructure composed of alumina–silica (mullite, 3Al2O3·2SiO2) was molded into tubes to be used in a microfiltration process for separating water\\/vegetable oil emulsions and to concentrate macromolecular suspensions. The microporous tubes were produced by the precipitation method using raw material supplied by Rhodia do Brasil Ltda, and sintered at a final temperature of 1450°C. The microporous medium was characterized by

  18. Modelling macromolecular networks: two meetings

    E-print Network

    Carbone, Alessandra

    for identifying the dynamics of macromolecular interactions, the morphodynamics of biologi- cal structures networks, where interactions mostly involve enzy- matic proteins and small molecules or metabolites protein­ protein interaction networks and genetic networks, where regulatory proteins interact with promoter

  19. Hierarchical amplification of macromolecular helicity of dynamic helical poly(phenylacetylene)s composed of chiral and achiral phenylacetylenes in dilute solution, liquid crystal, and two-dimensional crystal.

    PubMed

    Ohsawa, Sousuke; Sakurai, Shin-ichiro; Nagai, Kanji; Banno, Motonori; Maeda, Katsuhiro; Kumaki, Jiro; Yashima, Eiji

    2011-01-12

    Optically active poly(phenylacetylene) copolymers consisting of optically active and achiral phenylacetylenes bearing L-alanine decyl esters (1L) and 2-aminoisobutylic acid decyl esters (Aib) as the pendant groups (poly(1L(m)-co-Aib(n))) with various compositions were synthesized by the copolymerization of the optically active 1L with achiral Aib using a rhodium catalyst, and their chiral amplification of the macromolecular helicity in a dilute solution, a lyotropic liquid crystalline (LC) state, and a two-dimensional (2D) crystal on the substrate was investigated by measuring the circular dichroism of the copolymers, mesoscopic cholesteric twist in the LC state (cholesteric helical pitch), and high-resolution atomic force microscopy (AFM) images of the self-assembled 2D helix-bundles of the copolymer chains. We found that the macromolecular helicity of poly(1L(m)-co-Aib(n))s could be hierarchically amplified in the order of the dilute solution, LC state, and 2D crystal. In sharp contrast, almost no chiral amplification of the macromolecular helicity was observed for the homopolymer mixtures of 1L and Aib in the LC state and 2D crystal on graphite. PMID:21141965

  20. Self-consistent colloidal energy and diffusivity landscapes in macromolecular solutions.

    PubMed

    Beltran-Villegas, Daniel J; Edwards, Tara D; Bevan, Michael A

    2013-10-01

    We report a dynamic analysis to simultaneously measure colloidal forces and hydrodynamic interactions in the presence of both adsorbed and unadsorbed macromolecules. A Bayesian inference method is used to self-consistently obtain the position-dependent potential energy (i.e., energy landscape) and diffusivity (i.e., diffusivity landscape) from measured colloidal trajectories normal to a wall. Measurements are performed for particles and surfaces with adsorbed polyethylene oxide (PEO) copolymer as a function of unadsorbed PEO homopolymer concentration. Energy landscapes are well described by a steric repulsion between adsorbed brushes and depletion attraction due to unadsorbed macromolecules. Diffusivity landscapes show agreement with predicted short-range permeable brush models and long-range mobilities determined by the bulk solution viscosity. Lower than expected mobilities in the vicinity of overlapping depletion layers are attributed to interactions of adsorbed and unadsorbed macromolecules altering nonconservative lubrication forces. PMID:24067114

  1. Coarse-graining diblock copolymer solutions: a macromolecular version of the Widom-Rowlinson model

    E-print Network

    C. I. Addison; J. P. Hansen; V. Krakoviack; A. A. Louis

    2005-07-15

    We propose a systematic coarse-grained representation of block copolymers, whereby each block is reduced to a single ``soft blob'' and effective intra- as well as intermolecular interactions act between centres of mass of the blocks. The coarse-graining approach is applied to simple athermal lattice models of symmetric AB diblock copolymers, in particular to a Widom-Rowlinson-like model where blocks of the same species behave as ideal polymers (i.e. freely interpenetrate), while blocks of opposite species are mutually avoiding walks. This incompatibility drives microphase separation for copolymer solutions in the semi-dilute regime. An appropriate, consistent inversion procedure is used to extract effective inter- and intramolecular potentials from Monte Carlo results for the pair distribution functions of the block centres of mass in the infinite dilution limit.

  2. Macromolecular structures probed by combining single-shot free-electron laser diffraction with synchrotron coherent X-ray imaging.

    PubMed

    Gallagher-Jones, Marcus; Bessho, Yoshitaka; Kim, Sunam; Park, Jaehyun; Kim, Sangsoo; Nam, Daewoong; Kim, Chan; Kim, Yoonhee; Noh, Do Young; Miyashita, Osamu; Tama, Florence; Joti, Yasumasa; Kameshima, Takashi; Hatsui, Takaki; Tono, Kensuke; Kohmura, Yoshiki; Yabashi, Makina; Hasnain, S Samar; Ishikawa, Tetsuya; Song, Changyong

    2014-01-01

    Nanostructures formed from biological macromolecular complexes utilizing the self-assembly properties of smaller building blocks such as DNA and RNA hold promise for many applications, including sensing and drug delivery. New tools are required for their structural characterization. Intense, femtosecond X-ray pulses from X-ray free-electron lasers enable single-shot imaging allowing for instantaneous views of nanostructures at ambient temperatures. When combined judiciously with synchrotron X-rays of a complimentary nature, suitable for observing steady-state features, it is possible to perform ab initio structural investigation. Here we demonstrate a successful combination of femtosecond X-ray single-shot diffraction with an X-ray free-electron laser and coherent diffraction imaging with synchrotron X-rays to provide an insight into the nanostructure formation of a biological macromolecular complex: RNA interference microsponges. This newly introduced multimodal analysis with coherent X-rays can be applied to unveil nano-scale structural motifs from functional nanomaterials or biological nanocomplexes, without requiring a priori knowledge. PMID:24786694

  3. Teaching Structure: Student Use of Software Tools for Understanding Macromolecular Structure in an Undergraduate Biochemistry Course

    ERIC Educational Resources Information Center

    Jaswal, Sheila S.; O'Hara, Patricia B.; Williamson, Patrick L.; Springer, Amy L.

    2013-01-01

    Because understanding the structure of biological macromolecules is critical to understanding their function, students of biochemistry should become familiar not only with viewing, but also with generating and manipulating structural representations. We report a strategy from a one-semester undergraduate biochemistry course to integrate use of…

  4. Structure Solution - An Overview

    NASA Astrophysics Data System (ADS)

    McCusker, Lynne B.; Baerlocher, Christian

    The structure solution process consists of a series of steps, each requiring decisions and each depending upon the previous ones having been performed correctly. The preliminary steps involve selecting the best sample, choosing the most appropriate radiation, collecting the data, indexing the pattern, determining the most probable space group(s), and estimating the profile parameters. If extracted intensities are to be used for structure solution, something must be done about the overlapping reflections. They can be equipartitioned, or, if necessary, more sophisticated approaches can be applied to improve the partitioning. At this point, the structure solution algorithm most appropriate for the material and the data must be chosen and applied. Finally, the (partial) structural model has to be completed and refined. The art of structure determination from powder diffraction data lies in finding a viable path through the maze of possibilities.

  5. Determination by x-ray microscopy of the phases of the x-ray diffraction by macromolecular structures

    NASA Astrophysics Data System (ADS)

    Burge, Ronald E.; Buckley, Christopher J.; Foster, Guy F.; Bennett, Pauline

    1993-01-01

    The use of soft x-ray imaging is considered for the determination of the repeating macromolecular structure of biological fibers (e.g., collagen and muscle), within the available image resolution and subject to the effects of radiation damage. A comparison is made between the structure in sarcomere (2 (mu) to 3 (mu) long repeating unit) of striated muscle as seen directly by x-ray microscopy and as derived from published interpretations of x-ray diffraction data from whole muscle. The comparison shows that the loss by radiation damage of the ability of a muscle myofibril to contract is related to the loss of fine structure. Ways to minimize the effects of beam damage are discussed, including the use of images taken in phase, rather than amplitude contrast, and with photon energies above the `water window.'

  6. Macromolecular Structure Description: This course covers the principles of protein and nucleic acid structure, stability

    E-print Network

    Sherrill, David

    and nucleic acid structure, stability and dynamics. Topics will include interactions, conformations, forces of Biopolymers Amino Acids The Peptide Bond Protein Rotamers: Ramachandran plots The Nucleic Acid Bases The Nucleic Acid Backbone Nucleic Acid Rotamers Introduction to PYMOL: visualization software Introduction

  7. Platinum/iridium/carbon: a high-resolution shadowing material for TEM, STM and SEM of biological macromolecular structures.

    PubMed

    Wepf, R; Amrein, M; Bürkli, U; Gross, H

    1991-07-01

    Thin Pt/Ir/C coating films (1.5 nm) show a fine granularity and provide a high structural resolution in the transmission electron microscope (TEM) when applied to freeze-dried biological macromolecules. They keep their structure when exposed to atmospheric conditions, without the need of an additional stabilizing carbon layer, in contrast to conventional high-resolution shadowing materials such as Ta/W and Pt/C. However, the correct ratio of the components has turned out to be crucial. When evaporating Pt/Ir/C from the source electrode in an electron-beam-heated evaporator, the ratio of the three elements changes progressively, and, consequently, the properties of such films depend strongly on the mass that has been pre-evaporated. In this paper we present a quantitative analysis of the composition of Pt/Ir/C films by wavelength-dispersive X-ray analysis (WDX) undertaken in association with TEM experiments. We applied Pt/Ir/C shadowing to two regular biological test specimens, the phage T4 type III polyhead and the HPI-layer of Deinococcus radiodurans. It turns out that Pt/Ir/C films containing at least 25% C are three-dimensionally stable on the freeze-dried macromolecular samples. By the dramatically improved resolution power of the latest scanning electron microscopes (SEM) and the invention of the scanning tunnelling microscope (STM), two new surface-sensitive tools for the investigation of biological macromolecular structures became available. The Pt/Ir/C coating has proved to be well suited for STM and SEM imaging of freeze-dried biological structures because of its good electrical conductivity and its direct three-dimensional stability. We compare STM, SEM and TEM images of freeze-dried and Pt/Ir/C-coated polyheads. PMID:1920395

  8. Microbatch macromolecular crystallization in micropipettes

    Microsoft Academic Search

    Joseph R. Luft; Dawn M. Rak; George T. DeTitta

    1999-01-01

    A microbatch crystallization method suitable for macromolecular crystal growth is described. Solutions in the 1?l range are set up in micropipettes with very small inner diameter. The packaging is robust, compact and neat. Surface area of solution exposed to the atmosphere is much smaller than in a hanging drop vapor diffusion experiment. Small sample volumes make the packaging ideal for

  9. The effects of (macro)molecular structure on hydrophilic surface modification of polypropylene membranes via entrapment.

    PubMed

    Guo, Haofei; Ulbricht, Mathias

    2010-10-01

    Entrapment of a variety of ethyleneoxide-containing substances from nonpolar solutions into polypropylene (PP) microfiltration membrane surface for hydrophilic modification was studied. The results from gravimetric weight gain, surface characterization by contact angle measurements and ATR-IR spectroscopy, water flux measurements and protein adsorption revealed that poly(ethylene glycol)s (PEGs) were ineffective, while many nonionic amphiphilic substances, especially some tri-block copolymers of poly(ethyleneoxide) (PEO) and poly(propylene oxide) (PPO) were very effective for PP surface modification. The relationship between modifier structure and architecture and entrapment behavior was investigated by studying the micellization of the amphiphilic modifiers in nonpolar solutions via pyrene-probe fluorescence and (1)H NMR spectroscopy. We observed that the balanced structure of nonionic tri-block (macro)molecules tended to promote the formation of reverse micelles. For the most efficient polymeric modifiers, the lowest reverse critical micelle concentration (RCMC) had been observed. We conclude that a block copolymer structure and architecture promoting the self-association in the nonpolar solvent is the basis for a high modification efficiency, and that reverse micelles are involved in the entrapment modification performed at concentrations above RCMC. A different mechanism has been deduced for amphiphilic modifiers with low molar mass. This work provides more comprehensive insights in surface entrapment as a easy to perform physical surface modification method for polymeric materials. PMID:20621303

  10. Single-step antibody-based affinity cryo-electron microscopy for imaging and structural analysis of macromolecular assemblies.

    PubMed

    Yu, Guimei; Vago, Frank; Zhang, Dongsheng; Snyder, Jonathan E; Yan, Rui; Zhang, Ci; Benjamin, Christopher; Jiang, Xi; Kuhn, Richard J; Serwer, Philip; Thompson, David H; Jiang, Wen

    2014-07-01

    Single particle cryo-electron microscopy (cryo-EM) is an emerging powerful tool for structural studies of macromolecular assemblies (i.e., protein complexes and viruses). Although single particle cryo-EM requires less concentrated and smaller amounts of samples than X-ray crystallography, it remains challenging to study specimens that are low-abundance, low-yield, or short-lived. The recent development of affinity grid techniques can potentially further extend single particle cryo-EM to these challenging samples by combining sample purification and cryo-EM grid preparation into a single step. Here we report a new design of affinity cryo-EM approach, cryo-SPIEM, that applies a traditional pathogen diagnosis tool Solid Phase Immune Electron Microscopy (SPIEM) to the single particle cryo-EM method. This approach provides an alternative, largely simplified and easier to use affinity grid that directly works with most native macromolecular complexes with established antibodies, and enables cryo-EM studies of native samples directly from cell cultures. In the present work, we extensively tested the feasibility of cryo-SPIEM with multiple samples including those of high or low molecular weight, macromolecules with low or high symmetry, His-tagged or native particles, and high- or low-yield macromolecules. Results for all these samples (non-purified His-tagged bacteriophage T7, His-tagged Escherichiacoli ribosomes, native Sindbis virus, and purified but low-concentration native Tulane virus) demonstrated the capability of cryo-SPIEM approach in specifically trapping and concentrating target particles on TEM grids with minimal view constraints for cryo-EM imaging and determination of 3D structures. PMID:24780590

  11. Comprehensive objective maps of macromolecular conformations by quantitative SAXS analysis

    PubMed Central

    Hura, Greg L.; Budworth, Helen; Dyer, Kevin N.; Rambo, Robert P.; Hammel, Michal

    2013-01-01

    Comprehensive perspectives of macromolecular conformations are required to connect structure to biology. Here we present a small angle X-ray scattering (SAXS) Structural Similarity Map (SSM) and Volatility of Ratio (VR) metric providing comprehensive, quantitative and objective (superposition-independent) perspectives on solution state conformations. We validate VR and SSM utility on human MutS?, a key ABC ATPase and chemotherapeutic target, by revealing MutS? DNA sculpting and identifying multiple conformational states for biological activity. PMID:23624664

  12. Self-consistent treatment of the local dielectric permittivity and electrostatic potential in solution for polarizable macromolecular force fields

    NASA Astrophysics Data System (ADS)

    Hassan, Sergio A.

    2012-08-01

    A self-consistent method is presented for the calculation of the local dielectric permittivity and electrostatic potential generated by a solute of arbitrary shape and charge distribution in a polar and polarizable liquid. The structure and dynamics behavior of the liquid at the solute/liquid interface determine the spatial variations of the density and the dielectric response. Emphasis here is on the treatment of the interface. The method is an extension of conventional methods used in continuum protein electrostatics, and can be used to estimate changes in the static dielectric response of the liquid as it adapts to charge redistribution within the solute. This is most relevant in the context of polarizable force fields, during electron structure optimization in quantum chemical calculations, or upon charge transfer. The method is computationally efficient and well suited for code parallelization, and can be used for on-the-fly calculations of the local permittivity in dynamics simulations of systems with large and heterogeneous charge distributions, such as proteins, nucleic acids, and polyelectrolytes. Numerical calculation of the system free energy is discussed for the general case of a liquid with field-dependent dielectric response.

  13. WebFEATURE: an interactive web tool for identifying and visualizing functional sites on macromolecular structures

    Microsoft Academic Search

    Mike P. Liang; D. Rey Banatao; Teri E. Klein; Douglas L. Brutlag; Russ B. Altman

    2003-01-01

    WebFEATURE (http:\\/\\/feature.stanford.edu\\/webfeature\\/) is a web-accessible structural analysis tool that allows users to scan query structures for functional sites in both proteins and nucleic acids. WebFEATURE is the public interface to the scanning algorithm of the FEATURE package, a supervised learning algorithm for creating and identifying 3D, physicochemical motifs in molecular structures. Given an input structure or Protein Data Bank identifier

  14. Evolving Methods for Macromolecular Crystallography

    E-print Network

    Sussman, Joel L.

    Evolving Methods for Macromolecular Crystallography The Structural Path to the Understanding presented at the 2005 edition of the "Crystallography of Molecular Biology" courses that have been held is renowned for bringing leaders in the field of macromole- cular crystallography together with highly

  15. Macromolecular Crystallography is a technique used to study biological molecules such as proteins, viruses and nucleic acids (RNA and DNA) to a resolution higher than ~5 . This high resolution helps

    E-print Network

    Titov, Anatoly

    . (ESRF) #12;Macromolecular Crystallography is a technique used to study biological molecules of Mice #12;Basic techniques of STRUCTURAL BIOLOGY ·Macromolecular X-ray Crystallography ·Electron-ray crystallography becomes very difficult Molecules, complexes, assemblies - as single crystals Molecules in solution

  16. Chemical composition and structural features of the macromolecular components of Hibiscus cannabinus grown in Portugal

    Microsoft Academic Search

    C. Pascoal Neto; A. Seca; D. Fradinho; M. A. Coimbra; F. Domingues; D. Evtuguin; A. Silvestre; J. A. S. Cavaleiro

    1996-01-01

    Different morphological regions of Hibiscus cannabinus plants grown in Portugal were submitted to chemical composition studies. General chemical composition was determined by established methods. The polysaccharides were fractionated by successive extractions of holocellulose with aqueous KOH solutions. The sugar composition was determined by hydrolysis of polysaccharides followed by gas chromatography (GC) analysis of neutral sugars and spectrophotometric determination of uronic

  17. Structure Solution by Charge Flipping

    NASA Astrophysics Data System (ADS)

    Palatinus, Lukáš

    Charge flipping is an iterative structure solution method based on the alternating modification of an electron density in direct space and structure factors in reciprocal space. It has been successfully applied to a range of crystallographic problems, including structure solution from powder diffraction data and from electron diffraction data obtained by the precession electron diffraction method. For electron diffraction no modification of the basic algorithm is necessary. For the structure solution from powder diffraction the histogram matching technique proved to be a powerful method to improve the quality of the solutions and use the algorithm to solve quite complex structures.

  18. The effects of (macro)molecular structure on hydrophilic surface modification of polypropylene membranes via entrapment

    Microsoft Academic Search

    Haofei Guo; Mathias Ulbricht

    2010-01-01

    Entrapment of a variety of ethyleneoxide-containing substances from nonpolar solutions into polypropylene (PP) microfiltration membrane surface for hydrophilic modification was studied. The results from gravimetric weight gain, surface characterization by contact angle measurements and ATR-IR spectroscopy, water flux measurements and protein adsorption revealed that poly(ethylene glycol)s (PEGs) were ineffective, while many nonionic amphiphilic substances, especially some tri-block copolymers of poly(ethyleneoxide)

  19. ActaCryst.(1998).D54,1105-1108 Deposition of Macromolecular Structures

    E-print Network

    Barton, Geoffrey J.

    1998-01-01

    Outstation,European Bioinformatics Institute, Wellcome Trust Genome Campus,Hinxton, Cambridge CB10 LSD, it is essential to develop new techniquesto make deposition straightforward and less prone to error. Structural

  20. Macromolecular Structure Modeling from 3DEM Using VolRover 2.01

    PubMed Central

    Zhang, Qin; Bettadapura, Radhakrishna

    2012-01-01

    We report several tools for 3DEM structure identification and model-based refinement developed by our research group and implemented in our in-house software package, VolRover. For viral density maps with icosahedral symmetry, we segment the capsid, polymeric and monomeric subunits using segmentation techniques based on symmetry detection and fast marching. For large biomolecules without symmetry information, we use a multi-seeded fast-marching method to segment meaningful substructures. In either case, we subject the resulting segmented subunit to secondary structure detection when the EM resolution is sufficiently high, and rigid-body fitting when the corresponding crystal structure is available. Secondary structure elements are identified by our volume- and boundary-based skeletonization methods as well as a new method, currently in development, based on solving the grassfire flow equation. For rigid-body fitting, we use a translational fast Fourier based scheme. We apply our segmentation, secondary structure elements identification, and rigid-body fitting techniques to the PSB 2011 cryo-EM modeling challenge data, and compare our results to those submitted from other research groups. The comparisons show that our software is capable of segmenting relatively accurate subunits from a viral or protein assembly, and that the high segmentation quality leads in turn to high-quality results of secondary structure elements identification and rigid-body fitting. PMID:22696407

  1. Investigation of secondary structures and macromolecular interactions in bacteriophage P22 by laser Raman spectroscopy

    SciTech Connect

    Fish, S.R. (Univ. of Rhode Island, Kingston); Fuller, M.T.; King, J.; Thomas, G.J. Jr

    1980-10-01

    Laser Raman spectra of the DNA bacteriophage P22 and of its precursor particles and related structures have been obtained using 514.5-nm excitation. The spectra show that P22 DNA exists in the B form both inside of the phage head and after extraction from the phage. The major coat protein (gp5) contains a secondary structure composed of 18% ..cap alpha..-helix, 20% BETA-sheet and 62% irregular conformations. The scaffolding protein (gp8) in the phage prohead is substantially richer than gp5 in ..cap alpha..-helical content. Among the amino acid residues which give prominent Raman lines, the spectra show that tryptophans are exposed to solvent and most tyrosines are hydrogen bonded to positive donor groups. The above features of phage DNA and protein structures are nearly invariant to changes in temperature up to 80/sup 0/C, indicating a remarkable thermal stability of the phage head and its encapsulated DNA.

  2. Avoidable errors in deposited macromolecular structures: an impediment to efficient data mining

    PubMed Central

    Dauter, Zbigniew; Wlodawer, Alexander; Minor, Wladek; Jaskolski, Mariusz; Rupp, Bernhard

    2014-01-01

    Whereas the vast majority of the more than 85?000 crystal structures of macromolecules currently deposited in the Protein Data Bank are of high quality, some suffer from a variety of imperfections. Although this fact has been pointed out in the past, it is still worth periodic updates so that the metadata obtained by global analysis of the available crystal structures, as well as the utilization of the individual structures for tasks such as drug design, should be based on only the most reliable data. Here, selected abnormal deposited structures have been analysed based on the Bayesian reasoning that the correctness of a model must be judged against both the primary evidence as well as prior knowledge. These structures, as well as information gained from the corresponding publications (if available), have emphasized some of the most prevalent types of common problems. The errors are often perfect illustrations of the nature of human cognition, which is frequently influenced by preconceptions that may lead to fanciful results in the absence of proper validation. Common errors can be traced to negligence and a lack of rigorous verification of the models against electron density, creation of non-parsimonious models, generation of improbable numbers, application of incorrect symmetry, illogical presentation of the results, or violation of the rules of chemistry and physics. Paying more attention to such problems, not only in the final validation stages but during the structure-determination process as well, is necessary not only in order to maintain the highest possible quality of the structural repositories and databases but most of all to provide a solid basis for subsequent studies, including large-scale data-mining projects. For many scientists PDB deposition is a rather infrequent event, so the need for proper training and supervision is emphasized, as well as the need for constant alertness of reason and critical judgment as absolutely necessary safeguarding measures against such problems. Ways of identifying more problematic structures are suggested so that their users may be properly alerted to their possible shortcomings. PMID:25075337

  3. Improving the accuracy of macromolecular structure refinement at 7 Å resolution

    PubMed Central

    Brunger, Axel T.; Adams, Paul D.; Fromme, Petra; Fromme, Raimund; Levitt, Michael; Schröder, Gunnar F.

    2012-01-01

    SUMMARY In X-ray crystallography, molecular replacement and subsequent refinement is challenging at low resolution. We compared refinement methods using synchrotron diffraction data of photosystem I at 7.4 Å resolution, starting from different initial models with increasing deviations from the known high-resolution structure. Standard refinement spoiled the initial models moving them further away from the true structure and leading to high Rfree-values. In contrast, DEN-refinement improved even the most distant starting model as judged by Rfree, atomic root-mean-square differences to the true structure, significance of features not included in the initial model, and connectivity of electron density. The best protocol was DEN-refinement with initial segmented rigid-body refinement. For the most distant initial model, the fraction of atoms within 2 Å of the true structure improved from 24% to 60%. We also found a significant correlation between Rfree-values and the accuracy of the model, suggesting that Rfree is useful even at low resolution. PMID:22681901

  4. Neutron Scattering Investigation of the Structure and Dynamics of Macromolecular Systems

    Microsoft Academic Search

    Kenneth Forbes Bradley

    1991-01-01

    Elastic and Inelastic neutron scattering has been used to study the behavior of three different molecular and supramolecular systems whose structure and dynamics are consequences of both inter- and intra-molecular interactions. The design and construction of QENS, an inverse geometry, quasielastic and inelastic spectrometer built at the Intense Pulsed Neutron Source of Argonne National Laboratory is described. Measurements using QENS

  5. Macromolecular organisation of recombinant Yersinia pestis F1 antigen and the effect of structure on immunogenicity

    Microsoft Academic Search

    Julie Miller; E. Diane Williamson; Jeremy H Lakey; Martin J Pearce; Steven M Jones; Richard W Titball

    1998-01-01

    Yersinia pestis, the causative organism of plague, produces a capsular protein (fraction 1 or F1 antigen) that is one of the major virulence factors of the bacterium. We report here the production, structural and immunological characterisation of a recombinant F1 antigen (rF1). The rF1 was purified by ammonium sulfate fractionation followed by FPLC Superose gel filtration chromatography. Using FPLC gel

  6. Testing of the structure of macromolecular polymer films containing solid active pharmaceutical ingredient (API) particles

    NASA Astrophysics Data System (ADS)

    Bölcskei, É.; Süvegh, K.; Marek, T.; Regdon, G.; Pintye-Hódi, K.

    2011-07-01

    The aim of the present study was to investigate the structure of free films of Eudragit ® L 30D-55 containing different concentrations (0%, 1% or 5%) of diclofenac sodium by positron annihilation spectroscopy. The data revealed that the size of the free-volume holes and the lifetimes of ortho-positronium atoms decreased with increase of the API concentration. Films containing 5% of the API exhibited a different behavior during storage (17 °C, 65% relative humidity (RH)) in consequence of the uptake of water from the air.

  7. Reducing irreducible complexity: divergence of quaternary structure and function in macromolecular assemblies.

    PubMed

    Egelman, Edward H

    2010-02-01

    The bacterial flagellar system is an intricate assembly (containing approximately 40 different proteins) that is involved in both protein secretion and bacterial motility. It has also become the icon of the neo-creationist movement in the United States, with the argument that it shows 'irreducible complexity' and could not have been the product of evolution. Recent studies provide new insights into the evolution of the flagellar system and lead to the suggestion that the divergence of quaternary structure in protein assemblies may be an underappreciated mechanism for rapid evolutionary divergence. Work on the enzyme FucU, involved in fucose metabolism, may suggest similar conclusions. PMID:20006482

  8. AutoDep: a web-based system for deposition and validation of macromolecular structural -information.

    PubMed

    Lin, D; Manning, N O; Jiang, J; Abola, E E; Stampf, D; Prilusky, J; Sussman, J L

    2000-07-01

    This paper describes the design and full implementation of a new concept in data deposition and validation: AutoDep (copyright Brookhaven Science Associates LLC). AutoDep changes the traditional procedure for data acceptance and validation of the primary databases into an interactive depositor-driven operation which almost eliminates the delay between the acceptance of the data and its public release. The system takes full advantage of the knowledge and expertise of the experimenters, rather than relying on the database curators for the complete and accurate description of the structural experiment and its results. AutoDep, developed by the Protein Data Bank at Brookhaven National Laboratory (BNL) as a flexible and portable system, has already been adopted by other primary databases and implemented on different platforms/operating systems. AutoDep was introduced at BNL in 1996 [see Manning (1996), Protein Data Bank Quart. Newslett. 77, 2 (ftp://ftp.rcsb. org/pub/pdb/doc/newsletters/bnl/newsletter96jul/newslttr+ ++.txt); Manning (1996), Protein Data Bank Quart. Newslett. 78, 2 (ftp://ftp. rcsb.org/pub/pdb/doc/newsletters/bnl/newsletter96oct/+ ++newslttr.txt)]. PMID:10930830

  9. A Model for Macromolecular Crystallization

    NASA Technical Reports Server (NTRS)

    Pusey, Marc L.; Whitaker, Ann F. (Technical Monitor)

    2001-01-01

    Macromolecular crystallization is a complex process. involving a system which typically has 5 or more components (macromolecule, water, buffer + counter ion, and precipitant). Whereas small molecules have only several well defined contacts in the crystal lattice, macromolecules generally have 10's or even 100's of contacts between molecules. These can range from hydrogen bonds (direct or water-mediated), through van der Waals, hydrophobic, salt bridges, and ion-mediated contacts. The latter interactions are stronger and require some specificity in the molecular alignment, while the others are weaker, more prevalent, and more promiscuous, i.e., can often be readily broken and reformed between other sites. Formation of a consistent, ordered, 3D structure may be impossible in the absence of any or presence of too many strong interactions. Further complicating the process is the inherent structural asymmetry of monomeric single chain macromolecules. The process of crystal nucleation and growth involves the ordered assembly of growth units into a defined 3D lattice. We suggest that for many macromolecules, particularly those that are monomeric, this involves a preliminary solution-phase assembly process into a growth unit having some symmetry prior to addition to the lattice, recapitulating the initial stages of the nucleation process. If this model is correct then fluids and crystal growth models assuming a strictly monodisperse nutrient solution need to be revised. Experimental evidence, based upon face growth rate, AFM, and fluorescence energy transfer data, for a postulated model of the nucleation of tetragonal lysozyme crystals and how it transitions into crystal growth will be presented.

  10. Use of Site-Specifically Tethered Chemical Nucleases to Study Macromolecular Reactions

    PubMed Central

    Mukherjee, Srabani

    2003-01-01

    During a complex macromolecular reaction multiple changes in molecular conformation and interactions with ligands may occur. X-ray crystallography may provide only a limited set of snapshots of these changes. Solution methods can augment such structural information to provide a more complete picture of a macromolecular reaction. We analyzed the changes in protein conformation and protein:nucleic acid interactions which occur during transcription initiation by using a chemical nuclease tethered to cysteines introduced site-specifically into the RNA polymerase of bacteriophage T7 (T7 RNAP). Changes in cleavage patterns as the polymerase steps through transcription reveal a series of structural transitions which mediate transcription initiation. Cleavage by tethered chemical nucleases is seen to be a powerful method for revealing the conformational dynamics of macromolecular reactions, and has certain advantages over cross-linking or energy transfer approaches. PMID:12734553

  11. Visualizing Macromolecular Complexes with In Situ Liquid Scanning Transmission Electron Microscopy

    SciTech Connect

    Evans, James E.; Jungjohann, K. L.; Wong, Peony C. K.; Chiu, Po-Lin; Dutrow, Gavin H.; Arslan, Ilke; Browning, Nigel D.

    2012-11-01

    A central focus of biological research is understanding the structure/function relationship of macromolecular protein complexes. Yet conventional transmission electron microscopy techniques are limited to static observations. Here we present the first direct images of purified macromolecular protein complexes using in situ liquid scanning transmission electron microscopy. Our results establish the capability of this technique for visualizing the interface between biology and nanotechnology with high fidelity while also probing the interactions of biomolecules within solution. This method represents an important advancement towards allowing future high-resolution observations of biological processes and conformational dynamics in real-time.

  12. What Macromolecular Crowding Can Do to a Protein

    PubMed Central

    Kuznetsova, Irina M.; Turoverov, Konstantin K.; Uversky, Vladimir N.

    2014-01-01

    The intracellular environment represents an extremely crowded milieu, with a limited amount of free water and an almost complete lack of unoccupied space. Obviously, slightly salted aqueous solutions containing low concentrations of a biomolecule of interest are too simplistic to mimic the “real life” situation, where the biomolecule of interest scrambles and wades through the tightly packed crowd. In laboratory practice, such macromolecular crowding is typically mimicked by concentrated solutions of various polymers that serve as model “crowding agents”. Studies under these conditions revealed that macromolecular crowding might affect protein structure, folding, shape, conformational stability, binding of small molecules, enzymatic activity, protein-protein interactions, protein-nucleic acid interactions, and pathological aggregation. The goal of this review is to systematically analyze currently available experimental data on the variety of effects of macromolecular crowding on a protein molecule. The review covers more than 320 papers and therefore represents one of the most comprehensive compendia of the current knowledge in this exciting area. PMID:25514413

  13. Structural effect on degradability and in vivo contrast enhancement of polydisulfide Gd(III) complexes as biodegradable macromolecular MRI contrast agents

    PubMed Central

    Zong, Yuda; Wang, Xuli; Jeong, Eun-Kee; Parker, Dennis L.; Lu, Zheng-Rong

    2009-01-01

    Structural effect of polydisulfide Gd(III) chelates on their in vitro degradability, and cardiovascular and tumor imaging in mice were evaluated as biodegradable macromolecular MRI contrast agents. Polydisulfide Gd(III) chelates, Gd-DTPA cystamine copolymers (GDCC), Gd-DTPA L-cystine copolymers (GDCP), Gd-DTPA D-cystine copolymers (dGDCP) and Gd-DTPA glutathione (oxidized) copolymers (GDGP), with different sizes and narrow molecular weight distribution were prepared and evaluated both in vitro and in vivo in mice bearing MDA-MB-231 tumor xenografts. Large steric hindrance around the disulfide bonds in GDGP resulted in greater T1 and T2 relaxivities than GDCC, GDCP and dGDCP. The degradability of the polydisulfide by the endogenous thiols decreased with an increase in steric effects around the disulfide bonds in the order of GDCC > GDCP, dGDCP > GDGP. The size and degradability of the contrast agents had significant impact on vascular contrast enhancement kinetics. The agents with large size and low degradability resulted in more prolonged vascular enhancement than the agents with small size and high degradability. It seems that the size and degradability of the agents did not significantly affect tumor enhancement. All agents resulted in significant contrast enhancement in tumor tissue. This study has demonstrated that the vascular enhancement kinetics of the polydisulfide MRI contrast agents can be controlled by their sizes and structures. The polydisulfide Gd(III) chelates are promising biodegradable macromolecular MRI contrast agents for MR angiography and cancer imaging. PMID:18814987

  14. Crystal structure of Jararacussin-I: The highly negatively charged catalytic interface contributes to macromolecular selectivity in snake venom thrombin-like enzymes

    PubMed Central

    Ullah, A; Souza, T A C B; Zanphorlin, L M; Mariutti, R B; Santana, V S; Murakami, M T; Arni, R K

    2013-01-01

    Snake venom serine proteinases (SVSPs) are hemostatically active toxins that perturb the maintenance and regulation of both the blood coagulation cascade and fibrinolytic feedback system at specific points, and hence, are widely used as tools in pharmacological and clinical diagnosis. The crystal structure of a thrombin-like enzyme (TLE) from Bothrops jararacussu venom (Jararacussin-I) was determined at 2.48 Å resolution. This is the first crystal structure of a TLE and allows structural comparisons with both the Agkistrodon contortrix contortrix Protein C Activator and the Trimeresurus stejnegeri plasminogen activator. Despite the highly conserved overall fold, significant differences in the amino acid compositions and three-dimensional conformations of the loops surrounding the active site significantly alter the molecular topography and charge distribution profile of the catalytic interface. In contrast to other SVSPs, the catalytic interface of Jararacussin-I is highly negatively charged, which contributes to its unique macromolecular selectivity. PMID:23139169

  15. Complex structures – smart solutions

    PubMed Central

    2011-01-01

    The siliceous skeletal elements of the sponges, the spicules, represent one of the very few examples from where the molecule toolkit required for the formation of an extracellular mineral-based skeleton, has been elucidated. The distinguished feature of the inorganic matrix, the bio-silica, is its enzymatic synthesis mediated by silicatein. Ortho-silicate undergoes in the presence of silicatein a polycondensation reaction and forms bio-silica under release of reaction water. The protein silicatein aggregates non-covalently to larger filaments, a process that is stabilized by the silicatein-associated protein, silintaphin-1. These structured clusters form the axial filament that is located in the center of the spicules, the axial canal. Surprisingly it has now been found that the initial axial orientation, in which the spicules grow, is guided by cell processes through evagination. The approximately two µm wide cell extensions release silicatein that forms the first organic axial filament, which then synthesizes the inner core of the siliceous spicule rods. In parallel, the radial growth of the spicules is controlled by a telescopic arrangement of organic layers, into which bio-silica and ortho-silicate are deposited. Hence, the formation of a mature siliceous spicule is completed by a centrifugal accretion of bio-silica mediated by the silicatein in the axial filament, and a centripetal bio-silica deposition catalyzed by the extra-spicular silicatein. Finally this contribution highlights that for the ultimate determination of the spicule shapes, their species-specific morphologies, bio-silica hardens during a process which removes reaction water. The data presented can also provide new blueprints for the fabrication of novel biomaterials for biomedical applications.  PMID:22446527

  16. The role of macromolecular stability in desiccation tolerance

    Microsoft Academic Search

    W. Wolkers

    1998-01-01

    The work presented in this thesis concerns a study on the molecular interactions that play a role in the macromolecular stability of desiccation-tolerant higher plant organs. Fourier transform infrared microspectroscopy was used as the main experimental technique to assess macromolecular structures within their native environment.Protein secondary structure and membrane phase behavior of Typha latifolia pollen were studied in the course

  17. Screening Outside the Catalytic Site: Inhibition of Macromolecular Inter-actions Through Structure-Based Virtual Ligand Screening Experiments

    PubMed Central

    Sperandio, Olivier; Miteva, Maria A; Segers, Kenneth; Nicolaes, Gerry A. F; Villoutreix, Bruno O

    2008-01-01

    During these last 15 years, drug discovery strategies have essentially focused on identifying small molecules able to inhibit catalytic sites. However, other mechanisms could be targeted. Protein-protein interactions play crucial roles in a number of biological processes, and, as such, their disruption or stabilization is becoming an area of intense activity. Along the same line, inhibition of protein-membrane could be of major importance in several disease indications. Despite the many challenges associated with the development of such classes of interaction modulators, there has been considerable success in the recent years. Importantly, through the existence of protein hot-spots and the presence of druggable pockets at the macromolecular interfaces or in their vicinities, it has been possible to find small molecule effectors using a variety of screening techniques, including combined virtual ligand-in vitro screening strategy. Indeed such in silico-in vitro protocols emerge as the method of choice to facilitate our quest of novel drug-like compounds or of mechanistic probes aiming at facilitating the understanding of molecular reactions involved in the Health and Disease process. In this review, we comment recent successes of combined in silico-in vitro screening methods applied to modulating macromolecular interactions with a special emphasis on protein-membrane interactions. PMID:18949072

  18. in HS macromolecular structures associated with solution chemistry may be caused by the

    E-print Network

    Dunin-Borkowski, Rafal E.

    for soil HSs on substrate surfaces, such as mica and electron microscope sample substrates (13., Methods of Soil Analysis: Part 3, Chemical Methods (Soil Science Society of America, Madison, WI, 1996). 9, deprotonation, and metal complex- ation of HS functional groups. The noted dif- ferences between

  19. Continuous mutual improvement of macromolecular structure models in the PDB and of X-ray crystallographic software: the dual role of deposited experimental data

    SciTech Connect

    Terwilliger, Thomas C., E-mail: terwilliger@lanl.gov [Los Alamos National Laboratory, Mail Stop M888, Los Alamos, NM 87507 (United States); Bricogne, Gerard, E-mail: terwilliger@lanl.gov [Global Phasing Ltd, Sheraton House, Castle Park, Cambridge CB3 0AX (United Kingdom); Los Alamos National Laboratory, Mail Stop M888, Los Alamos, NM 87507 (United States)

    2014-10-01

    Macromolecular structures deposited in the PDB can and should be continually reinterpreted and improved on the basis of their accompanying experimental X-ray data, exploiting the steady progress in methods and software that the deposition of such data into the PDB on a massive scale has made possible. Accurate crystal structures of macromolecules are of high importance in the biological and biomedical fields. Models of crystal structures in the Protein Data Bank (PDB) are in general of very high quality as deposited. However, methods for obtaining the best model of a macromolecular structure from a given set of experimental X-ray data continue to progress at a rapid pace, making it possible to improve most PDB entries after their deposition by re-analyzing the original deposited data with more recent software. This possibility represents a very significant departure from the situation that prevailed when the PDB was created, when it was envisioned as a cumulative repository of static contents. A radical paradigm shift for the PDB is therefore proposed, away from the static archive model towards a much more dynamic body of continuously improving results in symbiosis with continuously improving methods and software. These simultaneous improvements in methods and final results are made possible by the current deposition of processed crystallographic data (structure-factor amplitudes) and will be supported further by the deposition of raw data (diffraction images). It is argued that it is both desirable and feasible to carry out small-scale and large-scale efforts to make this paradigm shift a reality. Small-scale efforts would focus on optimizing structures that are of interest to specific investigators. Large-scale efforts would undertake a systematic re-optimization of all of the structures in the PDB, or alternatively the redetermination of groups of structures that are either related to or focused on specific questions. All of the resulting structures should be made generally available, along with the precursor entries, with various views of the structures being made available depending on the types of questions that users are interested in answering.

  20. Macromolecular Chemistry and Physics

    E-print Network

    Guo, John Zhanhu

    , Mansfield Road, Oxford, OX1 3TA, United Kingdom L. Sun Department of Chemistry and Biochemistry, Texas State2429 Full Paper Macromolecular Chemistry and Physics wileyonlinelibrary.com Macromol. Chem. Phys Wang, Luyi Sun, Zhanhu Guo* PP nanocomposites containing different carbon nanofillers (CNTs, CNFs, Gn

  1. Neutron macromolecular crystallography

    Microsoft Academic Search

    M. P. Blakeley

    2009-01-01

    Neutron crystallography allows direct determination of the proton and deuteron positions of a macromolecule and its bound solvent. Key advances in neutron macromolecular crystallography have led to an expanding field addressing larger and more complex problems. In particular, improvements in neutron instrumentation, detection systems, data collection methods and perdeuterated sample preparation have dramatically lowered the sample volume requirements to ?0.1–0.2

  2. An upper limit for macromolecular crowding effects

    PubMed Central

    2011-01-01

    Background Solutions containing high macromolecule concentrations are predicted to affect a number of protein properties compared to those properties in dilute solution. In cells, these macromolecular crowders have a large range of sizes and can occupy 30% or more of the available volume. We chose to study the stability and ps-ns internal dynamics of a globular protein whose radius is ~2 nm when crowded by a synthetic microgel composed of poly(N-isopropylacrylamide-co-acrylic acid) with particle radii of ~300 nm. Results Our studies revealed no change in protein rotational or ps-ns backbone dynamics and only mild (~0.5 kcal/mol at 37°C, pH 5.4) stabilization at a volume occupancy of 70%, which approaches the occupancy of closely packing spheres. The lack of change in rotational dynamics indicates the absence of strong crowder-protein interactions. Conclusions Our observations are explained by the large size discrepancy between the protein and crowders and by the internal structure of the microgels, which provide interstitial spaces and internal pores where the protein can exist in a dilute solution-like environment. In summary, microgels that interact weakly with proteins do not strongly influence protein dynamics or stability because these large microgels constitute an upper size limit on crowding effects. PMID:21627822

  3. Clustering procedures for the optimal selection of data sets from multiple crystals in macromolecular crystallography

    SciTech Connect

    Foadi, James [Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE (United Kingdom); Imperial College, London SW7 2AZ (United Kingdom); Aller, Pierre [Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE (United Kingdom); Alguel, Yilmaz; Cameron, Alex [Imperial College, London SW7 2AZ (United Kingdom); Axford, Danny; Owen, Robin L. [Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE (United Kingdom); Armour, Wes [Oxford e-Research Centre (OeRC), Keble Road, Oxford OX1 3QG (United Kingdom); Waterman, David G. [Research Complex at Harwell (RCaH), Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0FA (United Kingdom); Iwata, So [Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE (United Kingdom); Imperial College, London SW7 2AZ (United Kingdom); Evans, Gwyndaf, E-mail: gwyndaf.evans@diamond.ac.uk [Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Oxfordshire OX11 0DE (United Kingdom)

    2013-08-01

    A systematic approach to the scaling and merging of data from multiple crystals in macromolecular crystallography is introduced and explained. The availability of intense microbeam macromolecular crystallography beamlines at third-generation synchrotron sources has enabled data collection and structure solution from microcrystals of <10 µm in size. The increased likelihood of severe radiation damage where microcrystals or particularly sensitive crystals are used forces crystallographers to acquire large numbers of data sets from many crystals of the same protein structure. The associated analysis and merging of multi-crystal data is currently a manual and time-consuming step. Here, a computer program, BLEND, that has been written to assist with and automate many of the steps in this process is described. It is demonstrated how BLEND has successfully been used in the solution of a novel membrane protein.

  4. Vibron transport in macromolecular chains

    E-print Network

    D. ?evizovi?; Z. Ivic.; S. Galovi?; A. Chizhov A.; A. Reshetnyak

    2014-12-16

    We study the hopping mechanism of the vibron excitation transport in the simple 1D model of biological macromolecular chains. We supposed that the vibron interaction with thermal oscillations of the macromolecular structural elements will result in vibron self -trapping, and the formation of the partial dressed vibron state. With use of the modified Holstein polaron model, we calculate vibron diffusivity in dependence of the basic system parameters and temperature. We obtain that the vibron diffusivity smoothly decreases in non adiabatic limit when the strength of the vibron-phonon coupling grows. However this dependence becomes by discontinuous one in case of growth of the adiabaticity of the system. The value of the critical point depends of the system temperature, and at room temperatures it belongs to the low or intermediate coupling regime. We discuss an application of these results to study of vibron transport to 3D bundles of such macromolecules chains considering it as polymer nanorods and to 2D polymer films organized from such macromolecules.

  5. Blueprinting macromolecular electronics

    Microsoft Academic Search

    Carlos-Andres Palma; Paolo Samorì

    2011-01-01

    Recently, by mastering either top-down or bottom-up approaches, tailor-made macromolecular nano-objects with semiconducting properties have been fabricated. These engineered nanostructures for organic electronics are based on conjugated systems predominantly made up of sp2-hybridized carbon, such as graphene nanoribbons. Here, we describe developments in a selection of these nanofabrication techniques, which include graphene carving, stimulus-induced synthesis of conjugated polymers and surface-assisted

  6. Continuum percolation in macromolecular fluids

    NASA Astrophysics Data System (ADS)

    Chatterjee, Avik P.

    2000-11-01

    A heuristic treatment of the connectedness Ornstein-Zernike equation is developed for macromolecular fluids within the framework of the polymer reference interaction site model (PRISM). Results are presented for the critical volume fraction at the percolation threshold and for the mean number of interchain contacts per molecule for athermal rodlike and Gaussian coil-like particles. The results for rodlike particles are in qualitative agreement with prior investigations based on fully numerical solutions of the PRISM equations, and with computer simulations of ellipsoids. The method proposed here leads to the physically reasonable result that the percolation threshold for direct connectivity on the length scale of the molecular dimensions is closely related to the semidilute crossover concentration as usually defined, and can be generalized directly to multicomponent systems.

  7. HIGH PRESSURE CRYOCOOLING FOR MACROMOLECULAR CRYSTALLOGRAPHY

    E-print Network

    Gruner, Sol M.

    HIGH PRESSURE CRYOCOOLING FOR MACROMOLECULAR CRYSTALLOGRAPHY A Dissertation Presented CRYOCOOLING FOR MACROMOLECULAR CRYSTALLOGRAPHY Chae Un Kim, Ph. D. Cornell University 2008 A novel high-pressure cryocooling technique to reduce radiation damage in macromolecular crystallography is developed and explored

  8. Practical macromolecular cryocrystallography

    PubMed Central

    Pflugrath, J. W.

    2015-01-01

    Cryocrystallography is an indispensable technique that is routinely used for single-crystal X-ray diffraction data collection at temperatures near 100?K, where radiation damage is mitigated. Modern procedures and tools to cryoprotect and rapidly cool macromolecular crystals with a significant solvent fraction to below the glass-transition phase of water are reviewed. Reagents and methods to help prevent the stresses that damage crystals when flash-cooling are described. A method of using isopentane to assess whether cryogenic temperatures have been preserved when dismounting screened crystals is also presented. PMID:26057787

  9. Non-ideality of aqueous solutions of polyethylene glycol: consequences for its use as a macromolecular crystallizing agent in vapor-diffusion experiments.

    PubMed

    Arakali, S V; Luft, J R; DeTitta, G T

    1995-09-01

    Microisopiestic measurements of the concentrations of polyethylene glycol (PEG 8000) paired with the salts sodium chloride, ammonium sulfate and magnesium sulfate heptahydrate have been made in a sitting-drop arrangement with PEG in the droplet and salt in the reservoir. Resulting graphs of the concentrations of PEG and salt that are equivalent with respect to the vapor pressure of water are non-linear, do not intersect their origins, and demonstrate that relatively low (mM) salt concentrations are equivalent to relatively high PEG concentrations. The consequences of each of these observations for macromolecular crystallization by the vapor-diffusion technique when PEG is employed as the crystallizing agent are discussed. PMID:15299808

  10. Macromolecular Crystallization in Microfluidics for the International Space Station

    NASA Technical Reports Server (NTRS)

    Monaco, Lisa A.; Spearing, Scott

    2003-01-01

    At NASA's Marshall Space Flight Center, the Iterative Biological Crystallization (IBC) project has begun development on scientific hardware for macromolecular crystallization on the International Space Station (ISS). Currently ISS crystallization research is limited to solution recipes that were prepared on the ground prior to launch. The proposed hardware will conduct solution mixing and dispensing on board the ISS, be fully automated, and have imaging functions via remote commanding from the ground. Utilizing microfluidic technology, IBC will allow for on orbit iterations. The microfluidics LabChip(R) devices that have been developed, along with Caliper Technologies, will greatly benefit researchers by allowing for precise fluid handling of nano/pico liter sized volumes. IBC will maximize the amount of science return by utilizing the microfluidic approach and be a valuable tool to structural biologists investigating medically relevant projects.

  11. RECENT ADVANCES IN MACROMOLECULAR HYDRODYNAMIC MODELING

    PubMed Central

    Aragon, Sergio R.

    2010-01-01

    The modern implementation of the boundary element method (S.R. Aragon, J. Comput. Chem. 25(2004)1191–12055) has ushered unprecedented accuracy and precision for the solution of the Stokes equations of hydrodynamics with stick boundary conditions. This article begins by reviewing computations with the program BEST of smooth surface objects such as ellipsoids, the dumbbell, and cylinders that demonstrate that the numerical solution of the integral equation formulation of hydrodynamics yields very high precision and accuracy. When BEST is used for macromolecular computations, the limiting factor becomes the definition of the molecular hydrodynamic surface and the implied effective solvation of the molecular surface. Studies on 49 different proteins, ranging in molecular weight from 9 to over 400 kDa, have shown that a model using a 1.1 A thick hydration layer describes all protein transport properties very well for the overwhelming majority of them. In addition, this data implies that the crystal structure is an excellent representation of the average solution structure for most of them. In order to investigate the origin of a handful of significant discrepancies in some multimeric proteins (over ?20% observed in the intrinsic viscosity), the technique of Molecular Dynamics simulation (MD) has been incorporated into the research program. A preliminary study of dimeric ?-chymotrypsin using approximate implicit water MD is presented. In addition I describe the successful validation of modern protein force fields, ff03 and ff99SB, for the accurate computation of solution structure in explicit water simulation by comparison of trajectory ensemble average computed transport properties with experimental measurements. This work includes small proteins such as lysozyme, ribonuclease and ubiquitin using trajectories around 10 ns duration. We have also studied a 150 kDa flexible monoclonal IgG antibody, trastuzumab, with multiple independent trajectories encompassing over 320 ns of simulation. The close agreement within experimental error of the computed and measured properties allows us to conclude that MD does produce structures typical of those in solution, and that flexible molecules can be properly described using the method of ensemble averaging over a trajectory. We review similar work on the study of a transfer RNA molecule and DNA oligomers that demonstrate that within 3% a simple uniform hydration model 1.1 A thick provides agreement with experiment for these nucleic acids. In the case of linear oligomers, the precision can be improved close to 1% by a non-uniform hydration model that hydrates mainly in the DNA grooves, in agreement with high resolution x-ray diffraction. We conclude with a vista on planned improvements for the BEST program to decrease its memory requirements and increase its speed without sacrificing accuracy. PMID:21073955

  12. Using NMR to Determine Protein Structure in Solution

    NASA Astrophysics Data System (ADS)

    Cavagnero, Silvia

    2003-02-01

    Nuclear magnetic resonance (NMR) is a marvelous spectroscopic technique that chemists, physicists, and biochemists routinely employ for their research around the world. This year half of the Nobel Prize for chemistry went to Kurt Wüthrich, who was recognized for the development of NMR-based techniques that lead to the structure determination of biomolecules in solution. In addition to implementing novel pulse sequences and software packages, Wüthrich also applied his methods to several biological systems of key importance to human health. These include the prion protein, which is heavily involved in the spongiform encephalopathy (best known as 'mad cow disease'), which recently caused numerous human deaths, particularly in the UK, due to ingestion of contaminated meat. Transverse relaxation optimized spectroscopy (TROSY) is the most intriguing new NMR method recently developed by Wüthrich and coworkers. This and other closely related pulse sequences promise to play a pivotal role in the extension of NMR to the conformational analysis of very large (up to the megadalton range) macromolecules and macromolecular complexes. More exciting new developments are expected in the near future.

  13. Automated error-tolerant macromolecular structure determination from multidimensional nuclear Overhauser enhancement spectra and chemical shift assignments

    PubMed Central

    Kuszewski, John J.; Thottungal, Robin Augustine; Schwieters, Charles D.; Clore, G. Marius

    2008-01-01

    We report substantial improvements to the previously introduced automated NOE assignment and structure determination protocol known as PASD. The improved protocol includes extensive analysis of input spectral data to create a low-resolution contact map of residues expected to be close in space. This map is used to obtain reasonable initial guesses of NOE assignment likelihoods which are refined during subsequent structure calculations. Information in the contact map about which residues are predicted to not be close in space is applied via conservative repulsive distance restraints which are used in early phases of the structure calculations. In comparison with the previous protocol, the new protocol requires significantly less computation time. We show results of running the new PASD protocol on six proteins and demonstrate that useful assignment and structural information is extracted on proteins of more than 220 residues. We show that useful assignment information can be obtained even in the case in which a unique structure cannot be determined. PMID:18668206

  14. Workshop on algorithms for macromolecular modeling. Final project report, June 1, 1994--May 31, 1995

    SciTech Connect

    Leimkuhler, B.; Hermans, J.; Skeel, R.D.

    1995-07-01

    A workshop was held on algorithms and parallel implementations for macromolecular dynamics, protein folding, and structural refinement. This document contains abstracts and brief reports from that workshop.

  15. Influence of hydrodynamic environment on composition and macromolecular organization of structural polysaccharides in Egregia menziesii cell walls

    Microsoft Academic Search

    J. M. Hackney; G. P. Kraemer; R. H. Atalla; D. L. VanderHart; D. J. Chapman

    1994-01-01

    To test whether secondary and tertiary structures of marine-algal structural polysaccharides may be altered during adaptive responses to hydrodynamic stresses, juvenile Egregia menziesii (Turn.) Aresch. sporophytes were cultured under three different regimes: (i) low-energy (LE) specimens were subjected to water motion produced by standard bubbling and circulation of tank water; (ii) high-energy (HE) specimens received additional movement in pumped streams

  16. 'Broken symmetries' in macromolecular crystallography: phasing from unmerged data.

    PubMed

    Schiltz, Marc; Bricogne, Gérard

    2010-04-01

    The space-group symmetry of a crystal structure imposes a point-group symmetry on its diffraction pattern, giving rise to so-called symmetry-equivalent reflections. Instances in macromolecular crystallography are discussed in which the symmetry in reciprocal space is broken, i.e. where symmetry-related reflections are no longer equivalent. Such a situation occurs when the sample suffers from site-specific radiation damage during the X-ray measurements. Another example of broken symmetry arises from the polarization anisotropy of anomalous scattering. In these cases, the genuine intensity differences between symmetry-related reflections can be exploited to yield phase information in the structure-solution process. In this approach, the usual separation of the data merging and phasing steps is abandoned. The data are kept unmerged down to the Harker construction, where the symmetry-breaking effects are explicitly modelled and refined and become a source of supplementary phase information. PMID:20382998

  17. ‘Broken symmetries’ in macromolecular crystallography: phasing from unmerged data

    PubMed Central

    Schiltz, Marc; Bricogne, Gérard

    2010-01-01

    The space-group symmetry of a crystal structure imposes a point-group symmetry on its diffraction pattern, giving rise to so-called symmetry-equivalent reflections. Instances in macromolecular crystallography are discussed in which the sym­metry in reciprocal space is broken, i.e. where symmetry-related reflections are no longer equivalent. Such a situation occurs when the sample suffers from site-specific radiation damage during the X-ray measurements. Another example of broken symmetry arises from the polarization anisotropy of anomalous scattering. In these cases, the genuine intensity differences between symmetry-related reflections can be exploited to yield phase information in the structure-solution process. In this approach, the usual separation of the data merging and phasing steps is abandoned. The data are kept unmerged down to the Harker construction, where the symmetry-breaking effects are explicitly modelled and refined and become a source of supplementary phase information. PMID:20382998

  18. Recent progress in macromolecular phasing, in part stimulated by the high-throughput structural biology initiatives, has made this

    E-print Network

    Met, is hard to automate. The aim of current structural genomic projects is to solve a large number of selected signal of such atoms as sulfur or phosphorus, inherently present in macromolecules. The current progress may become fully automatic. Addresses Synchrotron Radiation Research Section, National Cancer

  19. Macromolecular crystal growing system

    NASA Technical Reports Server (NTRS)

    Snyder, Robert S. (inventor); Herren, Blair J. (inventor); Carter, Daniel C. (inventor); Yost, Vaughn H. (inventor); Bugg, Charles E. (inventor); Delucas, Lawrence J. (inventor); Suddath, Fred L. (inventor)

    1991-01-01

    A macromolecular crystal growing system especially designed for growing crystals in the low gravity of space as well as the gravity of earth includes at least one tray assembly, a carrier assembly which receives the tray, and a refrigeration-incubation module in which the carrier assembly is received. The tray assembly includes a plurality of sealed chambers with a plastic syringe and a plug means for the double tip of the syringe provided therein. Ganging mechanisms operate the syringes and plugs simultaneously in a precise and smooth operation. Preferably, the tray assemblies are mounted on ball bearing slides for smooth operation in inserting and removing the tray assemblies into the carrier assembly. The plugging mechanism also includes a loading control mechanism. A mechanism for leaving a syringe unplugged is also provided.

  20. NOMAD-Ref: visualization, deformation and refinement of macromolecular structures based on all-atom normal mode analysis

    Microsoft Academic Search

    Erik Lindahl; Cyril Azuara; Patrice Koehl; Marc Delarue

    2006-01-01

    Normal mode analysis (NMA) is an efficient way to study collective motions in biomolecules that bypasses the computational costs and many limitationsassociatedwithfulldynamicssimulations. The NOMAD-Ref web server presented here provides tools for online calculation of the normal modes of large molecules (up to 100000 atoms) maintaining a full all-atom representation of their structures,aswellasaccesstoanumberofprograms that utilize these collective motions for deforma- tion

  1. Sequentially Structured Bayesian Solutions Simon Maskell

    E-print Network

    Maskell, Simon

    Sequentially Structured Bayesian Solutions Simon Maskell #12;#12;Sequentially Structured Bayesian Solutions Simon Maskell February 21, 2004 #12;Copyright c 2004 Simon Maskell. draft date: February, 2004 Green and Dr Arthur Williams of QinetiQ, Mr Matthew Orton, Dr Simon Godsill, Dr Jaco Vermaak

  2. Significance of Wall Structure, Macromolecular Composition, and Surface Polymers to the Survival and Transport of Cryptosporidium parvum Oocysts?

    PubMed Central

    Jenkins, Michael B.; Eaglesham, Barbara S.; Anthony, Larry C.; Kachlany, Scott C.; Bowman, Dwight D.; Ghiorse, William C.

    2010-01-01

    The structure and composition of the oocyst wall are primary factors determining the survival and hydrologic transport of Cryptosporidium parvum oocysts outside the host. Microscopic and biochemical analyses of whole oocysts and purified oocyst walls were undertaken to better understand the inactivation kinetics and hydrologic transport of oocysts in terrestrial and aquatic environments. Results of microscopy showed an outer electron-dense layer, a translucent middle layer, two inner electron-dense layers, and a suture structure embedded in the inner electron-dense layers. Freeze-substitution showed an expanded glycocalyx layer external to the outer bilayer, and Alcian Blue staining confirmed its presence on some but not all oocysts. Biochemical analyses of purified oocyst walls revealed carbohydrate components, medium- and long-chain fatty acids, and aliphatic hydrocarbons. Purified walls contained 7.5% total protein (by the Lowry assay), with five major bands in SDS-PAGE gels. Staining of purified oocyst walls with magnesium anilinonaphthalene-8-sulfonic acid indicated the presence of hydrophobic proteins. These structural and biochemical analyses support a model of the oocyst wall that is variably impermeable and resistant to many environmental pressures. The strength and flexibility of oocyst walls appear to depend on an inner layer of glycoprotein. The temperature-dependent permeability of oocyst walls may be associated with waxy hydrocarbons in the electron-translucent layer. The complex chemistry of these layers may explain the known acid-fast staining properties of oocysts, as well as some of the survival characteristics of oocysts in terrestrial and aquatic environments. The outer glycocalyx surface layer provides immunogenicity and attachment possibilities, and its ephemeral nature may explain the variable surface properties noted in oocyst hydrologic transport studies. PMID:20097810

  3. RapiData: a practical course in macromolecular X-ray diffraction data measurement and structure solving at the NSLS

    PubMed Central

    Sweet, R. M.; Soares, A.

    2010-01-01

    RapiData provides two days of high-level lectures, then two more of experimental work on several beamlines of the National Synchrotron Light Source, for about 50 students. Students are invited to bring their own research projects for measurement, and about half of them do. The students frequently solve half a dozen structures during the course. Tutorials by the lecturers run throughout the data-collection period. The crystal-preparation laboratory is popular for tutorials and practice, and often there is a beamline available for practice. This article provides details about the organization of the course and tells some of the reasons for its success. PMID:21695040

  4. Statistics of multiscale fluctuations in macromolecular systems.

    PubMed

    Yukalov, Vyacheslav I; Yukalova, Elizaveta P

    2012-07-26

    An approach is suggested for treating multiscale fluctuations in macromolecular systems. The emphasis is on the statistical properties of such fluctuations. The approach is illustrated by a macromolecular system with mesoscopic fluctuations between the states of atomic orbitals. Strong-orbital and weak-orbital couplings fluctuationally arise, being multiscale in space and time. Statistical properties of the system are obtained by averaging over the multiscale fluctuations. The existence of such multiscale fluctuations causes phase transitions between strong-coupling and weak-coupling states. These transitions are connected with structure and size transformations of macromolecules. An approach for treating density and size multiscale fluctuations by means of classical statistical mechanics is also advanced. PMID:22594677

  5. Structure and thermal stability of complexes of chromium, manganese, cobalt, and copper with nonhydrocarbon macromolecular compounds of petroleum

    SciTech Connect

    Paukku, A.N.; Posadov, I.A.; Rozental, D.A.; Gusev, V.P.; Sirotinkin, N.V.; Lozarev, S.Y.

    1982-11-10

    The structure and thermolysis parameters of complexes formed by Cr(III), Mn(II), Co(II), and Cu(II) with petroleum NHMC was studied. The following series of metal ions was chosen for evaluation of the influence of their electronic configuraton on the stability of the complexes formed: Cr/sup 3 +/(d/sup 3/), Mn/sup 2 +/(d/sup 5/), Co/sup 2 +/(d/sup 7/) and Cu/sup 2 +/(d/sup 9/). The complex compounds were synthesized from hydrated forms of the metal acetates in a salt of petroleum NHMC concentrates with rapid stirring at 70/sup 0/, at 50:1 molar ratio of ligand to metal acetate. Unreacted petroleum NHMC were removed from the complex compounds by extraction with n-hexane in a Soxhlet apparatus. The IR spectra of the petroleum NHMC concentrates and their complex compounds in KBr tablets were recorded in the region of 4000-400 cm/sup -1/ with the aid of the UR-20 spectrometer.

  6. Stochastic dynamics of macromolecular-assembly networks

    E-print Network

    Leonor Saiz; Jose M. G. Vilar

    2006-09-26

    The formation and regulation of macromolecular complexes provides the backbone of most cellular processes, including gene regulation and signal transduction. The inherent complexity of assembling macromolecular structures makes current computational methods strongly limited for understanding how the physical interactions between cellular components give rise to systemic properties of cells. Here we present a stochastic approach to study the dynamics of networks formed by macromolecular complexes in terms of the molecular interactions of their components. Exploiting key thermodynamic concepts, this approach makes it possible to both estimate reaction rates and incorporate the resulting assembly dynamics into the stochastic kinetics of cellular networks. As prototype systems, we consider the lac operon and phage lambda induction switches, which rely on the formation of DNA loops by proteins and on the integration of these protein-DNA complexes into intracellular networks. This cross-scale approach offers an effective starting point to move forward from network diagrams, such as those of protein-protein and DNA-protein interaction networks, to the actual dynamics of cellular processes.

  7. Significant Structure Theory Applied to Electrolyte Solution

    Microsoft Academic Search

    Jong Myung Lee; Mu Shik Jhon; Henry Eyring

    1979-01-01

    The significant structure theory has been successfully applied to an aqueous NaCl solution. Liquid water is assumed to have a domain structure and the ions are hydrated by water molecules. The partition function is composed of the partition function for the water and that for the salt, and the excess free energy term from the Debye-Huckel theory is also added.

  8. Macromolecular Crystallography Catalog No.3 Distributor Edition

    E-print Network

    Lebendiker, Mario

    Macromolecular Crystallography Catalog No.3 Distributor Edition How to get started Initial MacromolecularCrystallography How to get started 2 Teaching 2 JBS Crystallization Freshman Kits 2 Crystallization ­ Screen Formulations 20 #12;How to get started MacromolecularCrystallography 2 How to get started Teaching

  9. HIGHLY AUTOMATED BEAMLINE FOR MACROMOLECULAR CRYSTALLOGRAPHY (AMX)

    E-print Network

    Ohta, Shigemi

    HIGHLY AUTOMATED BEAMLINE FOR MACROMOLECULAR CRYSTALLOGRAPHY (AMX) SCIENTIFIC SCOPE BEAMLINE: · Macromolecular Crystallography PORT: 17-ID SOURCE: canted IVU21 Undulator ENERGY RANGE: 5 ­ 18 keV ENERGY The highly automated macromolecular crystallography beamline (AMX) is an undulator beamline at sector 17-ID

  10. Molecular Control of Macromolecular Properties

    NASA Astrophysics Data System (ADS)

    Holcombe, Thomas Wesley, III

    Molecular level control over macromolecules has been at the heart of human advancement, long before Hermann Staudinger coined the term Makromolekule. From the development of primitive pharmaceuticals to the advanced materials that sent Man into outer-space, We have been tinkering with God's paint since our inception. The work described herein primarily involves advances concerning poly-aromatic macromolecules for use in future electronic applications, particularly that of organic photovoltaics. There is a final chapter, however, that gives the reader a taste of how some molecular level changes can be directly visualized with modern microscopy techniques. Chapter 1 provides a very brief introduction to conjugated polymers and molecular level control over macromolecular properties. Chapters 2--4 introduces the concept of polymer substitution as a means by which to control and improve charge generation in organic photovoltaic devices. Chapters 5 and 6 show how these polymers can take on larger, defined structures, yet are still beholden to intrinsic molecular properties---such as regioregularity, a fancy word for the regularity of the position in which two aromatic rings are joined together. Chapter 7 re-examines the role of polymer substitution on photovoltaic performance, this time with an emphasis on homo-polymer packing rather than electron transfer at the donor/acceptor interface. Finally, Chapter 8 visualizes how controlling the environment about a single metal atom can lead directly to a cyclic polyolefin. Individually, these advances do not yield any breakthroughs noticeable to a general audience; collectively, they sit atop a mountain of human knowledge, waiting to provide a stepping stone for the next generation.

  11. Organic sulphur in macromolecular sedimentary organic matter: I. Structure and origin of sulphur-containing moieties in kerogen, asphaltenes and coal as revealed by flash pyrolysis

    NASA Astrophysics Data System (ADS)

    Sinninghe Damsté, Jaap S.; Eglinton, Timothy I.; De Leeuw, Jan W.; Schenck, P. A.

    1989-04-01

    The distributions of sulphur-containing compounds generated by flash pyrolysis of macromolecular sedimentary organic matter (kerogen, coal, asphaltenes) were studied by gas chromatography in combination with Sselective flame photometric detection or mass spectrometry. The abundance of S-containing pyrolysis products in the pyrolysates relative to other products was highly variable depending on the sample but the types of products were generally similar, being mainly composed of "gaseous" compounds ( e.g., hydrogen sulphide) and low molecular weight alkylthiophenes and alkylbenzothiophenes. The distribution patterns of the alkylated thiophenes were dominated by a limited number of all theoretically possible isomers. The alkyl substitution patterns of the dominant isomers bear a strong similarity to those of the organic S compounds present in the GC-amenable fractions of bitumens and immature oils. Therefore, it is suggested that these S-containing pyrolysis products are formed by pyrolysis of related thiophenic and benzothiophenic moieties present in the macromolecular sedimentary substances. Specific examples include those with linear alkyl, iso and anteiso alkyl, isoprenoid alkyl and steroidal carbon skeletons. The presence of higher molecular weight alkylthiophenes and alkylbenzothiophenes with these same carbon skeletons in pyrolysates of S-rich kerogens provided further evidence for the presence of these S-containing moieties. It is likely that these moieties have been formed by abiogenic S incorporation into sedimentary organic matter during early diagenesis.

  12. Structural Glazing Solutions for Protective Glazing

    Microsoft Academic Search

    Axel H. Giesecke; Kenneth Yarosh; Dow Corning

    Tragic world events have opened our eyes to the vulnerability and false sense of security in today's buildings around the globe. The horrific loss of life and property from terrorist attacks on these structures has forced building owners, investors, government authorities, building occupants and insurance companies to seek new solutions to protect people from these events as well as from

  13. Solution structure of RNase P RNA.

    PubMed

    Kazantsev, Alexei V; Rambo, Robert P; Karimpour, Sina; Santalucia, John; Tainer, John A; Pace, Norman R

    2011-06-01

    The ribonucleoprotein enzyme ribonuclease P (RNase P) processes tRNAs by cleavage of precursor-tRNAs. RNase P is a ribozyme: The RNA component catalyzes tRNA maturation in vitro without proteins. Remarkable features of RNase P include multiple turnovers in vivo and ability to process diverse substrates. Structures of the bacterial RNase P, including full-length RNAs and a ternary complex with substrate, have been determined by X-ray crystallography. However, crystal structures of free RNA are significantly different from the ternary complex, and the solution structure of the RNA is unknown. Here, we report solution structures of three phylogenetically distinct bacterial RNase P RNAs from Escherichia coli, Agrobacterium tumefaciens, and Bacillus stearothermophilus, determined using small angle X-ray scattering (SAXS) and selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) analysis. A combination of homology modeling, normal mode analysis, and molecular dynamics was used to refine the structural models against the empirical data of these RNAs in solution under the high ionic strength required for catalytic activity. PMID:21531920

  14. Structural studies of polyurethane ionomer solutions

    NASA Astrophysics Data System (ADS)

    Nomula, Srinivas; Cooper, Stuart

    1996-03-01

    Except for a number of conductivity and viscometric measurements, structural studies of polyurethane ionomer solutions are lacking in literature. Polyurethane ionomers in polar solvents are shown to exhibit polyelectrolyte behavior. So these ionomer solutions also form model systems to investigate the characteristic behavior of salt free polyelectrolyte solutions. In this study, viscometry and light scattering experiments have been performed on model polyurethane ionomers, which have regularly positioned ionic groups. The model system is synthesized as a 1:1 copolymer of polytetramethylene oxide (PTMO) and 4-4'-diphenyl methane diisocyanate (MDI) which is subsequently ionized by abstraction with sodium hydride (NaH) and derivatization with 1,3 propane sultone. The separation distance between the ionic groups is varied by varying the molecular weight of PTMO. Viscometric measurements of these ionomers in a polar solvent, N,N-dimethyl acetamide (DMAc), have verified that they exhibit polyelectrolyte behavior. Static and Dynamic Light Scattering have been applied to these ionomer solutions to reveal important information about the structures in solution. The results of the analysis of the light scattering data will be presented.

  15. Protein Diffusion and Macromolecular Crowding in Thylakoid Membranes1[W

    E-print Network

    Allen, John F.

    Protein Diffusion and Macromolecular Crowding in Thylakoid Membranes1[W] Helmut Kirchhoff*, Silvia by chlorophyll-binding protein complexes located in the thylakoid membranes within the chloroplasts. Thylakoid membranes have a complex structure, with lateral segregation of protein complexes into distinct membrane

  16. Studies on the macromolecular components of nonwood available in Bangladesh

    Microsoft Academic Search

    M. Sarwar Jahan; Sung Phil Mun

    2009-01-01

    The structural feature of macromolecular component of dhaincha, cotton stalks, jute fiber, rice straw and wheat straw, which are commonly used in paper pulp production in forest deficient countries, was thoroughly studied. Lignin was isolated by classical Bjorkman method and characterized by elemental and methoxyl analysis, alkaline nitrobenzene oxidation, FTIR and 1H NMR spectroscopy. The C9 formulas for cotton stalks,

  17. Quantum chemistry of macromolecular shape

    Microsoft Academic Search

    Paul G. Mezey

    1997-01-01

    Some of the new developments in the quantum-chemical study of macromolecular shapes are reviewed, with special emphasis on the additive fuzzy electron density fragmentation methods and on the algebraic-topological shape group analysis of global and local shape features of fuzzy three-dimensional bodies of electron densities of macromolecules. Earlier applications of these methods to actual macromolecules are reviewed, including studies on

  18. Automated protein NMR structure determination in solution.

    PubMed

    Gronwald, Wolfram; Kalbitzer, Hans Robert

    2010-01-01

    The main drawback of protein NMR spectroscopy today is still the extensive amount of time required for solving a single structure. The main bottleneck in this respect is the manual evaluation of the experimental spectra. A clear solution to this challenge is the development of automated methods for this purpose. At the current stage of development, this goal has been almost or in a few cases fully reached for favorable cases such as well-behaved, stably folding smaller proteins below the 25 kDa range. For larger and/or more difficult molecules, the input of a human expert is still required. However, even here, automated routines will substantially speed up the structure determination process. In this report, we will summarize recent developments in this field and especially emphasize practical aspects important for a successful automated protein structure determination in solution. An important aspect closely related to structure determination is structure validation. Therefore, we devote a section to automated approaches for this topic. PMID:20835795

  19. Macromolecular Crystal Quality

    NASA Technical Reports Server (NTRS)

    Snell, Edward H.; Borgstahl, Gloria E. O.; Bellamy, Henry D.; Curreri, Peter A. (Technical Monitor)

    2001-01-01

    There are many ways of judging a good crystal. Which we use depends on the qualities we seek. For gemstones size, clarity and impurity levels (color) are paramount. For the semiconductor industry purity is probably the most important quality. For the structural crystallographer the primary desideratum is the somewhat more subtle concept of internal order. In this chapter we discuss the effect of internal order (or the lack of it) on the crystal's diffraction properties.

  20. MACROMOLECULAR PHYSIOLOGY OF PLASTIDS

    PubMed Central

    Henningsen, K. W.; Boynton, J. E.

    1970-01-01

    Sequential changes occurring in the etioplasts of the primary leaf of 7-day-old dark-grown barley seedlings upon continuous illumination with 20 lux have been investigated by electron microscopy, in vivo spectrophotometry, and thin-layer chromatography. Following photoconversion of the protochlorophyllide pigment to chlorophyllide and the structural transformation of the crystalline prolamellar bodies, the tubules of the prolamellar bodies are dispersed into the primary lamellar layers. As both chlorophyll a and b accumulate, extensive formation of grana takes place. After 4 hr of greening, protochlorophyllide starts to reaccumulate, and concomitantly both large and small crystalline prolamellar bodies are formed. This protochlorophyllide is rapidly photoconverted upon exposure of the leaves to high light intensity, which also effects a rapid reorganization of the recrystallized prolamellar bodies into primary lamellar layers. PMID:5411076

  1. Static Structure of Polydisperse Micellar Solutions.

    PubMed

    Mileva

    2000-12-15

    A model study of polydisperse micellar solutions formed by ionic amphiphiles in the presence of added salt is proposed. The structural peculiarities of the system are determined by effective potentials including the screened electrostatic and the hardcore interactions. A perturbation procedure is applied to expand the characteristic parameters of the system around a reference system. The basic result is a model size distribution curve that accounts not only for the inherent polydispersity of the system but also includes the interaggregate interactions and the space correlation of the aggregates. Copyright 2000 Academic Press. PMID:11097753

  2. Analytical model for macromolecular partitioning during yeast cell division

    PubMed Central

    2014-01-01

    Background Asymmetric cell division, whereby a parent cell generates two sibling cells with unequal content and thereby distinct fates, is central to cell differentiation, organism development and ageing. Unequal partitioning of the macromolecular content of the parent cell — which includes proteins, DNA, RNA, large proteinaceous assemblies and organelles — can be achieved by both passive (e.g. diffusion, localized retention sites) and active (e.g. motor-driven transport) processes operating in the presence of external polarity cues, internal asymmetries, spontaneous symmetry breaking, or stochastic effects. However, the quantitative contribution of different processes to the partitioning of macromolecular content is difficult to evaluate. Results Here we developed an analytical model that allows rapid quantitative assessment of partitioning as a function of various parameters in the budding yeast Saccharomyces cerevisiae. This model exposes quantitative degeneracies among the physical parameters that govern macromolecular partitioning, and reveals regions of the solution space where diffusion is sufficient to drive asymmetric partitioning and regions where asymmetric partitioning can only be achieved through additional processes such as motor-driven transport. Application of the model to different macromolecular assemblies suggests that partitioning of protein aggregates and episomes, but not prions, is diffusion-limited in yeast, consistent with previous reports. Conclusions In contrast to computationally intensive stochastic simulations of particular scenarios, our analytical model provides an efficient and comprehensive overview of partitioning as a function of global and macromolecule-specific parameters. Identification of quantitative degeneracies among these parameters highlights the importance of their careful measurement for a given macromolecular species in order to understand the dominant processes responsible for its observed partitioning. PMID:25737777

  3. Structuring of polymer solutions upon solvent evaporation

    NASA Astrophysics Data System (ADS)

    Schaefer, C.; van der Schoot, P.; Michels, J. J.

    2015-02-01

    The morphology of solution-cast, phase-separated polymers becomes finer with increasing solvent evaporation rate. We address this observation theoretically for a model polymer where demixing is induced by steady solvent evaporation. In contrast to what is the case for a classical, thermal quench involving immiscible blends, the spinodal instability initially develops slowly and the associated length scale is not time invariant but decreases with time as t-1 /2. After a time lag, phase separation accelerates. Time lag and characteristic length exhibit power-law behavior as a function of the evaporation rate with exponents of -2 /3 and -1 /6 . Interestingly, at later stages the spinodal structure disappears completely while a second length scale develops. The associated structure coarsens but does not follow the usual Lifshitz-Slyozov-Wagner kinetics.

  4. Organoactinide chemistry: synthesis, structure, and solution dynamics

    SciTech Connect

    Brennan, J.G.

    1985-12-01

    This thesis considers three aspects of organoactinide chemistry. In chapter one, a bidentate phosphine ligand was used to kinetically stabilize complexes of the type Cp/sub 2/MX/sub 2/. Ligand redistribution processes are present throughout the synthetic work, as has often been observed in uranium cyclopentadienyl chemistry. The effects of covalent M-L bonding on the solution and solid state properties of U(III) coordination complexes are considered. In particular, the nature of the more subtle interaction between the metal and the neutral ligand are examined. Using relative basicity data obtained in solution, and solid state structural data (and supplemented by gas phase photoelectron measurements), it is demonstrated that the more electron rich U(III) centers engage in significant U ..-->.. L ..pi..-donation. Trivalent uranium is shown to be capable of acting either as a one- or two-electron reducing agent toward a wide variety of unsaturated organic and inorganic molecules, generating molecular classes unobtainable via traditional synthetic approaches, as well as offering an alternative synthetic approach to molecules accessible via metathesis reactions. Ligand redistribution processes are again observed, but given the information concerning ligand lability, this reactivity pattern is applied to the synthesis of pure materials inaccessible from redox chemistry. 214 refs., 33 figs., 10 tabs.

  5. Temperature-dependent macromolecular X-ray crystallography

    PubMed Central

    Weik, Martin; Colletier, Jacques-Philippe

    2010-01-01

    X-ray crystallography provides structural details of biological macromolecules. Whereas routine data are collected close to 100?K in order to mitigate radiation damage, more exotic temperature-controlled experiments in a broader temperature range from 15?K to room temperature can provide both dynamical and structural insights. Here, the dynamical behaviour of crystalline macromolecules and their surrounding solvent as a function of cryo-temperature is reviewed. Experimental strategies of kinetic crystallography are discussed that have allowed the generation and trapping of macromolecular intermediate states by combining reaction initiation in the crystalline state with appropriate temperature profiles. A particular focus is on recruiting X-ray-induced changes for reaction initiation, thus unveiling useful aspects of radiation damage, which otherwise has to be minimized in macromolecular crystallography. PMID:20382997

  6. Bridging the solution divide: comprehensive structural analyses of dynamic RNA, DNA, and protein assemblies by small-angle X-ray scattering.

    PubMed

    Rambo, Robert P; Tainer, John A

    2010-02-01

    Small-angle X-ray scattering (SAXS) is changing how we perceive biological structures, because it reveals dynamic macromolecular conformations and assemblies in solution. SAXS information captures thermodynamic ensembles, enhances static structures detailed by high-resolution methods, uncovers commonalities among diverse macromolecules, and helps define biological mechanisms. SAXS-based experiments on RNA riboswitches and ribozymes and on DNA-protein complexes including DNA-PK and p53 discover flexibilities that better define structure-function relationships. Furthermore, SAXS results suggest conformational variation is a general functional feature of macromolecules. Thus, accurate structural analyses will require a comprehensive approach that assesses both flexibility, as seen by SAXS, and detail, as determined by X-ray crystallography and NMR. Here, we review recent SAXS computational tools, technologies, and applications to nucleic acids and related structures. PMID:20097063

  7. Large structures in diblock copolymer micellar solution

    NASA Astrophysics Data System (ADS)

    Lombardo, Domenico; Micali, Norberto; Villari, Valentina; Kiselev, Mikhail A.

    2004-08-01

    The association properties in water solution of poly(dimethylsiloxane)-b-poly(ethyleneoxide) diblock copolymer was investigated by static and dynamic light scattering in a wide range of concentrations and temperatures. The presence of a long hydrophilic poly(ethyleneoxide) (PEO) chain causes a weak tendency to microphase separation of the system which is responsible for some relevant effects. First of all we observe a late micellization process which is characterized by an unusually high value of the critical micellar concentration (ccmc=0.007g/cm3) and by an unusually small aggregation number (?6) of the generated micelles. Moreover, the composition of the highly hydrated micelles has been found to change sensitively with temperature. On increasing temperature dehydration of micelles has been observed together with a contemporaneous increase in the aggregation number, whereas the hydrodynamic radius remains constant in the whole range investigated. The long hydrophilic chains also stimulate an efficient entanglement process between micelles. The interpenetrating PEO chains belonging to different micelles causes the depletion of the solvent in the outer layer of micelles. The result is the formation, just after the micellization process takes place, of thermodynamically stable clusters of entangled micelles. These large structures, which are present in the system in small concentrations, maintain their structural properties unchanged in a wide range of concentrations and temperatures, and provide indirect evidence of a weak attractive component to the intermicellar interaction potential.

  8. Large structures in diblock copolymer micellar solution.

    PubMed

    Lombardo, Domenico; Micali, Norberto; Villari, Valentina; Kiselev, Mikhail A

    2004-08-01

    The association properties in water solution of poly(dimethylsiloxane)-b-poly(ethyleneoxide) diblock copolymer was investigated by static and dynamic light scattering in a wide range of concentrations and temperatures. The presence of a long hydrophilic poly(ethyleneoxide) (PEO) chain causes a weak tendency to microphase separation of the system which is responsible for some relevant effects. First of all we observe a late micellization process which is characterized by an unusually high value of the critical micellar concentration (c(cmc) =0.007 g/cm3) and by an unusually small aggregation number (approximately 6) of the generated micelles. Moreover, the composition of the highly hydrated micelles has been found to change sensitively with temperature. On increasing temperature dehydration of micelles has been observed together with a contemporaneous increase in the aggregation number, whereas the hydrodynamic radius remains constant in the whole range investigated. The long hydrophilic chains also stimulate an efficient entanglement process between micelles. The interpenetrating PEO chains belonging to different micelles causes the depletion of the solvent in the outer layer of micelles. The result is the formation, just after the micellization process takes place, of thermodynamically stable clusters of entangled micelles. These large structures, which are present in the system in small concentrations, maintain their structural properties unchanged in a wide range of concentrations and temperatures, and provide indirect evidence of a weak attractive component to the intermicellar interaction potential. PMID:15447486

  9. Quantum chemistry of macromolecular shape

    NASA Astrophysics Data System (ADS)

    Mezey, Paul G.

    Some of the new developments in the quantum-chemical study of macromolecular shapes are reviewed, with special emphasis on the additive fuzzy electron density fragmentation methods and on the algebraic-topological shape group analysis of global and local shape features of fuzzy three-dimensional bodies of electron densities of macromolecules. Earlier applications of these methods to actual macromolecules are reviewed, including studies on the anticancer drug taxol, the proteins bovine insulin and HIV protease, and other macromolecules. The results of test calculations establishing the accuracy of these methods are also reviewed. The spherically weighted affine transformation technique is described and proposed for the deformation of electron densities approximating the changes occurring in small conformational displacements of atomic nuclei in macromolecules.

  10. Solvent-assisted NMR imaging or heterogeneous coal macromolecular networks

    SciTech Connect

    French, D.C.; Cody, G.D.; Botto, R.E.

    1993-09-01

    Solvent swelling has been employed to probe the physical structure of coal (1). The swelling behavior of bituminous coals in various solvents has been used to assess different strengths or types of secondary interactions which determine their macromolecular structures (2-5). The phenomenon of solvent transport into coal during solvent swelling has also been extensively investigated by numerous researchers (6-10). Recently, we have obtained important information concerning solvent accessibility in coals and maceral domains by proton NMR imaging of mobile proton distributions resulting from solvent swelling (11). Images of coals swollen with perdeuterated solvents were used to map mobile phases in the coal macromolecular structure, while images obtained with protic solvents mapped distributions of the ingressed solvent. For the present purposes 2-D images are sufficient and their acquisition is suitably fast. In order to ensure that the transport process was also two-dimensional, the upper and lower sample surfaces were protected from solvent infiltration by glass coverslips which restricted the flow of solvent to cross only the exposed faces of the sample. Each sample is rectangular with initial dimensions on the order of 2 {times} 2 {times} 1 mm. The experimental protocol involved immersing the sample in the solvent for a period of time, removing it from the solvent bath, acquiring an image, and re-immersing it. Figure 1 presents transient images together with one-dimensional projections for each of the three macromolecular systems.

  11. Studies of structure and dynamics of biological macro-molecular assemblies by low angle neutron diffraction and inelastic X-ray scattering

    E-print Network

    Liu, Yun, 1973-

    2005-01-01

    This thesis is organized into two parts which focus on the studies of the dynamic structure factor and static inter-particle structure factor respectively. In the first part, we have measured and analyzed the dynamic ...

  12. Water and Solute Flow in a Highly-Structured Soil 

    E-print Network

    Hallmark, C. Tom; Wilding, Larry P.; McInnes, Kevin J.; Heuvelman, Willem J.

    1993-01-01

    was related to changes in structural definition with depth. Convergence of water and solute flow is expected to increase the pollution potential of the soil because of increased bypassing of soil matrix and increased pore water velocities. Solute travel time...

  13. Biophysical Highlights from 54 Years of Macromolecular Crystallography

    PubMed Central

    Richardson, Jane S.; Richardson, David C.

    2014-01-01

    The United Nations has declared 2014 the International Year of Crystallography, and in commemoration, this review features a selection of 54 notable macromolecular crystal structures that have illuminated the field of biophysics in the 54 years since the first excitement of the myoglobin and hemoglobin structures in 1960. Chronological by publication of the earliest solved structure, each illustrated entry briefly describes key concepts or methods new at the time and key later work leveraged by knowledge of the three-dimensional atomic structure. PMID:24507592

  14. An autonomous structural health monitoring solution

    NASA Astrophysics Data System (ADS)

    Featherston, Carol A.; Holford, Karen M.; Pullin, Rhys; Lees, Jonathan; Eaton, Mark; Pearson, Matthew

    2013-05-01

    Combining advanced sensor technologies, with optimised data acquisition and diagnostic and prognostic capability, structural health monitoring (SHM) systems provide real-time assessment of the integrity of bridges, buildings, aircraft, wind turbines, oil pipelines and ships, leading to improved safety and reliability and reduced inspection and maintenance costs. The implementation of power harvesting, using energy scavenged from ambient sources such as thermal gradients and sources of vibration in conjunction with wireless transmission enables truly autonomous systems, reducing the need for batteries and associated maintenance in often inaccessible locations, alongside bulky and expensive wiring looms. The design and implementation of such a system however presents numerous challenges. A suitable energy source or multiple sources capable of meeting the power requirements of the system, over the entire monitoring period, in a location close to the sensor must be identified. Efficient power management techniques must be used to condition the power and deliver it, as required, to enable appropriate measurements to be taken. Energy storage may be necessary, to match a continuously changing supply and demand for a range of different monitoring states including sleep, record and transmit. An appropriate monitoring technique, capable of detecting, locating and characterising damage and delivering reliable information, whilst minimising power consumption, must be selected. Finally a wireless protocol capable of transmitting the levels of information generated at the rate needed in the required operating environment must be chosen. This paper considers solutions to some of these challenges, and in particular examines SHM in the context of the aircraft environment.

  15. Constructing efficient solutions structure of multiobjective linear programming

    Microsoft Academic Search

    Hong Yan; Quanling Wei; Jun Wang

    2005-01-01

    It is not a difficult task to find a weak Pareto or Pareto solution in a multiobjective linear programming (MOLP) problem. The difficulty lies in finding all these solutions and representing their structure. This paper develops an algorithm for solving this problem. We investigate the solutions and their relationships in the objective space. The algorithm determines finite number of weights,

  16. Automated error-tolerant macromolecular structure determination from multidimensional nuclear Overhauser enhancement spectra and chemical shift assignments: improved robustness and performance of the PASD algorithm.

    PubMed

    Kuszewski, John J; Thottungal, Robin Augustine; Clore, G Marius; Schwieters, Charles D

    2008-08-01

    We report substantial improvements to the previously introduced automated NOE assignment and structure determination protocol known as PASD (Kuszewski et al. (2004) J Am Chem Soc 26:6258-6273). The improved protocol includes extensive analysis of input spectral data to create a low-resolution contact map of residues expected to be close in space. This map is used to obtain reasonable initial guesses of NOE assignment likelihoods which are refined during subsequent structure calculations. Information in the contact map about which residues are predicted to not be close in space is applied via conservative repulsive distance restraints which are used in early phases of the structure calculations. In comparison with the previous protocol, the new protocol requires significantly less computation time. We show results of running the new PASD protocol on six proteins and demonstrate that useful assignment and structural information is extracted on proteins of more than 220 residues. We show that useful assignment information can be obtained even in the case in which a unique structure cannot be determined. PMID:18668206

  17. Low-resolution structures of proteins in solution retrieved from X-ray scattering with a genetic algorithm.

    PubMed Central

    Chacón, P; Morán, F; Díaz, J F; Pantos, E; Andreu, J M

    1998-01-01

    Small-angle x-ray solution scattering (SAXS) is analyzed with a new method to retrieve convergent model structures that fit the scattering profiles. An arbitrary hexagonal packing of several hundred beads containing the problem object is defined. Instead of attempting to compute the Debye formula for all of the possible mass distributions, a genetic algorithm is employed that efficiently searches the configurational space and evolves best-fit bead models. Models from different runs of the algorithm have similar or identical structures. The modeling resolution is increased by reducing the bead radius together with the search space in successive cycles of refinement. The method has been tested with protein SAXS (0.001 < S < 0.06 A(-1)) calculated from x-ray crystal structures, adding noise to the profiles. The models obtained closely approach the volumes and radii of gyration of the known structures, and faithfully reproduce the dimensions and shape of each of them. This includes finding the active site cavity of lysozyme, the bilobed structure of gamma-crystallin, two domains connected by a stalk in betab2-crystallin, and the horseshoe shape of pancreatic ribonuclease inhibitor. The low-resolution solution structure of lysozyme has been directly modeled from its experimental SAXS profile (0.003 < S < 0.03 A(-1)). The model describes lysozyme size and shape to the resolution of the measurement. The method may be applied to other proteins, to the analysis of domain movements, to the comparison of solution and crystal structures, as well as to large macromolecular assemblies. PMID:9635731

  18. Construction and asymptotic stability of structurally stable internal layer solutions

    Microsoft Academic Search

    Xiao-Biao Lin

    2001-01-01

    We introduce a geometric\\/asymptotic method to treat structurally stable internal layer solutions. We consider asymptotic expansions of the inter- nal layer solutions and the critical eigenvalues that determine their stability. Proofs of the existence of exact solutions and eigenvalue-eigenfunctions are outlined. Multi-layered solutions are constructed by a new shooting method through a sequence of pseudo Poincar e mappings that do

  19. Multi-crystal anomalous diffraction for low-resolution macromolecular phasing

    PubMed Central

    Liu, Qun; Zhang, Zhen; Hendrickson, Wayne A.

    2011-01-01

    Multiwavelength anomalous diffraction (MAD) and single-wavelength anomalous diffraction (SAD) are the two most commonly used methods for de novo determination of macromolecular structures. Both methods rely on the accurate extraction of anomalous signals; however, because of factors such as poor intrinsic order, radiation damage, inadequate anomalous scatterers, poor diffraction quality and other noise-causing factors, the anomalous signal from a single crystal is not always good enough for structure solution. In this study, procedures for extracting more accurate anomalous signals by merging data from multiple crystals are devised and tested. SAD phasing tests were made with a relatively large (1456 ordered residues) poorly diffracting (d min = 3.5?Å) selenomethionyl protein (20 Se). It is quantified that the anomalous signal, success in substructure determination and accuracy of phases and electron-density maps all improve with an increase in the number of crystals used in merging. Structure solutions are possible when no single crystal can support structural analysis. It is proposed that such multi-crystal strategies may be broadly useful when only weak anomalous signals are available. PMID:21206061

  20. Imaging the structure of water near hydrophobic solutes

    NASA Astrophysics Data System (ADS)

    Wong, Gerard C. L.; Coridan, Robert H.; Hwee Lai, Ghee; Schmidt, Nathan S.; Krisch, Michael; Abbamonte, Peter

    2007-03-01

    Theoretical studies of the structure of interfacial water on the surface of hydrophobic solutes show a strong dependence on the radius of the solute itself. At small radii, a hydrogen-bond network is still capable of forming around the solute, generally forbidding association between the solute molecules. At large radii water can no longer form a hydrogen-bond network around the solute molecule, resulting in the ``drying'' of the surface and a strong attraction between solute molecules. The crossover length between the two regimes is on the order of a nanometer. We will show that it is possible to make movies of water around hydrophobic solutes of varying size by extracting the density propagator from the dynamical structure factor measured via high-resolution inelastic x-ray scattering spectra at 3rd generation synchrotron sources.

  1. Development of highly chemoselective bulky zincate complex, tBu4ZnLi2: design, structure, and practical applications in small-/macromolecular synthesis.

    PubMed

    Furuyama, Taniyuki; Yonehara, Mitsuhiro; Arimoto, Sho; Kobayashi, Minoru; Matsumoto, Yotaro; Uchiyama, Masanobu

    2008-01-01

    We present full details of the unique reactivities of the newly developed dianion-type bulky zincate, dilithium tetra-tert-butylzincate (tBu(4)ZnLi(2)). With this reagent, halogen-zinc exchange reaction of variously functionalized haloaromatics and anionic polymerization of N-isopropylacrylamide (NIPAm)/styrene with excellent chemoselectivity were realized. Halogen-zinc exchange reaction followed by electrophilic trapping with propargyl bromide provided a convenient route to functionalized phenylallenes, particularly those with electrophilic functional groups (such as cyano, amide and halogens). Spectral and computational studies of the structure in the gas and liquid phases indicated extraordinary stabilization of this dianion-type zincate by its bulky ligands. PMID:18816554

  2. Adaptive Visuo-Haptic Rendering for Hybrid Modeling of Macromolecular Assemblies

    Microsoft Academic Search

    Stefan Birmanns; Maik Boltes; Herwig Zilken; Willy Wriggers

    We describe an immersive visualization system for structural biology using real-time load balancing of virtual reality and haptic render- ing. In structural biology a variety of image reconstruction techniques are employed to determine geometric aspects of large macromolecular assem- blies at various levels of resolution. Hybrid modeling techniques are the most promising approach to bridge the resolution gap between data

  3. Large structures in diblock copolymer micellar solution

    Microsoft Academic Search

    Domenico Lombardo; Norberto Micali; Valentina Villari; Mikhail A. Kiselev

    2004-01-01

    The association properties in water solution of poly(dimethylsiloxane)-b-poly(ethyleneoxide) diblock copolymer was investigated by static and dynamic light scattering in a wide range of concentrations and temperatures. The presence of a long hydrophilic poly(ethyleneoxide) (PEO) chain causes a weak tendency to microphase separation of the system which is responsible for some relevant effects. First of all we observe a late micellization

  4. Constructing efficient solutions structure of multiobjective linear programming

    NASA Astrophysics Data System (ADS)

    Yan, Hong; Wei, Quanling; Wang, Jun

    2005-07-01

    It is not a difficult task to find a weak Pareto or Pareto solution in a multiobjective linear programming (MOLP) problem. The difficulty lies in finding all these solutions and representing their structure. This paper develops an algorithm for solving this problem. We investigate the solutions and their relationships in the objective space. The algorithm determines finite number of weights, each of which corresponds to a weighted sum problemsE By solving these problems, we further obtain all weak Pareto and Pareto solutions of the MOLP and their structure in the constraint space. The algorithm avoids the degeneration problem, which is a major hurdle of previous works, and presents an easy and clear solution structure.

  5. Probing the structure of RNAs in solution.

    PubMed Central

    Ehresmann, C; Baudin, F; Mougel, M; Romby, P; Ebel, J P; Ehresmann, B

    1987-01-01

    During these last years, a powerful methodology has been developed to study the secondary and tertiary structure of RNA molecules either free or engaged in complex with proteins. This method allows to test the reactivity of every nucleotide towards chemical or enzymatic probes. The detection of the modified nucleotides and RNase cleavages can be conducted by two different paths which are oriented both by the length of the studied RNA and by the nature of the probes used. The first one uses end-labeled RNA molecule and allows to detect only scissions in the RNA chain. The second approach is based on primer extension by reverse transcriptase and detects stops of transcription at modified or cleaved nucleotides. The synthesized cDNA fragments are then sized by electrophoresis on polyacrylamide:urea gels. In this paper, the various structure probes used so far are described, and their utilization is discussed. Images PMID:2446263

  6. Large Structures: which Solutions for Health Monitoring?

    NASA Astrophysics Data System (ADS)

    Camp, G.; Carreaud, P.; Lançon, H.

    2013-07-01

    Whatever the age of a large structure (dam, viaduct, cooling tower, nuclear containment, tunnel, …) It has to be periodically monitored. It is a challenge to realise these services when the access is limited and difficult for Man. This paper introduces a global approach, developed by SITES, through examples of application on different concrete dams or cooling towers, and their results. This global method involves three techniques: the SCANSITES® (a visual inspection system), the LIDAR (3D laser scanning) and high resolution photogrammetry.

  7. Solution Structure of Human BCL-w

    Microsoft Academic Search

    Alexei Yu. Denisov; Murthy S. R. Madiraju; Gang Chen; Abdelkrim Khadir; Giorgio Attardo; Gordon C. Shore; Kalle Gehring

    2003-01-01

    The structure of human BCL-w, an anti-apoptotic member of the BCL-2 family, was determined by triple- resonance NMR spectroscopy and molecular modeling. Introduction of a single amino acid substitution (P117V) significantly improved the quality of the NMR spectra obtained. The cytosolic domain of BCL-w consists of 8 -helices, which adopt a fold similar to that of BCL-xL, BCL-2, and BAX

  8. NMR study of the solution structure of curcumin.

    PubMed

    Payton, Florastina; Sandusky, Peter; Alworth, William L

    2007-02-01

    Curcumin [1,7-bis(4-hydroxy-3-methoxyphenyl)-1,6-heptadiene-3,5-dione] is derived from the rhizomes of Curcuma longa. Although early studies concluded that curcumin exists predominantly as a keto-enol tautomer, 1b, in several recent articles the solution structure of curcumin has been represented as a beta-diketone tautomer, 1a. We have investigated the structure of curcumin in solvents ranging in polarity from CDCl3 to mixtures of DMSO-d6 in water, and in buffered aqueous DMSO-d6 solutions with pH values varying from 3 to 9. The solution structure of curcumin was determined on the basis of NMR techniques, including DEPT, HMQC, HMBC, and COSY. The results of the NMR studies show definitely that curcumin exists in solution as keto-enol tautomers, 1b. PMID:17315954

  9. [Macromolecular aromatic network characteristics of Chinese power coal analyzed by synchronous fluorescence and X-ray diffraction].

    PubMed

    Ye, Cui-Ping; Feng, Jie; Li, Wen-Ying

    2012-07-01

    Coal structure, especially the macromolecular aromatic skeleton structure, has a strong influence on coke reactivity and coal gasification, so it is the key to grasp the macromolecular aromatic skeleton coal structure for getting the reasonable high efficiency utilization of coal. However, it is difficult to acquire their information due to the complex compositions and structure of coal. It has been found that the macromolecular aromatic network coal structure would be most isolated if small molecular of coal was first extracted. Then the macromolecular aromatic skeleton coal structure would be clearly analyzed by instruments, such as X-ray diffraction (XRD), fluorescence spectroscopy with synchronous mode (Syn-F), Gel permeation chromatography (GPC) etc. Based on the previous results, according to the stepwise fractional liquid extraction, two Chinese typical power coals, PS and HDG, were extracted by silica gel as stationary phase and acetonitrile, tetrahydrofuran (THF), pyridine and 1-methyl-2-pyrollidinone (NMP) as a solvent group for sequential elution. GPC, Syn-F and XRD were applied to investigate molecular mass distribution, condensed aromatic structure and crystal characteristics. The results showed that the size of aromatic layers (La) is small (3-3.95 nm) and the stacking heights (Lc) are 0.8-1.2 nm. The molecular mass distribution of the macromolecular aromatic network structure is between 400 and 1 130 amu, with condensed aromatic numbers of 3-7 in the structure units. PMID:23016368

  10. Predicted Solution Structure of Zymogen Human Coagulation FVII

    E-print Network

    Perera, Lalith

    Predicted Solution Structure of Zymogen Human Coagulation FVII LALITH PERERA,1 THOMAS A. DARDEN,2-ray crystallographic structure of human coagulation FVIIa/TF complex bound with calcium ions (Banner et al., Nature dynamics simulations; FVII; tissue factor; EGF-like domains; serine protease Introduction Blood coagulation

  11. A data structure for the efficient Kronecker solution of GSPNs

    Microsoft Academic Search

    Gianfranco Ciardo; Andrew S. Miner

    1999-01-01

    Kronecker-based approaches have been proposed for the solution of structured GSPNs with extremely large state spaces. Representing the transition rate matrix using Kronecker sums and products of smaller matrices virtually eliminates its storage requirements, but introduces various sources of overhead. We show how, by using a new data structure which we call matrix diagrams, we are able to greatly reduce

  12. Solution processed organic microarray with inverted structure

    NASA Astrophysics Data System (ADS)

    Toglia, Patrick; Lewis, Jason; Lafalce, Evan; Jiang, Xiaomei

    2011-03-01

    We have fabricated inverted organic microarray using a novel solution-based technique. The array consists of 60 small (1 square mm) solar cells on a one inch by one inch glass substrate. The device utilizes photoactive materials such as a blend of poly(3-hexylthiophene) (P3HT) and [6,6]-phenyl-C61-butyric acid methyl ester (PCBM). Manipulation of active layer nanomorphology has been done by choice of solvents and annealing conditions. Detailed analysis of device physics including current voltage characteristics, external quantum efficiency and carrier recombinations will be presented and complimented by AFM images and glazing angle XRD of the active layer under different processing conditions. The procedure described here has the full potential for use in future fabrication of microarrays with single cell as small as 0.01 square mm for application in DC power supplies for electrostatic Microelectromechanical systems (MEMS) devices. This work was supported by New Energy Technology Inc. and Florida High Tech Corridor Matching Fund (FHT 09-18).

  13. Macromolecular prodrugs based on synthetic polyaminoacids: drug delivery and drug targeting in antitumor therapy.

    PubMed

    Cavallaro, Gennara; Pitarresi, Giovanna; Giammona, Gaetano

    2011-01-01

    In the last twenty years a depth study on potential pharmaceutical applications of synthetic polymers at proteinlike structure as carrier for macromolecular prodrug production has been performed in academia and in industry. In particular ?,?-poly(N-2-hydroxyethyl)-DL-aspartamide (PHEA), ?,?-polyaspartylhydrazide (PAHy), poly(glutamic acid) (PGA), poly(aspartic acid) (PAA) and polylysine (PLL) have been extensively studied in this field. In the present review, the use of PHEA, PAHy, PGA as starting materials to prepare macromolecular prodrugs is reported and drug delivery and targeting aspects have been considered. PMID:21671863

  14. Interactions affecting the mechanical properties of macromolecular microsphere composite hydrogels.

    PubMed

    Jiang, Fangzhi; Huang, Ting; He, Changcheng; Brown, Hugh R; Wang, Huiliang

    2013-10-31

    Macromolecular microsphere composite (MMC) hydrogel is a kind of tough hydrogel fabricated by using peroxidized macromolecular microspheres as polyfunctional initiating and cross-linking centers (PFICC). The contribution of chemical cross-linking (covalent bonding) and physical cross-linking (chain entanglement and hydrogen bonding) to the mechanical properties are understood by testing the hydrogels, which were swollen in water or aqueous urea solutions to different water contents. The as-prepared MMC gels exhibited moderate moduli (60-270 kPa), high fracture tensile stresses (up to 0.54 MPa), high extensibilities (up to 2500%), and high fracture energies (270-770 J m(-2)). The moduli of the swollen gels decrease dramatically, but there are no significant changes in fracture tensile strength and fracture strain, even slight increases. More interestingly, the swollen gels show much-enhanced fracture energies, higher than 2000 J m(-2). A gradual decrease in the hysteresis ratio and residual strain is also found in the cyclic tensile testing of the hydrogels that were swollen to different water contents. The covalent bonding determines the tensile strength and fracture energy of the MMC gels, whereas the physical entanglement and hydrogen bonding among the polymer chains contributes mainly to the modulus of the MMC gels, and they are also the main reason for the presence of hysteresis in the loading-unloading cycles. PMID:24093971

  15. Protein stabilization by macromolecular crowding through enthalpy rather than entropy.

    PubMed

    Senske, Michael; Törk, Lisa; Born, Benjamin; Havenith, Martina; Herrmann, Christian; Ebbinghaus, Simon

    2014-06-25

    The interior of the cell is a densely crowded environment in which protein stability is affected differently than in dilute solution. Macromolecular crowding is commonly understood in terms of an entropic volume exclusion effect based on hardcore repulsions among the macromolecules. We studied the thermal unfolding of ubiquitin in the presence of different cosolutes (glucose, dextran, poly(ethylene glycol), KCl, urea). Our results show that for a correct dissection of the cosolute-induced changes of the free energy into its enthalpic and entropic contributions, the temperature dependence of the heat capacity change needs to be explicitly taken into account. In contrast to the prediction by the excluded volume theory, we observed an enthalpic stabilization and an entropic destabilization for glucose, dextran, and poly(ethylene glycol). The enthalpic stabilization mechanism induced by the macromolecular crowder dextran was similar to the enthalpic stabilization mechanism of its monomeric building block glucose. In the case of poly(ethylene glycol), entropy is dominating over enthalpy leading to an overall destabilization. We propose a new model to classify cosolute effects in terms of their enthalpic contributions to protein stability. PMID:24888734

  16. Adaptive Visuo-Haptic Rendering for Hybrid Modeling of Macromolecular Assemblies

    E-print Network

    Wriggers, Willy

    Adaptive Visuo-Haptic Rendering for Hybrid Modeling of Macromolecular Assemblies Stefan Birmanns1-time load balancing of virtual reality and haptic render- ing. In structural biology a variety of image for the multi-resolution modeling problem that employs a novel load-balancing scheme for the visual and haptic

  17. Water structure in aqueous solutions of tetramethylammonium chloride

    Microsoft Academic Search

    J. Turner; A. K. Soper; J. L. Finney

    1992-01-01

    Neutron diffraction with hydrogen\\/deuterium isotope substitution is used to investigate the water structure and the solute distribution in aqueous solutions of tetramethylammonium chloride ((CH3)4NCl) between 2·0 and 8·0m concentrations at room temperature. The hydrogen-hydrogen (HH) pair correlation functions for the water indicate that the hydrogen-bonding geometry is not significantly changed over the concentration range compared to pure water, although the

  18. Macromolecular organization of chicken type X collagen in vitro

    PubMed Central

    1991-01-01

    The macromolecular structure of type X collagen in the matrices of primary cultures of chick hypertrophic chondrocytes was initially investigated using immunoelectron microscopy. Type X collagen was observed to assemble into a matlike structure with-in the matrix elaborated by hypertrophic chondrocytes. The process of self assembly was investigated at the molecular level using purified chick type X collagen and rotary-shadowing EM. It was shown that under neutral conditions at 34 degrees C, individual type X collagen molecules associate rapidly into multimeric clusters via their carboxy-terminal globular domains forming structures with a central nodule of carboxy- terminal domains and the triple helices radiating outwards. Prolonged incubation resulted in the formation of a regular hexagonal lattice by lateral association of the juxtaposed triple-helical domains from adjacent multimeric clusters. This extended lattice may play an important role in modifying the cartilage matrix for subsequent events occurring in endochondral bone formation. PMID:1860888

  19. Ions in water: The microscopic structure of concentrated hydroxide solutions

    NASA Astrophysics Data System (ADS)

    Imberti, S.; Botti, A.; Bruni, F.; Cappa, G.; Ricci, M. A.; Soper, A. K.

    2005-05-01

    Neutron-diffraction data on aqueous solutions of hydroxides, at solute concentrations ranging from 1 solute per 12 water molecules to 1 solute per 3 water molecules, are analyzed by means of a Monte Carlo simulation (empirical potential structure refinement), in order to determine the hydration shell of the OH- in the presence of the smaller alkali metal ions. It is demonstrated that the symmetry argument between H+ and OH- cannot be used, at least in the liquid phase at such high concentrations, for determining the hydroxide hydration shell. Water molecules in the hydration shell of K+ orient their dipole moment at about 45° from the K+-water oxygen director, instead of radially as in the case of the Li+ and Na+ hydration shells. The K+-water oxygen radial distribution function shows a shallower first minimum compared to the other cation-water oxygen functions. The influence of the solutes on the water-water radial distribution functions is shown to have an effect on the water structure equivalent to an increase in the pressure of the water, depending on both ion concentration and ionic radius. The changes of the water structure in the presence of charged solutes and the differences among the hydration shells of the different cations are used to present a qualitative explanation of the observed cation mobility.

  20. Structural cluster analysis of chemical reactions in solution

    NASA Astrophysics Data System (ADS)

    Gallet, Grégoire A.; Pietrucci, Fabio

    2013-08-01

    We introduce a simple and general approach to the problem of clustering structures from atomic trajectories of chemical reactions in solution. By considering distance metrics which are invariant under permutation of identical atoms or molecules, we demonstrate that it is possible to automatically resolve as distinct structural clusters the configurations corresponding to reactants, products, and transition states, even in presence of atom-exchanges and of hundreds of solvent molecules. Our approach strongly simplifies the analysis of large trajectories and it opens the way to the construction of kinetic network models of activated processes in solution employing the available efficient schemes developed for proteins conformational ensembles.

  1. Processes of ordered structure formation in polypeptide thin film solutions.

    SciTech Connect

    Botiz, I.; Schlaad, H.; Reiter, G. (Center for Nanoscale Materials); (Max Planck Inst. of Colloids and Interfaces); (Univ. of Freiburg)

    2010-06-17

    An experimental study is presented on the hierarchical assembly of {alpha}-helical block copolymers polystyrene-poly({gamma}-benzyl-L-glutamate) into anisotropic ordered structures. We transformed thin solid films into solutions through exposure to solvent vapor and studied the nucleation and growth of ordered three-dimensional structures in such solutions, with emphasis on the dependence of these processes on supersaturation with respect to the solubility limit. Interestingly, polymer solubility could be significantly influenced via variation of humidity in the surrounding gas phase. It is concluded that the interfacial tension between the ordered structures and the solution increased with humidity. The same effect was observed for other protic non-solvents in the surrounding gas phase and is attributed to a complexation of poly({gamma}-benzyl-L-glutamate) by protic non-solvent molecules (via hydrogen-bonding interactions). This change of polymer solubility was demonstrated to be reversible by addition or removal of small amounts of protic non-solvent in the surrounding gas phase. At a constant polymer concentration, ordered ellipsoidal structures could be dissolved by removing water or methanol present in the solution. Such structures formed once again when water or methanol was reintroduced via the vapor phase.

  2. AFM studies of the nucleation and growth mechanisms of macromolecular crystals

    NASA Astrophysics Data System (ADS)

    Kuznetsov, Yu. G.; Malkin, A. J.; McPherson, A.

    1999-01-01

    Atomic force microscopy (AFM) has been used to visualize events arising from the formation of intervening metastable phases at the surfaces of macromolecular crystals growing from solution. Crystals investigated were of the proteins canavalin, thaumatin, lipase, xylanase, and catalase, crystals of transfer RNA, and crystals of satellite tobacco mosaic virus. The appearance of aggregates on crystal surfaces was observed. The aggregates we infer to originate from liquid-protein droplets. These were particularly evident in freshly mixed mother liquor solutions. Droplets, upon sedimentation, have two possible fates. In some cases they immediately restructured as crystalline, multilayer stacks whose development was guided by, and contiguous with the underlying lattice. These contributed to the ordered growth of the crystal by serving as sources of growth steps. In other cases, liquid-protein droplets formed distinct microcrystals, somehow discontinuous with the underlying lattice, and these were subsequently incorporated into the growing substrate crystal. Scarring experiments with the AFM tip indicated that, detached from the crystal, molecules do not dissolve in the fluid phase but form metastable liquid-protein droplets with a potential to rapidly crystallize on the crystal surface. The molecular structure of the growth steps for thaumatin and lipase protein crystals were deduced. There is no step roughness due to thermal fluctuations, and each protein molecule which incorporated into the step edge remained. Growth steps propagate by addition of individual molecules which form subkinks of different size on the step edge.

  3. Macromolecular nanotheranostics for multimodal anticancer therapy

    NASA Astrophysics Data System (ADS)

    Huis in't Veld, Ruben; Storm, Gert; Hennink, Wim E.; Kiessling, Fabian; Lammers, Twan

    2011-10-01

    Macromolecular carrier materials based on N-(2-hydroxypropyl)methacrylamide (HPMA) are prototypic and well-characterized drug delivery systems that have been extensively evaluated in the past two decades, both at the preclinical and at the clinical level. Using several different imaging agents and techniques, HPMA copolymers have been shown to circulate for prolonged periods of time, and to accumulate in tumors both effectively and selectively by means of the Enhanced Permeability and Retention (EPR) effect. Because of this, HPMA-based macromolecular nanotheranostics, i.e. formulations containing both drug and imaging agents within a single formulation, have been shown to be highly effective in inducing tumor growth inhibition in animal models. In patients, however, as essentially all other tumor-targeted nanomedicines, they are generally only able to improve the therapeutic index of the attached active agent by lowering its toxicity, and they fail to improve the efficacy of the intervention. Bearing this in mind, we have recently reasoned that because of their biocompatibility and their beneficial biodistribution, nanomedicine formulations might be highly suitable systems for combination therapies. In the present manuscript, we briefly summarize several exemplary efforts undertaken in this regard in our labs in the past couple of years, and we show that long-circulating and passively tumor-targeted macromolecular nanotheranostics can be used to improve the efficacy of radiochemotherapy and of chemotherapy combinations.

  4. Atomistic molecular dynamics simulations of the structure of symmetric Polyelectrolyte block copolymer micelle in salt-free aqueous solution

    NASA Astrophysics Data System (ADS)

    Chockalingam, Rajalakshmi; Natarajan, Upendra

    2014-03-01

    The structure of a symmetric polystyrene- b - poly(acrylic acid) (PS- b - PAA) micelle in salt-free aqueous solution as a function of degree-of-neutralization (or ionization, f) of the PAA is studied via explicit-atom-ion MD simulations, for the first time for a polyelectrolyte block copolymer in a polar solvent. Micelle size increases with fin agreement with experimental observations in literature, due to extension of PAA at higher ionization. Pair RDF's with respect to water oxygens show that corona-water interaction becomes stronger with f due to an increase in number density of carboxylate (COO-) groups on the chain. Water-PAA coordination (carboxylate O's) increases with ionization. H-bonding between PAA and water increases with f due to greater extent of corona-water affinity. With increase in f, atom and counter-ion ? profiles confirm extension of corona blocks and micelle existing in the ``osmotic regime,'' and a decrease in scattering peak intensity, in agreement with neutron scattering experiments and mean-field theory in literature. Inter-chain distance in PS core is found to decrease with ionization. Macromolecular Simulation and Modeling Laboratory, Dept. of Chemical Engineering, Indian Institute of Technology Madras, Chennai 600036.

  5. Use of Capillaries for Macromolecular Crystallization in a Cryogenic Dewar

    NASA Technical Reports Server (NTRS)

    Ciszak, Ewa; Hammons, Aaron S.; Hong, Young Soo

    2002-01-01

    The enhanced gaseous nitrogen (EGN) dewar is a cryogenic dry shipper with a sealed cylinder inserted inside along with a temperature monitoring device, and is intended for macromolecular crystallization experiments on the International Space Station. Within the dewar, each crystallization experiment is contained as a solution within a plastic capillary tube. The standard procedure for loading samples in these tubes has involved rapid freezing of the precipitant and biomolecular solution, e.g., protein, directly in liquid nitrogen; this method, however, often resulted in uncontrolled formation of air voids, These air pockets, or bubbles, can lead to irreproducible crystallization results. A novel protocol has been developed to prevent formation of bubbles, and this has been tested in the laboratory as well as aboard the International Space Station during a 42-day long mission of July/August 2001. The gain or loss of mass from solutions within the plastic capillaries revealed that mass transport occurred among separated tubes, and that this mass transport was dependent upon the hygroscopic character of the solution contained in any given tube. The surface area of the plastic capillary tube also related to the observed mass transport. Furthermore, the decreased mass of solutions of-protein correlated to observed formation of protein crystals.

  6. Cooperative Macromolecular Disassembly via the Heat Shock Chaperone Hsc70

    NASA Astrophysics Data System (ADS)

    Puchalla, Jason; Krantz, Kelly; Austin, Robert; Rye, Hays

    2008-03-01

    Many essential cellular functions depend on the assembly and disassembly of macromolecular complexes. A general class of protein known as molecular chaperones regulates several of these processes. How can complex protein structure be quickly and efficiently disassembled by the action of a small number of these proteins? One such example is that of clathrin: a ubiquitous coat protein that stabilizes vesicular trafficking by forming a scaffold onto the membrane surface. This scaffold must be removed before the vesicle can deliver its cargo. We report on the cooperative disassembly of yeast-derived GFP-labeled clathrin baskets via its interaction with Hsc70. We exploit the highest signal-to-noise light bursts from single fluorescent baskets transiting a confocal excitation spot to recursively determine the brightness and size distribution of the baskets during the uncoating process. This minimal uncoating system demonstrates the ability of a surprisingly simple protein system to facilitate rapid structural changes through cooperative action.

  7. Solution structure of the tobramycin–RNA aptamer complex

    Microsoft Academic Search

    Licong Jiang; Dinshaw J. Patel

    1998-01-01

    We have solved the solution structure of the aminoglycoside antibiotic tobramycin complexed with a stem-loop RNA aptamer. The 14 base loop of the RNA aptamer 'zippers up' alongside the attached stem through alignment of four mismatches and one Watson-Crick pair on complex formation. The tobramycin inserts into the deep groove centered about the mismatch pairs and is partially encapsulated between

  8. Solution structure and dynamics of biomolecules from Raman optical activity

    Microsoft Academic Search

    L. D. Barron; L. Hecht; E. W. Blanch; A. F. Bell

    2000-01-01

    Raman optical activity (ROA) measures vibrational optical activity by means of a small difference in the intensity of Raman scattering from chiral molecules in right and left circularly polarized incident laser light. The ROA spectra of a wide range of biomolecules in aqueous solution can now be measured routinely. Because of its sensitivity to the chiral elements of biomolecular structure,

  9. An analytical solution for approximating simple structure in factor analysis

    Microsoft Academic Search

    John B. Carroll

    1953-01-01

    It is proposed that a satisfactory criterion for an approximation to simple structure is the minimization of the sums of cross-products (across factors) ofsquares of factor loadings. This criterion is completely analytical and yields a unique solution; it requires no plotting, nor any decisions as to the clustering of variables into subgroups. The equations involved appear to be capable only

  10. Solution-phase surface reconstruction and structural transformation in MWNTs

    Microsoft Academic Search

    Arunkumar Subramanian; Lixin Dong; Didi Xu; Bradley J. Nelson

    2009-01-01

    We report on structural changes induced in arc-grown multiwalled carbon nanotubes (MWNTs) due to ultrasonic agitation in an aqueous iron nitrate solution. The surface reconstructions were observed to follow three different pathways: (1) transformation from a tubular to a spherical \\/ polyhedral onion-like geometry that involves a lower surface energy, (2) surface reconstruction of shells resulting in NT shrinkage from

  11. Numerical Solution of Singular ODE Eigenvalue Problems in Electronic Structure

    E-print Network

    Koch, Othmar

    ) Corresponding Author Email addresses: rh@cms.tuwien.ac.at (Robert Hammerling ), othmar@othmar-koch.org (Othmar: http://www.cms.tuwien.ac.at/ (Robert Hammerling ), http://www.othmar-koch.org (Othmar Koch ), httpNumerical Solution of Singular ODE Eigenvalue Problems in Electronic Structure Computations Robert

  12. Extended structure of rat islet amyloid polypeptide in solution.

    PubMed

    Wei, Lei; Jiang, Ping; Manimekalai, Malathy Sony Subramanian; Hunke, Cornelia; Grüber, Gerhard; Pervushin, Konstantin; Mu, Yuguang

    2015-01-01

    The process of islet amyloid polypeptide (IAPP) formation and the prefibrillar oligomers are supposed to be one of the pathogenic agents causing pancreatic ?-cell dysfunction. The human IAPP (hIAPP) aggregates easily and therefore, it is difficult to characterize its structural features by standard biophysical tools. The rat version of IAPP (rIAPP) that differs by six amino acids when compared with hIAPP, is not prone to aggregation and does not form amyloid fibrils. Similar to hIAPP it also demonstrates random-coiled nature in solution. The structural propensity of rIAPP has been studied as a hIAPP mimic in recent works. However, the overall shape of it in solution still remains elusive. Using small angle X-ray scattering (SAXS) measurements combined with nuclear magnetic resonance (NMR) and molecular dynamics simulations (MD) the solution structure of rIAPP was studied. An unambiguously extended structural model with a radius of gyration of 1.83 nm was determined from SAXS data. Consistent with previous studies, an overall random-coiled feature with residual helical propensity in the N-terminus was confirmed. Combined efforts are necessary to unambiguously resolve the structural features of intrinsic disordered proteins. PMID:25387961

  13. Structural and Spectroscopic Properties of Water Around Small Hydrophobic Solutes

    PubMed Central

    Montagna, Maria; Sterpone, Fabio; Guidoni, Leonardo

    2013-01-01

    We investigated the structural, dynamical and spectroscopic properties of water molecules around a solvated methane by means of Car-Parrinello molecular dynamics simulations. Despite their mobility, in the first-shell water molecules are dynamically displaced in a clathrate-like cage around the hydrophobic solute. No significant differences in water geometrical parameters, in molecular dipole moments or in hydrogen bonding properties are observed between in-shell and out-shell molecules, indicating that liquid water can accommodate a small hydrophobic solute without altering its structural properties. The calculated contribution of the first shell water molecules to the infrared spectra does not show significant differences with respect the bulk signal once the effects of the missing polarization of second-shell molecules has been taken into account. Small fingerprints of the clathrate-like structure appear in the vibrational density of states in the libration and OH stretching regions. PMID:22946539

  14. Use of Capillaries for Macromolecular Crystallization in a Cryogenic Dewar

    NASA Technical Reports Server (NTRS)

    Ciszak, Ewa; Hammons, Aaron S.; Hong, Young Soo; Curreri, Peter A. (Technical Monitor)

    2001-01-01

    The Enhanced Gaseous Nitrogen (EGN) Dewar is a cryogenic dry shipper with a sealed cylinder inserted inside along with a temperature-monitoring device, and is intended for macromolecular crystallization experiments on the International Space Station. Within the Dewar, each crystallization experiment is contained as a solution within a plastic capillary. The standard procedure for loading samples in these tubes has involved rapid freezing of the precipitant and biomolecule solution directly in liquid nitrogen; this method, however, often results in uncontrolled formation of air voids. These air pockets, or bubbles, then can lead to irreproducible crystallization results. A novel protocol has been developed to prevent formation of bubbles, and this has been tested in the laboratory as well as aboard the International Space Station during a 42-day long mission of July/August of 2001. Furthermore, gain or loss of mass from solutions within the capillaries revealed that mass transport amongst separated tubes occurred, and that this mass transport was determined by the hygroscopic character of a solution contained in any given tube. The sample volume and the surface area of the plastic capillary tube also related to the observed mass transport.

  15. The Promise of Macromolecular Crystallization in Micro-fluidic Chips

    NASA Technical Reports Server (NTRS)

    vanderWoerd, Mark; Ferree, Darren; Pusey, Marc

    2003-01-01

    Micro-fluidics, or lab on a chip technology, is proving to be a powerful, rapid, and efficient approach to a wide variety of bio-analytical and microscale bio-preparative needs. The low materials consumption, combined with the potential for packing a large number of experiments in a few cubic centimeters, makes it an attractive technique for both initial screening and subsequent optimization of macromolecular crystallization conditions. Screening operations, which require equilibrating macromolecule solution with a standard set of premixed solutions, are relatively straightforward and have been successfully demonstrated in a micro-fluidics platform. More complex optimization methods, where crystallization solutions are independently formulated from a range of stock solutions, are considerably more complex and have yet to be demonstrated. To be competitive with either approach, a micro-fluidics system must offer ease of operation, be able to maintain a sealed environment over several weeks to months, and give ready access for the observation of crystals as they are grown.

  16. Effect of Solute Size on Transport in Structured Porous Media

    NASA Astrophysics Data System (ADS)

    Hu, Qinhong; Brusseau, Mark L.

    1995-07-01

    The purpose of this work was to investigate the effect of solute size on transport in structured porous media. Miscible displacement experiments were performed with tracers of different sizes (i.e., tritiated water (3H2O), pentafluorobenzoate (PFBA), 2,4-dichlorophenoxyacetic acid (2,4-D), and hydroxypropyl-?-cyclodextrin (HPCD)) in aggregated, stratified, and macroporous media. The breakthrough curves exhibited both early breakthrough and tailing, indicative of nonideal transport in these structured media. Comparison of breakthrough curves revealed that the extent of nonideality (e.g., tailing) was HPCD > PFBA, 2,4-D > 3H2O. This behavior is consistent with the impact of solute size on the relative degree of "nonequilibrium" experienced by solutes whose transport is constrained by diffusive mass transfer. The capability of the first-order, dual-porosity mobile-immobile model to represent solute transport in these structured systems was evaluated by comparing independently determined values of the input parameters to values obtained by curve fitting of the experimental measurements. The calculated and optimized values compared quite well for the aggregated and stratified media, but not for the macroporous media. xperiments performed with tracers of different size are useful for characterizing the nature of the porous medium through which transport is occurring.

  17. Effect of solute size on transport in structured porous media

    SciTech Connect

    Hu, Qinhong; Brusseau, M.L. [Univ. of Arizona, Tucson, AZ (United States)] [Univ. of Arizona, Tucson, AZ (United States)

    1995-07-01

    The purpose of this work was to investigate the effect of solute size on transport in structured porous media. Miscible displacement experiments were performed with tracers of different sizes (i.e., tritiated water {sup 3}H{sub 2}O), pentafluorobenzoate (PFBA), 2,4-dichlorophenoxyacetic acid (2,4-D), and hydroxypropyl-{beta}-cyclodextrin (HPCD) in aggregated, stratified, and macroporous media. The breakthrough curves exhibited both early breakthrough and tailing, indicative of nonideal transport in these structured media. Comparison of breakthrough curves revealed that the extent of nonideality (e.g., tailing) was HPCD > PFBA, 2,4-D > {sup 3}H{sub 2}O. This behavior is consistent with the impact of solute size on the relative degree of {open_quotes}nonequilibrium{close_quotes} experienced by solutes whose transport is constrained by diffusive mass transfer. The capability of the first-order, dual-porosity mobile-immobile model to represent solute transport in these structured systems was evaluated by comparing independently determined values of the input parameters to values obtained by curve fitting of the experimental measurements. The calculated and optimized values compared quite well for the aggregated and stratified media, but not for the macroporous media. Experiments performed with tracers of different size are useful for characterizing the nature of the porous medium through which transport is occurring. 25 refs., 13 figs., 5 tabs.

  18. Solution superstructures: truncated cubeoctahedron structures of pyrogallol[4]arene nanoassemblies.

    PubMed

    Kumari, Harshita; Kline, Steven R; Fowler, Drew A; Mossine, Andrew V; Deakyne, Carol A; Atwood, Jerry L

    2014-01-01

    Giant nanocapsules: the solution-phase structures of PgC1Ho and PgC3Ho have been investigated using in situ neutron scattering measurements. The SANS results show the presence of spherical nanoassemblies of radius 18.2 Å, which are larger than the previously reported metal-seamed PgC3 hexamers (radius = 10 Å). The spherical architectures conform to a truncated cubeoctahedron geometry, indicating formation of the first metal-containing pyrogallol[4]arene-based dodecameric nanoassemblies in solution. PMID:24217564

  19. Advances in macromolecular data storage

    NASA Astrophysics Data System (ADS)

    Mansuripur, Masud

    2014-09-01

    We propose to develop a new method of information storage to replace magnetic hard disk drives and other instruments of secondary/backup data storage. The proposed method stores petabytes of user-data in a sugar cube (1 cm3), and can read/write that information at hundreds of megabits/sec. Digital information is recorded and stored in the form of a long macromolecule consisting of at least two bases, 𝐴 and 𝐵. (This would be similar to DNA strands constructed from the four nucleic acids 𝐺, 𝐶, 𝐴, 𝑇.) The macromolecules initially enter the system as blank slates. A macromolecule with, say, 10,000 identical bases in the form of 𝐴𝐴𝐴𝐴𝐴. . . . 𝐴𝐴𝐴 may be used to record a kilobyte block of user-data (including modulation and error-correction coding), although, in this blank state, it can only represent the null sequence 00000....000. Suppose this blank string of 𝐴's is dragged before an atomically-sharp needle of a scanning tunneling microscope (STM). When electric pulses are applied to the needle in accordance with the sequence of 0s and 1s of a 1 𝑘𝐵 block of user-data, selected 𝐴 molecules will be transformed into 𝐵 molecules (e.g., a fraction of 𝐴 will be broken off and discarded). The resulting string now encodes the user-data in the form of 𝐴𝐴𝐵𝐴𝐵𝐵𝐴. . . 𝐵𝐴𝐵. The same STM needle can subsequently read the recorded information, as 𝐴 and 𝐵 would produce different electric signals when the strand passes under the needle. The macromolecule now represents a data block to be stored in a "parking lot" within the sugar cube, and later brought to a read station on demand. Millions of parking spots and thousands of Read/Write stations may be integrated within the micro-fabricated sugar cube, thus providing access to petabytes of user-data in a scheme that benefits from the massive parallelism of thousands of Read/Write stations within the same three-dimensionally micro-structured device.

  20. Flow-induced structured phase in nonionic micellar solutions.

    PubMed

    Cardiel, Joshua J; Tonggu, Lige; de la Iglesia, Pablo; Zhao, Ya; Pozzo, Danilo C; Wang, Liguo; Shen, Amy Q

    2013-12-17

    In this work, we consider the flow of a nonionic micellar solution (precursor) through an array of microposts, with focus on its microstructural and rheological evolution. The precursor contains polyoxyethylene(20) sorbitan monooleate (Tween-80) and cosurfactant monolaurin (ML). An irreversible flow-induced structured phase (NI-FISP) emerges after the nonionic precursor flows through the hexagonal micropost arrays, when subjected to strain rates ~10(4) s(-1) and strain ~10(3). NI-FISP consists of close-looped micellar bundles and multiconnected micellar networks as evidenced by transmission electron microscopy (TEM) and cryo-electron microscopy (cryo-EM). We also conduct small-angle neutron scattering (SANS) measurements in both precursor and NI-FISP to illustrate the structural transition. We propose a potential mechanism for the NI-FISP formation that relies on the micropost arrays and the flow kinematics in the microdevice to induce entropic fluctuations in the micellar solution. Finally, we show that the rheological variation from a viscous precursor solution to a viscoelastic micellar structured phase is associated with the structural evolution from the precursor to NI-FISP. PMID:24274648

  1. Travelling Wave Solutions in Multigroup Age-Structured Epidemic Models

    NASA Astrophysics Data System (ADS)

    Ducrot, Arnaut; Magal, Pierre; Ruan, Shigui

    2010-01-01

    Age-structured epidemic models have been used to describe either the age of individuals or the age of infection of certain diseases and to determine how these characteristics affect the outcomes and consequences of epidemiological processes. Most results on age-structured epidemic models focus on the existence, uniqueness, and convergence to disease equilibria of solutions. In this paper we investigate the existence of travelling wave solutions in a deterministic age-structured model describing the circulation of a disease within a population of multigroups. Individuals of each group are able to move with a random walk which is modelled by the classical Fickian diffusion and are classified into two subclasses, susceptible and infective. A susceptible individual in a given group can be crisscross infected by direct contact with infective individuals of possibly any group. This process of transmission can depend upon the age of the disease of infected individuals. The goal of this paper is to provide sufficient conditions that ensure the existence of travelling wave solutions for the age-structured epidemic model. The case of two population groups is numerically investigated which applies to the crisscross transmission of feline immunodeficiency virus (FIV) and some sexual transmission diseases.

  2. Development of macromolecular prodrug for rheumatoid arthritis.

    PubMed

    Yuan, Fang; Quan, Ling-dong; Cui, Liao; Goldring, Steven R; Wang, Dong

    2012-09-01

    Rheumatoid arthritis (RA) is a chronic autoimmune disease that is considered to be one of the major public health problems worldwide. The development of therapies that target tumor necrosis factor-? (TNF-?), interleukin-6 (IL-6) and co-stimulatory pathways that regulate the immune system have revolutionized the care of patients with RA. Despite these advances, many patients continue to experience symptomatic and functional impairment. To address this issue, more recent therapies that have been developed are designed to target intracellular signaling pathways involved in immunoregulation. Though this approach has been encouraging, there have been major challenges with respect to off-target organ side effects and systemic toxicities related to the widespread distribution of these signaling pathways in multiple cell types and tissues. These limitations have led to an increasing interest in the development of strategies for the macromolecularization of anti-rheumatic drugs, which could target them to the inflamed joints. This approach enhances the efficacy of the therapeutic agent with respect to synovial inflammation, while markedly reducing non-target organ adverse side effects. In this manuscript, we provide a comprehensive overview of the rational design and optimization of macromolecular prodrugs for treatment of RA. The superior and the sustained efficacy of the prodrug may be partially attributed to their Extravasation through Leaky Vasculature and subsequent Inflammatory cell-mediated Sequestration (ELVIS) in the arthritic joints. This biologic process provides a plausible mechanism, by which macromolecular prodrugs preferentially target arthritic joints and illustrates the potential benefits of applying this therapeutic strategy to the treatment of other inflammatory diseases. PMID:22433784

  3. Synthesis and characterization of macromolecular rhodamine tethers and their interactions with P-glycoprotein.

    PubMed

    Crawford, Lindsey; Putnam, David

    2014-08-20

    Rhodamine dyes are well-known P-glycoprotein (P-gp) substrates that have played an important role in the detection of inhibitors and other substrates of P-gp, as well as in the understanding of P-gp function. Macromolecular conjugates of rhodamines could prove useful as tethers for further probing of P-gp structure and function. Two macromolecular derivatives of rhodamine, methoxypolyethylene glycol-rhodamine6G and methoxypolyethylene glycol-rhodamine123, were synthesized through the 2'-position of rhodamine6G and rhodamine123, thoroughly characterized, and then evaluated by inhibition with verapamil for their ability to interact with P-gp and to act as efflux substrates. To put the results into context, the P-gp interactions of the new conjugates were compared to the commercially available methoxypolyethylene glycol-rhodamineB. FACS analysis confirmed that macromolecular tethers of rhodamine6G, rhodamine123, and rhodamineB were accumulated in P-gp expressing cells 5.2 ± 0.3%, 26.2 ± 4%, and 64.2 ± 6%, respectively, compared to a sensitive cell line that does not overexpress P-gp. Along with confocal imaging, the efflux analysis confirmed that the macromolecular rhodamine tethers remain P-gp substrates. These results open potential avenues for new ways to probe the function of P-gp both in vitro and in vivo. PMID:25050613

  4. Polydisulfide Gd(III) chelates as biodegradable macromolecular magnetic resonance imaging contrast agents

    PubMed Central

    Lu, Zheng-Rong; Mohs, Aaron M; Zong, Yuda; Feng, Yi

    2006-01-01

    Macromolecular gadolinium (Gd)(III) complexes have a prolonged blood circulation time and can preferentially accumulate in solid tumors, depending on the tumor blood vessel hyperpermeability, resulting in superior contrast enhancement in magnetic resonance (MR) cardiovascular imaging and cancer imaging as shown in animal models. Unfortunately, safety concerns related to these agents’ slow elimination from the body impede their clinical development. Polydisulfide Gd(III) complexes have been designed and developed as biodegradable macromolecular magnetic resonance imaging (MRI) contrast agents to facilitate the clearance of Gd(III) complexes from the body after MRI examinations. These novel agents can act as macromolecular contrast agents for in vivo imaging and excrete rapidly as low-molecular-weight agents. The rationale and recent development of the novel biodegradable contrast agents are reviewed here. Polydisulfide Gd(III) complexes have relatively long blood circulation time and gradually degrade into small Gd(III) complexes, which are rapidly excreted via renal filtration. These agents result in effective and prolonged in vivo contrast enhancement in the blood pool and tumor tissue in animal models, yet demonstrate minimal Gd(III) tissue retention as the clinically used low-molecular-weight agents. Structural modification of the agents can readily alter the contrast-enhancement kinetics. Polydisulfide Gd(III) complexes are promising for further clinical development as safe, effective, biodegradable macromolecular MRI contrast agents for cardiovascular and cancer imaging, and for evaluation of therapeutic response. PMID:17722260

  5. Revealing the macromolecular targets of complex natural products

    NASA Astrophysics Data System (ADS)

    Reker, Daniel; Perna, Anna M.; Rodrigues, Tiago; Schneider, Petra; Reutlinger, Michael; Mönch, Bettina; Koeberle, Andreas; Lamers, Christina; Gabler, Matthias; Steinmetz, Heinrich; Müller, Rolf; Schubert-Zsilavecz, Manfred; Werz, Oliver; Schneider, Gisbert

    2014-12-01

    Natural products have long been a source of useful biological activity for the development of new drugs. Their macromolecular targets are, however, largely unknown, which hampers rational drug design and optimization. Here we present the development and experimental validation of a computational method for the discovery of such targets. The technique does not require three-dimensional target models and may be applied to structurally complex natural products. The algorithm dissects the natural products into fragments and infers potential pharmacological targets by comparing the fragments to synthetic reference drugs with known targets. We demonstrate that this approach results in confident predictions. In a prospective validation, we show that fragments of the potent antitumour agent archazolid A, a macrolide from the myxobacterium Archangium gephyra, contain relevant information regarding its polypharmacology. Biochemical and biophysical evaluation confirmed the predictions. The results obtained corroborate the practical applicability of the computational approach to natural product ‘de-orphaning’.

  6. Large-volume protein crystal growth for neutron macromolecular crystallography.

    PubMed

    Ng, Joseph D; Baird, James K; Coates, Leighton; Garcia-Ruiz, Juan M; Hodge, Teresa A; Huang, Sijay

    2015-04-01

    Neutron macromolecular crystallography (NMC) is the prevailing method for the accurate determination of the positions of H atoms in macromolecules. As neutron sources are becoming more available to general users, finding means to optimize the growth of protein crystals to sizes suitable for NMC is extremely important. Historically, much has been learned about growing crystals for X-ray diffraction. However, owing to new-generation synchrotron X-ray facilities and sensitive detectors, protein crystal sizes as small as in the nano-range have become adequate for structure determination, lessening the necessity to grow large crystals. Here, some of the approaches, techniques and considerations for the growth of crystals to significant dimensions that are now relevant to NMC are revisited. These include experimental strategies utilizing solubility diagrams, ripening effects, classical crystallization techniques, microgravity and theoretical considerations. PMID:25849493

  7. Effects of macromolecular crowding on protein folding

    NASA Astrophysics Data System (ADS)

    Phuong Thuy, Bui; Thi Thu Huong, Hoang; Hoang, Trinh X.

    2015-06-01

    Folding of proteins in vivo is influenced by the presence of a high concentration of macromolecules in the cytosol. In this study we investigate the effects of macromolecular crowding on folding of proteins by using molecular dynamics simulation method with Langevin equations. The protein is considered in a Go-like model whereas crowders are modeled as soft spheres. In our simulations, protein and crowders are enclosed in a spherical container. It is shown that the crowders enhance the folding transition temperature as well as folding stability of protein. The effect of crowders on the folding free energy is found to agree with Minton's scaled particle theory.

  8. Crambin: a direct solution for a 400-atom structure.

    PubMed

    Weeks, C M; Hauptman, H A; Smith, G D; Blessing, R H; Teeter, M M; Miller R

    1995-01-01

    The crystal structure of crambin, a 46-residue protein containing the equivalent of approximately 400 fully occupied non-H-atom positions, was originally solved at 1.5 A by exploiting the anomalous scattering of its six S atoms at a single wavelength far removed from the absorption edge of sulfur. The crambin structure has now been resolved without the use of any anomalous-dispersion measurements. The technique employed was an ab initio 'shake-and-bake' method, consisting of a phase-refinement procedure based on the minimal function alternated with Fourier refinement. This method has successfully yielded solutions for a smaller molecule (28 atoms) using 1.2 A data, and a crambin solution was obtained at 1.1 A. PMID:15299333

  9. The Korteweg-de Vries hierarchy: structure and solution

    Microsoft Academic Search

    Subhendu Chakrabarti; J. Pal; J. Shamanna; B. Talukdar

    2002-01-01

    We attempt to realize the structure of the Korteweg-de Vries (KdV) hierarchy by using a simple dimensional analysis. The specific\\u000a results presented refer to equations of the hierarchy and conserved Hamiltonian densities associated with them. Based on the\\u000a Gel’fand-Levitan-Marchenko equation we construct a series expansion for the unstable solution of the KdV-like equations by\\u000a using the continuous part of the

  10. Structure and Flexibility of Individual Immunoglobulin G Molecules in Solution

    Microsoft Academic Search

    Sara Sandin; Lars-Göran Öfverstedt; Ann-Charlotte Wikström; Örjan Wrange; Ulf Skoglund

    2004-01-01

    In contrast to averaging methods of determining structure, such as X-ray diffraction, NMR, and single-particle tomography, cryo-electron tomography allows three-dimensional imaging of an individual object in solution. The method has previously been used to study cells and very large macromolecules. We have used cryo-electron tomography to analyze a monoclonal IgG, with a molecular weight of only 150 kDa. Tomograms reveal

  11. Light scattering measurements supporting helical structures for chromatin in solution.

    PubMed

    Campbell, A M; Cotter, R I; Pardon, J F

    1978-05-01

    Laser light scattering measurements have been made on a series of polynucleosomes containing from 50 to 150 nucleosomes. Radii of gyration have been determined as a function of polynucleosome length for different ionic strength solutions. The results suggest that at low ionic strength the chromatin adopts a loosely helical structure rather than a random coil. The helix becomes more regular on increasing the ionic strength, the dimension resembling those proposed by Finch and Klug for their solenoid model. PMID:662693

  12. Parameter degeneracy in neutrino oscillation — Solution network and structural overview

    NASA Astrophysics Data System (ADS)

    Minakata, Hisakazu; Uchinami, Shoichi

    2010-04-01

    It is known that there is a phenomenon called “parameter degeneracy” in neutrino oscillation measurement of lepton mixing parameters; A set of the oscillation probabilities, e.g., P( ? ? ? ? e ) and its CP-conjugate Pleft( {{{bar ? }_? } to {{bar ? }_e}} right) at a particular neutrino energy does not determine uniquely the values of ? 13 and ?. With use of the approximate form of the oscillation probability á la Cervera et al., a complete analysis of the eightfold parameter degeneracy is presented. We propose a unified view of the various types of the degeneracy as invariance of the oscillation probabilities under discrete mappings of the mixing parameters. Explicit form of the mapping is obtained either by symmetry argument, or by deriving exact analytic expressions of all the degeneracy solutions for a given true solution. Due to the one-to-one mapping structure the degeneracy solutions are shown to form a network. We extend our analysis into the parameter degeneracy in T- and CPT-conjugate measurement as well as to the setup with the golden and the silver channels, P( ? e ? ? ? ) and P( ? e ? ? ? ). Some characteristic features of the degeneracy solutions in CP-conjugate measurement, in particular their energy dependences, are illuminated by utilizing the explicit analytic solutions.

  13. Macromolecular Chemistry and Physics August 25 29 2014

    E-print Network

    Schubart, Christoph

    Macromolecular Chemistry and Physics August 25 ­ 29 2014 D. Richter, J. Allgaier, R. Biehl, W a bi- annual one week block course, "Macromolecular Physics and Chemistry" within the Helmholtz is open to students of Chemistry and Physics after Vordiplom, BSc or comparable level. Please send your

  14. Structure of polymer layers adsorbed from concentrated solutions

    NASA Astrophysics Data System (ADS)

    Auvray, Loïc; Auroy, Philippe; Cruz, Margarida

    1992-06-01

    We study by neutron scattering the interfacial strucuture of poly(dimethylsiloxane) layers irreversibly adsorbed from concentrated solutions or melts. We first measure the thickness h of the layers swollen by a good solvent as a function of the chain polymerisation index N and of the polymer volume fraction in the initial solution ?. The relation h ? N^{0.8}?^{0.3}, recently predicted from an analogy between irreversibly adsorbed layers and grafted polymer brushes, describes well our results. We can therefore deduce that there is at least one large loop of about N monomers per adsorbed chain. We also study the shape of the polymer concentration profile in the layers by measuring on two samples the polymer-solid partial structure factor, that is proportional to the Fourier transform of the profile. The model of pseudobrushes predicts a concentration decay varying with the distance of the wall z as z^{-2/5}. This power law profile accounts quantitatively for the angular variation of the polymer-solid cross structure factor but it is difficult to distinguish it without anbiguity from less singular profiles. It implies that the adsorption of PDMS onto silica is sufficiently strong and fast to quench completely the loop distribution in the initial layer. Nous étudions par diffusion de neutrons la structure interfaciale de couches de poly(diméthylsiloxane) irréversiblement adsorbées sur de la silice à partir de solutions semidiluées et de fondus. Nous mesurons d'abord l'épaisseur h des couches gonflées par un bon solvant en fonction du degré de polymérisation des chaînes N et de la fraction volumique dans la solution initiale ?. La relation h? N^{0.8}?^{0.3} récemment prédite à partir de l'analogie entre couches irréversiblement adsorbées et brosses de polymères greffés décrit bien nos résultats. Nous en déduisons qu'il existe au moins une grande boucle d'environ N monomères par chaîne adsorbée. Nous étudions aussi la forme du profil de concentration en polymère près de la paroi en mesurant sur deux échantillons le facteur de structure partiel polymère-solide qui est proportionnel à la transformée de Fourier du profil. Le modèle de pseudo-brosse prévoit une décroissance de la concentration avec la distance à la paroi z en z^{-2/5}. Ce profil en loi de puissance rend quantitativement compte de la dépendance angulaire du facteur de structure croisé polymère-solide, mais il est difficile de le distinguer sans ambiguïté de profils moins singuliers. Il implique que l'adsorption du PDMS sur la silice est suffisamment forte et rapide pour geler complètement la structure des boucles dans la couche adsorbée initiale.

  15. Gelation and micelle structure changes of aqueous polymer solutions

    NASA Astrophysics Data System (ADS)

    Guo, Liang

    Two topics of aqueous polymer solutions are covered in this thesis. The first addresses gelation kinetics and dynamics of aqueous gelatin solutions. The second deals with micelle structure changes in aqueous nonionic surfactant mixtures. Triple helix reversion kinetics of aqueous gelatin solutions is studied with optical rotation. A combination of first- and second-order concentration dependence of the reversion rate is observed and, based on this observation, a new two-step mechanism of helix formation distinct from the Flory and Weaver theory is proposed. The rate limiting step is formation of a two-stranded nucleus, either intramolecular (first-order) or intermolecular (second-order). The triple helix is formed by subsequent wrapping of a third strand onto the nucleus. Gelation dynamics of gelatin solutions is monitored with optical rotation and rheology. Viscosity data below the gel point are used to evaluate the gel point and the viscosity exponent, assuming dynamic scaling theory applies. Shear modulus data above the gel point are used to determine the dynamic scaling modulus exponent. As observed in the time-dependent optical rotation, an initial rapid growth region where new helices are formed is followed by a slower growth region involving helix lengthening. The viscosity and modulus exponents depend on concentration, but not on temperature for cases where the gel point occurs before the helix reversion slows down appreciably. However, anomalous exponents are measured at higher temperatures, where the helix reversion slows down appreciably before the gel point is reached. The observed concentration dependences of the dynamic scaling exponents are discussed in terms of chain overlap and entanglement. The structure of nonionic surfactant mixtures in water are probed by rheology and small-angle neutron scattering. Small amounts of a C14 diol (SurfynolRTM 104) cause enormous structural and rheological changes when added to aqueous solutions of an ethylene oxide-propylene oxide-ethylene oxide triblock copolymer (PluronicRTM P105). The hydrophobic diol incorporates into the existing copolymer micelles and causes a cascade of changes in micelle structure, with resultant changes in rheology. Particularly striking is the spherical to wormlike micelle transition, where the viscosity changes by a factor of more than 104.

  16. Nanoscale structure and dynamics of colloid-semiflexible polymer solutions

    NASA Astrophysics Data System (ADS)

    Huh, Ji Yeon; Furst, Eric M.

    2006-03-01

    Interactions and structure in colloid-polymer solutions control the phase behavior, viscoelasticity, stability, and vitrification, which play significant roles in many industrial applications. Filled semiflexible networks demonstrate distinctive rheological properties due to their large persistence length. They are important in many biological and surfactant systems, and display additional complexity because of the alignment and isotropic-nematic transition. In this work, we report diffusing wave spectroscopy studies of the dynamics of colloidal particles suspended in F-actin solutions in time scales 10-6solutions in the dilute limit^[1]. However, we find discrepancies in the entangled limit which may indicate the difference between local and bulk properties. Using a shell model for the local viscoelastic response^[2], we find that the response is consistent with a depletion-like structure surrounding the embedded colloidal particles^[3]. [1]Shankar et al., J. Rheol. 46, 1111 (2002) [2]A. Levine and T. Lubensky, Phys. Rev. E 63, 041510 (2001) [3]Y. L. Chen and K. S. Schweizer, J. Phys. Chem. B 108, 6687 (2004)

  17. Progress in rational methods of cryoprotection in macromolecular crystallography

    PubMed Central

    Alcorn, Thomas; Juers, Douglas H.

    2010-01-01

    Cryogenic cooling of macromolecular crystals is commonly used for X-ray data collection both to reduce crystal damage from radiation and to gather functional information by cryogenically trapping intermediates. However, the cooling process can damage the crystals. Limiting cooling-induced crystal damage often requires cryoprotection strategies, which can involve substantial screening of solution conditions and cooling protocols. Here, recent developments directed towards rational methods for cryoprotection are described. Crystal damage is described in the context of the temperature response of the crystal as a thermodynamic system. As such, the internal and external parts of the crystal typically have different cryoprotection requirements. A key physical parameter, the thermal contraction, of 26 different cryoprotective solutions was measured between 294 and 72?K. The range of contractions was 2–13%, with the more polar cryosolutions contracting less. The potential uses of these results in the development of cryocooling conditions, as well as recent developments in determining minimum cryosolution soaking times, are discussed. PMID:20382989

  18. The spliceosome: a flexible, reversible macromolecular machine

    PubMed Central

    Hoskins, Aaron A.; Moore, Melissa J.

    2012-01-01

    With more than a hundred individual RNA and protein parts and a highly dynamic assembly and disassembly pathway, the spliceosome is arguably the most complicated macromolecular machine in the eukaryotic cell. This complexity has made kinetic and mechanistic analysis of splicing incredibly challenging. Yet recent technological advances are now providing tools for understanding this process in much greater detail. Ranging from genome-wide analyses of splicing and creation of an orthogonal spliceosome in vivo, to purification of active spliceosomes and observation of single molecules in vitro, such new experimental approaches are yielding significant insight into the inner workings of this remarkable machine. These experiments are rewriting the textbooks, with a new picture emerging of a dynamic, malleable machine heavily influenced by the identity of its pre-mRNA substrate. PMID:22480731

  19. Nitric Oxide Release Part I. Macromolecular Scaffolds

    PubMed Central

    Riccio, Daniel A.; Schoenfisch, Mark H.

    2012-01-01

    Summary The roles of nitric oxide (NO) in physiology and pathophysiology merit the use of NO as a therapeutic for certain biomedical applications. Unfortunately, limited NO payloads, too rapid NO release, and the lack of targeted NO delivery have hindered the clinical utility of NO gas and low molecular weight NO donor compounds. A wide-variety of NO-releasing macromolecular scaffolds has thus been developed to improve NO’s pharmacological potential. In this tutorial review, we provide an overview of the most promising NO release scaffolds including protein, organic, inorganic, and hybrid organic-inorganic systems. The NO release vehicles selected for discussion were chosen based on their enhanced NO storage, tunable NO release characteristics, and potential as therapeutics. PMID:22362355

  20. The structure of the chromatin core particle in solution.

    PubMed Central

    Pardon, J F; Worcester, D L; Wooley, J C; Cotter, R I; Lilley, D M; Richards, R M

    1977-01-01

    The shape and size of the nucleosomal core particle from chromatin has been examined by analysis of neutron and X-ray scattering data from dilute solutions. Calculations of scattering for many different models have been made and only one model was able to account for both the X-ray and neutron profiles. This model is an oblate structure with height about 50A and diameter 110A. The DNA is mainly confined to two annuli located at the top and bottom respectively of the core particle positioned on the outside of a compact protein core which has a height of about 40A and diameter about 73A. PMID:561952

  1. The effectively specific recognition of bovine serum albumin imprinted silica nanoparticles by utilizing a macromolecularly functional monomer to stabilize and imprint template.

    PubMed

    Qian, Liwei; Hu, Xiaoling; Guan, Ping; Wang, Dan; Li, Ji; Du, Chunbao; Song, Renyuan; Wang, Chaoli; Song, Wenqi

    2015-07-16

    Structural stability of the template is one of the most important considerations during the preparation of protein imprinting technology. To address this limitation, we propose a novel and versatile strategy of utilizing macromolecularly functional monomers to imprint biomacromolecules. Results from circular dichroism and synchronous fluorescence experiments reflect the macromolecularly functional monomers tendency to interact with the protein surface instead of permeating it and destroying the hydrogen bonds that maintain the protein's structural stability, therefore stabilizing the template protein structure during the preparation of imprinted polymers. The imprinted polymers composed of macromolecularly functional monomers or their equivalent micromolecularly functional monomers over silica nanoparticles were characterized and carried out in batch rebinding test and competitive adsorption experiments. In batch rebinding test, the imprinted particles prepared with macromolecularly functional monomers exhibited an imprinting factor of 5.8 compared to those prepared by micromolecularly functional monomers with the imprinting factor of 3.4. The selective and competitive adsorption experiments also demonstrated the imprinted particles made by macromolecularly functional monomers possessed much better selectivity and specific recognition ability for template protein. Therefore, using macromolecularly functional monomers to imprint may overcome the mutability of biomacromolecule typically observed during the preparation of imprinted polymers, and thus promote the further development of imprinting technology. PMID:26073815

  2. Solution to certain problems in the failure of composite structures

    NASA Astrophysics Data System (ADS)

    Goodsell, Johnathan

    The present work contains the solution of two problems in composite structures. In the first, an approximate elasticity solution for prediction of the displacement, stress and strain fields within the m-layer, symmetric and balanced angle-ply composite laminate of finite-width subjected anticlastic bending deformation is developed. The solution is shown to recover classical laminated plate theory predictions at interior regions of the laminate and thereby illustrates the boundary layer character of this interlaminar phenomenon. The results exhibit the anticipated response in congruence with the solutions for uniform axial extension and uniform temperature change, where divergence of the interlaminar shearing stress is seen to occur at the intersection of the free-edge and planes between lamina of +theta and -theta orientation. The analytical results show excellent agreement with the finite-element predictions for the same boundary-value problem and thereby provide an efficient and compact solution available for parametric studies of the influence of geometry and material properties. The solution is combined with previously developed solutions for uniform axial extension and uniform temperature change of the identical laminate and the combined solution is exercised to compare the relative magnitudes of free-edge phenomenon arising from the different loading conditions, to study very thick laminates and laminates where the laminate width is less than the laminate thickness. Significantly, it was demonstrated that the solution is valid for arbitrary stacking sequence and the solution was exercised to examine antisymmetric and non-symmetric laminates. Finally, the solution was exercised to determine the dimensions of the boundary layer for very large numbers of layers. It was found that the dimension of the boundary layer width in bending is approximately twice that in uniform axial extension and uniform temperature change. In the second, the intrinsic flaw concept is extended to the determination of the intrinsic flaw length and the prediction of performance variability in the 10-degree off-axis specimen. The intrinsic flaw is defined as a fracture mechanics-type, through-thickness planar crack extending in the fiber direction from the failure initiation site of length, a. The distribution of intrinsic flaw lengths is postulated from multiple tests of 10-degree off-axis specimens by calculating the length of flaw that would cause fracture at each measured failure site and failure load given the fracture toughness of the material. The intrinsic flaw lengths on the homogeneous and micromechanical scales for unnotched (no hole) and specimens containing a centrally-located, through-thickness circular hole are compared. 8 hole-diameters ranging from 1.00--12.7 mm are considered. On the micromechanical scale, the intrinsic flaw ranges between approximately 10 and 100 microns in length, on the order of the relevant microstructural dimensions. The intrinsic flaw lengths on the homogeneous scale are determined to be an order of magnitude greater than that on the micromechanical scale. The effect of variation in the fiber volume fraction on the intrinsic flaw length is also considered. In the strength predictions for the specimens, the intrinsic flaw crack geometry and probability density function of intrinsic flaw lengths calculated from the unnotched specimens allow fracture mechanics predictions of strength variability. The strength prediction is dependent on the flaw density, the number of flaws per unit length along the free-edge. The flaw density is established by matching the predicted strength with the experimental strength. The distribution of intrinsic flaw lengths is used with the strength variability of the unnotched and of open-hole specimens to determine the flaw density at each hole-size. The flaw density is shown to be related to the fabrication machining speed suggesting machining damage as a mechanism for the hole-size dependence of the flaw density. (Abstract shortened by UMI.)

  3. Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7

    PubMed Central

    Langer, Gerrit G; Cohen, Serge X; Lamzin, Victor S; Perrakis, Anastassis

    2008-01-01

    ARP/wARP is a software suite to build macromolecular models in X-ray crystallography electron density maps. Structural genomics initiatives and the study of complex macromolecular assemblies and membrane proteins all rely on advanced methods for 3D structure determination. ARP/wARP meets these needs by providing the tools to obtain a macromolecular model automatically, with a reproducible computational procedure. ARP/wARP 7.0 tackles several tasks: iterative protein model building including a high-level decision-making control module; fast construction of the secondary structure of a protein; building flexible loops in alternate conformations; fully automated placement of ligands, including a choice of the best fitting ligand from a “cocktail”; and finding ordered water molecules. All protocols are easy to handle by a non-expert user through a graphical user interface or a command line. The time required is typically a few minutes although iterative model building may take a few hours. PMID:18600222

  4. Structure and dynamics of of solution polymerized polyureas

    NASA Astrophysics Data System (ADS)

    Choi, Taeyi; Jeong, Youmi; Runt, James

    2011-03-01

    Polyureas consisting of alternating soft and hard (urea containing) segments exhibit physical properties that are closely related to their microphase separated structure, which consist of rigid (high Tg and sometimes crystalline) hard domains embedded in a matrix dominated by flexible polyether segments. Polyurea properties can be controlled over a rather broad range by varying the chemical structures, molecular weight of the components, and reaction stoichiometry. In the present study, we focus primarily on linear polyureas synthesized using methylene diphenyl diisocyanate and polytetramethylene oxide-di-p-aminobenzoate using a solution polymerization method. Soft segment (diamine) molecular weights were varied from 460 to 860 to 1200 g/mol and characterize their morphology, hydrogen bonding, mechanical behavior and dielectric properties upon varying molecular weight of diamines. This presentation will focus on our latest findings, particularly details of the microphase separated morphology and molecular dynamics as measured using dielectric relaxation spectroscopy This work is supported by Office of Naval Research.

  5. Solution and structure of an alternating D,L-peptide.

    PubMed

    Alexopoulos, Eftichia; Küsel, Andrea; Sheldrick, George M; Diederichsen, Ulf; Usón, Isabel

    2004-11-01

    The crystal structure of H-(L-Tyr-D-Tyr)(4)-L-Lys-OH has been determined to 1.3 A resolution. The D,L-alternating peptide crystallizes in the tetragonal system, space group P4(3)2(1)2, with unit-cell parameters a = b = 27.99 (3), c = 78.93 (8) A. The crystals contain two molecules in the asymmetric unit that form a double-stranded right-handed antiparallel beta-helix. The structure has been solved by SIRAS using a crystal soaked in an iodide-containing solution for 1 min. The programs SHELXD and SHELXE were used to determine the iodide substructure and also the experimental electron-density map. Using the coordinates of known D,L-peptides deposited in the PDB, several attempts were made to solve the structure by molecular-replacement techniques. Although the backbone of the MR model selected shows great similarity and was used to trace the actual peptide structure in the map, it was not possible to obtain the correct solution before the experimental phases became available. The correct fragment orientations are easily determined, but the same does not apply to the translation search. Nevertheless, insights into fragment search and expansion were gained from the tests described in this paper. The correlation coefficient calculated with the resolution shell of data around 2.4 A, a distance corresponding to most 1-3 interatomic vectors, is a particularly good discriminator of correct orientations in the rotation search of small fragments. PMID:15502304

  6. The solution structure of apo-iron regulatory protein 1.

    PubMed

    Shand, O'Neil; Volz, Karl

    2013-07-25

    Iron is a cofactor for many proteins that are involved in essential metabolic processes. However, iron must be strictly regulated because it can react with oxygen to generate cytotoxic reactive oxygen intermediates. Iron regulatory protein 1 (IRP1) is a bi-functional protein that can act either as a post-transcriptional regulator of mRNAs containing iron responsive elements, or as a [4Fe-4S] cluster-containing cytosolic aconitase. Previous X-ray crystallography results show that IRP1 is in an open L-shape conformation when bound to IRE-RNAs, and in a globular conformation when it binds an iron-sulfur cluster. The structure of apo-IRP1 and the mechanism by which it transforms to either functional state is unknown. Therefore, small angle X-ray scattering was used to determine the low resolution solution structure of apo-IRP1 and to characterize its biophysical properties. These results show that apo-IRP1 has a radius of gyration (Rg) of 33.6±0.3Å, and a Dmax of 118±2Å. The ab initio and rigid-body modeling results show that apo-IRP1 is in an open conformation in solution, and the ensemble optimization results show that the molecules stay narrowly distributed about a Rg of 33-34Å. The open apo-IRP1 conformation seems optimal for subsequent conversion to either functional end state: RNA-binding, or cytosolic aconitase. PMID:23590984

  7. Solution structure of the HU protein from Bacillus stearothermophilus.

    PubMed

    Vis, H; Mariani, M; Vorgias, C E; Wilson, K S; Kaptein, R; Boelens, R

    1995-12-01

    The histone-like protein HU from Bacillus stearothermophilus is a dimer with a molecular mass of 19.5 kDa that is capable of bending DNA. An X-ray structure has been determined, but no structure could be established for a large part of the supposed DNA-binding beta-arms. Using distance and dihedral constraints derived from triple-resonance NMR data of a 13C/15N doubly-labelled HU protein 49 distance geometry structures were calculated, which were refined by means of restrained Molecular Dynamics. From this set a total of 25 refined structures were selected having low constraint energy and few constraint violations. The ensemble of 25 structures display a root-mea-square co-ordinate deviation of 0.36 A with respect to the average structure, calculated over the backbone heavy atoms of residues 2 to 54 and 75 to 90 (and residues 2' to 54' and 75' to 90' of the second monomer). The structure of the core is very similar to that observed in the X-ray structure, with a pairwise r.m.s.d. of 1.06 A. The structure of the beta-hairpin arm contains a double flip-over at the prolines in the two strands of the beta-arm. Strong 15N-NH heteronuclear nuclear Overhauser effects indicate that the beta-arm and especially the tip is flexible. This explains the disorder observed in the solution and X-ray structures of the beta-arm, in respect of the core of the protein. Overlayed onto itself the beta-arm is better defined, with an r.m.s.d. of 1.0 A calculated over the backbone heavy atoms of residues 54 to 59 and 69 to 74. The tip of the arm adopts a well-defined 4:6 beta-hairpin conformation similar to the iron co-ordinating beta-arms of rubredoxin. PMID:7500343

  8. Dilute-solution Structure of Charged Arborescent Graft Polymer

    SciTech Connect

    Yun, Seok [University of Maryland; Briber, R M [University of Maryland; Kee, R. Andrew [University of Waterloo, Canada; Gauthier, Mario [University of Waterloo, Canada

    2006-01-01

    The solutions of charged G1 arborescent polystyrene-graft-poly(2-vinylpyridine) copolymers in methanol-d4 and D{sub 2}O were investigated over a dilute concentration range {phi} = 0.005-0.05 ({phi}: mass fraction) using small-angle neutron scattering (SANS). Upon addition of acid (HCl) arborescent graft polymers became charged and a peak appeared in SANS data. The interparticle distance (d{sub exp}) calculated from a peak position corresponded to the expected value (d{sub uni}) for a uniform particle distribution. This indicates the formation of liquid-like ordering due to long-range Coulombic repulsions. The smaller dielectric constant of methanol-d4 resulted in long-range electrostatic repulsions persisting to lower polymer concentration than in D{sub 2}O. The slow mode scattering was observed by dynamic light scattering measurements for the same polymer solutions, indicating the presence of structural inhomogeneity in the solutions. Both the peak and slow mode disappeared by addition of NaCl or excess HCl into the solutions due to the screening of electrostatic interactions. The G1 polymer grafted with longer P2VP chains (M{sub w} {approx} 30,000 versus 5000 g mol) formed a gel on addition of HCl. This result reveals that molecular expansion is more significant for arborescent polymers with longer (M{sub w} {approx} 30,000) linear polyelectrolyte branches, resulting in gelation for {phi} > 0.01. Upon addition of NaCl or excess HCl a gel transformed back to a liquid resulted from the screening of electrostatic interactions.

  9. webSDA: a web server to simulate macromolecular diffusional association.

    PubMed

    Yu, Xiaofeng; Martinez, Michael; Gable, Annika L; Fuller, Jonathan C; Bruce, Neil J; Richter, Stefan; Wade, Rebecca C

    2015-07-01

    Macromolecular interactions play a crucial role in biological systems. Simulation of diffusional association (SDA) is a software for carrying out Brownian dynamics simulations that can be used to study the interactions between two or more biological macromolecules. webSDA allows users to run Brownian dynamics simulations with SDA to study bimolecular association and encounter complex formation, to compute association rate constants, and to investigate macromolecular crowding using atomically detailed macromolecular structures. webSDA facilitates and automates the use of the SDA software, and offers user-friendly visualization of results. webSDA currently has three modules: 'SDA docking' to generate structures of the diffusional encounter complexes of two macromolecules, 'SDA association' to calculate bimolecular diffusional association rate constants, and 'SDA multiple molecules' to simulate the diffusive motion of hundreds of macromolecules. webSDA is freely available to all users and there is no login requirement. webSDA is available at http://mcm.h-its.org/webSDA/. PMID:25883142

  10. webSDA: a web server to simulate macromolecular diffusional association

    PubMed Central

    Yu, Xiaofeng; Martinez, Michael; Gable, Annika L.; Fuller, Jonathan C.; Bruce, Neil J.; Richter, Stefan; Wade, Rebecca C.

    2015-01-01

    Macromolecular interactions play a crucial role in biological systems. Simulation of diffusional association (SDA) is a software for carrying out Brownian dynamics simulations that can be used to study the interactions between two or more biological macromolecules. webSDA allows users to run Brownian dynamics simulations with SDA to study bimolecular association and encounter complex formation, to compute association rate constants, and to investigate macromolecular crowding using atomically detailed macromolecular structures. webSDA facilitates and automates the use of the SDA software, and offers user-friendly visualization of results. webSDA currently has three modules: ‘SDA docking’ to generate structures of the diffusional encounter complexes of two macromolecules, ‘SDA association’ to calculate bimolecular diffusional association rate constants, and ‘SDA multiple molecules’ to simulate the diffusive motion of hundreds of macromolecules. webSDA is freely available to all users and there is no login requirement. webSDA is available at http://mcm.h-its.org/webSDA/. PMID:25883142

  11. Monomeric Solution Structure of the Prototypical ‘C’ Chemokine Lymphotactin†,‡

    PubMed Central

    Kulo?lu, E. Sonay; McCaslin, Darrell R.; Kitabwalla, Moiz; Pauza, C. David; Markley, John L.; Volkman, Brian F.

    2013-01-01

    Lymphotactin, the sole identified member of the C class of chemokines, specifically attracts T lymphocytes and natural killer cells. This 93-residue protein lacks 2 of the 4 conserved cysteine residues characteristic of the other 3 classes of chemokines and possesses an extended carboxyl terminus, which is required for chemotactic activity. We have determined the three-dimensional solution structure of recombinant human lymphotactin by NMR spectroscopy. Under the conditions used for the structure determination, lymphotactin was predominantly monomeric; however, pulsed field gradient NMR self-diffusion measurements and analytical ultracentrifugation revealed evidence of dimer formation. Sequence-specific chemical shift assignments were determined through analysis of two- and three-dimensional NMR spectra of 15N- and 13C/15N-enriched protein samples. Input for the torsion angle dynamics calculations used in determining the structure included 1258 unique NOE-derived distance constraints and 60 dihedral angle constraints obtained from chemical-shift-based searching of a protein conformational database. The ensemble of 20 structures chosen to represent the structure had backbone and heavy atom rms deviations of 0.46 ± 0.11 and 1.02 ± 0.14 Å, respectively. The results revealed that human lymphotactin adopts the conserved chemokine fold, which is characterized by a three-stranded antiparallel ?-sheet and a C-terminal ?-helix. Two regions are dynamically disordered as evidenced by 1H and 13C chemical shifts and {15N}-1H NOEs: residues 1–9 of the amino terminus and residues 69±93 of the C-terminal extension. A functional role for the C-terminal extension, which is unique to lymphotactin, remains to be elucidated. PMID:11601972

  12. Small-Angle X-Ray Scattering on Biological Macromolecules and Nanocomposites in Solution

    NASA Astrophysics Data System (ADS)

    Blanchet, Clement E.; Svergun, Dmitri I.

    2013-04-01

    Small-angle X-ray scattering (SAXS) is a powerful method to study the structural properties of materials at the nanoscale. Recent progress in instrumentation and analysis methods has led to rapidly growing applications of this technique for the characterization of biological macromolecules in solution. Ab initio and rigid-body modeling methods allow one to build three-dimensional, low-resolution models from SAXS data. With the new approaches, oligomeric states of proteins and macromolecular complexes can be assessed, chemical equilibria and kinetic reactions can be studied, and even flexible objects such as intrinsically unfolded proteins can be quantitatively characterized. This review describes the analysis methods of SAXS data from macromolecular solutions, ranging from the computation of overall structural parameters to advanced three-dimensional modeling. The efficiency of these methods is illustrated by recent applications to biological macromolecules and nanocomposite particles.

  13. Sequential recovery of macromolecular components of the nucleolus.

    PubMed

    Bai, Baoyan; Laiho, Marikki

    2015-01-01

    The nucleolus is involved in a number of cellular processes of importance to cell physiology and pathology, including cell stress responses and malignancies. Studies of macromolecular composition of the nucleolus depend critically on the efficient extraction and accurate quantification of all macromolecular components (e.g., DNA, RNA, and protein). We have developed a TRIzol-based method that efficiently and simultaneously isolates these three macromolecular constituents from the same sample of purified nucleoli. The recovered and solubilized protein can be accurately quantified by the bicinchoninic acid assay and assessed by polyacrylamide gel electrophoresis or by mass spectrometry. We have successfully applied this approach to extract and quantify the responses of all three macromolecular components in nucleoli after drug treatments of HeLa cells, and conducted RNA-Seq analysis of the nucleolar RNA. PMID:25311121

  14. JBluIce-EPICS control system for macromolecular crystallography.

    SciTech Connect

    Stepanov, S.; Makarov, O.; Hilgart, M.; Pothineni, S.; Urakhchin, A.; Devarapalli, S.; Yoder, D.; Becker, M.; Ogata, C.; Sanishvili, R.; Nagarajan, V.; Smith, J. L.; Fischetti, R. F. (Biosciences Division); (Univ. of Michigan)

    2011-01-01

    The trio of macromolecular crystallography beamlines constructed by the General Medicine and Cancer Institutes Collaborative Access Team (GM/CA-CAT) in Sector 23 of the Advanced Photon Source (APS) have been in growing demand owing to their outstanding beam quality and capacity to measure data from crystals of only a few micrometres in size. To take full advantage of the state-of-the-art mechanical and optical design of these beamlines, a significant effort has been devoted to designing fast, convenient, intuitive and robust beamline controls that could easily accommodate new beamline developments. The GM/CA-CAT beamline controls are based on the power of EPICS for distributed hardware control, the rich Java graphical user interface of Eclipse RCP and the task-oriented philosophy as well as the look and feel of the successful SSRL BluIce graphical user interface for crystallography. These beamline controls feature a minimum number of software layers, the wide use of plug-ins that can be written in any language and unified motion controls that allow on-the-fly scanning and optimization of any beamline component. This paper describes the ways in which BluIce was combined with EPICS and converted into the Java-based JBluIce, discusses the solutions aimed at streamlining and speeding up operations and gives an overview of the tools that are provided by this new open-source control system for facilitating crystallographic experiments, especially in the field of microcrystallography.

  15. Structure and dynamics of aqueous solution of uranyl ions

    SciTech Connect

    Chopra, Manish [Radiation Safety Systems Division, Bhabha Atomic Research Centre, Mumbai-400085 (India); Choudhury, Niharendu, E-mail: nihcho@barc.gov.in [Theoretical Chemistry Section, Bhabha Atomic Research Centre, Mumbai-400085 (India)

    2014-04-24

    The present work describes a molecular dynamics simulation study of structure and dynamics of aqueous solution of uranyl ions in water. Structural properties of the system in terms of radial distribution functions and dynamical characteristics as obtained through velocity autocorrelation function and mean square displacements have been analyzed. The results for radial distribution functions show the oxygen of water to form the first solvation shell at 2.4 Å around the uranium atom, whereas the hydrogen atoms of water are distributed around the uranium atom with the major peak at around 3.0 Å. Analyses of transport behaviors of ions and water through MSD indicates that the diffusion of the uranyl ion is much less as compared to that of the water molecules. It is also observed that the dynamical behavior of water molecules gets modified due to the presence of uranyl ion. The effect of increase in concentration of uranyl ions on the structure and dynamics of water molecules is also studied.

  16. Tertiary structure of conotoxin GIIIA in aqueous solution.

    PubMed

    Lancelin, J M; Kohda, D; Tate, S; Yanagawa, Y; Abe, T; Satake, M; Inagaki, F

    1991-07-16

    The three-dimensional structure of conotoxin GIIIA, an important constituent of the venom from the marine hunting snail Conus geographus L., was determined in aqueous solution by two-dimensional proton nuclear magnetic resonance and simulated annealing based methods. On the basis of 162 assigned nuclear Overhauser effect (NOE) connectivities obtained at the medium field strength frequency of 400 MHz, 74 final distance constraints of sequential and tertiary ones were derived and used together with 18 torsion angle (phi, chi 1) constraints and 9 distance constraints derived from disulfide bridges. A total of 32 converged structures were obtained from 200 runs of calculations. The atomic root-mean-square (RMS) difference about the mean coordinate positions (excluding the terminal residues 1 and 22) is 0.8 A for backbone atoms (N, C alpha, C). Conotoxin GIIIA is characterized by a particular folding of the 22 amino acid peptidic chain, which is stabilized by three disulfide bridges arranged in cage at the center of a discoidal structure of approximately 20-A diameter. The seven cationic side chains of lysine and arginine residues project radially into the solvent and form potential sites of interaction with the skeletal muscle sodium channel for which the toxin is a strong inhibitor. The present results provide a molecular basis to elucidate the remarkable physiological properties of this neurotoxin. PMID:2069951

  17. Hydration structure of salt solutions from ab initio molecular dynamics

    SciTech Connect

    Bankura, Arindam; Carnevale, Vincenzo; Klein, Michael L. [Institute for Computational Molecular Science and Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122 (United States)

    2013-01-07

    The solvation structures of Na{sup +}, K{sup +}, and Cl{sup -} ions in aqueous solution have been investigated using density functional theory (DFT) based Car-Parrinello (CP) molecular dynamics (MD) simulations. CPMD trajectories were collected for systems containing three NaCl or KCl ion pairs solvated by 122 water molecules using three different but commonly employed density functionals (BLYP, HCTH, and PBE) with electron correlation treated at the level of the generalized gradient approximation (GGA). The effect of including dispersion forces was analyzed through the use of an empirical correction to the DFT-GGA scheme. Special attention was paid to the hydration characteristics, especially the structural properties of the first solvation shell of the ions, which was investigated through ion-water radial distribution functions, coordination numbers, and angular distribution functions. There are significant differences between the present results obtained from CPMD simulations and those provided by classical MD based on either the CHARMM force field or a polarizable model. Overall, the computed structural properties are in fair agreement with the available experimental results. In particular, the observed coordination numbers 5.0-5.5, 6.0-6.4, and 6.0-6.5 for Na{sup +}, K{sup +}, and Cl{sup -}, respectively, are consistent with X-ray and neutron scattering studies but differ somewhat from some of the many other recent computational studies of these important systems. Possible reasons for the differences are discussed.

  18. Present status of SPring-8 macromolecular crystallography beamlines

    SciTech Connect

    Kawano, Yoshiaki; Hirata, Kunio; Ueno, Go; Hikima, Takaaki; Murakami, Hironori; Maeda, Daisuke; Nisawa, Atsushi; Yamamoto, Masaki [RIKEN SPring-8 Center, 1-1-1, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148 (Japan); Shimizu, Nobutaka; Baba, Seiki; Hasegawa, Kazuya; Makino, Masatomo; Mizuno, Nobuhiro; Hoshino, Takeshi; Ito, Ren; Wada, Izumi; Kumasaka, Takashi [JASRI/SPring-8, 1-1-1, Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198 (Japan)

    2010-06-23

    Seven beamlines are operated for macromolecular crystallography (MX) at SPring-8. The three undulator beamlines are developed for cutting edge target and four bending-magnet beamlines are developed for high throughput MX. The undulator beamline, BL41XU that provides the most brilliant beam, is dedicated to obtain high quality data even from small-size and weakly-diffracting crystals. The minimum beam size at sample position is achieved to 10 {mu}m diameter using a pin-hole collimator. Its photon flux at wavelength {lambda} = 1.0 A is 2.8x10{sup 11} photons/sec. This small beam coupled with irradiation point scanning method is quite useful to take diffraction dataset from small crystals by suppressing the radiation damage. These advanced technologies made a number of difficult protein structure analysis possible, (i.e. Sodium-potassium ATPase). The bending-magnet beamlines BL26B1/B2 and BL38B1 provide automatic data collection exploiting the high mobility of the beam. The beamline operation software 'BSS', sample auto-changer 'SPACE' and web-based data management software 'D-Cha' have made the automatic data collection possible. The 'Mail-in data collection system' that accepts distant users samples via courier service have made users possible to collect diffraction data without visiting SPring-8. The structural genomics research is promoted by these beamlines.

  19. Three-dimensional solution structure of Acanthamoeba profilin-I

    PubMed Central

    1993-01-01

    We have determined a medium resolution three-dimensional solution structure of Acanthamoeba profilin-I by multidimensional nuclear magnetic resonance spectroscopy. This 13-kD actin binding protein consists of a five stranded antiparallel beta sheet flanked by NH2- and COOH-terminal helices on one face and by a third helix and a two stranded beta sheet on the other face. Data from actin-profilin cross- linking experiments and the localization of conserved residues between profilins in different phyla indicate that actin binding occurs on the molecular face occupied by the terminal helices. The other face of the molecule contains the residues that differ between Acanthamoeba profilins-I and II and may be important in determining the difference in polyphosphoinositide binding between these isoforms. This suggests that lipids and actin bind to different faces of the molecule. PMID:8397216

  20. Revisiting the Solution Structure of Ceric Ammonium Nitrate.

    PubMed

    Demars, Thomas J; Bera, Mrinal K; Seifert, Soenke; Antonio, Mark R; Ellis, Ross J

    2015-06-22

    Ceric ammonium nitrate (CAN) is a single-electron-transfer reagent with unparalleled utility in organic synthesis, and has emerged as a vital feedstock in diverse chemical industries. Most applications use CAN in solution where it is assigned a monomeric [Ce(IV) (NO3 )6 ](2-) structure; an assumption traced to half-century old studies. Using synchrotron X-rays and Raman spectroscopy we challenge this tradition, converging instead on an oxo-bridged dinuclear complex, even in strong nitric acid. Thus, one equivalent of CAN is recast as a two-electron-transfer reagent and a redox-activated superbase, raising questions regarding the origins of its reactivity with organic molecules and giving new fundamental insight into the stability of polynuclear complexes of tetravalent ions. PMID:25906967

  1. The use of a mini-? goniometer head in macromolecular crystallography diffraction experiments

    PubMed Central

    Brockhauser, Sandor; Ravelli, Raimond B. G.; McCarthy, Andrew A.

    2013-01-01

    Most macromolecular crystallography (MX) diffraction experiments at synchrotrons use a single-axis goniometer. This markedly contrasts with small-molecule crystallography, in which the majority of the diffraction data are collected using multi-axis goniometers. A novel miniaturized ?-gonio­meter head, the MK3, has been developed to allow macromolecular crystals to be aligned. It is available on the majority of the structural biology beamlines at the ESRF, as well as elsewhere. In addition, the Strategy for the Alignment of Crystals (STAC) software package has been developed to facilitate the use of the MK3 and other similar devices. Use of the MK3 and STAC is streamlined by their incorporation into online analysis tools such as EDNA. The current use of STAC and MK3 on the MX beamlines at the ESRF is discussed. It is shown that the alignment of macromolecular crystals can result in improved diffraction data quality compared with data obtained from randomly aligned crystals. PMID:23793150

  2. Macromolecular Imaging Agents Containing Lanthanides: Can Conceptual Promise Lead to Clinical Potential?

    PubMed Central

    Bryson, Joshua; Reineke, Jeffrey W.; Reineke, Theresa M.

    2012-01-01

    Macromolecular magnetic resonance imaging (MRI) contrast agents are increasingly being used to improve the resolution of this noninvasive diagnostic technique. All clinically-approved T1 contrast agents are small molecule chelates of gadolinium [Gd(III)] that affect bound water proton relaxivity. Both the small size and monomeric nature of these agents ultimately limits the image resolution enhancement that can be achieved for both contrast enhancement and pharmacokinetic/biodistribution reasons. The multimeric nature of macromolecules, such as polymers, dendrimers, and noncovalent complexes of small molecule agents with proteins, have been shown to significantly increase the image contrast and resolution due to their large size and ability to incorporate multiple Gd(III) chlelation sites. Also, macromolecular agents are advantageous as they have the ability to be designed to be nontoxic, hydrophilic, easily purified, aggregation-resistant, and have controllable three-dimensional macromolecular structure housing the multiple lanthanide chelation sites. For these reasons, large molecule diagnostics have the ability to significantly increase the relaxivity of water protons within the targeted tissues and thus the image resolution for many diagnostic applications. The FDA approval of a contrast agent that consists of a reversible, non-covalent coupling of a small Gd(III) chelate with serum albumin for blood pool imaging (marketed under the trade names of Vasovist and Ablivar) proved to be one of the first diagnostic agent to capitalize on these benefits from macromolecular association in humans. However, much research and development is necessary to optimize the safety of these unique agents for in vivo use and potential clinical development. To this end, recent work in the field of polymer, dendrimer, and noncovalent complex-based imaging agents are reviewed herein and the future outlook of this field is discussed. PMID:23467737

  3. Macromolecular shape and interactions in layer-by-layer assemblies within cylindrical nanopores.

    PubMed

    Lazzara, Thomas D; Lau, K H Aaron; Knoll, Wolfgang; Janshoff, Andreas; Steinem, Claudia

    2012-01-01

    Layer-by-layer (LbL) deposition of polyelectrolytes and proteins within the cylindrical nanopores of anodic aluminum oxide (AAO) membranes was studied by optical waveguide spectroscopy (OWS). AAO has aligned cylindrical, nonintersecting pores with a defined pore diameter d(0) and functions as a planar optical waveguide so as to monitor, in situ, the LbL process by OWS. The LbL deposition of globular proteins, i.e., avidin and biotinylated bovine serum albumin was compared with that of linear polyelectrolytes (linear-PEs), both species being of similar molecular weight. LbL deposition within the cylindrical AAO geometry for different pore diameters (d(0) = 25-80 nm) for the various macromolecular species, showed that the multilayer film growth was inhibited at different maximum numbers of LbL steps (n(max)). The value of n(max) was greatest for linear-PEs, while proteins had a lower value. The cylindrical pore geometry imposes a physical limit to LbL growth such that n(max) is strongly dependent on the overall internal structure of the LbL film. For all macromolecular species, deposition was inhibited in native AAO, having pores of d(0) = 25-30 nm. Both, OWS and scanning electron microscopy showed that LbL growth in larger AAO pores (d(0) > 25-30 nm) became inhibited when approaching a pore diameter of d(eff,n_max) = 25-35 nm, a similar size to that of native AAO pores, with d(0) = 25-30 nm. For a reasonable estimation of d(eff,n_max), the actual volume occupied by a macromolecular assembly must be taken into consideration. The results clearly show that electrostatic LbL allowed for compact macromolecular layers, whereas proteins formed loosely packed multilayers. PMID:23019541

  4. The NMR solution structure of recombinant RGD-hirudin

    SciTech Connect

    Song, Xia [Center of Analysis and Measurement, Fudan University, Shanghai 200433 (China); Mo, Wei [Key Laboratory of Molecular Medicine, Ministry of Education, Fudan University, Shanghai 200032 (China); Liu, Xingang [Center of Analysis and Measurement, Fudan University, Shanghai 200433 (China); Zhu, Lina [Center of Analysis and Measurement, Fudan University, Shanghai 200433 (China); Yan, Xiaomin [Center of Analysis and Measurement, Fudan University, Shanghai 200433 (China); Song, Houyan [Key Laboratory of Molecular Medicine, Ministry of Education, Fudan University, Shanghai 200032 (China)]. E-mail: hysong@shmu.edu.cn; Dai, Linsen [Center of Analysis and Measurement, Fudan University, Shanghai 200433 (China)]. E-mail: lsdai@fudan.edu.cn

    2007-08-17

    The solution structure of a new recombinant RGD-hirudin, which has the activities of anti-thrombin and anti-platelet aggregation, was determined by {sup 1}H nuclear magnetic resonance spectroscopy and compared with the conformations of recombinant wild-type hirudin and hirudin (variant 2, Lys47) of the hirudin thrombin complex. On the basis of total 1284 distance and dihedral angle constraints derived from a series of NMR spectra, 20 conformers were computed with ARIA/CNS programs. The structure of residues 3-30 and 37-48 form a molecular core with two antiparallel {beta}-sheets as the other two hirudins. However, significant differences were found in the surface electrostatic charge distributions among the three hirudins, especially in the RGD segment of recombinant RGD-hirudin. This difference may be greatly beneficial to its additional function of anti-platelet aggregation. The difference in extended C-terminal makes its both ionic and hydrophobic interactions with the fibrinogen recognition exosite of thrombin more effective.

  5. Synchrotron radiation macromolecular crystallography: science and spin-offs

    PubMed Central

    Helliwell, John R.; Mitchell, Edward P.

    2015-01-01

    A current overview of synchrotron radiation (SR) in macromolecular crystallography (MX) instrumentation, methods and applications is presented. Automation has been and remains a central development in the last decade, as have the rise of remote access and of industrial service provision. Results include a high number of Protein Data Bank depositions, with an increasing emphasis on the successful use of microcrystals. One future emphasis involves pushing the frontiers of using higher and lower photon energies. With the advent of X-ray free-electron lasers, closely linked to SR developments, the use of ever smaller samples such as nanocrystals, nanoclusters and single molecules is anticipated, as well as the opening up of femtosecond time-resolved diffraction structural studies. At SR sources, a very high-throughput assessment for the best crystal samples and the ability to tackle just a few micron and sub-micron crystals will become widespread. With higher speeds and larger detectors, diffraction data volumes are becoming long-term storage and archiving issues; the implications for today and the future are discussed. Together with the rise of the storage ring to its current pre-eminence in MX data provision, the growing tendency of central facility sites to offer other centralized facilities complementary to crystallography, such as cryo-electron microscopy and NMR, is a welcome development. PMID:25866664

  6. Synchrotron radiation macromolecular crystallography: science and spin-offs.

    PubMed

    Helliwell, John R; Mitchell, Edward P

    2015-03-01

    A current overview of synchrotron radiation (SR) in macromolecular crystallography (MX) instrumentation, methods and applications is presented. Automation has been and remains a central development in the last decade, as have the rise of remote access and of industrial service provision. Results include a high number of Protein Data Bank depositions, with an increasing emphasis on the successful use of microcrystals. One future emphasis involves pushing the frontiers of using higher and lower photon energies. With the advent of X-ray free-electron lasers, closely linked to SR developments, the use of ever smaller samples such as nanocrystals, nanoclusters and single molecules is anticipated, as well as the opening up of femtosecond time-resolved diffraction structural studies. At SR sources, a very high-throughput assessment for the best crystal samples and the ability to tackle just a few micron and sub-micron crystals will become widespread. With higher speeds and larger detectors, diffraction data volumes are becoming long-term storage and archiving issues; the implications for today and the future are discussed. Together with the rise of the storage ring to its current pre-eminence in MX data provision, the growing tendency of central facility sites to offer other centralized facilities complementary to crystallography, such as cryo-electron microscopy and NMR, is a welcome development. PMID:25866664

  7. On a non approximated approach to Extended Thermodynamics for dense gases and macromolecular fluids

    E-print Network

    M. C. Carrisi; M. A. Mele; S. Pennisi

    2007-12-21

    Recently the 14 moments model of Extended Thermodynamics for dense gases and macromolecular fluids has been considered and an exact solution, of the restrictions imposed by the entropy principle and that of Galilean relativity, has been obtained through a non relativistic limit. Here we prove uniqueness of the above solution and exploit other pertinent conditions such us the convexity of the function $h'$ related to the entropy density, the problem of subsystems and the fact that the flux in the conservation law of mass must be the moment of order 1 in the conservation law of momentum. Also the solution of this last condition is here obtained without using expansions around equilibrium. The results present interesting aspects which were not suspected when only approximated solutions of this problem were known.

  8. Visualization of the atomic structure of solid solutions with the NaCl structure

    NASA Astrophysics Data System (ADS)

    Babanov, Yu. A.; Ponomarev, D. A.; Ustinov, V. V.

    2015-04-01

    It has been shown how an atomic cluster for a solid solution with a rock salt structure can be constructed using the Pauling model. Simulation has been performed for 343000 ions of Ni x Zn1 - x O3 ( x = 0, 0.3, 0.5, 0.7, 1.0) oxide substitutional solid solutions. Coordinates of all cluster ions are obtained and distribution functions of ion pairs (Ni-O, Ni-Ni, Ni-Zn, Zn-Zn, Zn-O, O-O) are constructed as functions of distance. The shape of the normal distribution indicates the existence of bounded chaos in the system of oxide solid solutions. The width of the Gaussian distribution function is determined by the difference of metal ionic radii. The results are in agreement with both X-ray diffraction and EXAFS spectroscopy data.

  9. Macromolecular query language (MMQL): prototype data model and implementation.

    PubMed

    Shindyalov, I N; Chang, W; Pu, C; Bourne, P E

    1994-11-01

    Macromolecular query language (MMQL) is an extensible interpretive language in which to pose questions concerning the experimental or derived features of the 3-D structure of biological macromolecules. MMQL portends to be intuitive with a simple syntax, so that from a user's perspective complex queries are easily written. A number of basic queries and a more complex query--determination of structures containing a five-strand Greek key motif--are presented to illustrate the strengths and weaknesses of the language. The predominant features of MMQL are a filter and pattern grammar which are combined to express a wide range of interesting biological queries. Filters permit the selection of object attributes, for example, compound name and resolution, whereas the patterns currently implemented query primary sequence, close contacts, hydrogen bonding, secondary structure, conformation and amino acid properties (volume, polarity, isoelectric point, hydrophobicity and different forms of exposure). MMQL queries are processed by MMQLlib; a C++ class library, to which new query methods and pattern types are easily added. The prototype implementation described uses PDBlib, another C(++)-based class library from representing the features of biological macromolecules at the level of detail parsable from a PDB file. Since PDBlib can represent data stored in relational and object-oriented databases, as well as PDB files, once these data are loaded they too can be queried by MMQL. Performance metrics are given for queries of PDB files for which all derived data are calculated at run time and compared to a preliminary version of OOPDB, a prototype object-oriented database with a schema based on a persistent version of PDBlib which offers more efficient data access and the potential to maintain derived information. MMQLlib, PDBlib and associated software are available via anonymous ftp from cuhhca.hhmi.columbia.edu. PMID:7700863

  10. a Procedural Solution to Model Roman Masonry Structures

    NASA Astrophysics Data System (ADS)

    Cappellini, V.; Saleri, R.; Stefani, C.; Nony, N.; De Luca, L.

    2013-07-01

    The paper will describe a new approach based on the development of a procedural modelling methodology for archaeological data representation. This is a custom-designed solution based on the recognition of the rules belonging to the construction methods used in roman times. We have conceived a tool for 3D reconstruction of masonry structures starting from photogrammetric surveying. Our protocol considers different steps. Firstly we have focused on the classification of opus based on the basic interconnections that can lead to a descriptive system used for their unequivocal identification and design. Secondly, we have chosen an automatic, accurate, flexible and open-source photogrammetric pipeline named Pastis Apero Micmac - PAM, developed by IGN (Paris). We have employed it to generate ortho-images from non-oriented images, using a user-friendly interface implemented by CNRS Marseille (France). Thirdly, the masonry elements are created in parametric and interactive way, and finally they are adapted to the photogrammetric data. The presented application, currently under construction, is developed with an open source programming language called Processing, useful for visual, animated or static, 2D or 3D, interactive creations. Using this computer language, a Java environment has been developed. Therefore, even if the procedural modelling reveals an accuracy level inferior to the one obtained by manual modelling (brick by brick), this method can be useful when taking into account the static evaluation on buildings (requiring quantitative aspects) and metric measures for restoration purposes.

  11. Solution Structures of Chemoenzymatically Synthesized Heparin and Its Precursors

    PubMed Central

    Zhang, Zhenqing; McCallum, Scott A.; Xie, Jin; Nieto, Lidia; Corzana, Francisco; Jiménez-Barbero, Jesús; Chen, Miao; Liu, Jian; Linhardt, Robert J.

    2009-01-01

    We report the first chemoenzymatic synthesis of the stable isotope-enriched heparin from a uniformly labeled [13C,15N]N-acetylheparosan (-GlcA(1,4)GlcNAc-) prepared from E. coli K5. Glycosaminoglycan (GAG) precursors and heparin were formed from N-acetylheparosan by the following steps: chemical N-deacetylation and N-sulfonation leading to N-sulfoheparosan (-GlcA(1,4)GlcNS-); enzyme-catalyzed C5-epimerization and 2-O-sulfonation leading to undersulfated heparin (-IdoA2S(1,4)GlcNS-); enzymatic 6-O-sulfonation leading to the heparin backbone (-IdoA2S(1,4)GlcNS6S-); and selective enzymatic 3-O-sulfonation leading to the anticoagulant heparin, containing the GlcNS6S3S residue. Heteronuclear, multidimensional nuclear magnetic resonance spectroscopy was employed to analyze the chemical composition and solution structure of [13C,15N]N-acetylheparosan, precursors, and heparin. Isotopic enrichment was found to provide well-resolved 13C spectra with the high sensitivity required for conformational studies of these biomolecules. Stable isotope-labeled heparin was indistinguishable from heparin derived from animal tissues and is a novel reagent for studying the interaction of heparin with proteins. PMID:18767845

  12. The secondary structure of ribosomal ribonucleic acid in solution

    PubMed Central

    Cox, R. A.

    1966-01-01

    1. The u.v.-absorption spectrum of ribosomal RNA from rabbit reticulocytes was studied as a function of temperature at different pH values. The changes in the spectrum over the range 220–320m? were interpreted on the basis of the assumption that the effect of denaturation and ionization are additive. The results suggest that in neutral salt solutions the secondary structure of the ribosomal RNA samples studied is due to two species of helical segments stabilized principally, if not solely, by complementary base pairs but differing in nucleotide composition: each species appears to be heterogeneous in other respects in view of the breadth of the melting ranges. 2. The number of base pairs per helical segment was estimated to be small (between 4 and 17) on the basis of the relation between melting temperature and chain length previously established by Lipsett and others for model compounds. Small fragments (about 2s) obtained by alkaline hydrolysis appeared to form the same helical segments as the intact molecule in accord with the estimated size of these segments. 3. Specific nucleotide sequences appear necessary to account for the hysteresis observed on titrating ribosomal RNA with acid or alkali within the range pH3·0–7·0 since this phenomenon was less pronounced for Escherichia coli transfer RNA and for RNA from turnip yellow-mosaic virus. PMID:5330109

  13. Ultrasoft primitive model of polyionic solutions: structure, aggregation, and dynamics

    E-print Network

    Daniele Coslovich; Jean-Pierre Hansen; Gerhard Kahl

    2011-06-30

    We introduce an ultrasoft core model of interpenetrating polycations and polyanions with continuous Gaussian charge distributions, to investigate polyelectrolyte aggregation in dilute and semi-dilute, salt-free solutions. The model is studied by a combination of approximate theories (random phase approximation and hypernetted chain theory) and numerical simulations. The calculated pair structure, thermodynamics, phase diagram and polyion dynamics of the symmetric version of the model (the "ultrasoft restricted primitive model" or UPRM) differ from the corresponding properties of the widely studied "restricted primitive model" (RPM) where ions have hard cores. At sufficiently low temperatures and densities, oppositely charged polyions form weakly interacting, polarizable neutral pairs. The clustering probabilities, dielectric behavior and electrical conductivity point to a line of sharp conductor-insulator transitions in the density-temperature plane. At very low temperatures the conductor-insulator transition line terminates near the top of a first order coexistence curve separating a high-density, liquid phase from a low-density, vapor phase. The simulation data hint at a tricritical behavior, reminiscent of that observed of the two-dimensional Coulomb Gas, which contrasts with the Ising criticality of its three-dimensional counterpart, the RPM.

  14. Davisson-Germer Prize in Atomic or Surface Physics Lecture: Line 'Em All Up: Macromolecular Assembly at Liquid Interfaces

    NASA Astrophysics Data System (ADS)

    Richmond, Geraldine

    2013-03-01

    Advances in our molecular level understanding of the ubiquitous fluid interface comprised of a hydrophobic fluid medium, and an aqueous solution of soluble ions and solutes has been slow until recently. This more recent upsurge in interest and progress comes from advances in both experimental and computational techniques as well as the increasingly important role that this interface is playing in such areas as green chemistry, nanoparticle synthesis, improved oil and mineral recovery and water purification. The presentation will focus on our most recent efforts in understanding (1) the molecular structure of the interface between two immiscible liquids, (2) the penetration of aqueous phase ions into the interfacial region and their effect on its properties, and (3) the structure and dynamics of the adsorption of surfactants, polymers and nanoparticles at this interface. To gain insights into these processes we use a combination of vibrational sum frequency spectroscopy, surface tension measurements using the pendant drop method, and molecular dynamics simulations. The results demonstrate that weak interactions between interfacial oil and water molecules create an interface that exhibits a high degree of molecular structuring and ordering, and with properties quite different than what is observed at the air-water interface. As a consequence of these interfacial oil-water interactions, the interface provides a unique environment for the adsorption and assembly of ions, polymers and nanoparticles that are drawn to its inner-most regions. Examples of our studies that provide new insights into the unique nature of adsorption, adsorption dynamics and macromolecular assembly at this interface will be provided.

  15. JBluIce–EPICS control system for macromolecular crystallography

    PubMed Central

    Stepanov, Sergey; Makarov, Oleg; Hilgart, Mark; Pothineni, Sudhir Babu; Urakhchin, Alex; Devarapalli, Satish; Yoder, Derek; Becker, Michael; Ogata, Craig; Sanishvili, Ruslan; Venugopalan, Nagarajan; Smith, Janet L.; Fischetti, Robert F.

    2011-01-01

    The trio of macromolecular crystallography beamlines constructed by the General Medicine and Cancer Institutes Collaborative Access Team (GM/CA-CAT) in Sector 23 of the Advanced Photon Source (APS) have been in growing demand owing to their outstanding beam quality and capacity to measure data from crystals of only a few micrometres in size. To take full advantage of the state-of-the-art mechanical and optical design of these beamlines, a significant effort has been devoted to designing fast, convenient, intuitive and robust beamline controls that could easily accommodate new beamline developments. The GM/CA-CAT beamline controls are based on the power of EPICS for distributed hardware control, the rich Java graphical user interface of Eclipse RCP and the task-oriented philosophy as well as the look and feel of the successful SSRL BluIce graphical user interface for crystallography. These beamline controls feature a minimum number of software layers, the wide use of plug-ins that can be written in any language and unified motion controls that allow on-the-fly scanning and optimization of any beamline com­ponent. This paper describes the ways in which BluIce was combined with EPICS and converted into the Java-based JBluIce, discusses the solutions aimed at streamlining and speeding up operations and gives an overview of the tools that are provided by this new open-source control system for facilitating crystallo­graphic experiments, especially in the field of microcrystallo­graphy. PMID:21358048

  16. Bonding of Macromolecular Hydrogels Using Perturbants Gavrielle M. Price, Kengyeh K. Chu, James G. Truslow, Min D. Tang-Schomer, Andrew P. Golden,

    E-print Network

    Tien, Joe

    of water). Stacked gels are thus unlikely to resist stresses imparted by mechanical pumping or by cellsBonding of Macromolecular Hydrogels Using Perturbants Gavrielle M. Price, Kengyeh K. Chu, James G form by self-assembly in water, we tested solutes known to affect hydrogen bonding in water (bond

  17. Dynamic Solution Code for Structural Analysis upon Joint Element

    Microsoft Academic Search

    S. A. Sadrnejad; M. Labibzadeh

    2006-01-01

    The analysis of large structures mostly requires a complete three dimensional finite element discretization. Stability of such structures includes not only the stability of structure itself but also that of foundation as well as interconnection elements. The general instability of a structure may be affected by two aspects, firstly, an inappropriate preliminary classical design of the structure and inadequate control

  18. Supraphysiologic L-tryptophan elicits cytoskeletal and macromolecular permeability alterations in hamster small intestinal epithelium in vitro.

    PubMed Central

    Madara, J L; Carlson, S

    1991-01-01

    We have previously shown that Na(+)-coupled transport of glucose and amino acids across the apical membrane of intestinal absorptive cells is accompanied by alterations in cytoskeletal structure and altered sieving of small hydrophilic solutes by tight junctions. Here we report that in response to the essential amino acid L-tryptophan at lumenal concentrations likely to be supraphysiological (1 mM or greater), these responses are so exaggerated as to induce disruption of tight junctions and transepithelial macromolecular leaks. Since these effects of L-tryptophan are energy and Na+ dependent and occur with mucosal but not serosal exposure to L-tryptophan, it appears they are triggered by activation of a Na(+)-nutrient cotransporter in the apical membrane of absorptive cells rather than by the presence of an unidentified trace contaminant. Our findings suggest the possibility that dietary supplementation by L-tryptophan may result in loss of the intestinal epithelial barrier to dietary antigens. We speculate that such a response to supraphysiologic tryptophan may contribute, in part, to the recently recognized curious tryptophan-induced eosinophilia myalgia syndrome. Images PMID:1991832

  19. Macromolecular Crowding Directs Extracellular Matrix Organization and Mesenchymal Stem Cell Behavior

    E-print Network

    Zeiger, Adam Scott

    Microenvironments of biological cells are dominated in vivo by macromolecular crowding and resultant excluded volume effects. This feature is absent in dilute in vitro cell culture. Here, we induced macromolecular crowding ...

  20. DOI: 10.1002/cbic.201000442 Mechanisms of Macromolecular Protease Inhibitors

    E-print Network

    Craik, Charles S.

    DOI: 10.1002/cbic.201000442 Mechanisms of Macromolecular Protease Inhibitors Christopher J. Farady by mac- romolecular inhibitors. Somewhat surprisingly, relatively few design principles underlie the mechanisms of inhibition of a myriad range of macromolecular protease inhibitors. Signifi- cant engineering

  1. Macromolecular crystallography beamline X25 at the NSLS

    PubMed Central

    Héroux, Annie; Allaire, Marc; Buono, Richard; Cowan, Matthew L.; Dvorak, Joseph; Flaks, Leon; LaMarra, Steven; Myers, Stuart F.; Orville, Allen M.; Robinson, Howard H.; Roessler, Christian G.; Schneider, Dieter K.; Shea-McCarthy, Grace; Skinner, John M.; Skinner, Michael; Soares, Alexei S.; Sweet, Robert M.; Berman, Lonny E.

    2014-01-01

    Beamline X25 at the NSLS is one of the five beamlines dedicated to macromolecular crystallography operated by the Brookhaven National Laboratory Macromolecular Crystallography Research Resource group. This mini-gap insertion-device beamline has seen constant upgrades for the last seven years in order to achieve mini-beam capability down to 20?µm × 20?µm. All major components beginning with the radiation source, and continuing along the beamline and its experimental hutch, have changed to produce a state-of-the-art facility for the scientific community. PMID:24763654

  2. Stability of the grain structure in 2219-O aluminum alloy friction stir welds during solution treatment

    Microsoft Academic Search

    Y. C.. Chen; J. C. Feng; H. J. Liu

    2007-01-01

    The stability of the grain structure in 2219-O aluminum alloy friction stir welds during solution treatment has been investigated. Experimental results show that the solution treatment causes drastic grain growth, Grain growth initiates at the surface and the bottom of the weld and then extends to the weld centre within several minutes. The solution treatment temperature and the welding heat

  3. The Lunar Internal Structure Model: Problems and Solutions

    NASA Astrophysics Data System (ADS)

    Nefedyev, Yuri; Gusev, Alexander; Petrova, Natalia; Varaksina, Natalia

    The report is devoted the problems of the internal structure and gravitational field of the Moon. New data received from 14 newest instruments installed on low-orbit satellite Kaguya essentially enriched our knowledge of the Moon. Chinese satellite ChagE-1 and Indian ?handrayan-1 have demonstrated strong potential of China and India in the field of lunar research and obtained new data on gravitational field, mascons, crust, and geochemical composition of the circumlunar space. Internal structure of the Moon: There are some essential arguments in favor of existence of a small-sized Moon’s core made of metallic iron alloyed with a small amount of sulfur and/or oxygen, and availability of hot viscous lower mantle. Structure of gravitational field of the Moon, determined by the comparison of high-precision trajectory measurements by Lunar Prospector (1998- 1999) with the results of laser altimetry obtained by Clementine (1994), as well as with data sets of laser ranging of the Moon (1970-2006), assumes the presence of a metal core. Interpretation of the polar moment value within the framework of chemical, thermal and density models of lunar crust and mantle informed conclusions about the weight and size of the core. LLR analysis of dissipation of rotation of the Moon points at two possible sources of dissipation: monthly solid-state inflows and liquid core, rotation of which differs from viscous-elastic mantle. Liquid (melted) core has its unique impact on the Moon’s rotation. In particular, there are two force moments due to topographical and phase interaction at the boundary between liquid core and elastic mantle (CMB). Liquid core can rotate independently from solid mantle Selenoid satellites (SS) open new and most perspective opportunities in the study of gravitational field and the Moon’s figure. SSs “Moon 10”, “Apollo”, “Clementine”, “Lunar Prospector” trajectory tracking data processing has allowed for identification of coefficients in decomposition of gravitational field of the Moon of members up to 165th order with a high degree of accuracy. Judging from the given data, the distinctive feature of the Moon’s gravitational field is that harmonics of the third and even the fourth order are comparable with harmonics of the second order, except for member J2. General conclusion: according to recent data, the true figure of the Moon is much more complex than a three-axis ellipsoid. Gravitational field and dynamic figure of the multilayered Moon: One of the main goals of selenodesy is the study of a dynamic figure of the Moon which determines distribution of the mass within the Moon’s body. A dynamic figure is shaped by the inertia ellipsoid set by values of resultant moments of inertia of the Moon A, B, C and their orientation in space. Selenoid satellites (SS) open new and most perspective opportunities in the study of gravitational field and the Moon’s figure. SSs “Moon 10”, “Apollo”, “Clementine”, “Lunar Prospector” trajectory tracking data processing has allowed for identification of coefficients in decomposition of gravitational field of the Moon of members up to 165th order with a high degree of accuracy. Judging from the given data, the distinctive feature of the Moon’s gravitational field is that harmonics of the third and even the fourth order are comparable with harmonics of the second order. Difference from zero of c-coefficients proves asymmetry of gravitational fields on the visible and invisible sides of the Moon. As a first attempt at solving the problem, the report presents the survey of internal structure of the Moon, tabulated values of geophysical parameters and geophysical profile of the Moon, including liquid lunar core, analytical solution of Clairaut’s equation for the two-layer model of the Moon; mathematical and bifurcational analysis of solution based on physically justified task options; original debugged software in VBA programming language for computer generated simulation for various intervals of radiuses, values of geometrical compression

  4. Application of finite-element-based solution technologies for viscoplastic structural analyses

    NASA Technical Reports Server (NTRS)

    Arya, V. K.

    1990-01-01

    Finite-element solution technology developed for use in conjunction with advanced viscoplastic models is described. The development of such solution technology is necessary for performing stress/life analyses of engineering structural problems where the complex geometries and loadings make the conventional analytical solutions difficult. The versatility of the solution technology is demonstrated by applying it to viscoplastic models possessing different mathematical structures and encompassing isotropic and anisotropic material. The computational results qualitatively replicate deformation behavior observed in experiments on prototypical structural components.

  5. Secondary structure effects on DNA hybridization kinetics: a solution versus surface comparison

    Microsoft Academic Search

    Yang Gao; Lauren K. Wolf; Rosina M. Georgiadis

    2006-01-01

    The hybridization kinetics for a series of designed 25mer probetarget pairs having varying degrees of secondary structure have been measured by UV absorbance and surface plasmon resonance (SPR) spectroscopy in solution and on the surface, res- pectively. Kinetic rate constants derived from the resultant data decrease with increasing probe and target secondary structure similarly in both solution and surface environments.

  6. HYBRID DIRECT-ITERATIVE LINEAR SOLUTION METHOD FOR STRUCTURAL ANALYSIS PROBLEM

    Microsoft Academic Search

    Seung-Jo KIM; Min-Ki KIM

    2005-01-01

    In this paper, hybrid direct-iterative linear solution method is proposed to solve large-scale structural analysis problem. Direct solution method is common to finite element structural analysis, but it has some disadvantage compared with iterative method. Iterative method is quite good performance to solve large scale problem, so we can combine both two method to get good performance to solve the

  7. HIGH PERFORMANCE DIRECT-ITERATIVE HYBRID LINEAR SOLUTION METHOD FOR LARGE SCALE STRUCTURAL ANALYSIS

    Microsoft Academic Search

    Seung Jo Kim; Min Ki Kim

    In this paper, hybrid direct-iterative linear solution method is proposed to solve large- scale structural analysis problem. Direct solution method is common to finite element structural analysis, but it has some disadvantage compared with iterative method. Iterative method is quite good performance to solve large scale problem, so we can combine both two method to get good performance to solve

  8. Structural and Dynamic Properties of Concentrated Alkali Halide Solutions:  A Molecular Dynamics Simulation Study

    Microsoft Academic Search

    Hao Du; Jayendran C. Rasaiah; Jan D. Miller

    2007-01-01

    The physicochemical properties of alkali halide solutions have long been attributed to the collective interactions between ions and water molecules in the solution, yet the structure of water in these systems and its effect on the equilibrium and dynamic properties of these systems are not clearly understood. Here, we present a systematic view of water structure in concentrated alkali halide

  9. Structures and properties of Sr-doped NdCrO 3 solid solutions

    Microsoft Academic Search

    Monan Liu; Yu Shen; Yuan Ji; Tianmin He

    2008-01-01

    Strontium doped NdCrO3 solid solutions (0.05?x?0.25) were synthesized using a solid-state reaction. The effects of Sr doping on the structures, electrical and thermal expansion properties of the solid solutions were studied. The results show that all the solid solutions prepared possess a single phase orthorhombic perovskite structure at room temperature. With the increase of Sr content in Nd site, the

  10. Spacetime structure of 5D hypercylindrical vacuum solutions with tension

    E-print Network

    Inyong Cho; Gungwon Kang; Sang Pyo Kim; Chul H. Lee

    2008-09-17

    We investigate geometrical properties of 5D cylindrical vacuum solutions with a transverse spherical symmetry. The metric is uniform along the fifth direction and characterized by tension and mass densities. The solutions are classified by the tension-to-mass ratio. One particular example is the well-known Schwarzschild black string which has a curvature singularity enclosed by a horizon. We focus mainly on geometry of other solutions which possess a naked singularity. The light signal emitted by an object approaching the singularity reaches a distant observer with finite time, but is infinitely red-shifted.

  11. Facilities for macromolecular crystallography at the Helmholtz-Zentrum Berlin.

    PubMed

    Mueller, Uwe; Darowski, Nora; Fuchs, Martin R; Förster, Ronald; Hellmig, Michael; Paithankar, Karthik S; Pühringer, Sandra; Steffien, Michael; Zocher, Georg; Weiss, Manfred S

    2012-05-01

    Three macromolecular crystallography (MX) beamlines at the Helmholtz-Zentrum Berlin (HZB) are available for the regional, national and international structural biology user community. The state-of-the-art synchrotron beamlines for MX BL14.1, BL14.2 and BL14.3 are located within the low-? section of the BESSY II electron storage ring. All beamlines are fed from a superconducting 7?T wavelength-shifter insertion device. BL14.1 and BL14.2 are energy tunable in the range 5-16?keV, while BL14.3 is a fixed-energy side station operated at 13.8?keV. All three beamlines are equipped with CCD detectors. BL14.1 and BL14.2 are in regular user operation providing about 200 beam days per year and about 600?user shifts to approximately 50 research groups across Europe. BL14.3 has initially been used as a test facility and was brought into regular user mode operation during the year 2010. BL14.1 has recently been upgraded with a microdiffractometer including a mini-? goniometer and an automated sample changer. Additional user facilities include office space adjacent to the beamlines, a sample preparation laboratory, a biology laboratory (safety level 1) and high-end computing resources. In this article the instrumentation of the beamlines is described, and a summary of the experimental possibilities of the beamlines and the provided ancillary equipment for the user community is given. PMID:22514183

  12. The surface structure of concentrated aqueous salt solutions E. Sloutskin

    E-print Network

    Ocko, Ben

    for more than a century.5 Most thermodynamical properties of the surfaces of such solutions are well the dependence on the anion and cation, and their size differences, we have chosen to study the alkali halides Rb

  13. Structural rearrangements in hairy-rod polymer solutions undergoing shear

    Microsoft Academic Search

    Loic Hilliou; Dimitris Vlassopoulos; Matthias Rehahn

    1999-01-01

    We report on a rheooptical investigation of hairy-rod poly(p-phenylene) solutions at different concentrations and temperatures. These polymers have a reasonably high persistence length\\u000a (about 28?nm) and behave as worm-like chains in dilute solutions, whereas they form nearly spherical fractal aggregates with\\u000a internal anisotropy at higher concentrations. By exposing these systems to time-dependent simple shear and following the evolution\\u000a of birefringence

  14. An investigation into methods of solution for nonlinear structural problems 

    E-print Network

    Henkel, Edwin Eugene

    1973-01-01

    procedure in which a correction factor is used to correct the drift of the solution. Reference 18 made use of a variational principle to derive a set of equations which contains the correction. This correction, called the unbalance of load, had been... dropped in previous research since it was assumed that the unbalance of load be zero throughout the analysis. The above authors realized that this was not the case when using an approximate solution procedure. 13 In much the same manner, Stricklin...

  15. Structural qualia: a solution to the hard problem of consciousness.

    PubMed

    Loorits, Kristjan

    2014-01-01

    The hard problem of consciousness has been often claimed to be unsolvable by the methods of traditional empirical sciences. It has been argued that all the objects of empirical sciences can be fully analyzed in structural terms but that consciousness is (or has) something over and above its structure. However, modern neuroscience has introduced a theoretical framework in which also the apparently non-structural aspects of consciousness, namely the so called qualia or qualitative properties, can be analyzed in structural terms. That framework allows us to see qualia as something compositional with internal structures that fully determine their qualitative nature. Moreover, those internal structures can be identified which certain neural patterns. Thus consciousness as a whole can be seen as a complex neural pattern that misperceives some of its own highly complex structural properties as monadic and qualitative. Such neural pattern is analyzable in fully structural terms and thereby the hard problem is solved. PMID:24672510

  16. Efficacy of macromolecular crowding in forcing proteins to fold

    Microsoft Academic Search

    Youxing Qu; D. W Bolen

    2002-01-01

    The intrinsically unstructured protein, reduced and carboxyamidated RNase T1 (TCAM) was used to determine the degree to which macromolecular crowding agents increase the equilibrium constant for folding. TCAM is not catalytically active in an aqueous assay system alone, but becomes catalytically active on addition of 400 mg\\/ml dextran 70. The activity observed accounts for approximately 16% of the total available

  17. Neutron Macromolecular Crystallography (NMC) can provide accurate hydrogen atom

    E-print Network

    Pennycook, Steve

    Neutron Macromolecular Crystallography (NMC) can provide accurate hydrogen atom positions crystals at a moderate 2 Å resolution. The advent of the Spallation Neutron Source (SNS neutron diffractometer (MaNDi) has been constructed at the SNS and is now operational. July 15-16, 2014

  18. Macromolecular Assemblage in the Design of a Synthetic AIDS Vaccine

    Microsoft Academic Search

    Jean-Philippe Defoort; Bernardetta Nardelli; Wolin Huang; David D. Ho; James P. Tam

    1992-01-01

    We describe a peptide vaccine model based on the mimicry of surface coat protein of a pathogen. This model used a macromolecular assemblage approach to amplify peptide antigens in liposomes or micelles. The key components of the model consisted of an oligomeric lysine scaffolding to amplify peptide antigens covalently 4-fold and a lipophilic membrane-anchoring group to further amplify noncovalently the

  19. Macromolecules in drug delivery Macromolecular targeting agents, carriers, and drugs

    E-print Network

    Barthelat, Francois

    Macromolecules in drug delivery Macromolecular targeting agents, carriers, and drugs 1gauthier@emt.inrs.ca #12;Why macromolecules in drug delivery? 2gauthier@emt.inrs.ca Classic chemotherapy Drug delivery? Targeting A carrier for small drugs A release mechanism (if necessary) Protection of drug cargo #12;How? 3

  20. Special quasirandom structure modeling of fluorite-structured oxide solid solutions with aliovalent cation substitutions

    NASA Astrophysics Data System (ADS)

    Wolff-Goodrich, Silas; Hanken, Benjamin E.; Solomon, Jonathan M.; Asta, Mark

    2015-07-01

    The accuracy of the special quasirandom structure (SQS) approach for modeling the structure and energetics of fluorite-structured oxide solid solutions with aliovalent cation substitutions is assessed in an ionic-pair potential study of urania and ceria based systems mixed with trivalent rare-earth ions. Mixing enthalpies for SQS supercells containing 96 and 324 lattice sites were calculated using ionic pair potentials for U0.5La0.5O1.75, U0.5Y0.5O1.75, Ce0.5La0.5O1.75, Ce0.5Y0.5O1.75, and Ce0.5Gd0.5O1.75, which all have stoichiometries of pyrochlores. The SQS results were compared to benchmark values for random substitutional disorder obtained using large supercell models. The calculations show significant improvement of the mixing enthalpy for the larger 324 site SQS, which is attributed to a better description of the structural distortions, as characterized by the radial distribution functions in relaxed systems.

  1. Ground Based Program for the Physical Analysis of Macromolecular Crystal Growth

    NASA Technical Reports Server (NTRS)

    Malkin, Alexander J.

    1998-01-01

    During the past year we have focused on application of in situ Atomic Force Microscopy (AFM) for studies of the growth mechanisms and kinetics of crystallization for different macromolecular systems. Mechanisms of macrostep formation and their decay, which are important in understanding of defect formation, were studied on the surfaces of thaumatin, catalase, canavalin and lysozyme crystals. Experiments revealed that step bunching on crystalline surfaces occurred either due to two- or three-dimensional nucleation on the terraces of vicinal slopes or as a result of uneven step generation by complex dislocation sources. No step bunching arising from interaction of individual steps in the course of the experiment was observed. The molecular structure of the growth steps for thaumatin and lipase crystals were deduced. It was further shown that growth step advance occurs by incorporation of single protein molecules. In singular directions growth steps move by one-dimensional nucleation on step edges followed by lateral growth. One-dimensional nuclei have different sizes, less then a single unit cell, varying for different directions of step movement. There is no roughness due to thermal fluctuations, and each protein molecule which incorporated into the step remained. Growth kinetics for catalase crystals was investigated over wide supersaturation ranges. Strong directional kinetic anisotropy in the tangential step growth rates in different directions was seen. The influence of impurities on growth kinetics and cessation of macromolecular crystals was studied. Thus, for catalase, in addition to pronounced impurity effects on the kinetics of crystallization, we were also able to directly observe adsorption of some impurities. At low supersaturation we repeatedly observed filaments which formed from impurity molecules sedimenting on the surfaces. Similar filaments were observed on the surfaces of thaumatin, canavalin and STMV crystals as well, but the frequency was low compared with catalase crystallization. Cessation of growth of xylanase and lysozyme crystals was also observed and appeared to be a consequence of the formation of dense impurity adsorption layers. Attachment: "An in situ AFM investigation of catalase crystallization", "Atomic force microscopy studies of living cells: visualization of motility, division, aggregation, transformation, and apoptosis", AFM studies on mechanisms of nucleation and growth of macromolecular crystals", and "In situ atomic force microscopy studies of surface morphology, growth kinetics, defect structure and dissolution in macromolecular crystallization".

  2. Solution of structural analysis problems on a parallel computer

    NASA Technical Reports Server (NTRS)

    Storaasli, Olaf; Poole, Eugene; Ortega, James; Cleary, Andrew; Vaughan, Courtenay

    1988-01-01

    The problems of a blade-stiffened panel with a hole subjected to compression, and a deployable space mast subjected to tip loads, are treated through the application of FEM to model generation followed by the solution of a linear system of equations. Direct and iterative approaches to the solution of the linear systems are solved in turn; for the panel problems using varying numbers of processors, the incomplete Cholesky-conjugate gradient method was the fastest iterative method on all but two instances in which the number of processors was large.

  3. Atomistic Modeling of Macromolecular Crowding Predicts Modest Increases in Protein Folding and Binding Stability

    PubMed Central

    Qin, Sanbo; Zhou, Huan-Xiang

    2009-01-01

    Abstract Theoretical models predict that macromolecular crowding can increase protein folding stability, but depending on details of the models (e.g., how the denatured state is represented), the level of stabilization predicted can be very different. In this study, we represented the native and denatured states atomistically, with conformations sampled from explicit-solvent molecular dynamics simulations at room temperature and high temperature, respectively. We then designed an efficient algorithm to calculate the allowed fraction, f, when the protein molecule is placed inside a box of crowders. That a fraction of placements of the protein molecule is disallowed because of volume exclusion by the crowders leads to an increase in chemical potential, given by ?? = ?kBT lnf. The difference in ?? between the native and denatured states predicts the effect of crowding on the folding free energy. Even when the crowders occupied 35% of the solution volume, the stabilization reached only 1.5 kcal/mol for cytochrome b562. The modest stabilization predicted is consistent with experimental studies. Interestingly, a mixture of different sized crowders was found to exert a greater effect than the sum of the individual species of crowders. The stabilization of crowding on the binding stability of barnase and barstar, based on atomistic modeling of the proteins, was similarly modest. These findings have profound implications for macromolecular crowding inside cells. PMID:19580740

  4. Microbatch macromolecular crystallization on a thermal gradient

    Microsoft Academic Search

    Joseph R. Luft; Dawn M. Rak; George T. DeTitta

    1999-01-01

    We can exploit the temperature dependence of protein solubility in a blind search for optimal crystallization conditions by conducting experiments on thermal gradients. A microbatch technique coupled with a specially constructed thermal gradient allows us to conduct polythermal experiments over the range 6–30°C using as little as 7?l of solution. The crystallization vessel is a micropipette commonly used in blood

  5. Nonpolar solutes enhance water structure within hydration shells while reducing

    E-print Network

    Raschke, Tanya M.

    an unfavorable free energy, a positive entropy at room temperature, and a large positive heat capacity (5, 6 correlation function of liquid water has been generated by applying maximum entropy methods to g(r) functions of a variety of nonpolar solutes and surfaces (1, 12), including proteins (13). Specific studies

  6. Solution NMR Structure of the 30S Ribosomal Protein S28E From Pyrococcus Horikoshii

    Microsoft Academic Search

    James M. Aramini; Yuanpeng Huang; John R. Cort; Sharon Goldsmith-Fischman; Rong Xiao; Liang-yu Shih; Chi K. Ho; Jinfeng Liu; Burkhard Rost; Barry Honig; Michael A. Kennedy; Thomas Acton; Gaetano Montelione

    2003-01-01

    We report NMR assignments and solution structure of the 71-residue 30S ribosomal protein S28E from the archaean Pyrococcus horikoshii, target JR19 of the Northeast Structural Genomics Consortium. The structure, determined rapidly with the aid of automated backbone resonance assignment (AutoAssign) and automated structure determination (AutoStructure) software, is characterized by a four-stranded -sheet with a classic Greek-key topology and an oligonucleotide\\/oligosaccharide

  7. Evidence for water structuring forces between surfaces

    SciTech Connect

    Stanley, Christopher B [ORNL; Rau, Dr. Donald [National Institutes of Health

    2011-01-01

    Structured water on apposing surfaces can generate significant energies due to reorganization and displacement as the surfaces encounter each other. Force measurements on a multitude of biological structures using the osmotic stress technique have elucidated commonalities that point toward an underlying hydration force. In this review, the forces of two contrasting systems are considered in detail: highly charged DNA and nonpolar, uncharged hydroxypropyl cellulose. Conditions for both net repulsion and attraction, along with the measured exclusion of chemically different solutes from these macromolecular surfaces, are explored and demonstrate features consistent with a hydration force origin. Specifically, the observed interaction forces can be reduced to the effects of perturbing structured surface water.

  8. A brief history of macromolecular crystallography, illustrated by a family tree and its Nobel fruits.

    PubMed

    Jaskolski, Mariusz; Dauter, Zbigniew; Wlodawer, Alexander

    2014-09-01

    As a contribution to the celebration of the year 2014, declared by the United Nations to be 'The International Year of Crystallography', the FEBS Journal is dedicating this issue to papers showcasing the intimate union between macromolecular crystallography and structural biology, both in historical perspective and in current research. Instead of a formal editorial piece, by way of introduction, this review discusses the most important, often iconic, achievements of crystallographers that led to major advances in our understanding of the structure and function of biological macromolecules. We identified at least 42 scientists who received Nobel Prizes in Physics, Chemistry or Medicine for their contributions that included the use of X-rays or neutrons and crystallography, including 24 who made seminal discoveries in macromolecular sciences. Our spotlight is mostly, but not only, on the recipients of this most prestigious scientific honor, presented in approximately chronological order. As a summary of the review, we attempt to construct a genealogy tree of the principal lineages of protein crystallography, leading from the founding members to the present generation. PMID:24698025

  9. Comparison of the crystal and solution structures of calmodulin and troponin C

    SciTech Connect

    Heidorn, D.B.; Trewhella, J.

    1988-02-09

    X-ray solution scattering data from skeletal muscle troponin C and from calmodulin have been measured. Modeling studies based on the crystal structure coordinates for these proteins show discrepancies between the solution data and the crystal structure that indicate that if the size and shape of the globular domains are the same in solution as in the crystal, the distances between them must be smaller by several angstroms. Bringing the globular domains closer together requires structural changes in the interconnecting helix that joins them.

  10. NMR solution structure of the human prion protein

    Microsoft Academic Search

    Ralph Zahn; Aizhuo Liu; Thorsten Lührs; Roland Riek; Christine von Schroetter; Francisco López García; Martin Billeter; Luigi Calzolai; Gerhard Wider; Kurt Wüthrich

    2000-01-01

    The NMR structures of the recombinant human prion protein, hPrP(23-230), and two C-terminal fragments, hPrP(90-230) and hPrP(121-230), include a globular domain extending from residues 125-228, for which a detailed structure was obtained, and an N-terminal flexibly disordered \\

  11. Structure solution with three-dimensional sets of precessed electron diffraction intensities

    Microsoft Academic Search

    Mauro Gemmi; Stavros Nicolopoulos

    2007-01-01

    The use of the precession technique for obtaining three-dimensional (3D) sets of electron diffraction intensities suitable for structure solution is discussed. The minerals uvarovite and åkermanite have been used as testing structures. The electron diffraction data sets obtained on these samples retain an acceptable linear relation with calculated structure factor amplitudes. The quality of these data is suitable to solve

  12. SOLUTION GROWN Ga,_,AI,As SUPERLATTICE STRUCTURES J. M. WOODALL

    E-print Network

    Woodall, Jerry M.

    SOLUTION GROWN Ga,_,AI,As SUPERLATTICE STRUCTURES J. M. WOODALL IBM Tlw~trtr.v J. W~rtsorr Rrscwch'). In a previous report'). Ga, _,AI,Ac superlattice structures with periods of about 2-3 pm and IO periods thick apparatus for the growth of the Ga, -,AI,As superlattice structure is shown in fig. I. This figure shows two

  13. Effect of Base Sequence on G-Wire Formation in Solution

    PubMed Central

    Spindler, Lea; Rigler, Martin; Drevenšek-Olenik, Irena; Ma'ani Hessari, Nason; Webba da Silva, Mateus

    2010-01-01

    The formation and dimensions of G-wires by different short G-rich DNA sequences in solution were investigated by dynamic light scattering (DLS) and polyacrilamide gel electrophoresis (PAGE). To explore the basic principles of wire formation, we studied the effects of base sequence, method of preparation, temperature, and oligonucleotide concentration. Both DLS and PAGE show that thermal annealing induces much less macromolecular self-assembly than dialysis. The degree of assembly and consequently length of G-wires (5-6?nm) are well resolved by both methods for DNA sequences with intermediate length, while some discrepancies appear for the shortest and longest sequences. As expected, the longest DNA sequence gives the longest macromolecular aggregates with a length of about 11?nm as estimated by DLS. The quadruplex topologies show no concentration dependence in the investigated DNA concentration range (0.1?mM–0.4?mM) and no structural change upon heating. PMID:20725621

  14. The concentration-dependence of macromolecular parameters.

    PubMed Central

    Harding, S E; Johnson, P

    1985-01-01

    Theories concerning the concentration-dependence of sedimentation and diffusion coefficients for macro-molecules in dilute solution are compared and discussed, together with their experimental basis. An attempt has been made to clarify an important uncertainty still present in the literature as to whether sedimentation coefficients should be corrected for solvent or solution density. It is pointed out that the two processes yield the same extrapolation limit but different concentration-dependencies, which have, however, been related. A general expression is derived thermodynamically for the concentration-dependence of diffusion that includes the coefficient of the concentration term involved in sedimentation (on the basis of sedimentation coefficients corrected from solution density). For rigid spherical particles the expression is shown to be exactly equivalent to one given by Batchelor [(1976) J. Fluid Mech. 74, 1-29], which was derived on the basis of sedimentation coefficients corrected from solvent density. Finally, we discuss the concentration-dependence of apparent weight-average relative molecular masses ('molecular weights') (from, e.g., sedimentation equilibrium) and note an important omission in some earlier representations. PMID:4074322

  15. Interfacial structure of photoresist thin films in developer solutions

    NASA Astrophysics Data System (ADS)

    Prabhu, Vivek M.; Vogt, Bryan D.; Wu, Wen-Li; Douglas, Jack F.; Lin, Eric K.; Satija, Sushil K.; Goldfarb, Dario L.; Ito, Hiroshi

    2005-05-01

    A depth profile of the base developer counterion concentration within thin photoresist films was measured in-situ using contrast variant specular neutron reflectivity to characterize the initial swelling stage of the film dissolution. We find a substantial counterion depletion near the substrate and an enrichment near the periphery of the film extending into the solution. These observations challenge our understanding of the charge distribution in photoresist and polyelectrolyte films and are important for understanding film dissolution in medical and technological applications.

  16. The thermodynamics and structure of nonaqueous solutions of electrolytes

    Microsoft Academic Search

    K. P. Mishchenko; G. M. Poltoratskii

    1964-01-01

    On the basis of measurements of the vapor pressure above solutions of tetrabutylammonium thiocyanate in benzene, values have been calculated for the nonideal fractions of the relative partial molal (t.p.m.) entropies of the solvent and its r.p.m, enthalpy Lz. It has been found that throughout the whole temperature range from 15 to 40* and at concentrations up to 8 moles

  17. Integrated Force Method Solution to Indeterminate Structural Mechanics Problems

    NASA Technical Reports Server (NTRS)

    Patnaik, Surya N.; Hopkins, Dale A.; Halford, Gary R.

    2004-01-01

    Strength of materials problems have been classified into determinate and indeterminate problems. Determinate analysis primarily based on the equilibrium concept is well understood. Solutions of indeterminate problems required additional compatibility conditions, and its comprehension was not exclusive. A solution to indeterminate problem is generated by manipulating the equilibrium concept, either by rewriting in the displacement variables or through the cutting and closing gap technique of the redundant force method. Compatibility improvisation has made analysis cumbersome. The authors have researched and understood the compatibility theory. Solutions can be generated with equal emphasis on the equilibrium and compatibility concepts. This technique is called the Integrated Force Method (IFM). Forces are the primary unknowns of IFM. Displacements are back-calculated from forces. IFM equations are manipulated to obtain the Dual Integrated Force Method (IFMD). Displacement is the primary variable of IFMD and force is back-calculated. The subject is introduced through response variables: force, deformation, displacement; and underlying concepts: equilibrium equation, force deformation relation, deformation displacement relation, and compatibility condition. Mechanical load, temperature variation, and support settling are equally emphasized. The basic theory is discussed. A set of examples illustrate the new concepts. IFM and IFMD based finite element methods are introduced for simple problems.

  18. Stationary solutions to a system of size-structured populations with nonlinear growth rate.

    PubMed

    Kato, Nobuyuki

    2012-01-01

    We study stationary solutions to a system of size-structured population models with nonlinear growth rate. Several characterizations of stationary solutions are provided. It is shown that the steady-state problem can be converted into different problems such as two types of eigenvalue problems and a fixed-point problem. In the two-species case, we give an existence result of nonzero stationary solutions by using the fixed-point problem. PMID:22873674

  19. The structure of the gamma-domain for H-infinity Riccati solutions

    NASA Technical Reports Server (NTRS)

    Li, X. P.; Chang, B. C.

    1992-01-01

    The authors investigated some properties of the solutions to H-infinity Riccati equations which play a key role in the state approach to H-infinity optimization problem. The structure of the gamma-domain for the Riccati solutions has been described. There are two kinds of lower bounds for the solutions to exist and to be positive semidefinite respectively. A quadratically convergent algorithm for computing the lower bound is discussed.

  20. Salt-stabilized globular protein structure in 7 M aqueous urea solution

    E-print Network

    Wider, Gerhard

    1 Salt-stabilized globular protein structure in 7 M aqueous urea solution V. Dötsch,1 G. Wider, G Hochschule- Hönggerberg, CH-8093 Zürich, Switzerland Keywords Protein folding; Urea denaturation; Salt changing the solution conditions. In this paper we describe the influence of various salts or non

  1. Gelation of aqueous gelatin solutions. I. Structural investigation Madeleine Djabourov, Jacques Leblond and Pierre Papon

    E-print Network

    Paris-Sud XI, Université de

    319 Gelation of aqueous gelatin solutions. I. Structural investigation Madeleine Djabourov, Jacques Physics Abstracts 82.70 - 07.60F - 61.40 The gelation of aqueous gelatin solutions is a process which has, the subject has regained a new stimulation arising both from the modern ideas on the gelation phenomenon

  2. Cone-angle Dependence of Ab-initio Structure Solutions Using Precession Electron Diffraction

    Microsoft Academic Search

    James Ciston; Christopher S. Own; Laurence D. Marks

    2008-01-01

    Precession electron diffraction (PED) is a technique which is gaining increasing interest due to its ease of use and reduction of the dynamical scattering problem in electron diffraction, leading to more direct structure solutions. We have performed a systematic study of the effect of precession angle for the mineral andalusite on kinematical extinctions and direct methods solutions where the semiangle

  3. Supramolecular porphyrinic prisms: coordinative assembly and solution phase X-ray structural characterization{

    E-print Network

    Supramolecular porphyrinic prisms: coordinative assembly and solution phase X-ray structural 2006 DOI: 10.1039/b610025b Supramolecular porphyrin prisms have been obtained via coordinative self of solution phase X-ray scattering and diffraction. Highly conjugated porphyrin dimers, trimers, and larger

  4. Scattering From Layered Structures With One Rough Interface: A Unified Formulation of Perturbative Solutions

    Microsoft Academic Search

    Giorgio Franceschetti; Pasquale Imperatore; Antonio Iodice; Daniele Riccio; Giuseppe Ruello

    2008-01-01

    In this paper, we investigate analytically the connection between the existing first-order small perturbation method solutions for the scattering from a layered structure with one rough interface. First of all, by using effectively the concept of generalized reflection coefficients, we cast the existing models in a unified more compact formulation and point out the connection between the different analytical solutions.

  5. A data structure for the efficient Kronecker solution of GSPNs Gianfranco Ciardo

    E-print Network

    Ciardo, Gianfranco

    A data structure for the efficient Kronecker solution of GSPNs Gianfranco Ciardo Andrew S. Miner Department of Computer Science College of William and Mary Williamsburg, VA, 23185 {ciardo as well to the study of absorbing CTMCs or the transient solution of arbitrary CTMCs. G. Ciardo's work

  6. Solution structure of a designed cyclic peptide ligand for nickel and copper ions.

    PubMed

    Eshelman, Matthew R; Aldous, Amanda R; Neupane, Kosh P; Kritzer, Joshua A

    2014-10-21

    Nuclear magnetic resonance (NMR) spectroscopy was used to study a cyclic peptide derived from the amino-terminal copper-and-nickel-binding (ATCUN) motif. The three-dimensional structure of the unliganded peptide in aqueous solution was solved by simulated annealing using distance constraints derived from Nuclear Overhauser Effects. A structural model for the Ni(II)-bound complex was also produced based on NMR evidence and prior spectroscopic data, which are consistent with crystal structures of linear ATCUN complexes. Structural interpolation, or "morphing," was used to understand the transition of this highly structured cyclic peptide from its unliganded structure to its metal-ion-bound structure. PMID:25414527

  7. Use of Plastic Capillaries for Macromolecular Crystallization

    NASA Technical Reports Server (NTRS)

    Potter, Rachel R.; Hong, Young-Soo; Ciszak, Ewa M.

    2003-01-01

    Methods of crystallization of biomolecules in plastic capillaries (Nalgene 870 PFA tubing) are presented. These crystallization methods used batch, free-interface liquid- liquid diffusion alone, or a combination with vapor diffusion. Results demonstrated growth of crystals of test proteins such as thaumatin and glucose isomerase, as well as protein studied in our laboratory such dihydrolipoamide dehydrogenase. Once the solutions were loaded in capillaries, they were stored in the tubes in frozen state at cryogenic temperatures until the desired time of activation of crystallization experiments.

  8. Multiple-bed solution mining of an inclined structure

    SciTech Connect

    Higgins, R.S.

    1983-12-06

    Solution mining method is disclosed particularly adapted for recovery of potash and the like from multiple beds of relatively thin, inclined strata at substantial depths. Dissolution of each ore strata overlain by an insoluble and impermeable strata takes place through a single borehole in sequential order beginning with the deepest ore strata. Water is injected down a borehole at a predetermined rate and, being much less dense than present brine, flows in an updip direction along the top of the cavity to the forward mining face remote from the drill hole. Loaded, heavy brine flows downdip along the bottom of the cavity to an outflow pipe communicating with the bottom of the cavity.

  9. On Computing Multiple Solutions of Nonlinear PDEs Without Variational Structure 

    E-print Network

    Wang, Changchun

    2012-07-16

    numerical solutions u1; :::; u7 to Example 2.3.5. 61 2.18 The pro les of the rst 8 numerical eigen functions u1; :::; u8 for Exam- ple 2.3.6 with v(x) = 0 at the energy level C = 900. The contours show that the eigen functions are not localized.... : : : : : : : : : : : : : : 63 2.19 The rst 8 numerical eigen functions u1; :::; u8 for Example 2.3.6 with v(x) = 0 at the energy level C = 10. The contours show that the eigen functions are not localized. : : : : : : : : : : : : : : : : : : : : : : 64 2.20 The rst 8...

  10. Supersymmetric solutions on S U (4 )-structure deformed Stenzel space

    NASA Astrophysics Data System (ADS)

    Prins, D. L. A.

    2015-05-01

    The Stenzel space fourfold is a noncompact Calabi-Yau (CY) which is a higher-dimensional analogue of the deformed conifold. We consider N =(1 ,1 ), type-IIA, N =1 M-theory and N =(2 ,0 ), type-IIB compactifications on this Stenzel space, thus examining the gravity side of potentially higher-dimensional analogues of Klebanov-Strassler-like compactifications. We construct families of S U (4 )-structures and solve associated moduli spaces, of complex and symplectic structures amongst others. By making use of these, we can construct IIA compactifications on manifolds homeomorphic to the Stenzel space fourfold, but with complex non-CY S U (4 )-structures. Such compactifications are sourced by a distribution of NS5-branes. The external metric is asymptotically conformal AdS3 and should thus be suitable for holography applications.

  11. On the variability of experimental data in macromolecular crystallography

    PubMed Central

    Pozharski, Edwin

    2012-01-01

    Experimental errors as determined by data-processing algorithms in macromolecular crystallography are compared with the direct error estimates obtained by a multiple crystal data-collection protocol. It is found that several-fold error inflation is necessary to account for crystal-to-crystal variation. It is shown that similar error inflation is observed for data collected from multiple sections of the same crystal, indicating non-uniform crystal growth as one of the likely sources of additional data variation. Other potential sources of error inflation include differential X-ray absorption for different reflections and variation of unit-cell parameters. The underestimation of the experimental errors is more severe in lower resolution shells and for reflections characterized by a higher signal-to-noise ratio. These observations partially account for the gap between the expected and the observed R values in macromolecular crystallography. PMID:22948908

  12. Solution NMR structure of the 30S ribosomal protein S28E from Pyrococcus horikoshii

    Microsoft Academic Search

    James M. Aramini; Yuanpeng J. Huang; John R. Cort; Sharon Goldsmith-Fischman; Rong Xiao; Liang-Yu Shih; Chi K. Ho; Jinfeng Liu; Burkhard Rost; Barry Honig; Michael A. Kennedy; Thomas B. Acton; Gaetano T. Montelione

    2003-01-01

    We report NMR assignments and solution structure of the 71-residue 30S ribosomal protein S28E from the archaean Pyrococcus horikoshii, target JR19 of the Northeast Structural Genomics Consortium. The struc- ture, determined rapidly with the aid of automated backbone resonance assignment (AutoAssign) and automated structure determination (AutoStructure) software, is characterized by a four-stranded -sheet with a classic Greek-key topology and an

  13. Axial growth and fusion of liposome regulated by macromolecular crowding and confinement.

    PubMed

    Liu, Yun; Zhu, Lin; Yang, Jingfa; Sun, Jianbo; Zhao, Jiang; Liang, Dehai

    2015-05-01

    The endomembrane system, including the endoplasmic reticulum, Golgi apparatus, lysosomes, and endosomes, is located in the crowded intracellular environment. An understanding of the cellular structure and functions requires knowledge of how macromolecular crowding and confinement affect the activity of membrane and its proteins. Using negatively charged liposome and the peptide K3L8K3 as a model system, we studied the aggregation behavior of liposome in a matrix of polyacrylamide and hyaluronic acid. Without matrix, the liposomes form spherical aggregates in the presence of K3L8K3. However, they orient in one dimension and fuse into a tube up to 40 ?m long in the matrix. The growth of the tube is via end-to-end connection. This anisotropic growth is mainly due to the macromolecular confinement provided by the polymer network. The study of the interactions between liposome and peptide in the crowded environment helps to reveal the mechanism of membrane-related processes in vivo. PMID:25874379

  14. Inflammasome activation causes dual recruitment of NLRC4 and NLRP3 to the same macromolecular complex.

    PubMed

    Man, Si Ming; Hopkins, Lee J; Nugent, Eileen; Cox, Susan; Glück, Ivo M; Tourlomousis, Panagiotis; Wright, John A; Cicuta, Pietro; Monie, Tom P; Bryant, Clare E

    2014-05-20

    Pathogen recognition by nucleotide-binding oligomerization domain-like receptor (NLR) results in the formation of a macromolecular protein complex (inflammasome) that drives protective inflammatory responses in the host. It is thought that the number of inflammasome complexes forming in a cell is determined by the number of NLRs being activated, with each NLR initiating its own inflammasome assembly independent of one another; however, we show here that the important foodborne pathogen Salmonella enterica serovar Typhimurium (S. Typhimurium) simultaneously activates at least two NLRs, whereas only a single inflammasome complex is formed in a macrophage. Both nucleotide-binding domain and leucine-rich repeat caspase recruitment domain 4 and nucleotide-binding domain and leucine-rich repeat pyrin domain 3 are simultaneously present in the same inflammasome, where both NLRs are required to drive IL-1? processing within the Salmonella-infected cell and to regulate the bacterial burden in mice. Superresolution imaging of Salmonella-infected macrophages revealed a macromolecular complex with an outer ring of apoptosis-associated speck-like protein containing a caspase activation and recruitment domain and an inner ring of NLRs, with active caspase effectors containing the pro-IL-1? substrate localized internal to the ring structure. Our data reveal the spatial localization of different components of the inflammasome and how different members of the NLR family cooperate to drive robust IL-1? processing during Salmonella infection. PMID:24803432

  15. Effects of Cannabinoids on Macromolecular Synthesis in Isolated Spermatogenic Cells

    Microsoft Academic Search

    S. K. Tilak; A. M. Zimmerman

    1984-01-01

    Effects of ?9-tetrahydrocannabinol (THC), cannabinol (CBN) and cannabidiol (CBD) (1, 3 or 5 ?M for 2 h) on macromolecular synthesis were investigated in homogeneous populations of pachytene spermatocytes and round spermatids obtained from CD-1 mice. Incorporation of 3H-uridine into the acid-insoluble fraction was used as an index of RNA synthesis. Treatment of pachytene spermatocytes with 5 ?M THC, CBN and

  16. A 3D cellular context for the macromolecular world

    PubMed Central

    Patwardhan, Ardan; Ashton, Alun; Brandt, Robert; Butcher, Sarah; Carzaniga, Raffaella; Chiu, Wah; Collinson, Lucy; Doux, Pascal; Duke, Elizabeth; Ellisman, Mark H; Franken, Erik; Grünewald, Kay; Heriche, Jean-Karim; Koster, Abraham; Kühlbrandt, Werner; Lagerstedt, Ingvar; Larabell, Carolyn; Lawson, Catherine L; Saibil, Helen R; Sanz-García, Eduardo; Subramaniam, Sriram; Verkade, Paul; Swedlow, Jason R; Kleywegt, Gerard J

    2015-01-01

    We report the outcomes of the discussion initiated at the workshop entitled A 3D Cellular Context for the Macromolecular World and propose how data from emerging three-dimensional (3D) cellular imaging techniques—such as electron tomography, 3D scanning electron microscopy and soft X-ray tomography—should be archived, curated, validated and disseminated, to enable their interpretation and reuse by the biomedical community. PMID:25289590

  17. Stable time domain PEEC solution for pulse interconnection structures

    Microsoft Academic Search

    Sergey V. Kochetov; Guenter Wollenberg

    2005-01-01

    Time domain methods for transient analysis of pulse excited interconnection structures are of big interest. Since frequency domain methods with IFT in a frequency range given by UWB pulses need much computation time, in particular, if system investigated have a low dissipation and the response time is relatively long in comparison with the exciting pulse. A further advantage of time

  18. Structure of the zodiacal cloud: new analytical and numerical solutions

    Microsoft Academic Search

    N. Gor'kavyi; L. Ozernoy; J. Mather; T. Taidakova

    1998-01-01

    Recent results of analytical and numerical modelling of the interplanetary dust (IPD) distribution are described. They have been obtained with a new techniques employing the continuity equation written in the space of orbital coordinates. A 3-D structure and the corresponding 2-D slices for the IPD cloud governed by the Poynting-Robertson drag are computed in the framework of our 'reference model',

  19. Vibration based structural health monitoring: Wavelet packet transform based solution

    Microsoft Academic Search

    Z. Sun; C.-C. Chang

    2007-01-01

    One prominent problem for vibration-based structural health monitoring is to extract condition indices which are sensitive to damage and yet insensitive to measurement noise. In this paper, a condition index extraction method based on the wavelet packet transform (WPT) is proposed. This transform leads to the formulation of a novel condition index: wavelet packet signature (WPS). The sensitivity of the

  20. Macromolecular Assemblage in the Design of a Synthetic AIDS Vaccine

    NASA Astrophysics Data System (ADS)

    Defoort, Jean-Philippe; Nardelli, Bernardetta; Huang, Wolin; Ho, David D.; Tam, James P.

    1992-05-01

    We describe a peptide vaccine model based on the mimicry of surface coat protein of a pathogen. This model used a macromolecular assemblage approach to amplify peptide antigens in liposomes or micelles. The key components of the model consisted of an oligomeric lysine scaffolding to amplify peptide antigens covalently 4-fold and a lipophilic membrane-anchoring group to further amplify noncovalently the antigens many-fold in liposomal or micellar form. A peptide antigen derived from the third variable domain of glycoprotein gp120 of human immunodeficiency virus type 1 (HIV-1), consisting of neutralizing, T-helper, and T-cytotoxic epitopes, was used in a macromolecular assemblage model (HIV-1 linear peptide amino acid sequence 308-331 in a tetravalent multiple antigen peptide system linked to tripalmitoyl-S-glycerylcysteine). The latter complex, in liposome or micelle, was used to immunize mice and guinea pigs without any adjuvant and found to induce gp120-specific antibodies that neutralize virus infectivity in vitro, elicit cytokine production, and prime CD8^+ cytotoxic T lymphocytes in vivo. Our results show that the macromolecular assemblage approach bears immunological mimicry of the gp120 of HIV virus and may lead to useful vaccines against HIV infection.

  1. Nanoscale Imaging with Resonant Coherent XRays: Extension of Multiple-Wavelength Anomalous Diffraction to Nonperiodic Structures

    Microsoft Academic Search

    A. Scherz; D. Zhu; R. Rick; W. F. Schlotter; S. Roy; J. Lüning; J. Stöhr

    2008-01-01

    The methodology of multiple-wavelength anomalous diffraction, widely used for macromolecular structure determination, is extended to the imaging of nonperiodic nanostructures. We demonstrate the solution of the phase problem by a combination of two resonantly recorded coherent scattering patterns at the carbon K edge (285 eV). Our approach merges iterative phase retrieval and x-ray holography approaches, yielding unique and rapid reconstructions.

  2. Atomic detail brownian dynamics simulations of concentrated protein solutions with a mean field treatment of hydrodynamic interactions.

    SciTech Connect

    Mereghetti, Paolo; Wade, Rebecca C.

    2012-07-26

    High macromolecular concentrations are a distinguishing feature of living organisms. Understanding how the high concentration of solutes affects the dynamic properties of biological macromolecules is fundamental for the comprehension of biological processes in living systems. In this paper, we describe the implementation of mean field models of translational and rotational hydrodynamic interactions into an atomically detailed many-protein brownian dynamics simulation method. Concentrated solutions (30-40% volume fraction) of myoglobin, hemoglobin A, and sickle cell hemoglobin S were simulated, and static structure factors, oligomer formation, and translational and rotational self-diffusion coefficients were computed. Good agreement of computed properties with available experimental data was obtained. The results show the importance of both solvent mediated interactions and weak protein-protein interactions for accurately describing the dynamics and the association properties of concentrated protein solutions. Specifically, they show a qualitative difference in the translational and rotational dynamics of the systems studied. Although the translational diffusion coefficient is controlled by macromolecular shape and hydrodynamic interactions, the rotational diffusion coefficient is affected by macromolecular shape, direct intermolecular interactions, and both translational and rotational hydrodynamic interactions.

  3. The accuracy, stability and convergence characteristics of solution procedures for nonlinear structural analysis 

    E-print Network

    Malek, Michele

    1974-01-01

    causes a large change in displacement, then the solution is likely to become unstable. However, if the structure stiffens as the load is increased then the solution will be stable. 28 aK NL, O fI q a. Unstabl. e Solution aK . o gq b. Stable.... tionally stable but the Adams-Moulton predictor-corrector has been used with succ. css in structural applications, It is also recommended that, where possible, the tangent stiffness matrix rather than a pseudo-forces vector be used to describe...

  4. Molecular Structure of Hydrochloric acid (if in aqueous solution)

    NSDL National Science Digital Library

    2002-09-10

    Hydrochloric acid (or hydrogen chloride) can be a colorless liquid with a sharp odor or a colorless to slightly yellow gas. It is a strong acid (it ionizes completely in aqueous solution) and highly corrosive. HCl is widely used as a laboratory reagent in the production of chlorides, in organic synthesis, ore reduction, hydrolyzing of starch and proteins, in the preparation of various food products, metal cleaning and pickling, for instance, and pharmaceutics acidifier. HCI is widely used in the manufacture e.g., in the conversion of cornstarch to syrup, in sugar refining, electroplating, soap refining, leather tanning etc. It is also used to remove scale and dust from boilers and heat exchange equipment, to clean membranes in desalination plants, increase oil well output and prepare metals for coatings.

  5. Structural characteristics of polyelectrolyte-surfactant complexes in aqueous solution

    NASA Astrophysics Data System (ADS)

    Nause, Richard; Strey, Helmut H.; Hoagland, David A.

    2001-03-01

    When polyelectrolytes and surfactants of opposite charge are mixed at a stoichiometric charge ratio, they self-assemble into ordered complexes. This contribution reports the self-assembly behavior of polyelectrolyte-surfactant complexes in aqueous solution. Of specific importance are the thermodynamics associated with polyelectrolyte-surfactant interactions, the morphological sensitivity to surfactant concentration, and the overall effect of ionic strength on the aggregation process. We have chosen to study the interaction of a model polyelectrolyte [sodium poly(styrene sulfonate)] with cetyltrimethylammonium chloride (CTAC), a cationic surfactant. We utilize turbidity, microcalorimetry, and small angle X-ray scattering to investigate the self-assembly process and specifically identify the factors that govern the aggregation behavior of polymer surfactant systems. We eventually plan to develop strategies to better control and predict the behavior of these systems.

  6. Assembly of a polytopic membrane protein structure from the solution structures of overlapping peptide fragments of bacteriorhodopsin.

    PubMed Central

    Katragadda, M; Alderfer, J L; Yeagle, P L

    2001-01-01

    Three-dimensional structures of only a handful of membrane proteins have been solved, in contrast to the thousands of structures of water-soluble proteins. Difficulties in crystallization have inhibited the determination of the three-dimensional structure of membrane proteins by x-ray crystallography and have spotlighted the critical need for alternative approaches to membrane protein structure. A new approach to the three-dimensional structure of membrane proteins has been developed and tested on the integral membrane protein, bacteriorhodopsin, the crystal structure of which had previously been determined. An overlapping series of 13 peptides, spanning the entire sequence of bacteriorhodopsin, was synthesized, and the structures of these peptides were determined by NMR in dimethylsulfoxide solution. These structures were assembled into a three-dimensional construct by superimposing the overlapping sequences at the ends of each peptide. Onto this construct were written all the distance and angle constraints obtained from the individual solution structures along with a limited number of experimental inter-helical distance constraints, and the construct was subjected to simulated annealing. A three-dimensional structure, determined exclusively by the experimental constraints, emerged that was similar to the crystal structure of this protein. This result suggests an alternative approach to the acquisition of structural information for membrane proteins consisting of helical bundles. PMID:11463644

  7. Robust, high-throughput solution structural analyses by small angle X-ray scattering (SAXS)

    SciTech Connect

    Hura, Greg L.; Menon, Angeli L.; Hammel, Michal; Rambo, Robert P.; Poole II, Farris L.; Tsutakawa, Susan E.; Jenney Jr, Francis E.; Classen, Scott; Frankel, Kenneth A.; Hopkins, Robert C.; Yang, Sungjae; Scott, Joseph W.; Dillard, Bret D.; Adams, Michael W. W.; Tainer, John A.

    2009-07-20

    We present an efficient pipeline enabling high-throughput analysis of protein structure in solution with small angle X-ray scattering (SAXS). Our SAXS pipeline combines automated sample handling of microliter volumes, temperature and anaerobic control, rapid data collection and data analysis, and couples structural analysis with automated archiving. We subjected 50 representative proteins, mostly from Pyrococcus furiosus, to this pipeline and found that 30 were multimeric structures in solution. SAXS analysis allowed us to distinguish aggregated and unfolded proteins, define global structural parameters and oligomeric states for most samples, identify shapes and similar structures for 25 unknown structures, and determine envelopes for 41 proteins. We believe that high-throughput SAXS is an enabling technology that may change the way that structural genomics research is done.

  8. The structure factor of dense two-dimensional polymer solutions

    Microsoft Academic Search

    H. Meyer; N. Schulmann; J. E. Zabel; J. P. Wittmer

    2011-01-01

    According to the generalized Porod law the intramolecular structure factor F(q) of compact objects with surface dimension ds scales as F(q)\\/N?1\\/(R(N)q)2d?ds in the intermediate range of the wave vector q with d being the dimension of the embedding space, N the mass of the objects and R(N)?N1\\/d their typical size. By means of molecular-dynamics simulations of a bead-spring model with

  9. Phase Transitions and Relaxation Processes in Macromolecular Systems: The Case of Bottle-brush Polymers

    E-print Network

    Hsiao-Ping Hsu; Wolfgang Paul; Panagiotis E. Theodorakis; Kurt Binder

    2009-10-22

    As an example for the interplay of structure, dynamics, and phase behavior of macromolecular systems, this article focuses on the problem of bottle-brush polymers with either rigid or flexible backbones. On a polymer with chain length $N_b$, side-chains with chain length $N$ are endgrafted with grafting density $\\sigma$. Due to the multitude of characteristic length scales and the size of these polymers (typically these cylindrical macromolecules contain of the order of 10000 effective monomeric units) understanding of the structure is a challenge for experiment. But due to excessively large relaxation times (particularly under poor solvent conditions) such macromolecules also are a challenge for simulation studies. Simulation strategies to deal with this challenge, both using Monte Carlo and Molecular Dynamics Methods, will be briefly discussed, and typical results will be used to illustrate the insight that can be gained.

  10. MOLECULAR SIZE OF HUMIC SUBSTANCES. SUPRAMOLECULAR ASSOCIATIONS VERSUS MACROMOLECULAR POLYMERS

    Microsoft Academic Search

    ALESSANDRO PICCOLO; PELLEGRINO CONTE

    This work illustrates recent experiments conducted by low- and high-pressure size exclusion chromatography (HPSEC) on humic substances of different origin and molecular structure. Solutions of humic substances were either injected as such into the HPSEC system that operated with eluents which differed in composition but were constant in ionic strength, or were previously modified with mineral and organic acids and

  11. A Global Solution for the Structured Total Least Squares Problem with Block Circulant Matrices

    Microsoft Academic Search

    Amir Beck; Aharon Ben-Tal

    2005-01-01

    We study the structured total least squares (STLS) problem of system of linear equations Ax = b, where A has a block circulant structure with N blocks. We show that by applying the discrete Fourier transform (DFT), the STLS problem decomposes into N unstructured total least squares (TLS) problems. The N solutions of these problems are then assembled to generate

  12. Double-layer structure, corrosion and corrosion inhibition of copper in aqueous solution

    Microsoft Academic Search

    O. M. Magnussen; M. R. Vogt; J. Scherer; R. J. Behm

    1998-01-01

    In situ STM results on the surface structure of Cu(100) electrodes in sulfuric and hydrochloric acid solution, both at potentials in the double-layer range and at the onset of anodic Cu dissolution, are presented. The Cu surface structure, morphology and dynamic behavior are found to depend strongly on the anion species and on the potential. In both electrolytes dissolution of

  13. Solution structure of Archaeglobus fulgidis peptidyl-tRNA hydrolase (Pth2) provides evidence

    E-print Network

    Powers, Robert

    Solution structure of Archaeglobus fulgidis peptidyl-tRNA hydrolase (Pth2) provides evidence for an extensive conserved family of Pth2 enzymes in archea, bacteria, and eukaryotes ROBERT POWERS,1 NEBOJSA, and Sulfolobus solfataricus reveals that AF2095 is a peptidyl- tRNA hydrolase (Pth2). This structural comparison

  14. Structure Controlled Synthesis of Single-Walled Carbon Nanotubes Using Solution Based Catalyst Deposition

    E-print Network

    Mellor-Crummey, John

    and physical properties, single-walled carbon nanotube (SWCNT) has been considered for many applications. We, mechanical application, etc. #12;Structure Controlled Synthesis of Carbon Nanotubes Theerapol Thurakitseree1Structure Controlled Synthesis of Single-Walled Carbon Nanotubes Using Solution Based Catalyst

  15. Asymmetric Silver "Nanocarrot" Structures: Solution Synthesis and Their Asymmetric Plasmonic Resonances

    E-print Network

    Asymmetric Silver "Nanocarrot" Structures: Solution Synthesis and Their Asymmetric Plasmonic the wet-chemical synthesis of asymmetric one-dimensional (1D) silver "nanocarrot" structures that exhibit of the longitudinal surface plasmon resonance peaks. The silver nanocarrots also show very high sensitivity

  16. Inverse Sensitivity Analysis of Singular Solutions of FRF matrix in Structural System Identification

    Microsoft Academic Search

    S. Venkatesha; R. Rajender; C. S. Manohar

    2009-01-01

    The problem of structural damage detection based on measured fre- quency response functions of the structure in its damaged and undamaged states is considered. A novel procedure that is based on inverse sensitivity of the sin- gular solutions of the system FRF matrix is proposed. The treatment of possibly ill-conditioned set of equations via regularization scheme and questions on spatial

  17. Interfacial Structural Transition in Hydration Shells of a Polarizable Solute

    NASA Astrophysics Data System (ADS)

    Dinpajooh, Mohammadhasan; Matyushov, Dmitry V.

    2015-05-01

    Electrostatics of polar solvation is typically described by harmonic free energy functionals. Polarizability contributes a negative polarization term that can make the harmonic free energy negative. The harmonic truncation fails in this regime. Simulations of polarizable ideal dipoles in water show that water's susceptibility passes through a maximum in the range of polarizabilities zeroing the harmonic term out. The microscopic origin of the nonmonotonic behavior is an interfacial structural transition involving the density collapse of the first hydration layer and enhanced number of dangling OH bonds.

  18. Aromatic units from the macromolecular material in meteorites: Molecular probes of cosmic environments

    NASA Astrophysics Data System (ADS)

    Sephton, Mark A.

    2013-04-01

    Ancient meteorites contain several percent of organic matter that represents a chronicle of chemical evolution in the early solar system. Aromatic hydrocarbon units make up the majority of meteorite organic matter but reading their record of organic evolution is not straightforward and their formation mechanisms have remained elusive. Most aromatic units reside in a macromolecular material and new perceptions of its structure have been provided by a novel on-line hydrogenation approach. When applied to the Orgueil (CI1) and Murchison (CM2) meteorites the technique releases a range of aromatic hydrocarbons along with some oxygen, sulphur and nitrogen-containing aromatic units. When on-line hydrogenation is compared to conventional pyrolysis, more high molecular weight units and a wider range of liberated entities are evident. Comparisons of results from Orgueil and Murchison reveal variations that are most likely related to differing levels of parent body alteration. The enhancement of straight-chain hydrocarbons (n-alkanes) in the hydrogenation products imply a source of these common contaminants from straight-chain carboxylic acid (n-alkanoic acid) precursors, perhaps from bacterial contributions on Earth. The on-line hydrogenation data also highlight a long-standing but unexplained observation related to the relative preference for specific isomers in methyl-substituted benzenes (meta-, ortho- and para-xylenes). The new hydrogenation approach appears to release and transform macromolecular material meta-structures (benzenes with substituents separated by single carbon atoms) into their free hydrocarbon counterparts. Their release characteristics suggest that the meta-structures are bound by oxygen-linkages. The meta-structures may be molecular probes of specific ancient cosmic environments. Parent body processing may have performed a similar function as hydrogenation to produce the most common meta configuration for free substituted benzenes. Notably, this isomeric preference for substituted benzenes is relatively distinctive for meteorites and can help in the discrimination of meteorite-derived and fossil biology-derived organic matter on Earth and on Mars.

  19. Determination of domain structure of proteins from X-ray solution scattering.

    PubMed Central

    Svergun, D I; Petoukhov, M V; Koch, M H

    2001-01-01

    An ab initio method for building structural models of proteins from x-ray solution scattering data is presented. Simulated annealing is employed to find a chain-compatible spatial distribution of dummy residues which fits the experimental scattering pattern up to a resolution of 0.5 nm. The efficiency of the method is illustrated by the ab initio reconstruction of models of several proteins, with known and unknown crystal structure, from experimental scattering data. The new method substantially improves the resolution and reliability of models derived from scattering data and makes solution scattering a useful technique in large-scale structural characterization of proteins. PMID:11371467

  20. High-accuracy deterministic solution of the Boltzmann equation for the shock wave structure

    NASA Astrophysics Data System (ADS)

    Malkov, E. A.; Bondar, Ye. A.; Kokhanchik, A. A.; Poleshkin, S. O.; Ivanov, M. S.

    2015-07-01

    A new deterministic method of solving the Boltzmann equation has been proposed. The method has been employed in numerical studies of the plane shock wave structure in a hard sphere gas. Results for Mach numbers and have been compared with predictions of the direct simulation Monte Carlo (DSMC) method, which has been used to obtain the reference solution. Particular attention in estimating the solution accuracy has been paid to a fine structural effect: the presence of a total temperature peak exceeding the temperature value further downstream. The results of solving the Boltzmann equation for the shock wave structure are in excellent agreement with the DSMC predictions.

  1. Isomerization kinetics of AT hook decapeptide solution structures.

    PubMed

    Schenk, Emily R; Ridgeway, Mark E; Park, Melvin A; Leng, Fenfei; Fernandez-Lima, Francisco

    2014-01-21

    The mammalian high mobility group protein HMGA2 contains three DNA binding motifs associated with many physiological functions including oncogenesis, obesity, stem cell youth, human height, and human intelligence. In the present paper, trapped ion mobility spectrometry-mass spectrometry (TIMS-MS) has been utilized to study the conformational dynamics of the third DNA binding motif using the "AT hook" decapeptide unit (Lys(1)-Arg(2)-Prol(3)-Arg(4)-Gly(5)-Arg(6)-Prol(7)-Arg(8)-Lys(9)-Trp(10), ATHP) as a function of the solvent state. Solvent state distributions were preserved during electrospray ion formation, and multiple IMS bands were identified for the [M + 2H](2+) and for the [M + 3H](3+) charge states. Conformational isomer interconversion rates were measured as a function of the trapping time for the [M + 2H](2+) and [M + 3H](3+) charge states. Candidate structures were proposed for all IMS bands observed. Protonation site, proline residue conformation, and side chain orientations were identified as the main motifs governing the conformational interconversion processes. Conformational dynamics from the solvent state distribution to the gas-phase "de-solvated" state distribution demonstrated that ATHP is "structured", and relative abundances are associated with the relative stability between the proposed conformers. The most stable ATHP [M + 2H](2+) conformation at the "de-solvated" state corresponds to the AT hook motif observed in AT-rich DNA regions. PMID:24364733

  2. Implementation and performance of SIBYLS: a dual endstation small-angle X-ray scattering and macromolecular crystallography beamline at the Advanced Light Source

    PubMed Central

    Classen, Scott; Hura, Greg L.; Holton, James M.; Rambo, Robert P.; Rodic, Ivan; McGuire, Patrick J.; Dyer, Kevin; Hammel, Michal; Meigs, George; Frankel, Kenneth A.; Tainer, John A.

    2013-01-01

    The SIBYLS beamline (12.3.1) of the Advanced Light Source at Lawrence Berkeley National Laboratory, supported by the US Department of Energy and the National Institutes of Health, is optimized for both small-angle X-ray scattering (SAXS) and macromolecular crystallography (MX), making it unique among the world’s mostly SAXS or MX dedicated beamlines. Since SIBYLS was commissioned, assessments of the limitations and advantages of a combined SAXS and MX beamline have suggested new strategies for integration and optimal data collection methods and have led to additional hardware and software enhancements. Features described include a dual mode monochromator [containing both Si(111) crystals and Mo/B4C multilayer elements], rapid beamline optics conversion between SAXS and MX modes, active beam stabilization, sample-loading robotics, and mail-in and remote data collection. These features allow users to gain valuable insights from both dynamic solution scattering and high-resolution atomic diffraction experiments performed at a single synchrotron beamline. Key practical issues considered for data collection and analysis include radiation damage, structural ensembles, alternative conformers and flexibility. SIBYLS develops and applies efficient combined MX and SAXS methods that deliver high-impact results by providing robust cost-effective routes to connect structures to biology and by performing experiments that aid beamline designs for next generation light sources. PMID:23396808

  3. Implementation and performance of SIBYLS: a dual endstation small-angle X-ray scattering and macromolecular crystallography beamline at the Advanced Light Source.

    PubMed

    Classen, Scott; Hura, Greg L; Holton, James M; Rambo, Robert P; Rodic, Ivan; McGuire, Patrick J; Dyer, Kevin; Hammel, Michal; Meigs, George; Frankel, Kenneth A; Tainer, John A

    2013-02-01

    The SIBYLS beamline (12.3.1) of the Advanced Light Source at Lawrence Berkeley National Laboratory, supported by the US Department of Energy and the National Institutes of Health, is optimized for both small-angle X-ray scattering (SAXS) and macromolecular crystallography (MX), making it unique among the world's mostly SAXS or MX dedicated beamlines. Since SIBYLS was commissioned, assessments of the limitations and advantages of a combined SAXS and MX beamline have suggested new strategies for integration and optimal data collection methods and have led to additional hardware and software enhancements. Features described include a dual mode monochromator [containing both Si(111) crystals and Mo/B(4)C multilayer elements], rapid beamline optics conversion between SAXS and MX modes, active beam stabilization, sample-loading robotics, and mail-in and remote data collection. These features allow users to gain valuable insights from both dynamic solution scattering and high-resolution atomic diffraction experiments performed at a single synchrotron beamline. Key practical issues considered for data collection and analysis include radiation damage, structural ensembles, alternative conformers and flexibility. SIBYLS develops and applies efficient combined MX and SAXS methods that deliver high-impact results by providing robust cost-effective routes to connect structures to biology and by performing experiments that aid beamline designs for next generation light sources. PMID:23396808

  4. Charge distribution and local structure of americium-bearing thorium oxide solid solutions.

    PubMed

    Carvajal-Nunez, U; Prieur, D; Vitova, T; Somers, J

    2012-11-01

    The electronical and structural properties of Th(0.80)Am(0.20)O(2-x) materials have been studied by the coupling of X-ray diffraction and X-ray absorption spectroscopy techniques. A substoichiometric fluorite Th(IV)(0.80)Am(III)(0.20)O(1.90) solid solution is found following sintering in moisturized Ar-H(2). In contrast, heating of this sample in air leads to a nondefective fluorite Th(IV)(0.80)Am(IV)(0.20)O(2.00) solid solution. The structures of these solid solution compounds were fully characterized by assessing the interatomic distances, the coordination numbers, and the structural disorder. The effect of the sintering atmosphere on these crystallographical parameters and on the cation valences has been determined and the capability of ThO(2) to accommodate tri- and tetravalent actinides in the fluorite structure assessed. PMID:23072315

  5. An Analytical Solution for Transient Thermal Response of an Insulated Structure

    NASA Technical Reports Server (NTRS)

    Blosser, Max L.

    2012-01-01

    An analytical solution was derived for the transient response of an insulated aerospace vehicle structure subjected to a simplified heat pulse. This simplified problem approximates the thermal response of a thermal protection system of an atmospheric entry vehicle. The exact analytical solution is solely a function of two non-dimensional parameters. A simpler function of these two parameters was developed to approximate the maximum structural temperature over a wide range of parameter values. Techniques were developed to choose constant, effective properties to represent the relevant temperature and pressure-dependent properties for the insulator and structure. A technique was also developed to map a time-varying surface temperature history to an equivalent square heat pulse. Using these techniques, the maximum structural temperature rise was calculated using the analytical solutions and shown to typically agree with finite element simulations within 10 to 20 percent over the relevant range of parameters studied.

  6. The structure and dynamics in solution of Cu(I) pseudoazurin from Paracoccus pantotrophus.

    PubMed Central

    Thompson, G. S.; Leung, Y. C.; Ferguson, S. J.; Radford, S. E.; Redfield, C.

    2000-01-01

    The solution structure and backbone dynamics of Cu(I) pseudoazurin, a 123 amino acid electron transfer protein from Paracoccus pantotrophus, have been determined using NMR methods. The structure was calculated to high precision, with a backbone RMS deviation for secondary structure elements of 0.35+/-0.06 A, using 1,498 distance and 55 torsion angle constraints. The protein has a double-wound Greek-key fold with two alpha-helices toward its C-terminus, similar to that of its oxidized counterpart determined by X-ray crystallography. Comparison of the Cu(I) solution structure with the X-ray structure of the Cu(II) protein shows only small differences in the positions of some of the secondary structure elements. Order parameters S2, measured for amide nitrogens, indicate that the backbone of the protein is rigid on the picosecond to nanosecond timescale. PMID:10850794

  7. Minimizing distortion in truss structures -- a Hopfield network solution

    NASA Technical Reports Server (NTRS)

    Fu, B.; Hajela, P.

    1993-01-01

    Distortions in truss structures can result from random errors in elemental lengths that are typical of a manufacturing process. These distortions may be minimized by an optimal selection of elements from those available for placement between the prescribed nodes -- a combinatorial optimization problem requiring significant investment of computational resource for all but the smallest problems. The present paper describes a formulation in which near-optimal element assignments are obtained as minimum energy, stable states, of an analogous Hopfield neural network. This requires mapping of the optimization problem into an energy function of the appropriate Lyapunov form. The computational architecture is ideally suited to a parallel processor implementation and offers significant savings in computational effort. A numerical implementation of the approach is discussed with reference to planar truss problems.

  8. Minimizing distortion in truss structures - A Hopfield network solution

    NASA Technical Reports Server (NTRS)

    Fu, B.; Hajela, P.

    1992-01-01

    Distortions in truss structures can result from random errors in element lengths that are typical of a manufacturing process. These distortions may be minimized by an optimal selection of elements from those available for placement between the prescribed nodes - a combinatorial optimization problem requiring significant investment of computational resource for all but the smallest problems. The present paper describes a formulation in which near-optimal element assignments are obtained as minimum-energy stable states, of an analogous Hopfield neural network. This requires mapping of the optimization problem into an energy function of the appropriate Liapunov form. The computational architecture is ideally suited to a parallel processor implementation and offers significant savings in computational effort. A numerical implementation of the approach is discussed with reference to planar truss problems.

  9. Structure and solid solution properties of Cu-Ag nanoalloys.

    PubMed

    Atanasov, Ivailo; Ferrando, Riccardo; Johnston, Roy L

    2014-07-01

    The nanoparticle phase diagram of an immiscible system is studied at the atomic level. Cu-Ag clusters with sizes 1000 and 2000 atoms, resulting from a global minimum search and belonging to icosahedral and crystalline structural motifs, are considered. We present the statistical analysis of the effect of temperature on the solubility of the two elements based on Metropolis Monte Carlo importance sampling. Our results suggest that the relevance of bulk phase diagrams to nanoparticles is limited to cases where the internal stress distribution does not deviate very much from uniform (e.g. sufficiently large crystalline clusters). In the general case, the principal interdependence between partial phase compositions and the overall cluster composition in nanoparticle phase diagrams need to be taken into account. PMID:24918748

  10. Structure and solid solution properties of Cu-Ag nanoalloys

    NASA Astrophysics Data System (ADS)

    Atanasov, Ivailo; Ferrando, Riccardo; Johnston, Roy L.

    2014-07-01

    The nanoparticle phase diagram of an immiscible system is studied at the atomic level. Cu-Ag clusters with sizes 1000 and 2000 atoms, resulting from a global minimum search and belonging to icosahedral and crystalline structural motifs, are considered. We present the statistical analysis of the effect of temperature on the solubility of the two elements based on Metropolis Monte Carlo importance sampling. Our results suggest that the relevance of bulk phase diagrams to nanoparticles is limited to cases where the internal stress distribution does not deviate very much from uniform (e.g. sufficiently large crystalline clusters). In the general case, the principal interdependence between partial phase compositions and the overall cluster composition in nanoparticle phase diagrams need to be taken into account.

  11. We Can Rebuild It: Reconstructive Solutions for Structural Urologic Diseases.

    PubMed

    Abdullah, Newaj M; Lakshmanan, Yegappan

    2015-07-01

    Bladder augmentation and urinary diversion have become standard of care as surgical treatments for structural and functional disorders affecting the bladder, both in children and adults. With improved medical care, long-term survival of these patients is expected. Common medical problems that can occur such as metabolic side effects including acid-base imbalances and nutritional issues need to be anticipated and addressed. In addition, surgical problems caused by impaired urinary drainage, namely stones and urinary tract infections, and mechanical factors related to catheterizable channels and continence also may compound postoperative management. The risk of malignancy after bladder augmentation and substitution, and appropriate surveillance for this, remains to be clearly defined. PMID:26088077

  12. Holographic methods in X-ray crystallography. IV. A fast algorithm and its application to macromolecular crystallography.

    PubMed

    Somoza, J R; Szöke, H; Goodman, D M; Béran, P; Truckses, D; Kim, S H; Szöke, A

    1995-09-01

    The holographic method makes use of partially modeled electron density and experimentally measured structure-factor amplitudes to recover electron density corresponding to the unmodeled part of a crystal structure. This paper describes a fast algorithm that makes it possible to apply the holographic method to sizable crystallographic problems. The algorithm uses positivity constraints on the electron density and can incorporate a 'target' electron density, making it similar to solvent flattening. The potential for applying the holographic method to macromolecular X-ray crystallography is assessed using both synthetic and experimental data. PMID:7576377

  13. Structure solution with three-dimensional sets of precessed electron diffraction intensities.

    PubMed

    Gemmi, Mauro; Nicolopoulos, Stavros

    2007-01-01

    The use of the precession technique for obtaining three-dimensional (3D) sets of electron diffraction intensities suitable for structure solution is discussed. The minerals uvarovite and åkermanite have been used as testing structures. The electron diffraction data sets obtained on these samples retain an acceptable linear relation with calculated structure factor amplitudes. The quality of these data is suitable to solve both structures using direct methods opening the possibility to use 3D precession ED data for solving unknown mineral structures. PMID:17222513

  14. Conduit network structural controls on groundwater flow and solute breakthrough in karst aquifers

    NASA Astrophysics Data System (ADS)

    Ronayne, M. J.

    2014-12-01

    The structure of the conduit network is a key factor that governs flow and transport behavior in karst aquifers. The network inlet (recharge) and outlet (karst spring) locations may be known, but direct measurements of the conduit network and associated structural properties (volume fraction, sinuosity) are generally limited for the aquifer interior. This study considers the information content of indirect solute tracer data for inferring structural properties of the network. Observations from selected karst aquifers in the USA provide motivation for a numerical investigation that utilizes synthetic models characterized by a branching conduit network surrounded by permeable matrix material, with focused discharge at a single karst spring. The permeable matrix allows for solute exchange between the conduits and diffuse flow domain. Results from physics-based flow and transport simulations demonstrate how variations in conduit network geometry influence solute breakthrough at the outlet. Solute particle arrival time distributions, generated from synthetic tracer tests, are described by the mean, variance, skewness, and early (5th percentile) breakthrough times. The results indicate a clear relationship between these statistical moments and structural properties of the network, highlighting the potential signature of conduit network structure on hydrologic response and solute transport in karst aquifers.

  15. Transformations of the macromolecular landscape at mitochondria during DNA-damage-induced apoptotic cell death.

    PubMed

    Yadav, N; Pliss, A; Kuzmin, A; Rapali, P; Sun, L; Prasad, P; Chandra, D

    2014-01-01

    Apoptosis is a dynamic process regulated by mitochondrion critical for cellular respiration and survival. Execution of apoptosis is mediated by multiple protein signaling events at mitochondria. Initiation and progression of apoptosis require numerous apoptogenic factors that are either released from or sequestered in mitochondria, which may transform the biomolecular makeup of the organelle. In this communication, using Raman microspectroscopy, we demonstrate that transformation in biomolecular composition of mitochondrion may be used as apoptosis marker in an individual cell. For the first time, we show that significant changes occur in the concentrations of RNA, DNA, protein, and lipid constituents of mitochondria during apoptosis. The structural analysis of proteins on mitochondria demonstrated a decrease in ?-helix secondary structure content, and an increase in the levels of random coils and ?-sheets on mitochondria. This may represent an additional hallmark of apoptosis. Strikingly, we observed nearly identical changes in macromolecular content of mitochondria both in the presence and absence of a key proapoptotic protein, Bax (Bcl-2-associated X protein). Increased DNA level in mitochondria corresponded with higher mitochondrial DNA (mtDNA), cellular reactive oxygen species (ROS), and mitochondrial ROS production. Upregulation of polymerase-? (POLG), mitochondrial helicase Twinkle, and mitochondrial transcription factor A (Tfam) in response to DNA damage correlated with increased mtDNA and RNA synthesis. Elevated activity of oxidative phosphorylation complexes supports functional mitochondrial respiration during apoptosis. Thus, we define previously unknown dynamic correlation of macromolecular structure of mitochondria and apoptosis progression in the presence and absence of Bax protein. These findings open up a new approach for monitoring physiological status of cells by non invasive single-cell method. PMID:25299778

  16. Structure solution of DNA-binding proteins and complexes with ARCIMBOLDO libraries

    SciTech Connect

    Pröpper, Kevin [University of Göttingen, (Germany); Instituto de Biologia Molecular de Barcelona (IBMB-CSIC), (Spain); Meindl, Kathrin; Sammito, Massimo [Instituto de Biologia Molecular de Barcelona (IBMB-CSIC), (Spain); Dittrich, Birger; Sheldrick, George M. [University of Göttingen, (Germany); Pohl, Ehmke, E-mail: ehmke.pohl@durham.ac.uk [Durham University, (United Kingdom); Usón, Isabel, E-mail: ehmke.pohl@durham.ac.uk [Instituto de Biologia Molecular de Barcelona (IBMB-CSIC), (Spain); Institucio Catalana de Recerca i Estudis Avancats (ICREA), (Spain); University of Göttingen, (Germany)

    2014-06-01

    The structure solution of DNA-binding protein structures and complexes based on the combination of location of DNA-binding protein motif fragments with density modification in a multi-solution frame is described. Protein–DNA interactions play a major role in all aspects of genetic activity within an organism, such as transcription, packaging, rearrangement, replication and repair. The molecular detail of protein–DNA interactions can be best visualized through crystallography, and structures emphasizing insight into the principles of binding and base-sequence recognition are essential to understanding the subtleties of the underlying mechanisms. An increasing number of high-quality DNA-binding protein structure determinations have been witnessed despite the fact that the crystallographic particularities of nucleic acids tend to pose specific challenges to methods primarily developed for proteins. Crystallographic structure solution of protein–DNA complexes therefore remains a challenging area that is in need of optimized experimental and computational methods. The potential of the structure-solution program ARCIMBOLDO for the solution of protein–DNA complexes has therefore been assessed. The method is based on the combination of locating small, very accurate fragments using the program Phaser and density modification with the program SHELXE. Whereas for typical proteins main-chain ?-helices provide the ideal, almost ubiquitous, small fragments to start searches, in the case of DNA complexes the binding motifs and DNA double helix constitute suitable search fragments. The aim of this work is to provide an effective library of search fragments as well as to determine the optimal ARCIMBOLDO strategy for the solution of this class of structures.

  17. Algorithmic aspect of the solution of transient heat transfer in structures

    NASA Astrophysics Data System (ADS)

    Kadivar, M. H.

    1980-06-01

    The analysis and design of high speed reentry vehicles requires the solution of the transient heat transfer equations in the structure. The application of the finite element method to such a problem results in a system of stiff ordinary differential equations. Variable step, of such systems of explicit algorithms for the solution of such systems of differential equations are investigated. An efficient solution algorithm with an efficient storage strategy for the ill-conditioned large set of algebraic equations which arises from the use of implicit algorithms applied to the system of differential equations is developed. The performance of the algorithm is compared to other algorithms for the solution of two and three dimensional transient heat transfer problems in structures.

  18. Spatial structure of transition metal complexes in solution determined by EXAFS spectroscopy

    NASA Astrophysics Data System (ADS)

    Erenburg, S. B.; Bausk, N. V.; Zemskova, S. M.; Mazalov, L. N.

    2000-06-01

    CdK EXAFS, ZnK and CuK EXAFS and XANES spectra were measured for solutions of cadmium, zinc and copper dialkyldithiocarbamates in organic solvents with varying donating abilities: tributylphosphine, methylene chloride, benzene, dibutylsulfide, pyridine, dimethylsulfoxide and for some model compounds. The parameters of the local surroundings of the Cd, Zn and Cu atoms for complex forms in solutions were determined using EXAFS spectroscopy. Spatial structure models of the complex forms in a metal chelate - nonaqueous solvent system are suggested.

  19. Linear structural evolution induced tunable photoluminescence in clinopyroxene solid-solution phosphors

    PubMed Central

    Xia, Zhiguo; Zhang, Yuanyuan; Molokeev, Maxim S.; Atuchin, Victor V.; Luo, Yi

    2013-01-01

    Clinopyroxenes along the Jervisite (NaScSi2O6) – Diopside (CaMgSi2O6) join have been studied, and a solid-solution of the type (Na1?xCax)(Sc1?xMgx)Si2O6 has been identified in the full range of 0 ? x ? 1. The powder X-ray patterns of all the phases indicate a structural similarity to the end compounds and show smooth variation of structural parameters with composition. The linear structural evolution of iso-structural (Na1?xCax)(Sc1?xMgx)Si2O6 solid-solutions obeying Vegard's rule has also been examined and verified by high resolution transmission electron microscopy (HRTEM). The continuous solid-solutions show the same structural type, therefore the photoluminescence spectra of Eu2+ doped samples possess the superposition of spectral features from blue-emitting component (CaMgSi2O6:Eu2+) and yellow-emitting one (NaScSi2O6:Eu2+). This indicates that the spectroscopic properties of (Na1?xCax)(Sc1?xMgx)Si2O6 clinopyroxene solid-solutions are in direct relations with structural parameters, and it is helpful for designing color-tunable photoluminescence with predetermined parameters. PMID:24264556

  20. Small-angle x-ray scattering investigation of the solution structure of troponin C.

    PubMed

    Hubbard, S R; Hodgson, K O; Doniach, S

    1988-03-25

    X-ray crystallographic studies of troponin C (Herzberg, O., and James, M.N.G. (1985) Nature 313, 653-659; Sundaralingam, M., Bergstrom, R., Strasburg, G., Rao, S.T., and Roychowdhury, P. (1985a) Science 227, 945-948) have revealed a novel protein structure consisting of two globular domains, each containing two Ca2+-binding sites, connected via a nine-turn alpha-helix, three turns of which are fully exposed to solvent. Since the crystals were grown at pH approximately 5, it is of interest to determine whether this structure is applicable to the protein in solution under physiological conditions. We have used small-angle x-ray scattering to examine the solution structure of troponin C at pH 6.8 and the effect of Ca2+ on the structure. The scattering data are consistent with an elongated structure in solution with a radius of gyration of approximately 23.0 A, which is quite comparable to that computed for the crystal structure. The experimental scattering profile and the scattering profile computed from the crystal structure coordinates do, however, exhibit differences at the 40-A level. A weak Ca2+-facilitated dimerization of troponin C was observed. The data rule out large Ca2+-induced structural changes, indicating rather that the molecule with Ca2+ bound is only slightly more compact than the Ca2+-free molecule. PMID:3346242

  1. Exciton Structure and Dynamics in Solution Aggregates of a Low-Bandgap Copolymer.

    PubMed

    Guo, Zhi; Lee, Doyun; Gao, Haifeng; Huang, Libai

    2015-06-18

    In this work, we elucidate exciton structure, dynamics, and charge generation in the solution phase aggregates of a low-bandgap donor-acceptor polymer, poly(4,8-bis-alkyloxybenzo[1,2-b:4,5-b']dithiophene-2,6-diyl-alt-(alkylthieno[3,4-b]thiophene-2carboxylate)-2,6-diyl (PBDTTT). The polymer aggregates in the solution phase serve as precursors for thin film morphologies. We have identified intrachain and interchain exciton transitions and resolved their relaxation pathways by comparing excitons in solution aggregates to those in isolated polymer chains. Hot intrachain excitons have led to the generation of stabilized interchain charge-separated states in solution aggregates, which could serve as the intermediate state to the hot exciton charge separation in bulk heterojunctions (BHJs). These results have important implications for controlling morphology dependent exciton dynamics in solution processed BHJs. PMID:25666173

  2. On the structure of solutions to a class of quasilinear elliptic Neumann problems. Part II

    PubMed Central

    Zhao, Chunshan; Li, Yi

    2010-01-01

    We continue our work (Y. Li, C. Zhao in J Differ Equ 212:208–233, 2005) to study the structure of positive solutions to the equation ?m ?mu ? um?1 + f(u) = 0 with homogeneous Neumann boundary condition in a smooth bounded domain of RN (N ? 2). First, we study subcritical case for 2 < m < N and show that after passing by a sequence positive solutions go to a constant in C1, ? sense as ? ? ?. Second, we study the critical case for 1 < m < N and prove that there is a uniform upper bound independent of ? ? [1, ?) for the least-energy solutions. Third, we show that in the critical case for 1 < m ? 2 the least energy solutions must be a constant if ? is sufficiently large and for 2 < m < N the least energy solutions go to a constant in C1, ? sense as ? ? ?. PMID:20700388

  3. Yang-Mills Solutions and Dyons on Cylinders over Coset Spaces with Sasakian Structure

    E-print Network

    Maike Tormählen

    2014-12-22

    We present solutions of the Yang-Mills equation on cylinders $\\mathbb R\\times G/H$ over coset spaces with Sasakian structure and odd dimension $2m+1$. The gauge potential is assumed to be $SU(m)$-equivariant, parametrized by two real, scalar-valued functions. Yang-Mills theory with torsion in this setup reduces to the Newtonian mechanics of a point particle moving in $\\mathbb R^2$ under the influence of an inverted potential. We analyze the critical points of this potential and present an analytic as well as several numerical finite-action solutions. Apart from the Yang-Mills solutions that constitute $SU(m)$-equivariant instanton configurations, we construct periodic sphaleron solutions on $S^1\\times G/H$ and dyon solutions on $i\\mathbb R\\times G/H$.

  4. Patchy worm-like micelles: solution structure studied by small-angle neutron scattering

    E-print Network

    S. Rosenfeldt; F. Luedel; C. Schulreich; T. Hellweg; A. Radulescu; J. Schmelz; H. Schmalz; L. Harnau

    2012-09-20

    Triblock terpolymers exhibit a rich self-organization behavior including the formation of fascinating cylindrical core-shell structures with a phase separated corona. After crystallization-induced self-assembly of polystryrene-(block)-polyethylene-(block)-poly(methyl methacrylate) triblock terpolymers (abbreviated as SEMs = Styrene-Ethylene-Methacrylates) from solution, worm-like core-shell micelles with a patchy corona of polystryrene and poly(methyl methacrylate) were observed by transmission electron microscopy. However, the solution structure is still a matter of debate. Here, we present a method to distinguish in-situ between a Janus-type (two faced) and a patchy (multiple compartments) configuration of the corona. To discriminate between both models the scattering intensity must be determined mainly by one corona compartment. Contrast variation in small-angle neutron scattering enables us to focus on one compartment of the SEMs. The results validate the existence of the patchy structure also in solution.

  5. Mathieu function solutions for photoacoustic waves in sinusoidal one-dimensional structures

    NASA Astrophysics Data System (ADS)

    Wu, Binbin; Diebold, Gerald J.

    2012-07-01

    The photoacoustic effect for a one-dimensional structure, the sound speed of which varies sinusoidally in space, is shown to be governed by an inhomogeneous Mathieu equation with the forcing term dependent on the spatial and temporal properties of the exciting optical radiation. New orthogonality relations, traveling wave Mathieu functions, and solutions to the inhomogeneous Mathieu equation are found, which are used to determine the character of photoacoustic waves in infinite and finite length phononic structures. Floquet solutions to the Mathieu equation give the positions of the band gaps, the damping of the acoustic waves within the band gaps, and the dispersion relation for photoacoustic waves. The solutions to the Mathieu equation give the photoacoustic response of the structure, show the space equivalent of subharmonic generation and acoustic confinement when waves are excited within band gaps.

  6. Self-organization of amphiphilic macromolecules with local helix structure in concentrated solutions.

    PubMed

    Glagolev, M K; Vasilevskaya, V V; Khokhlov, A R

    2012-08-28

    Concentrated solutions of amphiphilic macromolecules with local helical structure were studied by means of molecular dynamic simulations. It is shown that in poor solvent the macromolecules are assembled into wire-like aggregates having complex core-shell structure. The core consists of a hydrophobic backbone of the chains which intertwine around each other. It is protected by the shell of hydrophilic side groups. In racemic mixture of right-hand and left-hand helix macromolecules the wire-like complex is a chain of braid bundles of macromolecules with the same chirality stacking at their ends. The average number of macromolecules in the wire cross-section is close to that of separate bundles observed in dilute solutions of such macromolecules. The effects described here could serve as a simple model of self-organization in solutions of macromolecules with local helical structure. PMID:22938259

  7. Extracellular biodegradable macromolecular gadolinium(III) complexes for MRI.

    PubMed

    Lu, Zheng-Rong; Parker, Dennis L; Goodrich, K Craig; Wang, Xinghe; Dalle, John G; Buswell, Henry R

    2004-01-01

    The clinical application of macromolecular gadolinium (Gd) complexes as MRI contrast agents is limited by the slow excretion of Gd(III) complexes and consequent long-term tissue accumulation of toxic Gd ions. To alleviate the problem of slow excretion, biodegradable polydisulfide-based macromolecular Gd(III) complexes were designed and prepared based on the disulfide-thiol exchange to allow degradation of the macromolecules by endogenous thiols and to facilitate excretion of Gd(III) complexes after the MRI examination. The in vitro degradation study showed that the polydisulfide agent was readily degraded by cysteine at plasma thiol concentrations. No cross-reaction was observed between the cysteine-34 on human serum albumin (HSA) with the agent. Concentration-dependent blood pool contrast enhancement was observed for the polydisulfide agents. The agents of both high molecular weight (35,000 Da) and low molecular weight (17,700 Da) produced significant contrast enhancement in the heart and aorta in rats at relatively high doses. Except for the bladder, the signal intensities gradually decreased over time. Significant blood pool contrast enhancement was also observed for the high molecular weight agent at a low dose (0.03 mmol-Gd/kg), but not for the agent with a lower molecular weight. The contrast enhancement in the urinary bladder increased over time for the polydisulfide agents and Gd(III)-(DTPA-BMA). Degradation products were identified by mass spectrometry in the urine samples from the rats administered with both polydisulfide agents, which confirmed that the polydisulfide agents were degraded in vivo and excreted through renal filtration. The preliminary results demonstrated the in vitro and in vivo degradability, superior blood pool contrast enhancement, and rapid clearance through renal filtration of the novel biodegradable macromolecular agent. This agent has a great potential for further preclinical and clinical development with application in contrast-enhanced blood pool and cancer MR imaging. PMID:14705042

  8. A structural study of saturated aqueous solutions of some alkali halides by X-ray diffraction

    Microsoft Academic Search

    Hitoshi Ohtaki; Nobuhiro Fukushima

    1992-01-01

    The structure of nearly saturated or supersaturated aqueous solutions of NaCI [6.18 mol (kg H2O)-1], KCI [4.56 mol (kg H2O)-1], KF [16.15 mol (kg H2O)-1] and CsF [31.96 mol (kg H2O)-1] has been investigated by means of solution X-ray diffraction at 25°C. In the NaCI and KCI solutions about 30% and 60%, respectively, of the ions form ion pairs and

  9. Solution Structure of the Human Oncogenic Protein Gankyrin Containing Seven Ankyrin Repeats and Analysis of Its Structure?Function Relationship † , ‡

    Microsoft Academic Search

    Chunhua Yuan; Junan Li; Anjali Mahajan; Ming Jye Poi; In-Ja L. Byeon; Ming-Daw Tsai

    2004-01-01

    Human gankyrin (226 residues, 24.4 kDa) is a liver oncoprotein that plays an important role in the development of human hepatocellular carcinomas. In this paper, its solution structure is reported, which is the largest ankyrin protein ever determined by NMR. The highly degenerate primary sequences of the seven ankyrin repeats presented a major challenge, which was overcome by combined use

  10. Effect of tumour cell-conditioned medium on endothelial macromolecular permeability and its correlation with collagen.

    PubMed Central

    Utoguchi, N.; Mizuguchi, H.; Dantakean, A.; Makimoto, H.; Wakai, Y.; Tsutsumi, Y.; Nakagawa, S.; Mayumi, T.

    1996-01-01

    Conditioned medium prepared from mouse melanoma B16 cells (B16-CM) increases the macromolecular permeability of bovine aortic, venous and human umbilical vein endothelial monolayer. Collagen, which is synthesised by endothelial cells, has an important function in regulating the permeability of endothelial monolayer. Briefly, low collagen content leads to hyperpermeable structure of the endothelial monolayer. In the present studies, we examined the relationship between the increase of endothelial permeability and content of synthesised collagen of endothelial cells cultured with B16-CM. The B16-CM reduced endothelial collagen content but did not digest collagen directly. Matrix metalloproteinase inhibitor, 1,10-phenanthroline, inhibited the increase in permeability due to addition of B16-CM. These data suggest that B16-CM acts on endothelial cells, stimulating the digestion of endothelial collagen, and that the reduced content of collagen leads to the hyperpermeability of the endothelial monolayer. PMID:8554978

  11. DNA translocation through ?-hemolysin nanopores with potential application to macromolecular data storage

    NASA Astrophysics Data System (ADS)

    Khulbe, Pramod K.; Mansuripur, Masud; Gruener, Raphael

    2005-05-01

    Digital information can be encoded in the building-block sequence of macromolecules, such as RNA and single-stranded DNA. Methods of "writing" and "reading" macromolecular strands are currently available, but they are slow and expensive. In an ideal molecular data storage system, routine operations such as write, read, erase, store, and transfer must be done reliably and at high speed within an integrated chip. As a first step toward demonstrating the feasibility of this concept, we report preliminary results of DNA readout experiments conducted in miniaturized chambers that are scalable to even smaller dimensions. We show that translocation of a single-stranded DNA molecule (consisting of 50 adenosine bases followed by 100 cytosine bases) through an ion channel yields a characteristic signal that is attributable to the two-segment structure of the molecule. We also examine the dependence of the translocation rate and speed on the adjustable parameters of the experiment.

  12. Engineering human immunodeficiency virus 1 protease heterodimers as macromolecular inhibitors of viral maturation.

    PubMed

    McPhee, F; Good, A C; Kuntz, I D; Craik, C S

    1996-10-15

    Dimerization of human immunodeficiency virus type 1 protease (HIV-1 PR) monomers is an essential prerequisite for viral proteolytic activity and the subsequent generation of infectious virus particles. Disruption of the dimer interface inhibits this activity as does formation of heterodimers between wild-type and defective monomers. A structure-based approach was used to identify amino acid substitutions at the dimer interface of HIV-1 PR that facilitate preferential association of heterodimers and inhibit self-association of the defective monomers. Expression of the designed PR monomers inhibits activity of wild-type HIV-1 PR and viral infectivity when assayed in an ex vivo model system. These results show that it is possible to design PR monomers as macromolecular inhibitors that may provide an alternative to small molecule inhibitors for the treatment of HIV infection. PMID:8876160

  13. The kinetic dose limit in room-temperature time-resolved macromolecular crystallography

    PubMed Central

    Schmidt, M.; Šrajer, V.; Purwar, N.; Tripathi, S.

    2012-01-01

    Protein X-ray structures are determined with ionizing radiation that damages the protein at high X-ray doses. As a result, diffraction patterns deteriorate with the increased absorbed dose. Several strategies such as sample freezing or scavenging of X-ray-generated free radicals are currently employed to minimize this damage. However, little is known about how the absorbed X-ray dose affects time-resolved Laue data collected at physiological temperatures where the protein is fully functional in the crystal, and how the kinetic analysis of such data depends on the absorbed dose. Here, direct evidence for the impact of radiation damage on the function of a protein is presented using time-resolved macromolecular crystallography. The effect of radiation damage on the kinetic analysis of time-resolved X-ray data is also explored. PMID:22338689

  14. Macromolecular Crowding as a Suppressor of Human IAPP Fibril Formation and Cytotoxicity

    PubMed Central

    Seeliger, Janine; Werkmüller, Alexander; Winter, Roland

    2013-01-01

    The biological cell is known to exhibit a highly crowded milieu, which significantly influences protein aggregation and association processes. As several cell degenerative diseases are related to the self-association and fibrillation of amyloidogenic peptides, understanding of the impact of macromolecular crowding on these processes is of high biomedical importance. It is further of particular relevance as most in vitro studies on amyloid aggregation have been performed in diluted solution which does not reflect the complexity of their cellular surrounding. The study presented here focuses on the self-association of the type-2 diabetes mellitus related human islet amyloid polypeptide (hIAPP) in various crowded environments including network-forming macromolecular crowding reagents and protein crowders. It was possible to identify two competing processes: a crowder concentration and type dependent stabilization of globular off-pathway species and a – consequently - retarded or even inhibited hIAPP fibrillation reaction. The cause of these crowding effects was revealed to be mainly excluded volume in the polymeric crowders, whereas non-specific interactions seem to be most dominant in protein crowded environments. Specific hIAPP cytotoxicity assays on pancreatic ?-cells reveal non-toxicity for the stabilized globular species, in contrast to the high cytotoxicity imposed by the normal fibrillation pathway. From these findings it can be concluded that cellular crowding is able to effectively stabilize the monomeric conformation of hIAPP, hence enabling the conduction of its normal physiological function and prevent this highly amyloidogenic peptide from cytotoxic aggregation and fibrillation. PMID:23922768

  15. A Solution Adaptive Structured/Unstructured Overset Grid Flow Solver with Applications to Helicopter Rotor Flows

    NASA Technical Reports Server (NTRS)

    Duque, Earl P. N.; Biswas, Rupak; Strawn, Roger C.

    1995-01-01

    This paper summarizes a method that solves both the three dimensional thin-layer Navier-Stokes equations and the Euler equations using overset structured and solution adaptive unstructured grids with applications to helicopter rotor flowfields. The overset structured grids use an implicit finite-difference method to solve the thin-layer Navier-Stokes/Euler equations while the unstructured grid uses an explicit finite-volume method to solve the Euler equations. Solutions on a helicopter rotor in hover show the ability to accurately convect the rotor wake. However, isotropic subdivision of the tetrahedral mesh rapidly increases the overall problem size.

  16. Effects of Hydrophobic Macromolecular Crowders on Amyloid ? (16-22) Aggregation.

    PubMed

    Latshaw, David C; Hall, Carol K

    2015-07-01

    In Alzheimer's disease (AD), the amyloid ? (A?) peptide aggregates in the brain to form progressively larger oligomers, fibrils, and plaques. The aggregation process is strongly influenced by the presence of other macromolecular species, called crowders, that can exert forces on the proteins. One very common attribute of macromolecular crowders is their hydrophobicity. We examined the effect of hydrophobic crowders on protein aggregation by using discontinuous molecular dynamics (DMD) simulations in combination with an intermediate resolution protein model, PRIME20. The systems considered contained 48 A? (16-22) peptides and crowders with diameters of 5 Å, 20 Å, and 40 Å, represented by hard spheres or spheres with square-well/square-shoulder interactions, at a crowder volume fraction of ? = 0.10. Results show that low levels of crowder hydrophobicity are capable of increasing the fibrillation lag time and high levels of crowder hydrophobicity can fully prevent the formation of fibrils. The types of structures that remain during the final stages of the simulations are summarized in a global phase diagram that shows fibril, disordered oligomer, or ?-sheet phases in the space spanned by crowder size and crowder hydrophobicity. In particular, at high levels of hydrophobicity, simulations with 5 Å crowders result in only disordered oligomers and simulations with 40 Å crowders result in only ?-sheets. The presence of hydrophobic crowders reduces the antiparallel ?-sheet content of fibrils, whereas hard sphere crowders increase it. Finally, strong hydrophobic crowders alter the secondary structure of the A? (16-22) monomers, bending them into a shape that is incapable of forming ordered ?-sheets or fibrils. These results qualitatively agree with previous theoretical and experimental work. PMID:26153709

  17. Characterization of the macromolecular components of the articular cartilage surface

    Microsoft Academic Search

    K. Noyori; T. Takagi; H. E. Jasin

    1998-01-01

    The intact surface of articular cartilage is a highly organized structure composed of a variety of macromolecules. The studies\\u000a reported here deal with a partial characterization of the non-covalently bound components of the outermost layer of articular\\u000a cartilage. Normal bovine and human cartilage articular surfaces were extracted for 5 min with 4-M guanidine HCl solution.\\u000a Analysis and quantitation of small

  18. Effects of solvent on the solution properties, structural characteristics and properties of silk sericin.

    PubMed

    Jo, Yoon Nam; Um, In Chul

    2015-07-01

    Sericin films have attracted much attention from researchers in biomedical and cosmetic fields because of its unique properties, including good cytocompatibility and its promotion of wound healing. However, poor mechanical properties of sericin films have restricted its application in these fields. In this study, a new solvent, formic acid, was used to fabricate sericin solutions and films. The effects of formic acid on the structural characteristics and mechanical properties of the sericin solutions and films were examined and compared with water. The sericin/formic acid solution showed fewer aggregated sericin molecules, resulting in a lower turbidity than that of the sericin/water solution. In addition, the gelation of the sericin solution was retarded in formic acid compared to that of water. Sericin films cast from the formic acid solution exhibited a much higher crystallinity index than that produced from water. The tensile strength and elongation of the sericin films cast from the formic acid solution were more than double that of the sericin films cast from water. It is expected that the more stable sericin solution and high-crystallinity sericin films, which have significantly improved mechanical properties, produced by using formic acid as the solvent could be utilized in biomedical and cosmetic applications. PMID:25869308

  19. Mapping in Solution Shows the Peach Latent Mosaic Viroid To Possess a New Pseudoknot in a Complex, Branched Secondary Structure

    Microsoft Academic Search

    F. Bussiere; J. Ouellet; F. Cote; D. Levesque; J. P. Perreault

    2000-01-01

    We have investigated the secondary structure of peach latent mosaic viroid (PLMVd) in solution, and we present here the first description of the structure of a branched viroid in solution. Different PLMVd transcripts of plus polarity were produced by using the circularly permuted RNA method and the exploitation of RNA internal secondary structure to position the 5* and 3* termini

  20. Solution structure of an informationally complex high-affinity RNA aptamer to GTP

    Microsoft Academic Search

    JAMES M. CAROTHERS; JONATHAN H. DAVIS; JAMES J. CHOU; JACK W. SZOSTAK

    2006-01-01

    Higher-affinity RNA aptamers to GTP are more informationally complex than lower-affinity aptamers. Analog binding studies have shown thatthe additional informationneeded toimproveaffinity doesnot specify moreinteractions withthe ligand. Inlightof those observations, we would like to understand the structural characteristics that enable complex aptamers to bind their ligands with higher affinity. Here we present the solution structure of the 41-nt Class I GTP

  1. Atomistic Modeling of Macromolecular Crowding Predicts Modest Increases in Protein Folding and Binding Stability

    E-print Network

    Weston, Ken

    Atomistic Modeling of Macromolecular Crowding Predicts Modest Increases in Protein Folding that macromolecular crowding can increase protein folding stability, but depending on details of the models (e.g., how on the effects of macro- molecular crowding on protein folding and binding stability has been reached. Crowders

  2. Using macromolecular-crystallography beamline and microfluidic platform for small-angle diffraction studies of lipidic

    E-print Network

    Kenis, Paul J. A.

    Using macromolecular-crystallography beamline and microfluidic platform for small-angle diffraction, 600 S. Matthews Ave., Urbana, IL 61801, USA Abstract Macromolecular-crystallography (MX) beamlines Crystallography (MX) would facilitate the studies of crystallogenesis. Some MX synchrotron beamlines have SAXS

  3. Normal Mode Analysis of Macromolecular Motions in a Database Framework: Developing Mode Concentration as a

    E-print Network

    Gerstein, Mark

    Normal Mode Analysis of Macromolecular Motions in a Database Framework: Developing Mode ABSTRACT We investigated protein motions us- ing normal modes within a database framework, deter- mining motions and normal mode calculations in the Macromolecular Motions Database, through a new ranking

  4. PRIGo: a new multi-axis goniometer for macromolecular crystallography.

    PubMed

    Waltersperger, Sandro; Olieric, Vincent; Pradervand, Claude; Glettig, Wayne; Salathe, Marco; Fuchs, Martin R; Curtin, Adrian; Wang, Xiaoqiang; Ebner, Simon; Panepucci, Ezequiel; Weinert, Tobias; Schulze-Briese, Clemens; Wang, Meitian

    2015-07-01

    The Parallel Robotics Inspired Goniometer (PRIGo) is a novel compact and high-precision goniometer providing an alternative to (mini-)kappa, traditional three-circle goniometers and Eulerian cradles used for sample reorientation in macromolecular crystallography. Based on a combination of serial and parallel kinematics, PRIGo emulates an arc. It is mounted on an air-bearing stage for rotation around ? and consists of four linear positioners working synchronously to achieve x,?y,?z translations and ? rotation (0-90°), followed by a ? stage (0-360°) for rotation around the sample holder axis. Owing to the use of piezo linear positioners and active correction, PRIGo features spheres of confusion of <1?µm, <7?µm and <10?µm for ?, ? and ?, respectively, and is therefore very well suited for micro-crystallography. PRIGo enables optimal strategies for both native and experimental phasing crystallographic data collection. Herein, PRIGo hardware and software, its calibration, as well as applications in macromolecular crystallography are described. PMID:26134792

  5. PRIGo: a new multi-axis goniometer for macromolecular crystallography

    PubMed Central

    Waltersperger, Sandro; Olieric, Vincent; Pradervand, Claude; Glettig, Wayne; Salathe, Marco; Fuchs, Martin R.; Curtin, Adrian; Wang, Xiaoqiang; Ebner, Simon; Panepucci, Ezequiel; Weinert, Tobias; Schulze-Briese, Clemens; Wang, Meitian

    2015-01-01

    The Parallel Robotics Inspired Goniometer (PRIGo) is a novel compact and high-precision goniometer providing an alternative to (mini-)kappa, traditional three-circle goniometers and Eulerian cradles used for sample reorientation in macromolecular crystallography. Based on a combination of serial and parallel kinematics, PRIGo emulates an arc. It is mounted on an air-bearing stage for rotation around ? and consists of four linear positioners working synchronously to achieve x,?y,?z translations and ? rotation (0–90°), followed by a ? stage (0–360°) for rotation around the sample holder axis. Owing to the use of piezo linear positioners and active correction, PRIGo features spheres of confusion of <1?µm, <7?µm and <10?µm for ?, ? and ?, respectively, and is therefore very well suited for micro-crystallography. PRIGo enables optimal strategies for both native and experimental phasing crystallographic data collection. Herein, PRIGo hardware and software, its calibration, as well as applications in macromolecular crystallography are described. PMID:26134792

  6. Bioelectrochemical activity of an electroactive macromolecular weight coenzyme derivative

    NASA Astrophysics Data System (ADS)

    Liu, Pu; Zheng, Haitao; Nie, Pingping; Wei, Yaotian; Feng, Zhenchao; Sun, Tao

    2009-07-01

    As coenzyme utilized by more than hundreds of dehydrogenases, the efficient immobilization and regeneration of nicotinamide adenine dinucleotide (NAD+) are of great importance and have practical applications in industrial, analytical and biomedical field. In this paper, an electroactive macromolecular weight coenzyme derivative (PEI-DHBNAD) was prepared by attaching both NAD+ and 3,4-dihydroxybenzaldehyde (3,4-DHB) to a water-soluble polyelectrolyte, poly(ethylenimine) (PEI). The functional polymer exhibited both electrochemical properties of catechol unites and coenzymatic activity of NAD moieties. The macromolecular NAD analogue showed a substantial degree of efficiency relative to free NAD+ with alcohol dehydrogenase (ADH) and glucose-6-phophate dehydrogenase (G6PDH), and a litter higher Michaelis-Menton constant (Km) was obtained for the coenzyme derivative than free NAD+. The bioelectrochemical properties of PEI-DHB-NAD were investigated by using G6PDH as the model enzyme, and both of them were retained on electrode surface by ultrafiltration membrane. The modified electrode showed typical response to substrate without the addition of free coenzyme, which indicated that PEI-DHB-NAD can carry out the electron transfer between electrode and NAD-dependent dehydrogenase. The utilization of polymer-based PEI-DHB-NAD is convenient for the immobilization of both electron mediator and coenzyme, and offers a practical approach for the construction of reagentless biosensors.

  7. Effect of light intensity on macromolecular synthesis in cyanobacteria.

    PubMed

    Konopka, A; Schnur, M

    1980-12-01

    The light-dependent incorporation of NaH(14)CO3 into low molecular weight compounds, polysaccharide, or protein was determined in cultures of the cyanobacteriumMerismopedia tenuissima incubated at a series of light intensities. There was an inverse relationship between incorporation into polysaccharide and protein. At light intensities of 90 ?E/m(2)/sec or above, relative incorporation of radioisotope into polysaccharide was greatest and relative incorporation into protein was lowest. Optimal relative protein accumulation occurred in samples incubated at 20 ?E/m(2)/sec. A broader optimum of light intensity for maximal protein accumulation was found if ammonia rather than nitrate was the nitrogen source. Physiological adaptation of cultures to growth at a particular light intensity did not alter the pattern of macromolecular incorporation when those cultures were tested over the series of light intensities. The response of cultures ofOscillatoria rubescens to light intensity was similar to that ofM. tenuissima, although incorporation into low molecular weight compounds was significantly greater.The effect of light intensity on macromolecular synthesis in a natural population ofOscillatoria rubescens was also determined. A pattern similar to that observed in batch cultures ofO. rubescens was occasionally found, but in other experiments there was no increase in relative protein incorporation when light intensity was decreased. PMID:24227225

  8. Crowding and hydrodynamic interactions likely dominate in vivo macromolecular motion

    PubMed Central

    Ando, Tadashi; Skolnick, Jeffrey

    2010-01-01

    To begin to elucidate the principles of intermolecular dynamics in the crowded environment of cells, employing Brownian dynamics (BD) simulations, we examined possible mechanism(s) responsible for the great reduction in diffusion constants of macromolecules in vivo from that at infinite dilution. In an Escherichia coli cytoplasm model comprised of 15 different macromolecule types at physiological concentrations, BD simulations of molecular-shaped and equivalent sphere representations were performed with a soft repulsive potential. At cellular concentrations, the calculated diffusion constant of GFP is much larger than experiment, with no significant shape dependence. Next, using the equivalent sphere system, hydrodynamic interactions (HI) were considered. Without adjustable parameters, the in vivo experimental GFP diffusion constant was reproduced. Finally, the effects of nonspecific attractive interactions were examined. The reduction in diffusivity is very sensitive to macromolecular radius with the motion of the largest macromolecules dramatically slowed down; this is not seen if HI dominate. In addition, long-lived clusters involving the largest macromolecules form if attractions dominate, whereas HI give rise to significant, size independent intermolecular dynamic correlations. These qualitative differences provide a testable means of differentiating the importance of HI vs. nonspecific attractive interactions on macromolecular motion in cells. PMID:20937902

  9. Local structures and Raman spectra in the Ca(Zr,Ti)O3 perovskite solid solutions

    SciTech Connect

    Levin,I.; Cockayne, E.; Lufaso, M.; Woicik, J.; Masler, J.

    2006-01-01

    Local structures and cation distributions in perovskite Ca(Zr,Ti)O{sub 3} solid solutions were analyzed using X-ray absorption fine structure and pair-distribution functions obtained from total neutron scattering. The analyses revealed that the Zr-O and Ti-O bond distances in the solid solutions remain distinct and close to their respective values in the end-compounds, CaZrO{sub 3} and CaTiO{sub 3}. The structural strain in the solid solutions, which results from the ionic size mismatch between Zr and Ti, is accommodated by adjustment of the tilting angles for the different [BO6] octahedra. Additionally, the octahedra are distorted by bending, which affects the O-O distances while preserving a uniform distribution of the B-O distances. Combined experimental and theoretical analyses of Raman spectra demonstrated that high-frequency modes associated with the breathing of oxygen octahedra arise even in the nearly disordered solid solutions. Our results suggest a coexistence of both localized and extended Raman-active breathing vibrations, associated with the octahedra hosting the minority and majority B-cations, respectively. For the dilute solid solutions (<25 at. %), these modes yield two well-resolved Raman peaks.

  10. Structural Properties of High and Low Density Water in a Supercooled Aqueous Solution of Salt

    E-print Network

    D. Corradini; M. Rovere; P. Gallo

    2011-01-27

    We consider and compare the structural properties of bulk TIP4P water and of a sodium chloride aqueous solution in TIP4P water with concentration c = 0.67 mol/kg, in the metastable supercooled region. In a previous paper [D. Corradini, M. Rovere and P. Gallo, J. Chem. Phys. 132, 134508 (2010)] we found in both systems the presence of a liquid-liquid critical point (LLCP). The LLCP is believed to be the end point of the coexistence line between a high density liquid (HDL) and a low density liquid (LDL) phase of water. In the present paper we study the different features of water-water structure in HDL and LDL both in bulk water and in the solution. We find that the ions are able to modify the bulk LDL structure, rendering water-water structure more similar to the bulk HDL case. By the study of the hydration structure in HDL and LDL, a possible mechanism for the modification of the bulk LDL structure in the solution is identified in the substitution of the oxygen by the chloride ion in oxygen coordination shells.

  11. Solution structures of Alzheimer's amyloid A?13-23 peptide: NMR studies in solution and in SDS

    NASA Astrophysics Data System (ADS)

    Usachev, K. S.; Filippov, A. V.; Filippova, E. A.; Antzutkin, O. N.; Klochkov, V. V.

    2013-10-01

    To be believed that interaction of amyloid peptides with the cellular membrane is one of the mechanisms for the neurotoxicity of A?. Therefore, structural studies of beta-amyloid in solution and in a "peptide-bio-membrane" complex are of intense interest. The aim of this study was to acquire a better understanding of the mechanism of "A? peptide-micelle surface" complex formation. Previous studies of A? peptides binding on the micelle surface show the presence of helical region between 15-24 residues and that fragment between 11-28 residues have a tendency to exit the hydrophobic environment of the micelle core and to bind to the micelle surface. In present paper we considered the fragment of A? from 13 to 23 residues and found that L17, F19 and F20 residues region play a great role in the process of binding of A? to the micelle surface.

  12. Structural and dynamic heterogeneity in a telechelic polymer solution Dmitry Bedrova,*, Grant Smitha

    E-print Network

    Utah, University of

    dynamics in a model telechelic polymer solution. The transient structural heterogeneity associated-micelle separation at long times. As with associating polymers, glass-forming liquids and other complex heterogeneous at temperatures ðTÞ much higher than Tg [6]. Dynamic heterogeneity has been also reported in associating polymer

  13. Formation and thermodynamic stability of (polymer + porphyrin) supramolecular structures in aqueous solutions

    E-print Network

    Annunziata, Onofrio

    of (polymer + porphyrin) supramolecular structures and their competition with porphyrin self-association were) self-association and TPPS binding to the polymer poly(vinylpyrrolidone) (PVP, 40 kg/mol) in aqueous. However, (polymer + porphyrin) binding competes with porphyrin self-association in solution, and accurate

  14. Protein folding, protein structure and the origin of life: Theoretical methods and solutions of dynamical problems

    NASA Technical Reports Server (NTRS)

    Weaver, D. L.

    1982-01-01

    Theoretical methods and solutions of the dynamics of protein folding, protein aggregation, protein structure, and the origin of life are discussed. The elements of a dynamic model representing the initial stages of protein folding are presented. The calculation and experimental determination of the model parameters are discussed. The use of computer simulation for modeling protein folding is considered.

  15. Structural heterogeneity and its effect on the glass transition in sucrose solutions containing protein and polysaccharide

    Microsoft Academic Search

    M. A. Rogers; Y. H. Roos; H. D. Goff

    2006-01-01

    Foods systems containing polysaccharides and proteins tend to be structurally heterogeneous due to polymer incompatibility and phase separation, at least on a microscopic scale. This study was designed to determine the effect of such phase separation on the bulk glass transition temperature of frozen solutions containing sucrose, lactose, milk salts, protein from skim milk powder and guar or locust bean

  16. Tomatoes Production, Marketing Structure and Solution Recommendations for Problems of Farmers: A Case Study

    Microsoft Academic Search

    Kemal Esengun; Murat Sayili; Hasan Akca

    2005-01-01

    This study focus on production of tomatoes, its marketing structure, problems faced by farmers and solution recommendations for the problems. Data were collected from 90 tomatoes farms via survey. Average tomatoes production area was found as 6.69 decare (1 dacare = 1000 m2). Two-thirds of the farms produces only indeterminate tomatoes. The ratio of farmers growing both determinate and indeterminate

  17. Surface Structural Studies of Methanesulfonic Acid at Air /Aqueous Solution Interfaces Using Vibrational Sum Frequency Spectroscopy

    E-print Network

    Richmond, Geraldine L.

    Surface Structural Studies of Methanesulfonic Acid at Air /Aqueous Solution Interfaces Using Form: NoVember 28, 2000 Atmospheric gas phase species such as methanesulfonic acid (MSA) are adsorbed orientation in which the methyl group points away from the liquid surface. The surrounding surface water

  18. Neutron reflectivity study of the swollen structure of polyzwitterion and polyeletrolyte brushes in aqueous solution.

    PubMed

    Kobayashi, Motoyasu; Ishihara, Kazuhiko; Takahara, Atsushi

    2014-01-01

    The swollen brush structures of polycation and zwitterionic polymer brushes, such as poly(2-methacryloyloxyethyltrimethylammonium chloride) (PMTAC), poly(2-methacryloyloxyethyl phosphorylcholine) (PMPC), and poly[3-(N-2-methacryloyloxyethyl-N,N-dimethyl)ammonatopropanesulfonate] (PMAPS), in aqueous solutions of various ionic strengths were characterized by neutron reflectivity (NR) measurements. A series of the polyelectrolyte brushes were prepared by surface-initiated controlled radical polymerization on silicon substrates. A high-graft-density PMTAC brush in salt-free water (D2O) adopted a two-region step-like structure consisting of a shrunk region near the Si substrate surface and a diffuse brush region with a relatively stretched chain structure at the solution interface. The diffuse region of PMTAC was reduced with increase in salt (NaCl) concentration. The PMAPS brush in D2O formed a collapsed structure due to the strong molecular interaction between betaine groups, while significant increase in the swollen thickness was observed in salt aqueous solution. In contrast, no change was observed in the depth profile of the swollen PMPC brush in D2O with various salt concentrations. The unique solution behaviors of zwitterionic polymer brushes were described. PMID:25178564

  19. HOUSEHOLD AND STRUCTURAL INSECTS Laboratory Evaluation of Boric Acid-Sugar Solutions as Baits

    E-print Network

    HOUSEHOLD AND STRUCTURAL INSECTS Laboratory Evaluation of Boric Acid-Sugar Solutions as Baits of boric acid and tend to be less efÞcacious than other insecticide baits. The purpose of this study and expressed as lethal time90, the time taken to kill 90% of the cockroaches. Results showed that boric acid

  20. Restoring Low Resolution Structure of Biological Macromolecules from Solution Scattering Using Simulated Annealing

    Microsoft Academic Search

    D. I. Svergun

    1999-01-01

    A method is proposed to restore ab initio low resolution shape and internal structure of chaotically oriented particles (e.g., biological macromolecules in solution) from isotropic scattering. A multiphase model of a particle built from densely packed dummy atoms is characterized by a configuration vector assigning the atom to a specific phase or to the solvent. Simulated annealing is employed to

  1. An Analytical Solution of Equivalent Stress for Structure Fatigue Life Prediction under Broad Band Random Loading

    Microsoft Academic Search

    Xiaoyun Liu; Pengmin Lü

    1997-01-01

    An analytical solution of an equivalent stress-range calculation, based on the power-spectral density of stress in critical points of structures, and a statistical theory for the peak distribution of a stationary Gaussian random process are presented in this paper for fatigue life assessment under broad-band random loading. This model has more advantages than similar existing models.

  2. Solution-State NMR Studies of the Surface Structure and Dynamics of Semiconductor Nanocrystals

    E-print Network

    Solution-State NMR Studies of the Surface Structure and Dynamics of Semiconductor Nanocrystals nuclear magnetic resonance (NMR) relaxation studies of thiophenol-capped CdS nanocrystals are presented. The transverse and longitudinal relaxation times were investigated as a function of nanocrystal radius

  3. Work function tuning for high-performance solution-processed organic photodetectors with inverted structure.

    PubMed

    Saracco, Emeline; Bouthinon, Benjamin; Verilhac, Jean-Marie; Celle, Caroline; Chevalier, Nicolas; Mariolle, Denis; Dhez, Olivier; Simonato, Jean-Pierre

    2013-12-01

    Organic photodetectors with inverted structure are fabricated by solution process techniques. A very thin interfacing layer of polyethyleneimine leads to a homogenous interface with low work function. The devices exhibit excellent performances, in particular in terms of low dark current density, wide range linearity, high detectivity, and remarkable stability in ambient air without encapsulation. PMID:24136640

  4. The structure of 12-silicotungstate and 12-phosphomolybdate anions in saturated aqueous solutions

    Microsoft Academic Search

    A. A. Babad-Zakhryapin; N. S. Gorbunov

    1962-01-01

    Employing x-rays, it was shown by the radial distribution method that in aqueous saturated solutions of 12-silicotungstic and 12-phosphomolybdic acids the structure of the corresponding complex anions is the same as in crystals at differing moisture contents.

  5. Aqueous Solutions of Amino Acid Based Ionic Liquids. Dispersion and Structure

    E-print Network

    Chaban, Vitaly V

    2014-01-01

    New ionic liquids (ILs) are continuously introduced involving an increasing number of organic and inorganic ions. Amino acid based ILs (AAILs) represent a specific interest due to their natural origin and, allegedly, low cost. We apply our recently developed force field for imidazolium-based AAILs to investigate structure properties in their aqueous solutions via molecular dynamics (MD) simulations. By reporting cluster analysis, radial distribution functions and spatial distribution functions, we argue that AAIL ions are well dispersed in the aqueous media, irrespective of the AAIL content. Aqueous solutions of AAILs exhibit desirable properties as solvents for chemical engineering. The AAILs in relatively dilute aqueous solutions (10 mol% AAIL) exist as ion pairs, while more concentrated solutions feature certain amount of larger ionic aggregates.

  6. Structure and properties of regenerated Antheraea pernyi silk fibroin in aqueous solution.

    PubMed

    Tao, Wei; Li, Mingzhong; Zhao, Chunxia

    2007-04-10

    Antheraea pernyi silk fibroin fibers were dissolved by aqueous lithium thiocyanate to obtain regenerated A. pernyi silk fibroin solution. By means of circular dichroism, (13)C NMR and Raman spectroscopy, the molecular conformation of regenerated A. pernyi silk fibroin in aqueous solution was investigated. The relationship of environmental factors and sol-gel transformation behavior of regenerated A. pernyi silk fibroin was also studied. The molecular conformations of regenerated A. pernyi silk fibroin mainly were alpha-helix and random coil in solution. There also existed a little beta-sheet conformation. It was obviously different with Bombyx mori silk fibroin, whose molecular conformation in solution was only random coil but no alpha-helix existence. With the increase of temperature and solution concentration and with the decrease of solution pH value, the gelation velocity of regenerated A. pernyi silk fibroin solution increased. Especially, it showed that A. pernyi silk fibroin was more sensitive to temperature than B. mori silk fibroin during the sol-gel transformation. The velocity increased obviously when the temperature was above 30 degrees C. During the sol-gel transformation, the molecular conformation of regenerated A. pernyi silk fibroin changed from random coil to beta-sheet structure. The results of these studies provided important insight into the preparation of new biomaterials by silk fibroin protein. PMID:17173967

  7. Application of in situ diffraction in high-throughput structure determination platforms.

    PubMed

    Aller, Pierre; Sanchez-Weatherby, Juan; Foadi, James; Winter, Graeme; Lobley, Carina M C; Axford, Danny; Ashton, Alun W; Bellini, Domenico; Brandao-Neto, Jose; Culurgioni, Simone; Douangamath, Alice; Duman, Ramona; Evans, Gwyndaf; Fisher, Stuart; Flaig, Ralf; Hall, David R; Lukacik, Petra; Mazzorana, Marco; McAuley, Katherine E; Mykhaylyk, Vitaliy; Owen, Robin L; Paterson, Neil G; Romano, Pierpaolo; Sandy, James; Sorensen, Thomas; von Delft, Frank; Wagner, Armin; Warren, Anna; Williams, Mark; Stuart, David I; Walsh, Martin A

    2015-01-01

    Macromolecular crystallography (MX) is the most powerful technique available to structural biologists to visualize in atomic detail the macromolecular machinery of the cell. Since the emergence of structural genomics initiatives, significant advances have been made in all key steps of the structure determination process. In particular, third-generation synchrotron sources and the application of highly automated approaches to data acquisition and analysis at these facilities have been the major factors in the rate of increase of macromolecular structures determined annually. A plethora of tools are now available to users of synchrotron beamlines to enable rapid and efficient evaluation of samples, collection of the best data, and in favorable cases structure solution in near real time. Here, we provide a short overview of the emerging use of collecting X-ray diffraction data directly from the crystallization experiment. These in situ experiments are now routinely available to users at a number of synchrotron MX beamlines. A practical guide to the use of the method on the MX suite of beamlines at Diamond Light Source is given. PMID:25502203

  8. Automating crystallographic structure solution and refinement of protein–ligand complexes

    PubMed Central

    Echols, Nathaniel; Moriarty, Nigel W.; Klei, Herbert E.; Afonine, Pavel V.; Bunkóczi, Gábor; Headd, Jeffrey J.; McCoy, Airlie J.; Oeffner, Robert D.; Read, Randy J.; Terwilliger, Thomas C.; Adams, Paul D.

    2014-01-01

    High-throughput drug-discovery and mechanistic studies often require the determination of multiple related crystal structures that only differ in the bound ligands, point mutations in the protein sequence and minor conformational changes. If performed manually, solution and refinement requires extensive repetition of the same tasks for each structure. To accelerate this process and minimize manual effort, a pipeline encompassing all stages of ligand building and refinement, starting from integrated and scaled diffraction intensities, has been implemented in Phenix. The resulting system is able to successfully solve and refine large collections of structures in parallel without extensive user intervention prior to the final stages of model completion and validation. PMID:24419387

  9. Solution of quadratic matrix equations for free vibration analysis of structures.

    NASA Technical Reports Server (NTRS)

    Gupta, K. K.

    1973-01-01

    An efficient digital computer procedure and the related numerical algorithm are presented herein for the solution of quadratic matrix equations associated with free vibration analysis of structures. Such a procedure enables accurate and economical analysis of natural frequencies and associated modes of discretized structures. The numerically stable algorithm is based on the Sturm sequence method, which fully exploits the banded form of associated stiffness and mass matrices. The related computer program written in FORTRAN V for the JPL UNIVAC 1108 computer proves to be substantially more accurate and economical than other existing procedures of such analysis. Numerical examples are presented for two structures - a cantilever beam and a semicircular arch.

  10. Solution Structure of a DNA Quadruplex Containing the Fragile X Syndrome Triplet Repeat

    Microsoft Academic Search

    Abdelali Kettani; Ajay R. Kumar; Dinshaw J. Patel

    1995-01-01

    Both X-ray and NMR structural studies have defined the polymorphic nature of G-quadruplexes generated through mutual stacking of G·G·G·G tetrads by guanine rich telomeric sequences. Recently, the fragile X syn- drome d(C-G-G)ntriplet nucleotide repeat has been shown to form a stable quadruplex of undefined structure in monovalent cation solution. We have undertaken a structural characterization of the d(G-C-G-G-T3-G-C-G-G) undecanucleotide to

  11. Surface evolution of a gradient structured Ti in hydrogen peroxide solution

    NASA Astrophysics Data System (ADS)

    Wen, Ming; Gu, Jian-Feng; Liu, Gang; Wang, Zhen-Bo; Lu, Jian

    2008-02-01

    In this work, the interaction between hydrogen peroxide (H 2O 2) and a gradient structured Ti was investigated extensively. The gradient structured Ti (SMAT Ti) was produced by surface mechanical attrition treatment (SMAT), and then it was immersed in H 2O 2 solution for different time until 48 h at room temperature (25 °C). The structure and surface morphology evolution were examined by Raman spectra and scanning electron microscopy (SEM). The formation mechanism of nanoporous titania was discussed based on above results.

  12. Contrast-enhanced MRI with new biodegradable macromolecular Gd(III) complexes in tumor-bearing mice.

    PubMed

    Zong, Yuda; Wang, Xinghe; Goodrich, K Craig; Mohs, Aaron M; Parker, Dennis L; Lu, Zheng-Rong

    2005-04-01

    The structures of polydisulfide-based biodegradable macromolecular Gd(III) complexes were modified to improve their in vivo retention time and MRI contrast enhancement. Steric hindrance was introduced around the disulfide bonds to control their access to free thiols in order to alter the degradation rate of the copolymers. Two new macromolecular agents, (Gd-DTPA)-cystine copolymers (GDCP) and (Gd-DTPA)-cystine diethyl ester copolymers (GDCEP), were prepared. Both agents were readily degraded in vitro and in vivo by the disulfide-thiol exchange reaction, but at a slow rate. The introduction of COOH and COOEt groups slowed down the degradation of the copolymers in the incubation with 15 microM cysteine. Metabolic degradation products were identified by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry in the urine samples from rats injected with the agents. The T(1) relaxivity (r(1)) was 5.43 mM(-1)s(-1) for GDCP, and 5.86 mM(-1)s(-1) for GDCEP, respectively, at 3T. MRI contrast enhancement of both agents was studied in nude mice bearing MDA-BM-231 human breast carcinoma xenografts, on a Siemens Trio 3T scanner. The modified agents resulted in more significant contrast enhancement in the blood pool and tumor periphery than (Gd-DTPA)-cystamine copolymers (GDCC) and a low-molecular-weight control agent, Gd-(DTPA-BMA), at a dose of 0.1 mmol-Gd/kg. The results demonstrate that the structural modification of the biodegradable macromolecular Gd(III) complexes resulted in a relatively slow degradation of the macromolecules and significantly improved in vivo contrast enhancement. The modified agents show promise for use in investigations of blood pool and cancer by contrast-enhanced (CE) MRI. PMID:15799038

  13. Solution structure of CEH-37 homeodomain of the nematode Caenorhabditis elegans

    SciTech Connect

    Moon, Sunjin [Structural Biochemistry and Molecular Biophysics Lab, Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749 (Korea, Republic of)] [Structural Biochemistry and Molecular Biophysics Lab, Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749 (Korea, Republic of); Lee, Yong Woo; Kim, Woo Taek [Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749 (Korea, Republic of)] [Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749 (Korea, Republic of); Lee, Weontae, E-mail: wlee@spin.yonsei.ac.kr [Structural Biochemistry and Molecular Biophysics Lab, Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749 (Korea, Republic of)] [Structural Biochemistry and Molecular Biophysics Lab, Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749 (Korea, Republic of)

    2014-01-10

    Highlights: •We have determined solution structures of CEH-37 homedomain. •CEH-37 HD has a compact ?-helical structure with HTH DNA binding motif. •Solution structure of CEH-37 HD shares its molecular topology with that of the homeodomain proteins. •Residues in the N-terminal region and HTH motif are important in binding to Caenorhabditis elegans telomeric DNA. •CEH-37 could play an important role in telomere function via DNA binding. -- Abstract: The nematode Caenorhabditis elegans protein CEH-37 belongs to the paired OTD/OTX family of homeobox-containing homeodomain proteins. CEH-37 shares sequence similarity with homeodomain proteins, although it specifically binds to double-stranded C. elegans telomeric DNA, which is unusual to homeodomain proteins. Here, we report the solution structure of CEH-37 homeodomain and molecular interaction with double-stranded C. elegans telomeric DNA using nuclear magnetic resonance (NMR) spectroscopy. NMR structure shows that CEH-37 homeodomain is composed of a flexible N-terminal region and three ?-helices with a helix-turn-helix (HTH) DNA binding motif. Data from size-exclusion chromatography and fluorescence spectroscopy reveal that CEH-37 homeodomain interacts strongly with double-stranded C. elegans telomeric DNA. NMR titration experiments identified residues responsible for specific binding to nematode double-stranded telomeric DNA. These results suggest that C. elegans homeodomain protein, CEH-37 could play an important role in telomere function via DNA binding.

  14. Dynamic structure factor of a stiff polymer in a glassy solution

    E-print Network

    J. Glaser; O. Hallatschek; K. Kroy

    2008-05-29

    We provide a comprehensive overview of the current theoretical understanding of the dynamic structure factor of stiff polymers in semidilute solution based on the wormlike chain (WLC) model. We extend previous work by computing exact numerical coefficients and an expression for the dynamic mean square displacement (MSD) of a free polymer and compare various common approximations for the hydrodynamic interactions, which need to be treated accurately if one wants to extract quantitative estimates for model parameters from experimental data. A recent controversy about the initial slope of the dynamic structure factor is thereby resolved. To account for the interactions of the polymer with a surrounding (sticky) polymer solution, we analyze an extension of the WLC model, the glassy wormlike chain (GWLC), which predicts near power-law and logarithmic long-time tails in the dynamic structure factor.

  15. Solution structure of sialyl Lewis X mimics studied by two-dimensional NMR

    NASA Astrophysics Data System (ADS)

    Demura, Makoto; Noda, Masatoshi; Kajimoto, Tetsuya; Uchiyama, Taketo; Umemoto, Kimiko; Wong, Chi-Huey; Asakura, Tetsuo

    2002-01-01

    A structure of the peptidic mimic of sialyl Lewis X (Sle X) (?- N-acetyl-neuraminyl-(2,3)-?- D-galactopyranosyl-(1,4)-[?- L-fucopyranosyl-(1,3)-?- D- N-acetyl-glucosamine]) in an aqueous solution was studied using two-dimensional 1H NMR spectroscopy. Complete assignments of 1H NMR chemical shift of the SLe X mimic have been performed. The presence of three conformers of the SLe X mimic in a solution was proposed by using distance geometry calculation based on NOE constraints, which were obtained from NOESY experiments. In addition, intermolecular interaction between the mimic and the crystal structure of E-selectin was refined using molecular dynamics. This suggested the conformational rearrangement of the functional groups of the conformers to the active sites of E-selectin. The relationship between the binding activities toward E-selectin and the three-dimensional structures of other mimics was also discussed.

  16. Uniqueness of Topological Solutions and the Structure of Solutions for the Chern-Simons System with Two Higgs Particles

    NASA Astrophysics Data System (ADS)

    Chern, Jann-Long; Chen, Zhi-You; Lin, Chang-Shou

    2010-06-01

    The existence of topological solutions for the Chern-Simons equation with two Higgs particles has been proved by Lin, Ponce and Yang [16]. However, both the uniqueness problem and the existence of non-topological solutions have been left open. In this paper, we consider the case of one vortex at origin. Among others, we prove the uniqueness of topological solutions and give a complete study of the radial solutions, in particular, the existence of some non-topological solutions.

  17. A hybrid computational-experimental approach for automated crystal structure solution.

    PubMed

    Meredig, Bryce; Wolverton, C

    2013-02-01

    Crystal structure solution from diffraction experiments is one of the most fundamental tasks in materials science, chemistry, physics and geology. Unfortunately, numerous factors render this process labour intensive and error prone. Experimental conditions, such as high pressure or structural metastability, often complicate characterization. Furthermore, many materials of great modern interest, such as batteries and hydrogen storage media, contain light elements such as Li and H that only weakly scatter X-rays. Finally, structural refinements generally require significant human input and intuition, as they rely on good initial guesses for the target structure. To address these many challenges, we demonstrate a new hybrid approach, first-principles-assisted structure solution (FPASS), which combines experimental diffraction data, statistical symmetry information and first-principles-based algorithmic optimization to automatically solve crystal structures. We demonstrate the broad utility of FPASS to clarify four important crystal structure debates: the hydrogen storage candidates MgNH and NH(3)BH(3); Li(2)O(2), relevant to Li-air batteries; and high-pressure silane, SiH(4). PMID:23178265

  18. Physical and structural stability of the monoclonal antibody, trastuzumab (Herceptin®), intravenous solutions.

    PubMed

    Pabari, Ritesh M; Ryan, Benedict; Ahmad, Wazir; Ramtoola, Zebunnissa

    2013-01-01

    A major limitation of biological therapeutics is their propensity for degradation particularly in aqueous solutions hence resulting in their short shelf-life. In this study, the stability of trastuzumab (Herceptin®) intravenous (i.v.) solutions, an IgG1 monoclonal antibody (mAb), indicated for the treatment of HER2 positive breast cancer, stored under refrigerated conditions, was evaluated over 28 days. No change in visual appearance or average particle size was observed. The pH values of the trastuzumab i.v. solutions remained stable over time. Interestingly, no change in trastuzumab monomer concentration was observed throughout the 28-day study, as determined by SEC-HPLC. SDSPAGE showed only a monomer band corresponding to the molecular weight of trastuzumab. Circular dichroism spectra obtained following 28-day storage demonstrated integrity of the secondary structural conformation of trastuzumab. Results from this study show that trastuzumab i.v. solutions remain physically and structurally stable on storage at 2-8°C for 28 days. These findings suggest that trastuzumab in solution may not be as sensitive to degradation as expected for a mAb and therefore may have important implications in extending trastuzumab shelf life for clinical use and reducing associated healthcare cost. PMID:23360264

  19. An integrated method for the transient solution of reduced order models of geometrically nonlinear structures

    NASA Astrophysics Data System (ADS)

    Lülf, Fritz Adrian; Tran, Duc-Minh; Matthies, Hermann G.; Ohayon, Roger

    2015-02-01

    For repeated transient solutions of geometrically nonlinear structures, the numerical effort often poses a major obstacle. Thus it may become necessary to introduce a reduced order model which accelerates the calculations considerably while taking into account the nonlinear effects of the full order model in order to maintain accuracy. This work yields an integrated method that allows for rapid, accurate and parameterisable transient solutions. It is applicable if the structure is discretised in time and in space and its dynamic equilibrium described by a matrix equation. The projection on a reduced basis is introduced to obtain the reduced order model. Three approaches, each responding to one of the requirements of rapidity, accuracy and parameterisation, are united to form the integrated method. The polynomial formulation of the nonlinear terms renders the solution of the reduced order model autonomous from the finite element formulation and ensures a rapid solution. The update and augmentation of the reduced basis ensures the accuracy, because the simple introduction of a constant basis seems to be insufficient to account for the nonlinear behaviour. The interpolation of the reduced basis allows adapting the reduced order model to different external parameters. A Newmark-type algorithm provides the backbone of the integrated method. The application of the integrated method on test-cases with geometrically nonlinear finite elements confirms that this method enables a rapid, accurate and parameterisable transient solution.

  20. Structure and dimerization of translation initiation factor aIF5B in solution

    SciTech Connect

    Rasmussen, Louise Caroe Vohlander [Department of Molecular Biology, Aarhus University, Gustav Wieds Vej 10, DK-8000 Aarhus C (Denmark)] [Department of Molecular Biology, Aarhus University, Gustav Wieds Vej 10, DK-8000 Aarhus C (Denmark); Oliveira, Cristiano Luis Pinto [Department of Chemistry, Centre for mRNP Biogenesis and Metabolism, and iNANO Interdisciplinary Nanoscience Center, Aarhus University, Langelandsgade 140, DK-8000 Aarhus C (Denmark)] [Department of Chemistry, Centre for mRNP Biogenesis and Metabolism, and iNANO Interdisciplinary Nanoscience Center, Aarhus University, Langelandsgade 140, DK-8000 Aarhus C (Denmark); Byron, Olwyn [Glasgow Biomedical Research Center, University of Glasgow, Glasgow G12 8QQ, Scotland (United Kingdom)] [Glasgow Biomedical Research Center, University of Glasgow, Glasgow G12 8QQ, Scotland (United Kingdom); Jensen, Janni Mosgaard [Department of Molecular Biology, Aarhus University, Gustav Wieds Vej 10, DK-8000 Aarhus C (Denmark)] [Department of Molecular Biology, Aarhus University, Gustav Wieds Vej 10, DK-8000 Aarhus C (Denmark); Pedersen, Jan Skov [Department of Chemistry, Centre for mRNP Biogenesis and Metabolism, and iNANO Interdisciplinary Nanoscience Center, Aarhus University, Langelandsgade 140, DK-8000 Aarhus C (Denmark)] [Department of Chemistry, Centre for mRNP Biogenesis and Metabolism, and iNANO Interdisciplinary Nanoscience Center, Aarhus University, Langelandsgade 140, DK-8000 Aarhus C (Denmark); Sperling-Petersen, Hans Uffe [Department of Molecular Biology, Aarhus University, Gustav Wieds Vej 10, DK-8000 Aarhus C (Denmark)] [Department of Molecular Biology, Aarhus University, Gustav Wieds Vej 10, DK-8000 Aarhus C (Denmark); Mortensen, Kim Kusk, E-mail: kkm@science.au.dk [Department of Molecular Biology, Aarhus University, Gustav Wieds Vej 10, DK-8000 Aarhus C (Denmark)

    2011-12-09

    Highlights: Black-Right-Pointing-Pointer aIF5B forms maximum 5.0-6.8% irreversible dimers in solution. Black-Right-Pointing-Pointer Sedimentation coefficients for monomer and dimer are 3.64 and 5.51 {+-} 0.29 S. Black-Right-Pointing-Pointer Adding only 2% glycerol prevents dimerization. Black-Right-Pointing-Pointer SAXS on aIF5B monomer gave an R{sub g} of 37.5 {+-} 0.2 A and a D{sub max} of {approx}130 A. Black-Right-Pointing-Pointer There are universal structural differences between aIF5B and Escherichia coli IF2. -- Abstract: Translation initiation factor 5B (IF5B) is required for initiation of protein synthesis. The solution structure of archaeal IF5B (aIF5B) was analysed by small-angle X-ray scattering (SAXS) and dynamic light scattering (DLS) and was indicated to be in both monomeric and dimeric form. Sedimentation equilibrium (SE) analytical ultracentrifugation (AUC) of aIF5B indicated that aIF5B forms irreversible dimers in solution but only to a maximum of 5.0-6.8% dimer. Sedimentation velocity (SV) AUC at higher speed also indicated the presence of two species, and the sedimentation coefficients s{sub 20,w}{sup 0} were determined to be 3.64 and 5.51 {+-} 0.29 S for monomer and dimer, respectively. The atomic resolution (crystallographic) structure of aIF5B (Roll-Mecak et al. ) was used to model monomer and dimer, and theoretical sedimentation coefficients for these models were computed (3.89 and 5.63 S, respectively) in good agreement with the sedimentation coefficients obtained from SV analysis. Thus, the structure of aIF5B in solution must be very similar to the atomic resolution structure of aIF5B. SAXS data were acquired in the same buffer with the addition of 2% glycerol to inhibit dimerization, and the resultant monomeric aIF5B in solution did indeed adopt a structure very similar to the one reported earlier for the protein in crystalline form. The p(r) function indicated an elongated conformation supported by a radius of gyration of 37.5 {+-} 0.2 A and a maximum dimension of {approx}130 A. The effects of glycerol on the formation of dimers are discussed. This new model of aIF5B in solution shows that there are universal structural differences between aIF5B and the homologous protein IF2 from Escherichia coli.

  1. Polydimethylsiloxane as a Macromolecular Additive for Enhanced Performance of Molecular Bulk Heterojunction Organic Solar Cells

    SciTech Connect

    Graham, Kenneth; Mei, Jianguo; Stalder, Romain; Shim, Jae Won; Cheun, Hyeunseok; Steffy, Fred; So, Franky; Kippelen, Bernard; Reynolds, John R.

    2011-04-27

    The effect of the macromolecular additive, polydimethylsiloxane (PDMS), on the performance of solution processed molecular bulk heterojunction solar cells is investigated, and the addition of PDMS is shown to improve device power conversion efficiency by ?70% and significantly reduce cell-to-cell variation, from a power conversion efficiency of 1.25 ± 0.37% with no PDMS to 2.16 ± 0.09% upon the addition of 0.1 mg/mL PDMS to the casting solution. The cells are based on a thiophene and isoindigo containing oligomer as the electron donor and [6,6]-phenyl-C61 butyric acid methyl ester (PC{sub 61}BM) as the electron acceptor. PDMS is shown to have a strong influence on film morphology, with a significant decrease in film roughness and feature size observed. The morphology change leads to improved performance parameters, most notably an increase in the short circuit current density from 4.3 to 6.8 mA/cm{sup 2} upon addition of 0.1 mg/mL PDMS. The use of PDMS is of particular interest, as this additive appears frequently as a lubricant in plastic syringes commonly used in device fabrication; therefore, PDMS may unintentionally be incorporated into device active layers.

  2. Theory of Polymer Chains in Poor Solvent: Single-Chain Structure, Solution Thermodynamics and Theta Point

    E-print Network

    Rui Wang; Zhen-Gang Wang

    2014-06-05

    Using the language of the Flory chi parameter, we develop a theory that unifies the treatment of the single-chain structure and the solution thermodynamics of polymers in poor solvents. The structure of a globule and its melting thermodynamics is examined using the self-consistent filed theory. Our results show that the chain conformation involves three states prior to the globule-to-coil transition: the fully-collapsed globule, the swollen globule and the molten globule, which are distinguished by the core density and the interfacial thickness. By examining the chain-length dependence of the melting of the swollen globule, we find universal scaling behavior in the chain properties near the Theta point. The information of density profile and free energy of the globule is used in the dilute solution thermodynamics to study the phase equilibrium of polymer solution. Our results show different scaling behavior of the solubility of polymers in the dilute solution compared to the F-H theory, both in the chi dependence and the chain-length dependence. From the perspectives of single chain structure and solution thermodynamics, our results verifies the consistency of the Theta point defined by different criteria in the limit of infinite chain length: the disappearance of the second viral coefficient, the abrupt change in chain size and the critical point in the phase diagram of the polymer solution. Our results show the value of chi at the Theta point is 0.5 (for the case of equal monomer and solvent volume), which coincides with the value predicted from the F-H theory.

  3. Structure determination of the seven-helical transmembrane receptor sensory rhodopsin II by solution NMR spectroscopy

    PubMed Central

    Gautier, Antoine; Mott, Helen R.; Bostock, Mark J.; Kirkpatrick, John P.; Nietlispach, Daniel

    2010-01-01

    Seven-helical membrane proteins represent a challenge for structural biology. Here, we report the first NMR structure determination of a detergent-solubilized seven-helical transmembrane (7TM) protein, the phototaxis receptor sensory rhodopsin II (pSRII) from Natronomonas pharaonis, as a proof of principle. The overall quality of the structure ensemble is extremely good (backbone root mean squared deviation of 0.48 Å) and agrees well with previously determined X-ray structures. Furthermore, measurements in more native-like small phospholipid bicelles indicate that the protein structure is the same as in detergent micelles, suggesting that environment specific effects are minimal when using mild detergents. We use our case study as a platform to discuss the feasibility of similar solution NMR studies for other 7TM proteins including members of the family of G protein-coupled receptors (GPCRs). PMID:20512150

  4. Relaxation matrix refinement of the solution structure of squash trypsin inhibitor.

    PubMed

    Nilges, M; Habazettl, J; Brünger, A T; Holak, T A

    1991-06-01

    The structure of the small squash trypsin inhibitor CMTI-I is refined by directly minimizing the difference between the observed two-dimensional nuclear Overhauser enhancement (NOE) intensities and those calculated by the full relaxation matrix approach. To achieve this, a term proportional to this difference was added to the potential energy function of the molecular dynamics program X-PLOR. Derivatives with respect to atomic co-ordinates are calculated analytically. Spin diffusion effects are thus accounted for fully during the refinement. Initial structures for the refinement were those determined recently by solution nuclear magnetic resonance using the isolated two-spin approximation to derive distance range estimates. The fits to the nuclear magnetic resonance data improve significantly with only small shifts in the refined structures during a few cycles of conjugate gradient minimization. However, larger changes (approximately 1 A) in the conformation occur during simulated annealing, which is accompanied by a further reduction of the difference between experimental and calculated two-dimensional NOE intensities. The refined structures are closer to the X-ray structure of the inhibitor complexed with trypsin than the initial structures. The root-mean-square difference for backbone atoms between the initial structures and the X-ray structure is 0.96 A, and that between the refined structures and the X-ray structure 0.61 A. PMID:2051485

  5. Capturing Transient Structures in the Elimination Reaction of Haloalkane in Solution by Transient X-ray Diffraction

    E-print Network

    Ihee, Hyotcherl

    Capturing Transient Structures in the Elimination Reaction of Haloalkane in Solution by Transient X,2- diiodotetrafluoroethane (C2F4I2) in methanol solution using transient X-ray diffraction (TXD).1 The iodine elimination unanswered. For example, transient absorption spectroscopy in solution phase2b could not elucidate

  6. Liquid crystalline ordering of nucleosome core particles under macromolecular crowding conditions: evidence for a discotic columnar hexagonal phase.

    PubMed Central

    Leforestier, A; Livolant, F

    1997-01-01

    Macromolecular crowding conditions occurring inside the cell nucleus were reproduced experimentally with solutions of mononucleosome core particles to study their supramolecular organization. We report here that under these conditions, and over a large range of monovalent salt concentrations, mononucleosome core particles self-assemble to form a discotic liquid crystalline phase characterized in polarizing and freeze-fracture electron microscopy. Mononucleosomes are stacked on each other to form columns, which are themselves closely packed into an hexagonal array. The nucleosome concentration, estimated from the network parameters, falls in the range of values measured in cell nuclei. We suggest that these concentrated solutions, although their organization cannot be immediately compared to the organization of chromatin in vivo, may be used to investigate the nucleosome-nucleosome interactions. Furthermore, this approach may be complexified to take into account the complexity of the eucaryotic chromatin. Images FIGURE 1 FIGURE 2 FIGURE 4 PMID:9336172

  7. Effects of macromolecular crowding on the collapse of biopolymers

    E-print Network

    Hongsuk Kang; Philip A. Pincus; Changbong Hyeon; D. Thirumalai

    2015-01-13

    Experiments show that macromolecular crowding modestly reduces the size of intrinsically disordered proteins (IDPs) even at volume fraction ($\\phi$) similar to that in the cytosol whereas DNA undergoes a coil-to-globule transition at very small $\\phi$. We show using a combination of scaling arguments and simulations that the polymer size $\\overline{R}_g(\\phi)$ depends on $x = \\overline{R}_g(0)/D$ where $D$ is the $\\phi$-dependent distance between the crowders. If $x\\lesssim \\mathcal{O}(1)$, there is only a small decrease in $\\overline{R}_g(\\phi)$ as $\\phi$ increases. When $x\\gg \\mathcal{O}(1)$, a cooperative coil-to-globule transition is induced. Our theory quantitatively explains a number of experiments.

  8. Solution studies and structural model of the extracellular domain of the human amyloid precursor protein.

    PubMed Central

    Gralle, Matthias; Botelho, Michelle M; de Oliveira, Cristiano L P; Torriani, Iris; Ferreira, Sérgio T

    2002-01-01

    The amyloid precursor protein (APP) is the precursor of the beta-amyloid peptide (Abeta), which is centrally related to the genesis of Alzheimer's disease (AD). In addition, APP has been suggested to mediate and/or participate in events that lead to neuronal degeneration in AD. Despite the fact that various aspects of the cell biology of APP have been investigated, little information on the structure of this protein is available. In this work, the solution structure of the soluble extracellular domain of APP (sAPP, composing 89% of the amino acid residues of the whole protein) has been investigated through a combination of size-exclusion chromatography, circular dichroism, and synchrotron radiation small-angle x-ray scattering (SAXS) studies. sAPP is monomeric in solution (65 kDa obtained from SAXS measurements) and exhibits an anisometric molecular shape, with a Stokes radius of 39 or 51 A calculated from SAXS or chromatographic data, respectively. The radius of gyration and the maximum molecular length obtained by SAXS were 38 A and 130 A, respectively. Analysis of SAXS data further allowed building a structural model for sAPP in solution. Circular dichroism data and secondary structure predictions based on the amino acid sequence of APP suggested that a significant fraction of APP (30% of the amino acid residues) is not involved in standard secondary structure elements, which may explain the elongated shape of the molecule recovered in our structural model. Possible implications of the structure of APP in ligand binding and molecular recognition events involved in the biological functions of this protein are discussed. PMID:12496118

  9. Hepatitis B virus peptide inhibitors: solution structures and interactions with the viral capsid.

    PubMed

    Muhamad, Azira; Ho, Kok Lian; Abdul Rahman, Mohd Basyaruddin; Tejo, Bimo A; Uhrín, Dušan; Tan, Wen Siang

    2015-07-01

    Hepatitis B virus (HBV) infection remains a health problem globally despite the availability of effective vaccines. In the assembly of the infectious virion, both the preS and S regions of the HBV large surface antigen (L-HBsAg) interact synergistically with the viral core antigen (HBcAg). Peptides preS and S based on the L-HBsAg were demonstrated as potential inhibitors to block the viral assembly. Therefore, the objectives of this study were to determine the solution structures of these peptides and study their interactions with HBcAg. The solution structures of these peptides were solved using (1)H, (13)C, and (15)N NMR spectroscopy. Peptide preS has several structured regions of ?-turns at Ser7-Pro8-Pro9, Arg11-Thr12-Thr13 and Ser22-Thr23-Thr24 sequences whereas peptide S has only one structured region observed at Ser3-Asn4-His5. Both peptides contain bend-like structures surrounding the turn structures. Docking studies revealed that both peptides interacted with the immunodominant region of HBcAg located at the tip of the viral capsid spikes. Saturation Transfer Difference (STD) NMR experiments identified several aromatic residues in peptides preS and S that interact with HBcAg. This study provides insights into the contact regions of L-HBsAg and HBcAg at atomic resolution which can be used to design antiviral agents that inhibit HBV morphogenesis. PMID:26100394

  10. Radiation damage to nucleoprotein complexes in macromolecular crystallography

    PubMed Central

    Bury, Charles; Garman, Elspeth F.; Ginn, Helen Mary; Ravelli, Raimond B. G.; Carmichael, Ian; Kneale, Geoff; McGeehan, John E.

    2015-01-01

    Significant progress has been made in macromolecular crystallography over recent years in both the understanding and mitigation of X-ray induced radiation damage when collecting diffraction data from crystalline proteins. In contrast, despite the large field that is productively engaged in the study of radiation chemistry of nucleic acids, particularly of DNA, there are currently very few X-ray crystallographic studies on radiation damage mechanisms in nucleic acids. Quantitative comparison of damage to protein and DNA crystals separately is challenging, but many of the issues are circumvented by studying pre-formed biological nucleoprotein complexes where direct comparison of each component can be made under the same controlled conditions. Here a model protein–DNA complex C.Esp1396I is employed to investigate specific damage mechanisms for protein and DNA in a biologically relevant complex over a large dose range (2.07–44.63?MGy). In order to allow a quantitative analysis of radiation damage sites from a complex series of macromolecular diffraction data, a computational method has been developed that is generally applicable to the field. Typical specific damage was observed for both the protein on particular amino acids and for the DNA on, for example, the cleavage of base-sugar N1—C and sugar-phosphate C—O bonds. Strikingly the DNA component was determined to be far more resistant to specific damage than the protein for the investigated dose range. At low doses the protein was observed to be susceptible to radiation damage while the DNA was far more resistant, damage only being observed at significantly higher doses. PMID:25723923

  11. Solution Structure of the 2A Protease from a Common Cold Agent, Human Rhinovirus C2, Strain W12

    E-print Network

    Solution Structure of the 2A Protease from a Common Cold Agent, Human Rhinovirus C2, Strain W12 al. (2014) Solution Structure of the 2A Protease from a Common Cold Agent, Human Rhinovirus C2 of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any

  12. Nuclear magnetic resonance solution structure of the Arc repressor using relaxation matrix calculations.

    PubMed

    Bonvin, A M; Vis, H; Breg, J N; Burgering, M J; Boelens, R; Kaptein, R

    1994-02-11

    The Arc repressor of Salmonella bacteriophage P22 is a dimeric sequence-specific DNA-binding protein. The solution structure of Arc has been determined from 2D NMR data using an "ensemble" iterative relaxation matrix approach (IRMA) followed by direct NOE refinement with DINOSAUR. A set of 51 structures was generated with distance geometry and further refined with a combination of restrained energy minimization and restrained molecular dynamics in a parallel refinement protocol. Distance constraints were obtained from an extensive set of NOE build-ups in H2O and 2H2O via relaxation matrix calculations from the ensemble of structures. Methyl group rotation, aromatic ring flaps and internal mobility effects (via order parameters obtained from a free molecular dynamics run in water) were included in these calculations. The best structures were finally refined with direct NOE constraints following a slow-cooling simulated annealing protocol. In this final refinement stage, theoretical NOE intensities were directly compared with the experimental data and forces were derived using a simple two-spin approximation for the gradient of the NOE function. Dynamic assignment was applied to the peaks involving unassigned diastereotopic groups. The structure is determined to a precision (r.m.s.d. from the average excluding the ill defined C and N-terminal region) of 0.55 and 1.10 A for backbone and all atoms, respectively. The final structures, with R factor values around 0.35, have good stereochemical qualities, contain an extensive network of hydrogen bonds consistent with the secondary structure elements and structural features in concordance with genetic data. The overall folding of the solution and crystal structures is the same. PMID:8107113

  13. Cone-angle Dependence of Ab-initio Structure Solutions Using Precession Electron Diffraction

    NASA Astrophysics Data System (ADS)

    Ciston, James; Own, Christopher S.; Marks, Laurence D.

    2008-04-01

    Precession electron diffraction (PED) is a technique which is gaining increasing interest due to its ease of use and reduction of the dynamical scattering problem in electron diffraction, leading to more direct structure solutions. We have performed a systematic study of the effect of precession angle for the mineral andalusite on kinematical extinctions and direct methods solutions where the semiangle was varied from 6.5 to 32 mrad in five discrete steps. We show that the intensities of kinematically forbidden reflections decay exponentially as the precession semiangle (?) is increased and that the amount of information provided by direct methods increases monotonically but non-systematically as ? increases. We have also investigated the zeolite-framework mineral mordenite with PED and have found a direct methods solution where the 12-ring is clearly resolved for the first time.

  14. Finite difference approximations for measure-valued solutions of a hierarchically size-structured population model.

    PubMed

    Ackleh, Azmy S; Chellamuthu, Vinodh K; Ito, Kazufumi

    2015-04-01

    We study a quasilinear hierarchically size-structured population model presented in [4]. In this model the growth, mortality and reproduction rates are assumed to depend on a function of the population density. In [4] we showed that solutions to this model can become singular (measure-valued) in finite time even if all the individual parameters are smooth. Therefore, in this paper we develop a first order finite difference scheme to compute these measure-valued solutions. Convergence analysis for this method is provided. We also develop a high resolution second order scheme to compute the measure-valued solution of the model and perform a comparative study between the two schemes. PMID:25811433

  15. Solution structure of the cyclic-nucleotide binding homology domain of a KCNH channel.

    PubMed

    Li, Qingxin; Ng, Hui Qi; Yoon, Ho Sup; Kang, Congbao

    2014-04-01

    The carboxy-terminal region of the KCNH family of potassium channels contains a cyclic-nucleotide binding homology domain (CNBHD) that is important for channel gating and trafficking. The solution structure of the CNBHD of the KCNH potassium of zebrafish was determined using solution NMR spectroscopy. This domain exists as a monomer under solution conditions and adopts a similar fold to that determined by X-ray crystallography. The CNBHD does not bind cAMP because residue Y740 blocks the entry of cyclic-nucleotide to the binding pocket. Relaxation results show that the CNBHD is rigid except that some residues in the loop between ?6 and ?7 are flexible. Our results will be useful to understand the gating mechanism of KCNH family members through the CNBHD. PMID:24632450

  16. NMR Solution Structure and Condition-Dependent Oligomerization of the Antimicrobial Peptide Human Defensin 5

    PubMed Central

    Wommack, Andrew J.; Robson, Scott A.; Wanniarachchi, Yoshitha A.; Wan, Andrea; Turner, Christopher J.; Wagner, Gerhard; Nolan, Elizabeth M.

    2012-01-01

    Human defensin 5 (HD5) is a 32-residue host-defense peptide expressed in the gastrointestinal, reproductive, and urinary tracts that has antimicrobial activity. It exhibits six cysteine residues that are regiospecifically oxidized to form three disulfide bonds (Cys3—Cys31, Cys5—Cys20, and Cys10—Cys30) in the oxidized form (HD5ox). To probe the solution structure and oligomerization properties of HD5ox, and select mutant peptides lacking one or more disulfide bonds, NMR solution studies and analytical ultracentrifugation experiments are reported in addition to in vitro peptide stability assays. The NMR solution structure of HD5ox, solved at pH 4 in 90:10 H2O/D2O, is presented (PDB: 2LXZ). Relaxation T1/T2 measurements and the rotational correlation time (Tc) estimated from a [15N,1H]-TRACT experiment demonstrate that HD5ox is dimeric under these experimental conditions. Exchange broadening of the H? signals in the NMR spectra suggests that residues 19-21 (Val19-Cys20-Glu21) contribute to the dimer interface in solution. Exchange broadening is also observed for residues 7-14 comprising the loop. Sedimentation velocity and equilibrium studies conducted in buffered aqueous solution reveal that the oligomerization state of HD5ox is pH-dependent. Sedimentation coefficients of ca. 1.8 S and a molecular weight of 14,363 Da were determined for HD5ox at pH 7, supporting a tetrameric form ([HD5ox] ? 30 ?M). At pH 2, a sedimentation coefficient of ca. 1.0 S and a molecular weight of 7,079 Da, corresponding to a HD5ox dimer, were obtained. Millimolar concentrations of NaCl, CaCl2, and MgCl2 have negligible effect on the HD5ox sedimentation coefficients in buffered aqueous solution at neutral pH. Removal of a single disulfide bond results in a loss of peptide fold and quaternary structure. These biophysical investigations highlight the dynamic and environment-sensitive behavior of HD5ox in solution, and provide important insights into HD5ox structure/activity relationships and the requirements for antimicrobial action. PMID:23163963

  17. Solvent-induced changes in the structure and rheology of polyelectrolyte solutions.

    NASA Astrophysics Data System (ADS)

    Breedveld, Victor

    2006-03-01

    By integrating microfluidics and particle tracking microrheology, we have constructed a dialysis cell for microrheology, which provides unique opportunities for studying the dynamics of microstructural changes induced by changes in solvent composition. Such experiments are virtually impossible with mechanical rheometers. The concept and design of the microdialysis cell will be discussed, and data will be presented on the structural and rheological response of polyelectrolyte solutions to changes in ionic strength. Sulphonated polystyrene is a water-soluble polymer and its molecular conformation in solution strongly depends on ionic strength of the solution. It will be shown that quantitative measurements of transient solution viscosity during solvent exchange can be performed with the new dialysis cell. Experiments were also performed on amphiphilic block copolypeptide (BCP) hydrogels, which self-assemble into fibrillar structures due to a subtle balance between attractive and repulsive intermolecular forces. Electrostatic repulsion between the hydrophilic L-lysine blocks plays a key role. Therefore, changes in ionic strength have a significant effect on the self-assembled local structure and mechanical properties of the BCP gels, as was previously observed in rheometer experiments. Microrheology in the dialysis cell provided a much more complete picture, revealing the occurrence of microscopic phase separation upon the addition of salt. For example, in a K160L40 lysine-leucine block copolypeptide, the motion of tracer particles in the hydrogel is homogeneous in DI water. After the addition of salt, microrheology reveals the co-existence of populations of freely moving and immobilized particles. The changes in local microstructure were found to be reversible when the ionic strength of the solution was lowered again. Data will be presented on the dynamics of the morphological and rheological changes of various block copolypeptide hydrogels.

  18. Characterization of swollen structure of high-density polyelectrolyte brushes in salt solution by neutron reflectivity

    NASA Astrophysics Data System (ADS)

    Kobayashi, Motoyasu; Terayama, Yuki; Hino, Masahiro; Ishihara, Kazuhiko; Takahara, Atsushi

    2009-08-01

    Zwitterionic and cationic polyelectrolyte brushes on quartz substrate were prepared by surface-initiated atom transfer radical polymerization of 2-(methacryloyloxy)ethyl phosphorylcholine (MPC) and 2-(methacryloyloxy)ethyltrimethylammonium chloride (METAC), respectively. The effects of ionic strength on brush structure and surface properties of densely grafted polyelectrolyte brushes were analysed by neutron reflectivity (NR) measurements. NR at poly(METAC)/D2O and poly(MPC)/D2O interface revealed that the grafted polymer chains were fairly extended from the substrate surface, while the thickness reduction of poly(METAC) brush was observed in 5.6 M NaCl/D2O solution due to the screening of the repulsive interaction between polycations by hydrated salt ions. Interestingly, no structural change was observed in poly(MPC) brush even in a salt solution probably due to the unique interaction properties of phosphorylcholine units.

  19. Numerical solution of quadratic matrix equations for free vibration analysis of structures

    NASA Technical Reports Server (NTRS)

    Gupta, K. K.

    1975-01-01

    This paper is concerned with the efficient and accurate solution of the eigenvalue problem represented by quadratic matrix equations. Such matrix forms are obtained in connection with the free vibration analysis of structures, discretized by finite 'dynamic' elements, resulting in frequency-dependent stiffness and inertia matrices. The paper presents a new numerical solution procedure of the quadratic matrix equations, based on a combined Sturm sequence and inverse iteration technique enabling economical and accurate determination of a few required eigenvalues and associated vectors. An alternative procedure based on a simultaneous iteration procedure is also described when only the first few modes are the usual requirement. The employment of finite dynamic elements in conjunction with the presently developed eigenvalue routines results in a most significant economy in the dynamic analysis of structures.

  20. Upgrade of IMCA-CAT Bending Magnet Beamline 17-BM for Macromolecular Crystallography at the Advanced Photon Source

    SciTech Connect

    Koshelev, I.; Huang, R.; Muir, J. L.; Battaile, K.; Mulichak, A. M.; Keefe, L. J. [IMCA-CAT, The Center for Advanced Radiation Sources, University of Chicago, Chicago, Illinois 60637 (United States); Graber, T.; Meron, M. [ChemMatCARS, The Center for Advanced Radiation Sources, University of Chicago, Chicago, Illinois 60637 (United States); Lavender, W. [Biological, Chemical, and Physical Sciences Department, Illinois Institute of Technology, Chicago, Illinois, 60616 (United States)

    2007-01-19

    Pharmaceutical research depends on macromolecular crystallography as a tool in drug design and development. To solve the de novo three-dimensional atomic structure of a protein, it is essential to know the phases of the X-rays scattered by a protein crystal. Experimental phases can be obtained from multiwavelength anomalous dispersion (MAD) experiments. Dedicated to macromolecular crystallography, the IMCA-CAT bending magnet beamline at sector 17 of the Advanced Photon Source (APS) was upgraded to provide the energy resolution required to successfully perform synchrotron radiation-based MAD phasing of protein crystal structures. A collimating mirror was inserted into the beam path upstream of a double-crystal monochromator, thus increasing the monochromatic beam throughput in a particular bandwidth without sacrificing the energy resolution of the system. The beam is focused horizontally by a sagittally bent crystal and vertically by a cylindrically bent mirror, delivering a beam at the sample of 130 {mu}m (vertically) x 250 {mu}m (horizontally) FWHM. As a result of the upgrade, the beamline now operates with an energy range of 7.5x17.5 keV, delivers 8 x 10+11 photons/sec at 12.398 keV at the sample, and has an energy resolution of {delta}E/E = 1.45 x 10-4 at 10 keV, which is suitable for MAD experiments.

  1. Upgrade of IMCA-CAT Bending Magnet Beamline 17-BM for Macromolecular Crystallography at the Advanced Photon Source

    SciTech Connect

    Koshelev, I.; Huang, R.; Graber, T.; Meron, M.; Muir, J.L.; Lavender, W.; Battaile, K.; Mulichak, A.M.; Keefe, L.J. (UC)

    2007-05-15

    Pharmaceutical research depends on macromolecular crystallography as a tool in drug design and development. To solve the de novo three-dimensional atomic structure of a protein, it is essential to know the phases of the X-rays scattered by a protein crystal. Experimental phases can be obtained from multiwavelength anomalous dispersion (MAD) experiments. Dedicated to macromolecular crystallography, the IMCA-CAT bending magnet beamline at sector 17 of the Advanced Photon Source (APS) was upgraded to provide the energy resolution required to successfully perform synchrotron radiation-based MAD phasing of protein crystal structures. A collimating mirror was inserted into the beam path upstream of a double-crystal monochromator, thus increasing the monochromatic beam throughput in a particular bandwidth without sacrificing the energy resolution of the system. The beam is focused horizontally by a sagittally bent crystal and vertically by a cylindrically bent mirror, delivering a beam at the sample of 130 {micro}m (vertically) x 250 {micro}m (horizontally) FWHM. As a result of the upgrade, the beamline now operates with an energy range of 7.5 x 17.5 keV, delivers 8 x 10{sup +11} photons/sec at 12.398 keV at the sample, and has an energy resolution of {delta}E/E = 1.45 x 10{sup -4} at 10 keV, which is suitable for MAD experiments.

  2. Water structure changes induced by hydrophobic and polar solutes revealed by simulations and infrared spectroscopy

    NASA Astrophysics Data System (ADS)

    Sharp, Kim A.; Madan, Bhupinder; Manas, Eric; Vanderkooi, Jane M.

    2001-01-01

    A combination of simulations and Fourier transform infrared spectroscopy was used to examine the effect of three ionic solutes (KCl, NaCl, and KSCN), the polar solute urea, and the osmolyte trimethylamine-N-oxide (TMAO) on a water structure. The ionic solutes increase the mean water-water H-bond angle in their first hydration shell concomitantly shifting the OH stretching mode to higher frequency, and shifting the HOH bending mode to lower frequency. TMAO decreases the mean water-water H-bond angle in its first hydration shell, shifts the OH stretching mode frequency down, and shifting the HOH bending mode frequency up. Urea has no effect on the mean H-bond angle, OH stretch, and HOH bend frequencies. These results can be explained in terms of changes in the relative proportions of two H-bond angle populations: Ionic solutes increase the population of more distorted (larger angle) H bonds relative to the less distorted population, TMAO has the reverse effect, while urea does not affect the H-bond angle probability distribution. The negligible effect of urea on water structure supports the direct binding model for urea-induced protein denaturation.

  3. Thorium nanochemistry: the solution structure of the Th(IV)-hydroxo pentamer.

    PubMed

    Walther, Clemens; Rothe, Jörg; Schimmelpfennig, Bernd; Fuss, Markus

    2012-08-28

    Tetravalent thorium exhibits a strong tendency towards hydrolysis and subsequent polymerization. Polymeric species play a crucial role in understanding thorium solution chemistry, since their presence causes apparent solubility several orders of magnitude higher than predicted by thermodynamic data bases. Although electrospray mass spectrometry (ESI MS) identifies Th(IV) dimers and pentamers unequivocally as dominant species close to the solubility limit, the molecular structure of Th(5)(OH)(y) polymers was hitherto unknown. In the present study, X-ray absorption fine structure (XAFS) spectroscopy, high energy X-ray scattering (HEXS) measurements, and quantum chemical calculations are combined to solve the pentamer structure. The most favourable structure is represented by two Th(IV) dimers linked by a central Th(IV) cation through hydroxide bridges. PMID:22565635

  4. Solution structure of PcFK1, a spider peptide active against Plasmodium falciparum

    PubMed Central

    Pimentel, Cyril; Choi, Soo-Jin; Chagot, Benjamin; Guette, Catherine; Camadro, Jean-Michel; Darbon, Hervé

    2006-01-01

    Psalmopeotoxin I (PcFK1) is a 33-amino-acid residue peptide isolated from the venom of the tarantula Psalmopoeus cambridgei. It has been recently shown to possess strong antiplasmodial activity against the intra-erythrocyte stage of Plasmodium falciparum in vitro. Although the molecular target for PcFK1 is not yet determined, this peptide does not lyse erythrocytes, is not cytotoxic to nucleated mammalian cells, and does not inhibit neuromuscular function. We investigated the structural properties of PcFK1 to help understand the unique mechanism of action of this peptide and to enhance its utility as a lead compound for rational development of new antimalarial drugs. In this paper, we have determined the three-dimensional solution structure by 1H two-dimensional NMR means of recombinant PcFK1, which is shown to belong to the ICK structural superfamily with structural determinants common to several neurotoxins acting as ion channels effectors. PMID:16452619

  5. Solution structure of PcFK1, a spider peptide active against Plasmodium falciparum.

    PubMed

    Pimentel, Cyril; Choi, Soo-Jin; Chagot, Benjamin; Guette, Catherine; Camadro, Jean-Michel; Darbon, Hervé

    2006-03-01

    Psalmopeotoxin I (PcFK1) is a 33-amino-acid residue peptide isolated from the venom of the tarantula Psalmopoeus cambridgei. It has been recently shown to possess strong antiplasmodial activity against the intra-erythrocyte stage of Plasmodium falciparum in vitro. Although the molecular target for PcFK1 is not yet determined, this peptide does not lyse erythrocytes, is not cytotoxic to nucleated mammalian cells, and does not inhibit neuromuscular function. We investigated the structural properties of PcFK1 to help understand the unique mechanism of action of this peptide and to enhance its utility as a lead compound for rational development of new antimalarial drugs. In this paper, we have determined the three-dimensional solution structure by (1)H two-dimensional NMR means of recombinant PcFK1, which is shown to belong to the ICK structural superfamily with structural determinants common to several neurotoxins acting as ion channels effectors. PMID:16452619

  6. 800 MHz 1H NMR solution structure refinement of oxidized cytochrome c7 from Desulfuromonas acetoxidans.

    PubMed

    Assfalg, M; Banci, L; Bertini, I; Bruschi, M; Turano, P

    1998-09-01

    The solution structure of Desulfuromonas acetoxidans cytochrome c7 has been refined by using 1H-NMR spectra recorded at 800 MHz and by using pseudocontact shifts in the final energy minimization procedure. The protein, composed of 68 amino acids, contains three paramagnetic heme moieties, each with one unpaired electron. The largely distributed paramagnetism broadens the lines in several protein parts. The structure is now relatively well resolved all over the backbone by the use of 1315 meaningful NOEs and 90 pseudocontact shifts. The statistical analysis of the structure indicates its satisfactory quality. The protein-fold is quite similar to that of the analogous four-heme cytochromes c3 for those parts which can be considered homologous. The solvent accessibility and the electrostatic potential surfaces surrounding the three hemes have been analyzed in terms of their reduction potentials. The resulting magnetic susceptibility anisotropy data obtained from pseudocontact shifts are analyzed in terms of structural data. PMID:9760163

  7. XtalView, protein structure solution and protein graphics, a short history.

    PubMed

    McRee, Duncan E; Israel, Mark

    2008-09-01

    From a user's point-of-view we are in the Golden Age of protein crystallographic software. In the past few decades, solving protein structures has gone from a task requiring man-months of effort to a process requiring minutes on an ordinary laptop with no human intervention required. The birth of XtalView coincided with the mainstream use of synchrotron radiation, seleno-Met phasing and it continues to be used in this age of robotic crystallization, Fed-Ex data collection and fully automated structure solution "pipelines". This article is a retrospective history of protein crystallographic computing and a discussion of the current state of the art. PMID:18411057

  8. Reversible pressure-induced structure changes in turbostratic BN-C solid solutions.

    PubMed

    Solozhenko, Vladimir L; Kurakevych, Oleksandr O

    2005-10-01

    The results obtained by Rietveld analysis and numerical modeling of B-C-N layered clusters with various types of lattice defects explain the evolution of diffraction patterns of turbostratic graphite-like BN-C solid solutions which are experimentally observed at room temperature at pressures up to 30 GPa. Above 20 GPa a reversible diffusionless transformation of the initial turbostratic structure takes place, giving a high-pressure phase formed by close-packed buckled layers having a diamond-like structure. PMID:16186650

  9. Mechanical and structural properties of solution-cast high-amylose maize starch films.

    PubMed

    Koch, Kristine; Gillgren, Thomas; Stading, Mats; Andersson, Roger

    2010-01-01

    Environmental issues have forced the introduction of sustainable solutions such as annually renewable resources being used as a raw material for packaging and disposables. This paper examined the effects of time and temperature during manufacturing and plasticiser content on the molecular structure of high-amylose maize starch films. It also analysed how manufacturing conditions, plasticiser content and molecular structure of the films affected their material properties. It was found that increased time or temperature increased the degradation of amylose and of amylopectin, which in turn negatively affected film cohesiveness. However, neither time nor temperature had any effect on tensile properties. PMID:19828118

  10. Effective protein-protein interaction from structure factor data of a lysozyme solution

    SciTech Connect

    Abramo, M. C.; Caccamo, C.; Costa, D.; Ruberto, R.; Wanderlingh, U. [Dipartimento di Fisica e di Scienze della Terra, Università degli Studi di Messina and CNISM (Consorzio Nazionale Interuniversitario di Struttura della Materia) Viale F. Stagno d'Alcontres 31, 98166 Messina (Italy)] [Dipartimento di Fisica e di Scienze della Terra, Università degli Studi di Messina and CNISM (Consorzio Nazionale Interuniversitario di Struttura della Materia) Viale F. Stagno d'Alcontres 31, 98166 Messina (Italy); Cavero, M. [School of Chemistry and Physics, University of Kwazulu-Natal, Private Bag X01, Scottsville 3209, Pietermaritzburg (South Africa)] [School of Chemistry and Physics, University of Kwazulu-Natal, Private Bag X01, Scottsville 3209, Pietermaritzburg (South Africa); Pellicane, G. [School of Chemistry and Physics, University of Kwazulu-Natal, Private Bag X01, Scottsville 3209, Pietermaritzburg (South Africa) [School of Chemistry and Physics, University of Kwazulu-Natal, Private Bag X01, Scottsville 3209, Pietermaritzburg (South Africa); National Institute for Theoretical Physics (NITheP), KZN node, Pietermaritzburg (South Africa)

    2013-08-07

    We report the determination of an effective protein-protein central potential for a lysozyme solution, obtained from the direct inversion of the total structure factor of the system, as extracted from small angle neutron scattering. The inversion scheme rests on a hypernetted-chain relationship between the effective potential and the structural functions, and is preliminarily tested for the case of a Lennard-Jones interaction. The characteristics of our potential are discussed in comparison with current models of effective interactions in complex fluids. The phase behavior predictions are also investigated.

  11. Structural and thermoelectric properties of Zr 1 ? x Er x NiSn solid solutions

    Microsoft Academic Search

    Yu. V. Stadnyk; A. M. Goryn’; V. V. Romaka; Yu. K. Gorelenko; L. P. Romaka; N. A. Mel’nichenko

    2011-01-01

    We have studied the electronic and crystal structures and temperature-dependent resistivity and thermopower of Zr1 ? x\\u000a Er\\u000a x\\u000a NiSn (x = 0–0.20) substitutional semiconductor solid solutions (so-called half-Heusler alloys) in the temperature range 80–380 K.\\u000a Heavily erbium doped semiconductors with the MgAgAs structure are described in terms of an amorphous semiconductor model.\\u000a The erbium atoms in Zr1 ? x

  12. Restoring low resolution structure of biological macromolecules from solution scattering using simulated annealing.

    PubMed Central

    Svergun, D I

    1999-01-01

    A method is proposed to restore ab initio low resolution shape and internal structure of chaotically oriented particles (e.g., biological macromolecules in solution) from isotropic scattering. A multiphase model of a particle built from densely packed dummy atoms is characterized by a configuration vector assigning the atom to a specific phase or to the solvent. Simulated annealing is employed to find a configuration that fits the data while minimizing the interfacial area. Application of the method is illustrated by the restoration of a ribosome-like model structure and more realistically by the determination of the shape of several proteins from experimental x-ray scattering data. PMID:10354416

  13. Homologous size-extension of hybrid vanadate capsules - solid state structures, solution stability and surface deposition.

    PubMed

    Mahimaidoss, Mariyatra B; Krasnikov, Sergey A; Reck, Lukas; Onet, Camelia I; Breen, John M; Zhu, Nianyong; Marzec, Bartosz; Shvets, Igor V; Schmitt, Wolfgang

    2014-03-01

    The dimensions and cavity sizes of the molecular capsules with the general formula [V10O18L4](10-) can be controlled modularly through the nature of the bifunctional, rigid organophosphonate ligands L(1) and L(2) (L(1) = bis(4-phosphonatophenyl)ethyne and L(2) = bis(4-phosphonatophenyl)butadiyne); the solution stability of the molecular entities as demonstrated by ESI-MS studies permits their assembly on the Au(111) surface on a sub-monolayer scale giving rise to a 2D supramolecular structure that is comparable to the packing arrangements of the capsules in the crystal structures. PMID:24435072

  14. Solution structure and dynamics of C-terminal regulatory domain of Vibrio vulnificus extracellular metalloprotease

    SciTech Connect

    Yun, Ji-Hye; Kim, Heeyoun [Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749 (Korea, Republic of)] [Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749 (Korea, Republic of); Park, Jung Eun [Department of Biotechnology, College of Natural Sciences, Chosun University, Gwangju 501-759 (Korea, Republic of)] [Department of Biotechnology, College of Natural Sciences, Chosun University, Gwangju 501-759 (Korea, Republic of); Lee, Jung Sup, E-mail: jsplee@mail.chosun.ac.kr [Department of Biotechnology, College of Natural Sciences, Chosun University, Gwangju 501-759 (Korea, Republic of); Lee, Weontae, E-mail: wlee@spin.yonsei.ac.kr [Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749 (Korea, Republic of)] [Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749 (Korea, Republic of)

    2013-01-11

    Highlights: Black-Right-Pointing-Pointer We have determined solution structures of vEP C-terminal regulatory domain. Black-Right-Pointing-Pointer vEP C-ter100 has a compact {beta}-barrel structure with eight anti-parallel {beta}-strands. Black-Right-Pointing-Pointer Solution structure of vEP C-ter100 shares its molecular topology with that of the collagen-binding domain of collagenase. Black-Right-Pointing-Pointer Residues in the {beta}3 region of vEP C-ter100 might be important in putative ligand/receptor binding. Black-Right-Pointing-Pointer vEP C-ter100 interacts strongly with iron ion. -- Abstract: An extracellular metalloprotease (vEP) secreted by Vibrio vulnificus ATCC29307 is a 45-kDa proteolytic enzyme that has prothrombin activation and fibrinolytic activities during bacterial infection. The action of vEP could result in clotting that could serve to protect the bacteria from the host defense machinery. Very recently, we showed that the C-terminal propeptide (C-ter100), which is unique to vEP, is involved in regulation of vEP activity. To understand the structural basis of this function of vEP C-ter100, we have determined the solution structure and backbone dynamics using multidimensional nuclear magnetic resonance spectroscopy. The solution structure shows that vEP C-ter100 is composed of eight anti-parallel {beta}-strands with a unique fold that has a compact {beta}-barrel formation which stabilized by hydrophobic and hydrogen bonding networks. Protein dynamics shows that the overall structure, including loops, is very rigid and stabilized. By structural database analysis, we found that vEP C-ter100 shares its topology with that of the collagen-binding domain of collagenase, despite low sequence homology between the two domains. Fluorescence assay reveals that vEP C-ter100 interacts strongly with iron (Fe{sup 3+}). These findings suggest that vEP protease might recruit substrate molecules, such as collagen, by binding at C-ter100 and that vEP participates in iron uptake from iron-withholding proteins of the host cell during infection.

  15. The water structure around the chloride ion in aqueous polyethylene oxide solutions

    NASA Astrophysics Data System (ADS)

    Barnes, A. C.; Enderby, J. E.; Breen, J.; Leyte, J. C.

    1987-12-01

    Neutron diffraction and nuclear magnetic relaxation yield complementary information on the interaction of ions and water molecules in solution. In the present study the two techniques are used to investigate the influence of poly (ethyleneoxide) on the Cl - hydration sphere. It is concluded that the important effect of PEO on the 35Cl relaxation rate is due to the occurrence of a long correlation time rather than structural changes.

  16. Implicit SUPG solution of Euler equations using edge-based data structures

    Microsoft Academic Search

    Lucia Catabriga; Alvaro L. G. A. Coutinho

    2002-01-01

    In this work we present an implicit, edge-based implementation of the semi-discrete SUPG formulation with shock-capturing for the Euler equations in conservative variables. By disassembling the resulting finite element matrices into their edge contributions, sparse matrix coefficients, residuals and matrix-vector products needed in Krylov-update techniques are computed based on edge data structures. The resulting solution method requires less memory and

  17. Structural and photoluminescence studies of TiO2 nanoparticles synthesized by solution combustion method

    NASA Astrophysics Data System (ADS)

    Balamurugan, M.; Silambarasan, M.; Saravanan, S.; Soga, Tetsuo

    2015-06-01

    In this study titanium dioxide nanoparticle is prepared by simple solution combustion method. The powder X-ray diffraction pattern indicates the prepared titanium dioxide nanoparticles crystalline nature with tetragonal structure. Also it shows the nanoparticle is anatase and rutile mixed phase. The Field Emission Scanning Electron Microscopy image shows the nanostructure of particles in the size range about 50 nm. Room temperature photoluminescence shows intrinsic defects of oxygen vacancies.

  18. Solution Structure of ERK2 Binding Domain of MAPK Phosphatase MKP-3

    Microsoft Academic Search

    Amjad Farooq; Gaurav Chaturvedi; Shiraz Mujtaba; Olga Plotnikova; Lei Zeng; Christophe Dhalluin; Robert Ashton; Ming-Ming Zhou

    2001-01-01

    MAP kinases (MAPKs), which control mitogenic signal transduction in all eukaryotic organisms, are inactivated by dual specificity MAPK phosphatases (MKPs). MKP-3, a prototypical MKP, achieves substrate specificity through its N-terminal domain binding to the MAPK ERK2, resulting in the activation of its C-terminal phosphatase domain. The solution structure and biochemical analysis of the ERK2 binding (EB) domain of MKP-3 show

  19. Solution Structure of the Major a-Amylase Inhibitor of the Crop Plant Amaranth

    Microsoft Academic Search

    Shanyun Lu; Pengchi Deng; Xiucai Liu; Jingchu Luo; Rushan Han; Xiaocheng Gu; Songping Liangi; Xianchun Wangi; Feng Lii; Valentin Lozanov; Andras Patthy; Sandor Pongor

    a-Amylase inhibitor (AAI), a 32-residue miniprotein from the Mexican crop plant amaranth (Amaranthus hypochondriacus), is the smallest known a-amylase in- hibitor and is specific for insect a-amylases (Chagolla- Lopez, A., Blanco-Labra, A., Patthy, A., Sanchez, R., and Pongor, S. (1994) J. Biol. Chem. 269, 23675-23680). Its disulfide topology was confirmed by Edman degrada- tion, and its three-dimensional solution structure was

  20. Synthesis of partially exfoliated EPDM\\/LDH nanocomposites by solution intercalation: Structural characterization and properties

    Microsoft Academic Search

    H. Acharya; S. K. Srivastava; Anil K. Bhowmick

    2007-01-01

    Partially exfoliated ethylene propylene diene terpolymer (EPDM)\\/Mg–Al layered double hydroxide (LDH) nanocomposites have been synthesized by solution intercalation using organically modified LDH (DS-LDH) as nanofiller obtained by reconstruction method using sodium dodecyl sulfate and LDH. The nanocomposite structure has been elucidated by the X-ray diffraction (XRD), transmission electron microscopy (TEM), atomic force microscopy (AFM), Fourier transform infrared (FTIR) spectroscopy and

  1. Improved PML for the FDTD solution of wave-structure interaction problems

    Microsoft Academic Search

    Jean-Pierre Berenger

    1997-01-01

    In a previous paper, an optimum perfectly matched layer has been designed for the finite-difference time-domain (FDTD) solution of wave-structure interaction problems. The present paper shows the results of subsequent investigations that were done with the intention of reducing the thickness of this optimum PML. Four improvements to the PML are presented. The resulting reductions of the thickness are discussed

  2. Total assignment and structure in solution of tetrandrine by NMR spectroscopy and molecular modelling

    NASA Astrophysics Data System (ADS)

    Thevand, André; Stanculescu, Ioana; Mandravel, Cristina; Woisel, Patrice; Surpateanu, Gheorghe

    2004-07-01

    High-resolution 1- and 2D NMR spectra of tetrandrine and molecular modelling were employed to characterise its structure in solution. Complete and unambiguous assignment of all proton and carbon resonance signals is reported. Scalar couplings were determined from dihedral angles with the Karplus equation. Inter-proton distances were evaluated from NOE correlation peaks. Comparison of simulated and X-ray conformations of tetrandrine reveals only small differences.

  3. A Method for Solution NMR Structural Studies of Large Integral Membrane Proteins: Reverse Micelle Encapsulation

    PubMed Central

    Kielec, Joseph M.; Valentine, Kathleen G.; Wand, A. Joshua

    2009-01-01

    The structural study of membrane proteins perhaps represents one of the greatest challenges of the post-genomic era. While membrane proteins comprise over 50% of current and potential drug targets, their structural characterization lags far behind that of soluble proteins. Nuclear magnetic resonance (NMR) offers great potential not only with respect to structural characterization of integral membrane proteins but may also provide the ability to study the details of small ligand interactions. However, the size limitations of solution NMR have restricted comprehensive structural characterization of membrane protein NMR structures to the relatively small ?-barrel proteins or helical proteins of relatively simple topology. In an effort to escape the barriers presented by slow molecular reorientation of large integral membrane proteins solubilized by detergent micelles in water, we have adapted the reverse micelle encapsulation strategy originally developed for the study of large soluble proteins by solution NMR methods. Here we review a novel approach to the solubilization of large integral membrane proteins in reverse micelle surfactants dissolved in low viscosity alkane solvents. The procedure is illustrated with a 54 kDa construct of the homotetrameric KcsA potassium channel. PMID:19665988

  4. Discovering Free Energy Basins for Macromolecular Systems via Guided Multiscale Simulation

    PubMed Central

    Sereda, Yuriy V.; Singharoy, Abhishek B.; Jarrold, Martin F.; Ortoleva, Peter J.

    2012-01-01

    An approach for the automated discovery of low free energy states of macromolecular systems is presented. The method does not involve delineating the entire free energy landscape but proceeds in a sequential free energy minimizing state discovery, i.e., it first discovers one low free energy state and then automatically seeks a distinct neighboring one. These states and the associated ensembles of atomistic configurations are characterized by coarse-grained variables capturing the large-scale structure of the system. A key facet of our approach is the identification of such coarse-grained variables. Evolution of these variables is governed by Langevin dynamics driven by thermal-average forces and mediated by diffusivities, both of which are constructed by an ensemble of short molecular dynamics runs. In the present approach, the thermal-average forces are modified to account for the entropy changes following from our knowledge of the free energy basins already discovered. Such forces guide the system away from the known free energy minima, over free energy barriers, and to a new one. The theory is demonstrated for lactoferrin, known to have multiple energy-minimizing structures. The approach is validated using experimental structures and traditional molecular dynamics. The method can be generalized to enable the interpretation of nanocharacterization data (e.g., ion mobility – mass spectrometry, atomic force microscopy, chemical labeling, and nanopore measurements). PMID:22423635

  5. Organic solid solution composed of two structurally similar porphyrins for organic solar cells.

    PubMed

    Zhen, Yonggang; Tanaka, Hideyuki; Harano, Koji; Okada, Satoshi; Matsuo, Yutaka; Nakamura, Eiichi

    2015-02-18

    A solid solution of a 75:25 mixture of tetrabenzoporphyrin (BP) and dichloroacenaphtho[q]tribenzo[b,g,l]porphyrin (CABP) forms when they are generated in a matrix of (dimethyl(o-anisyl)silylmethyl)(dimethylphenylsilylmethyl)[60]fullerene. This solid solution provides structural and optoelectronic properties entirely different from those of either pristine compounds or a mixture at other blending ratios. The use of this BP:CABP solid solution for organic solar cell (OSC) devices resulted in a power conversion efficiency (PCE) value higher by 16 and 300% than the PCE values obtained for the devices using the single donor BP and CABP, respectively, in a planar heterojunction architecture. This increase originates largely from the increase in short circuit current density, and hence by enhanced charge carrier separation at the donor/acceptor interface, which was probably caused by suitable energy level for the solid solution state, where electronic coupling between the two porphyrins occurred. The results suggest that physical and chemical modulation in solid solution is beneficial as an operationally simple method to enhance OSC performance. PMID:25626088

  6. proteinsSTRUCTURE O FUNCTION O BIOINFORMATICS Solution structure and function of YndB, an

    E-print Network

    Powers, Robert

    protein structure was solved,2 numerous other proteins from among eukaryotes, archaea, and bacteria have protein from birch is a major allergen with high sequence similarity to the plant PR-10 pathogenesisAR-related lipid transfer (START) family (1026 sequen- ces). The sequence similarity among the different Bet v 1

  7. Ion aggregation in high salt solutions. II. Spectral graph analysis of water hydrogen-bonding network and ion aggregate structures

    NASA Astrophysics Data System (ADS)

    Choi, Jun-Ho; Cho, Minhaeng

    2014-10-01

    Graph theory in mathematics and computer science is the study of graphs that are structures with pairwise connections between any objects. Here, the spectral graph theory and molecular dynamics simulation method are used to describe both morphological variation of ion aggregates in high salt solutions and ion effects on water hydrogen-bonding network structure. From the characteristic value analysis of the adjacency matrices that are graph theoretical representations of ion clusters, ion networks, and water H-bond structures, we obtained the ensemble average eigenvalue spectra revealing intricate connectivity and topology of ion aggregate structure that can be classified as either ion cluster or ion network. We further show that there is an isospectral relationship between the eigenvalue spectra of ion networks in high KSCN solutions and those of water H-bonding networks. This reveals the isomorphic relationship between water H-bond structure and ion-ion network structure in KSCN solution. On the other hand, the ion clusters formed in high NaCl solutions are shown to be graph-theoretically and morphologically different from the ion network structures in KSCN solutions. These observations support the bifurcation hypothesis on large ion aggregate growth mechanism via either ion cluster or ion network formation. We thus anticipate that the present spectral graph analyses of ion aggregate structures and their effects on water H-bonding network structures in high salt solutions can provide important information on the specific ion effects on water structures and possibly protein stability resulting from protein-water interactions.

  8. Structure of thallium(III) chloride, bromide, and cyanide complexes in aqueous solution

    SciTech Connect

    Blixt, J.; Glaser, J.; Sandstroem, M. [Royal Inst. of Technology, Stockholm (Sweden); Mink, J. [Royal Inst. of Technology, Stockholm (Sweden)]|[Inst. of Isotopes, Budapest (Hungary); Persson, I. [Swedish Univ. of Agricultural Sciences, Uppsala (Sweden); Persson, P. [Umea Univ. (Sweden)

    1995-05-10

    The structures of the hydrated thallium(III) halide and pseudohalide complexes, [TlX{sub n}(OH{sub 2}){sub m}]{sup (3-d)+}, X = Cl, Br, CN, in aqueous solution have been studied by a combination of X-ray absorption fine structure spectroscopy (XAFS), large-angle X-ray scattering (LAXS), and vibrational spectroscopic (Raman and IR) techniques including far-infrared studies of aqueous solutions and some solid phases with known structures. The vibrational Tl-X frequencies of all complexes are reported, force constants are calculated using normal coordinate analysis, and assignments are given. The structural results are consistent with octahedral six-coordination for the cationic complexes Tl(OH{sub 2}){sub 6}{sup 3$PLU}, TlX(OH{sub 2}){sub 5}{sup 2+}, and trans-TlX{sub 2}(OH{sub 2}){sub 4}{sup +}. The coordination geometry changes to trigonal bipyramidal for the neutral TlBr{sub 3}(OH{sub 2}){sub 2} complex and possibly also for TlCl{sub 3}(OH{sub 2}){sub 2}. The TlX{sub 4}{sup -} complexes are all tetrahedral. Higher chloride complexes, TlCl{sub 5}(OH{sub 2}){sup 2-} and TlCl{sub 6}{sup 3-}, are formed and have again octahedral coordination geometry. 65 refs., 7 figs., 5 tabs.

  9. Effect of Macromolecular Polydispersity on Diffusion Coefficients Measured by Rayleigh Interferometry

    E-print Network

    Annunziata, Onofrio

    determination of diffusion coefficients for binary and ternary liquid mixtures. For ternary mixtures, the 2 × 2Effect of Macromolecular Polydispersity on Diffusion Coefficients Measured by Rayleigh matrix of multicomponent diffusion coefficients is obtained. Polydispersity adds complexity

  10. P-95-09-062-iii Randomly Crosslinked Macromolecular Systems: Vulcanisation

    E-print Network

    Goldbart, Paul M.

    Goodyear discovered in 1839, when he #12;rst vulcanised rubber, a macromolecular liquid is transformed, especially in the regime of Goodyear's vulcanisation transition. This approach rests #12;rmly on techniques

  11. An Alternative Hypothesis for How Microgravity Improves Macromolecular Crystal Quality

    NASA Technical Reports Server (NTRS)

    Pusey, Marc

    2003-01-01

    There is a substantial body of experimental evidence, from this and other laboratories, that strongly suggests that for many proteins crystal nucleation and growth is by addition of associated species that are preformed by reversible concentration-driven self association processes in the bulk solution. We have developed a self-association model for the crystal nucleation and growth of the protein chicken egg lysozyme. The model accounts for the obtained crystal symmetry, explains the observed surface structures, and shows the importance of the symmetry obtained by self-association in solution to the process as a whole. This model also offers a possible mechanism for fluid flow effects on the growth process and how microgravity may affect it. While a single lysozyme molecule is relatively small an octamer in the 43 helix configuration (the proposed average sized growth unit) would have a M.W. approx. 115,000 and dimensions of 5.6 x 5.6 x 7.6 nm. Direct AFM measurements of growth unit incorporation indicate that units as wide as 11.2 nm and as long as 11.4 nm (a 24-mer) commonly attach to the crystal. AFM results from Weichmann et al. (Ultramicroscopy 86, 159-166, 2001) suggest that associated species of up to 40-mers in size add to the (101) faces. These measurements reflect the sizes of units that both added and desorbed from the crystal surface. The larger and less isotropic the associated species the more likely that it will be oriented to some degree in a flowing boundary layer, even at the low flow velocities measured about macromolecule crystals. On Earth, concentration gradient driven flow will maintain a high interfacial concentration, i.e., a high level (essentially that of the bulk solution) of solute association at the interface and higher growth rate. Higher growth rates mean an increased probability that misaligned growth units are trapped by subsequent growth layers before they can be desorbed and try again, or that the desorbing species is more likely to be smaller than the adsorbing species. In microgravity the extended diffusive boundary layer will lower the interfacial concentration. This results in a net dissociation of aggregated species that diffuse in from the bulk solution, i.e., smaller associated species, which are more likely able to make multiple attempts to correctly bind, yielding higher quality crystals.

  12. Structural Stability of Riemann Solutions for a Multiphase Kinematic Conservation Law Model that Changes Type.

    NASA Astrophysics Data System (ADS)

    Vinod, Vaidyanath

    We consider a model for 2-way traffic flow introduced by Bick and Newell in 1960 (2). The model problem is: p_{t} + (pu)_{x } = 0; quad q_{t} + (qv)_ {x} = 0.eqno(0.1)Here p and q are the densities of cars in the two directions of flow and u and v are the respective velocities in the p and q directions; a choice suggested in (2) is u = 1 - p - beta q, v = -1 + q + beta p.. In this model, beta is a measure of the interaction between the two directions of flow. For the problem to be physically feasible, we require 0<=beta<1.. Equation (0.1) is a conservation law that changes type. The domain of the solution is p>=0, q<=0, 1 - p - beta q>=0, and -1 + q + beta p>=0.. When beta = 0, there is no interaction between the two directions of flow and then the system (0.1) reduces to a system of scalar equation for which the Riemann problem (Cauchy problem) to (0.1) with initial data of the form: U(x,0) = cases{{U_0,quad x < 0} crcr{U_1,quad x > 0} cr}has a unique solution in the class of Lax entropy or admissible wave solutions. In this case, there is an open set of initial states (U_0, U_1) for which the solution exhibits the phenomenon of 'overlapping rarefaction waves'. These waves occupy the same position in the physical plane and they are stable. When beta>0, for the same initial values U_0 and U_1, these overlapping rarefaction solutions disappear due to the presence of an elliptic region. For these states, we introduce a new shock solution which we term a critical shock (this is qualitatively similar to a Buckley-Leverett shock). The strength of the shock goes to zero as beta tends to zero; and this solution approaches the overlapping wave solution. The main result of this thesis is that these constructed solutions are structurally stable as beta approaches zero (that is, the elliptic region shrinks to a line); and that they converge strongly in L^1. The construction might prove useful in solving other problems that change type, for example models for three-phase flow in porous media (1) or compressible two-phase flow (19). In this dissertation, we present the stability result for one new case, which typifies the difficulties involved.

  13. Analysis of the size dependence of macromolecular crowding shows that smaller is better

    PubMed Central

    Sharp, Kim A.

    2015-01-01

    The aqueous milieu inside cells contains as much as 30–40% dissolved protein and RNA by volume. This large concentration of macromolecules is expected to cause significant deviations from solution ideality. In vivo biochemical reaction rates and equilibria might differ significantly from those measured in the majority of in vitro experiments that are performed at much lower macromolecule concentrations. Consequently crowding, a nonspecific phenomenon believed to arise from the large excluded volume of these macromolecules, has been studied extensively by experimental and theoretical methods. However, the relevant theory has not been applied consistently. When the steric effects of macromolecular crowders and small molecules like water and ions are treated on an equal footing, the effect of the macromolecules is opposite to that commonly believed. Large molecules are less effective at crowding than water and ions. There is also a surprisingly weak dependence on crowder size. Molecules of medium size, ?5 Å radius, have the same effect as much larger macromolecules like proteins and RNA. These results require a reassessment of observed high-concentration effects and of strategies to mimic in vivo conditions with in vitro experiments. PMID:26080429

  14. Structure and aggregation proclivity of C12E3 in aqueous solution

    NASA Astrophysics Data System (ADS)

    Zahariev, Ts.; Ivanova, A.; Velinova, M.; Tadjer, A.

    2013-01-01

    Olygo(ethylene glycol) alkyl ethers - CxEy are well known for their high surface activity and rich phase behavior. These substances exhibit some unusual aggregation characteristics in aqueous solution even at concentrations well below CMC attributed to the formation of pre-aggregates of small size, e.g., dimers. To verify this, a series of C12E3 dimers with initial geometries taken from coarse-grained molecular dynamics simulations is subject to geometry optimization with two quantum chemical methods: DFT and ONIOM in implicit water solvent. The resulting structures are classified into groups based on structural parameters. Their stability is assessed by relative and binding energy and rationalized in terms of molecular characteristics. All studied dimers are stable and various mutual alignments of the surfactants therein are feasible. The loss of surface area is outlined as the predominant stabilizing factor. Substantial number of the structures is suitable for further aggregation.

  15. NMR characterization and solution structure determination of the oxidized cytochrome c7 from Desulfuromonas acetoxidans.

    PubMed

    Banci, L; Bertini, I; Bruschi, M; Sompornpisut, P; Turano, P

    1996-12-10

    The solution structure of the three-heme electron transfer protein cytochrome c7 from Desulfuromonas acetoxidans is reported. The determination of the structure is obtained through NMR spectroscopy on the fully oxidized, paramagnetic form. The richness of structural motifs and the presence of three prosthetic groups in a protein of 68 residues is discussed in comparison with the four-heme cytochromes c3 already characterized through x-ray crystallography. In particular, the orientation of the three hemes present in cytochrome c7 is similar to that of three out of four hemes of cytochromes c3. The reduction potentials of the individual hemes, which have been obtained through the sequence-specific assignment of the heme resonances, are discussed with respect to the properties of the protein matrix. This information is relevant for any attempt to understand the electron transfer pathway. PMID:8962062

  16. Structure and flow properties of micelle-nanoparticle solutions from Molecular Dynamics simulations

    NASA Astrophysics Data System (ADS)

    Sureshkumar, Radhakrishna; Dhakal, Subas; Sambasivam, Abhinanden

    2014-03-01

    In aqueous media, cationic surfactant molecules spontaneously self-assemble into diverse morphologies depending upon temperature, surfactant concentration and solution ionic strength. Spherical, cylindrical and long (~ microns) flexible wormlike structures with or without branches with distinct rheological properties are observed. Inclusion of nanoparticles (NPs) provides additional means to manipulate structure and create active ``nano-fluids'' that respond to optical, magnetic or electrical stimuli. We study self-assembly, dynamics and rheology of such fluids using coarse-grained Molecular Dynamics simulations in presence of explicit solvent and salt. Specifically, we will discuss the mechanisms underlying fascinating phenomenology observed experimentally such as the pronounced non-monotonic dependence of the zero shear viscosity on salt/NP concentration, shear-induced structure formation, and isotropic to nematic transitions. NSF grants 1049489, 1049454 for the financial support, and Pittsburg Super Computer Centre for providing HPC resources.

  17. Structures in solid state and solution of dimethoxy curcuminoids: regioselective bromination and chlorination

    PubMed Central

    2013-01-01

    Background Several papers described the structure of curcumin and some other derivatives in solid and in solution. In the crystal structure of curcumin, the enol H atom is located symmetrically between both oxygen atoms of the enolone fragment with an O···O distance of 2.455 Å, which is characteristic for symmetrical H-bonds. In the solution, the geometry of the enolone fragment is attributed to the inherent disorder of the local environment, which solvates one of the basic sites better than the other, stabilizing one tautomer over the other. In this paper, how the position of methoxy groups in dimethoxy curcuminoids influence the conformation of molecules and how the halogen atoms change it when they are bonded at ?-position in keto-enol part of molecules is described. Results Six isomers of dimethoxy curcuminoids were prepared. Conformations in solid state, which were determined by X-ray single crystallography and 1H MAS and 13C CPMAS NMR measurements, depend on the position of methoxy groups in curcuminoid molecules. In solution, a fast equilibrium between both keto-enol forms exists. A theoretical calculation finding shows that the position of methoxy groups changes the energy of HOMO and LUMO. An efficient protocol for the highly regioselective bromination and chlorination leading to ?-halogenated product has been developed. All ?-halogenated compounds are present mainly in cis keto-enol form. Conclusions The structures in solid state of dimethoxy curcuminoids depend on the position of methoxy groups. The NMR data of crystalline solid samples of 3,4-diOCH3 derivative, XRD measurements and X-ray structures lead us to the conclusion that polymorphism exists in solids. The same conclusion can be done for 3,5-diOCH3 derivative. In solution, dimethoxy curcuminoids are present in the forms that can be described as the coexistence of two equivalent tautomers being in fast equilibrium. The position of methoxy groups has a small influence on the enolic hydrogen bond. Theoretical calculations show that the energy gap between HOMO and LUMO depend on the position of methoxy groups and are lower in solution. Chlorination and bromination on ?-position of 1,3-diketone moiety do not change the preferential form being cis keto-enol as in parent compounds. PMID:23800041

  18. Structure and interaction in protein solutions as studied by small-angle neutron scattering

    SciTech Connect

    Chodankar, S.; Aswal, V.K. [Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai-400 085 (India)

    2005-10-01

    Small-angle neutron scattering (SANS) measurements have been performed to compare the effect of the salts KF, KCl, and KBr on crystallization in aqueous solution of lysozyme protein. It is found that the propensity of the salt to crystallize protein follows the Hoffmeister series (KFsolution, lysozyme macromolecules are prolate ellipsoidal with semimajor and semiminor axes as 22 and 13.5 A, respectively. SANS also gives that the effective (structural+counterion) charge (Z) on the protein as obtained by taking into account screened Coulomb interaction between the protein macromolecules is found to be much smaller than the structural charge. There is decrease in Z suggesting the higher counterion condensation on protein with the increase in the concentration. The counterion condensation seems to be responsible for the differences in the effect of different salts. It is also found that with the addition of salts, lysozyme macromolecules convert to dimers, and for the same salt concentration the comparative effect of different salts follows the Hoffmeister series. Time evolved measurements prior to and after the crystallization show that the protein solution mostly consists of monomers and dimers. Interestingly, higher-mers are not observed in these measurements as perhaps they are formed in very small numbers towards the process that leads to the crystallization. The time dependent data have been used to obtain the fraction of crystallization as a function of time.

  19. Solution structure of the pseudo-5? splice site of a retroviral splicing suppressor

    PubMed Central

    CABELLO-VILLEGAS, JAVIER; GILES, KEITH E.; SOTO, ANA MARIA; YU, PING; MOUGIN, ANNIE; BEEMON, KAREN L.; WANG, YUN-XING

    2004-01-01

    Control of Rous sarcoma virus RNA splicing depends in part on the interaction of U1 and U11 snRNPs with an intronic RNA element called the negative regulator of splicing (NRS). A 23mer RNA hairpin (NRS23) of the NRS directly binds U1 and U11 snRNPs. Mutations that disrupt base-pairing between the loop of NRS23 and U1 snRNA abolish its negative control of splicing. We have determined the solution structure of NRS23 using NOEs, torsion angles, and residual dipolar couplings that were extracted from multidimensional heteronuclear NMR spectra. Our structure showed that the 6-bp stem of NRS23 adopts a nearly A-form duplex conformation. The loop, which consists of 11 residues according to secondary structure probing, was in a closed conformation. U913, the first residue in the loop, was bulged out or dynamic, and loop residues G914–C923, G915–U922, and U916–A921 were base-paired. The remaining UUGU tetraloop sequence did not adopt a stable structure and appears flexible in solution. This tetraloop differs from the well-known classes of tetraloops (GNRA, CUYG, UNCG) in terms of its stability, structure, and function. Deletion of the bulged U913, which is not complementary to U1 snRNA, increased the melting temperature of the RNA hairpin. This hyperstable hairpin exhibited a significant decrease in binding to U1 snRNP. Thus, the structure of the NRS RNA, as well as its sequence, is important for interaction with U1 snRNP and for splicing suppression. PMID:15317975

  20. Macromolecular crowding: chemistry and physics meet biology (Ascona, Switzerland, 10-14 June 2012)

    NASA Astrophysics Data System (ADS)

    Foffi, G.; Pastore, A.; Piazza, F.; Temussi, P. A.

    2013-08-01

    More than 60 years of biochemical and biophysical studies have accustomed us to think of proteins as highly purified entities that act in isolation, more or less freely diffusing until they find their cognate partner to bind to. While in vitro experiments that reproduce these conditions largely remain the only way to investigate the intrinsic properties of molecules, this approach ignores an important factor: in their natural milieu , proteins are surrounded by several other molecules of different chemical nature, and this crowded environment can considerably modify their behaviour. About 40% of the cellular volume on average is occupied by all sorts of molecules. Furthermore, biological macromolecules live and operate in an extremely structured and complex environment within the cell (endoplasmic reticulum, Golgi apparatus, cytoskeletal structures, etc). Hence, to further complicate the picture, the interior of the cell is by no means a simply crowded medium, rather, a most crowded and confining one. In recent times, several approaches have been developed in the attempt to take into account important factors such as the ones mentioned above, at both theoretical and experimental levels, so that this field of research is now emerging as one of the most thriving in molecular and cell biology (see figure 1). Figure 1. Figure 1. Left: number of articles containing the word 'crowding' as a keyword limited to the biological and chemical science domains (source: ISI Web of Science). The arrow flags the 2003 'EMBO Workshop on Biological Implications of Macromolecular Crowding' (Embo, 2012). Right: number of citations to articles containing the word 'crowding' limited to the same domains (bars) and an exponential regression curve (source: Elsevier Scopus). To promote the importance of molecular crowding and confinement and provide researchers active in this field an interdisciplinary forum for meeting and exchanging ideas, we recently organized an international conference held in Ascona from 10 to 14 June 2012. In the unique scenario of the Maggiore lake and absorbed in the magic atmosphere of the Centro Stefano Franscini (CSF) at Monte Verità, we enjoyed three-and-a-half days of intense and inspiring activity, where not only many of the most prominent scientists working on macromolecular crowding, but also experts in closely related fields such as colloids and soft matter presented their work. The meeting was intended and has been organized to bring theoreticians and experimentalists together in the attempt to promote an active dialogue. Moreover, we wanted different disciplines to be represented, notably physics and chemistry, besides biology, as cross-fertilization is proving an increasingly fundamental source of inspiration and advancement. This issue of Physical Biology (PB) features a selection of the oral contributions presented at the conference, expanded in the form of research or review articles. PB, one of the scientific journals of the Institute of Physics (IOP), is one of the most dynamic and lively forums active at the interface between biology on one side, and physics and mathematics on the other. As its mission is stated by IOP, PB 'focuses on research in which physics-based approaches lead to new insights into biological systems at all scales of space and time, and all levels of complexity'. For these reasons, and also in view of its high reputation and broad readership, PB appears to be the ideal place for disseminating the thriving pieces of research presented at the conference. We are extremely grateful to PB and its kind and efficient editorial staff who helped make this issue a great scientific follow-up to the conference. The opening lecture of the conference, the first of four day-opening keynote lectures, was given by Allen P Minton from NIH (USA), possibly the most influential among the pioneers in the field. He provided a lucid and well-thought-out overview of the concept of macromolecular crowding through an exhaustive chronological account of the major milestones. It is clear that the concept of excl

  1. The Effect of Liquid Crystalline Structures on Antiseizure Properties of Aqueous Solutions of Ethoxylated Alcohols

    PubMed Central

    Sulek, Marian Wlodzimierz; Bak, Anna

    2010-01-01

    Aqueous solutions of ethoxylated alcohols which form lyotropic liquid crystals at high concentrations (40–80%) were selected as model lubricating substances. Microscopic studies under polarized light and viscosity measurements were carried out in order to confirm the presence of liquid crystalline structures in the case of alcohol solutions with ethoxylation degrees of 3, 5, 7 and 10. Microscopic images and viscosity coefficient values characteristic of various mesophases were obtained. As expected, the viscosity of LLCs decreases considerably with an increase in shearing rate which is characteristic of liquid crystals being non-Newtonian liquids. Antiseizure properties were determined by means of a four-ball machine (T-02 Tester) and characterized by scuffing load (Pt), seizure load (Poz) and limiting pressure of seizure (poz). Alcohol ethoxylates forming mesophases in aqueous solutions have the strongest effect on the Pt values which are several times higher than those measured in the presence of water. Ethoxylates with higher degrees of ethoxylation exhibit higher values of scuffing load. Those changes have been interpreted as a result of higher cloud points at which those compounds lose their amphiphilic properties. In general, the presence of mesophases in the bulk phase and particularly in the surface phase may lead to the formation of a lubricant film which separates the frictionally cooperating elements of a friction pair. The antiseizure efficiency of alcohol solutions is highest up to the load value which does not exceed the scuffing load value. PMID:20162010

  2. Effects of inorganic salts on the structural heterogeneity of serum albumin solutions.

    PubMed

    Rozhkov, S P; Goryunov, A S

    2000-01-01

    The formation of protein clusters or a protein-rich phase in undersaturated solutions of biopolymers is considered theoretically on the basis of phase diagrams of a water-protein-salt system. Concentrated (50-200 mg/ml of protein) water-salt solutions of human serum albumin molecules modified by a maleimide spin-label have been studied experimentally using the ESR technique to characterize the significant general features of the system behaviour suggested by the model phase diagrams. The inorganic ion content (NaCl, KSCN, MgCl(2), and CaCl(2)) was varied in the range of 10(-3)-4 M. Salt-induced changes in different experimental ESR spin-label parameters based on relations between spectral line widths and amplitudes were determined and compared with the same parameters in salt-free solution. The data on dipole-dipole interactions of spin labels obtained at 77 K and on spin exchange at normal temperatures are indicative of local protein concentration inhomogeneities. The results have been described in terms of salt-induced dissociation of stabilized supramolecular structures in protein solution-protein clusters, liquid-liquid phase transition between the hydration water of clusters and that of individual proteins, and a rise in surface tension which results in protein stabilization. PMID:10663531

  3. The effect of liquid crystalline structures on antiseizure properties of aqueous solutions of ethoxylated alcohols.

    PubMed

    Sulek, Marian Wlodzimierz; Bak, Anna

    2010-01-01

    Aqueous solutions of ethoxylated alcohols which form lyotropic liquid crystals at high concentrations (40-80%) were selected as model lubricating substances. Microscopic studies under polarized light and viscosity measurements were carried out in order to confirm the presence of liquid crystalline structures in the case of alcohol solutions with ethoxylation degrees of 3, 5, 7 and 10. Microscopic images and viscosity coefficient values characteristic of various mesophases were obtained. As expected, the viscosity of LLCs decreases considerably with an increase in shearing rate which is characteristic of liquid crystals being non-Newtonian liquids. Antiseizure properties were determined by means of a four-ball machine (T-02 Tester) and characterized by scuffing load (P(t)), seizure load (P(oz)) and limiting pressure of seizure (p(oz)). Alcohol ethoxylates forming mesophases in aqueous solutions have the strongest effect on the P(t) values which are several times higher than those measured in the presence of water. Ethoxylates with higher degrees of ethoxylation exhibit higher values of scuffing load. Those changes have been interpreted as a result of higher cloud points at which those compounds lose their amphiphilic properties. In general, the presence of mesophases in the bulk phase and particularly in the surface phase may lead to the formation of a lubricant film which separates the frictionally cooperating elements of a friction pair. The antiseizure efficiency of alcohol solutions is highest up to the load value which does not exceed the scuffing load value. PMID:20162010

  4. Structural and Optical Properties Thin Film Copper Oxides Formed by Chemical Solution Deposition Process Technique

    SciTech Connect

    Lockman, Zainovia; Abidin, Noor Rehan Zainal; Hutagalung, Sabar Derita [School of Materials and Mineral Resources Engineering, Engineering Campus Universiti Sains Malaysia, 14300 Nibong Tebal (Malaysia)

    2007-05-09

    Cu2O films were prepared by chemical deposition process (CSD) using solutions of copper nitrate, dip-coated onto glass substrates. The precursor solutions were altered in an effort to seek the best solution for successful deposition. Organic additive of ethanolamine (EA) and (poly)ethylene glycol (PEG, H(OCH2CH2)nOH) was added to the solution and had shown positive effect in terms of the wetability and hence homogenous films resulted. Most films characterised by XRD gave (002) Cu2O, cuprite structure. To avoid films cracking and inhomogeneous coverage, multiple coatings were done with drying in between the successive coatings. Five to eight coatings were carried out for better coverage to ensure surface homogeneity. The microstructure of the surface oxides consisted of nanostructured oxides with uniform size distribution of 60-80nm. The optical transmittance of optimized Cu2O film reaches around 80% at wavelength of {approx} 700nm and the calculated direct optical band gaps were {approx} 2eV for the Cu2O films.

  5. Structural and Optical Properties Thin Film Copper Oxides Formed by Chemical Solution Deposition Process Technique

    NASA Astrophysics Data System (ADS)

    Lockman, Zainovia; Abidin, Noor Rehan Zainal; Hutagalung, Sabar Derita

    2007-05-01

    Cu2O films were prepared by chemical deposition process (CSD) using solutions of copper nitrate, dip-coated onto glass substrates. The precursor solutions were altered in an effort to seek the best solution for successful deposition. Organic additive of ethanolamine (EA) and (poly)ethylene glycol (PEG, H(OCH2CH2)nOH) was added to the solution and had shown positive effect in terms of the wetability and hence homogenous films resulted. Most films characterised by XRD gave (002) Cu2O, cuprite structure. To avoid films cracking and inhomogeneous coverage, multiple coatings were done with drying in between the successive coatings. Five to eight coatings were carried out for better coverage to ensure surface homogeneity. The microstructure of the surface oxides consisted of nanostructured oxides with uniform size distribution of 60-80nm. The optical transmittance of optimized Cu2O film reaches around 80% at wavelength of ˜ 700nm and the calculated direct optical band gaps were ˜ 2eV for the Cu2O films.

  6. Biomimetic Branched Hollow Fibers Templated by Self-assembled Fibrous Polyvinylpyrrolidone (PVP) Structures in Aqueous Solution

    PubMed Central

    Qiu, Penghe; Mao, Chuanbin

    2010-01-01

    Branched hollow fibers are common in nature, but to form artificial fibers with a similar branched hollow structure is still a challenge. We discovered that polyvinylpyrrolidone (PVP) could self-assemble into branched hollow fibers in an aqueous solution after aging the PVP solution for about two weeks. Based on this finding, we demonstrated two approaches by which the self-assembly of PVP into branched hollow fibers could be exploited to template the formation of branched hollow inorganic fibers. First, inorganic material such as silica with high affinity against the PVP could be deposited on the surface of the branched hollow PVP fibers to form branched hollow silica fibers. To extend the application of PVP self-assembly in templating the formation of hollow branched fibers, we then adopted a second approach where the PVP molecules bound to inorganic nanoparticles (using gold nanoparticles as a model) co-self-assemble with the free PVP molecules in an aqueous solution, resulting in the formation of the branched hollow fibers with the nanoparticles embedded in the PVP matrix constituting the walls of the fibers. Heating the resultant fibers above the glass transition temperature of PVP led to the formation of branched hollow gold fibers. Our work suggests that the self-assembly of the PVP molecules in the solution can serve as a general method for directing the formation of branched hollow inorganic fibers. The branched hollow fibers may find potential applications in microfluidics, artificial blood vessel generation, and tissue engineering. PMID:20158250

  7. Effect of ionic liquid treatment on the structures of lignins in solutions

    SciTech Connect

    Cheng, Gang [Joint Bioenergy Institute; Kent, Michael S [ORNL; He, Lilin [ORNL; Varanasi, Patanjali [Joint Bioenergy Institute; Dibble, Dean [Joint Bioenergy Institute; Melnichenko, Yuri B [ORNL; Simmons, Blake [Sandia National Laboratories (SNL); Singh, Seema [Joint Bioenergy Institute

    2012-01-01

    The solution structures of three types of isolated lignin - organosolv (OS), Kraft (K), and low sulfonate (LS) - before and after treatment with 1-ethyl-3-methylimidazolium acetate were studied using small-angle neutron scattering (SANS) and dynamic light scattering (DLS) over a concentration range of 0.3-2.4 wt %. The results indicate that each of these lignins is comprised of aggregates of well-defined basal subunits, the shapes and sizes of which, in D{sub 2}O and DMSO-d{sub 6}, are revealed using these techniques. LS lignin contains a substantial amount of nanometer-scale individual subunits. In aqueous solution these subunits have a well-defined elongated shape described well by ellipsoidal and cylindrical models. At low concentration the subunits are highly expanded in alkaline solution, and the effect is screened with increasing concentration. OS lignin dissolved in DMSO was found to consist of a narrow distribution of aggregates with average radius 200 {+-} 30 nm. K lignin in DMSO consists of aggregates with a very broad size distribution. After ionic liquid (IL) treatment, LS lignin subunits in alkaline solution maintained the elongated shape but were reduced in size. IL treatment of OS and K lignins led to the release of nanometer-scale subunits with well-defined size and shape.

  8. Operation of the Australian Store.Synchrotron for macromolecular crystallography

    SciTech Connect

    Meyer, Grischa R. [Monash University, Clayton, Victoria 3800 (Australia); Aragão, David; Mudie, Nathan J.; Caradoc-Davies, Tom T. [Australian Synchrotron, 800 Blackburn Road, Clayton, Victoria 3168 (Australia); McGowan, Sheena; Bertling, Philip J.; Groenewegen, David; Quenette, Stevan M. [Monash University, Clayton, Victoria 3800 (Australia); Bond, Charles S. [The University of Western Australia, 35 Stirling Highway, Crawley 6009, Western Australia (Australia); Buckle, Ashley M. [Monash University, Clayton, Victoria 3800 (Australia); Androulakis, Steve, E-mail: steve.androulakis@monash.edu [Monash Bioinformatics Platform, Monash University, Clayton, Victoria 3800 (Australia)

    2014-10-01

    The Store.Synchrotron service, a fully functional, cloud computing-based solution to raw X-ray data archiving and dissemination at the Australian Synchrotron, is described. The Store.Synchrotron service, a fully functional, cloud computing-based solution to raw X-ray data archiving and dissemination at the Australian Synchrotron, is described. The service automatically receives and archives raw diffraction data, related metadata and preliminary results of automated data-processing workflows. Data are able to be shared with collaborators and opened to the public. In the nine months since its deployment in August 2013, the service has handled over 22.4 TB of raw data (?1.7 million diffraction images). Several real examples from the Australian crystallographic community are described that illustrate the advantages of the approach, which include real-time online data access and fully redundant, secure storage. Discoveries in biological sciences increasingly require multidisciplinary approaches. With this in mind, Store.Synchrotron has been developed as a component within a greater service that can combine data from other instruments at the Australian Synchrotron, as well as instruments at the Australian neutron source ANSTO. It is therefore envisaged that this will serve as a model implementation of raw data archiving and dissemination within the structural biology research community.

  9. Hypoxic Tumor Environments Exhibit Disrupted Collagen I Fibers and Low Macromolecular Transport

    PubMed Central

    Kakkad, Samata M.; Penet, Marie-France; Akhbardeh, Alireza; Pathak, Arvind P.; Solaiyappan, Meiyappan; Raman, Venu; Leibfritz, Dieter; Glunde, Kristine; Bhujwalla, Zaver M.

    2013-01-01

    Hypoxic tumor microenvironments result in an aggressive phenotype and resistance to therapy that lead to tumor progression, recurrence, and metastasis. While poor vascularization and the resultant inadequate drug delivery are known to contribute to drug resistance, the effect of hypoxia on molecular transport through the interstitium, and the role of the extracellular matrix (ECM) in mediating this transport are unexplored. The dense mesh of fibers present in the ECM can especially influence the movement of macromolecules. Collagen 1 (Col1) fibers form a key component of the ECM in breast cancers. Here we characterized the influence of hypoxia on macromolecular transport in tumors, and the role of Col1 fibers in mediating this transport using an MDA-MB-231 breast cancer xenograft model engineered to express red fluorescent protein under hypoxia. Magnetic resonance imaging of macromolecular transport was combined with second harmonic generation microscopy of Col1 fibers. Hypoxic tumor regions displayed significantly decreased Col1 fiber density and volume, as well as significantly lower macromolecular draining and pooling rates, than normoxic regions. Regions adjacent to severely hypoxic areas revealed higher deposition of Col1 fibers and increased macromolecular transport. These data suggest that Col1 fibers may facilitate macromolecular transport in tumors, and their reduction in hypoxic regions may reduce this transport. Decreased macromolecular transport in hypoxic regions may also contribute to poor drug delivery and tumor recurrence in hypoxic regions. High Col1 fiber density observed around hypoxic regions may facilitate the escape of aggressive cancer cells from hypoxic regions. PMID:24349142

  10. Effects of 940 Hz EMF on luciferase solution: structure, function, and dielectric studies.

    PubMed

    Sefidbakht, Yahya; Hosseinkhani, Saman; Mortazavi, Mojtaba; Tavakkolnia, Iman; Khellat, Mohammad R; Shakiba-Herfeh, Mahdi; Saviz, Mehrdad; Faraji-Dana, Reza; Saboury, Ali A; Sheibani, Nader; Moosavi-Movahedi, Ali A

    2013-09-01

    We designed a rectangular waveguide exposure system to study the effects of mobile phone frequency (940 MHz) electromagnetic fields (EMF) on luciferase structure and activity. The luciferase activity of exposed samples was significantly higher than that of unexposed samples. Dynamic light scattering of the exposed samples showed smaller hydrodynamic radii compared to unexposed samples (20 nm vs. 47 nm ± 5%). The exposed samples also showed less tendency to form aggregates, monitored by turbidity measurements at l = 360 nm. A microwave dielectric measurement was performed to study the hydration properties of luciferase solutions with a precision network analyzer over frequency ranges from 0.2 to 20 GHz before and after exposure. The change in the dielectric properties of the exposed luciferase solution was related to the disaggregation potency of the applied field. Together, our results suggested that direct interactions with luciferase molecules and its dipole moment were responsible for the reduced aggregation and enhanced luciferase activity upon exposure to the EMF. PMID:23633149

  11. Surface structure and electrical properties of solution processed lanthanum nickelate films

    NASA Astrophysics Data System (ADS)

    Pandya, Nirav C.; Joshi, U. S.

    2014-04-01

    Conducting oxides with perovskite crystal structure have many advantages over the simple Pt or Au, Pt based metal bottom electrodes (BE), particularly in fabrication of ferroelectric as well as resistive random access memory devices, if they possess smooth surface morphology. LaNiO3 (LNO) thin films were prepared by modified chemical solution deposition method. Precursor solutions were spin coated onto SiO2-substrates. Deposited layers were thermally treated in a pre-heated furnace at 550 °C and oxygenated up to 800 °C. Results of AFM and FESEM showed that films are very smooth (Ra = 1.69 nm), dense, crack-free and with monodispersed nanocrystallites. Growth conditions such as spinning rate, annealing rates and temperatures etc. have been optimized for mono dispersed crystallinity with very smooth surface morphology. Sheet resistivity, carrier concentration and RMS roughness were correlated with growth temperatures.

  12. Recent Advances in the Analysis of Macromolecular Interactions Using the Matrix-Free Method of Sedimentation in the Analytical Ultracentrifuge

    PubMed Central

    Harding, Stephen E.; Gillis, Richard B.; Almutairi, Fahad; Erten, Tayyibe; Kök, M. ?amil; Adams, Gary G.

    2015-01-01

    Sedimentation in the analytical ultracentrifuge is a matrix free solution technique with no immobilisation, columns, or membranes required and can be used to study self-association and complex or “hetero”-interactions, stoichiometry, reversibility and interaction strength of a wide variety of macromolecular types and across a very large dynamic range (dissociation constants from 10?12 M to 10?1 M). We extend an earlier review specifically highlighting advances in sedimentation velocity and sedimentation equilibrium in the analytical ultracentrifuge applied to protein interactions and mucoadhesion and to review recent applications in protein self-association (tetanus toxoid, agrin), protein-like carbohydrate association (aminocelluloses), carbohydrate-protein interactions (polysaccharide-gliadin), nucleic-acid protein (G-duplexes), nucleic acid-carbohydrate (DNA-chitosan) and finally carbohydrate-carbohydrate (xanthan-chitosan and a ternary polysaccharide complex) interactions. PMID:25756246

  13. Recent advances in the analysis of macromolecular interactions using the matrix-free method of sedimentation in the analytical ultracentrifuge.

    PubMed

    Harding, Stephen E; Gillis, Richard B; Almutairi, Fahad; Erten, Tayyibe; Kök, M ?amil; Adams, Gary G

    2015-01-01

    Sedimentation in the analytical ultracentrifuge is a matrix free solution technique with no immobilisation, columns, or membranes required and can be used to study self-association and complex or "hetero"-interactions, stoichiometry, reversibility and interaction strength of a wide variety of macromolecular types and across a very large dynamic range (dissociation constants from 10-12 M to 10-1 M). We extend an earlier review specifically highlighting advances in sedimentation velocity and sedimentation equilibrium in the analytical ultracentrifuge applied to protein interactions and mucoadhesion and to review recent applications in protein self-association (tetanus toxoid, agrin), protein-like carbohydrate association (aminocelluloses), carbohydrate-protein interactions (polysaccharide-gliadin), nucleic-acid protein (G-duplexes), nucleic acid-carbohydrate (DNA-chitosan) and finally carbohydrate-carbohydrate (xanthan-chitosan and a ternary polysaccharide complex) interactions. PMID:25756246

  14. Structure solution with automated electron diffraction tomography data: different instrumental approaches.

    PubMed

    Gorelik, T E; Stewart, A A; Kolb, U

    2011-12-01

    Over the past few years automated electron diffraction tomography has become an established technique for structure solution of nano-crystalline material. The intentional choice of an arbitrary tilt axis and thus, the use of nonoriented diffraction patterns (off-zone acquisition) together with fine equidistant sampling of the reciprocal space result in high quality intensity data sets. Coupling automated electron diffraction tomography with electron beam precession (Vincent & Midgley, 1994) enables sampling of intensities between the static slices of reciprocal space and therefore enhances the quality of intensity data further; relatively complex structures have been solved using 3D electron diffraction intensities extracted from automated electron diffraction tomography data. Automated electron diffraction tomography data was collected initially using a dedicated automated module. In this manuscript we demonstrate that electron diffraction data of comparable quality can be collected using manual technique that mimics the automated process. A rather difficult material, i.e. a low symmetric (triclinic) sodium tetratungstate (Na(2) W(4) O(13) ) including heavy and light scatterers, was selected for testing. In this paper we show, that all collected data sets - automatic and manual, with and without electron beam precession - were able to provide data slightly different but suitable for?ab initio?structure solution and refinement. PMID:21992494

  15. Human alpha-lactalbumin as a marker of macromolecular absorption.

    PubMed Central

    Jakobsson, I; Lindberg, T; Lothe, L; Axelsson, I; Benediktsson, B

    1986-01-01

    alpha-Lactalbumin was purified from human milk and a competitive radioimmunoassay for measuring serum concentrations of human alpha-lactalbumin was developed. Human alpha-lactalbumin was not detected (less than 5 micrograms/l) in serum from adult men (n = 4), non-pregnant women (n = 6) or in serum from seven of eight formula fed infants. alpha-Lactalbumin was found in serum from pregnant women (19-130 micrograms/l, n = 4), cord blood (22-72 micrograms/l, median value 35 micrograms/l, n = 9), and from newborn non-fed infants (less than 1 day old) (less than 5-50 micrograms/l, median value 15 micrograms/l, n = 11). In breast fed infants the serum concentration of alpha-lactalbumin was highest in preterm infants (140-952 micrograms/l serum/l human milk/kg body weight, n = 4) and decreased in term infants successively with maturity (age 5-30 days: median value 85 micrograms/l serum/l human milk/kg body weight, n = 7; age 31-60 days: median value 43, n = 6; age 61-135 days: median value 12, n = 6). A human milk feeding to three infants one month of age gave serum peak values of alpha-lactalbumin after 30 to 60 minutes. We suggest that human alpha-lactalbumin is a suitable marker for investigating macromolecular absorption in physiological and pathological conditions. Images Fig. 1 PMID:3758816

  16. Solution Structural Analysis of the Single-Domain Parvulin TbPin1

    PubMed Central

    Sun, Lifang; Wu, Xueji; Peng, Yu; Goh, Jian Yuan; Liou, Yih-Cherng; Lin, Donghai; Zhao, Yufen

    2012-01-01

    Background Pin1-type parvulins are phosphorylation-dependent peptidyl-prolyl cis-trans isomerases. Their functions have been widely reported to be involved in a variety of cellular responses or processes, such as cell division, transcription, and apoptosis, as well as in human diseases including Alzheimer's disease and cancers. TbPin1 was identified as a novel class of Pin1-type parvulins from Trypanosoma brucei, containing a unique PPIase domain, which can catalyze the isomerization of phosphorylated Ser/Thr-Pro peptide bond. Methodology/Principal Findings We determined the solution structure of TbPin1 and performed 15N relaxation measurements to analyze its backbone dynamics using multi-dimensional heteronuclear NMR spectroscopy. The average RMSD values of the 20 lowest energy structures are 0.50±0.05 Å for backbone heavy atoms and 0.85±0.08 Å for all heavy atoms. TbPin1 adopts the typical catalytic tertiary structure of Pin1-type parvulins, which comprises a globular fold with a four-stranded anti-parallel ?-sheet core surrounded by three ?-helices and one 310-helix. The global structure of TbPin1 is relatively rigid except the active site. The 2D EXSY spectra illustrate that TbPin1 possesses a phosphorylation-dependent PPIase activity. The binding sites of TbPin1 for a phosphorylated peptide substrate {SSYFSG[p]TPLEDDSD} were determined by the chemical shift perturbation approach. Residues Ser15, Arg18, Asn19, Val21, Ser22, Val32, Gly66, Ser67, Met83, Asp105 and Gly107 are involved in substantial contact with the substrate. Conclusions/Significance The solution structure of TbPin1 and the binding sites of the phosphorylated peptide substrate on TbPin1 were determined. The work is helpful for further understanding the molecular basis of the substrate specificity for Pin1-type parvulin family and enzyme catalysis. PMID:22900083

  17. Structural, functional, and evolutionary relationships among extracellular solute-binding receptors of bacteria.

    PubMed Central

    Tam, R; Saier, M H

    1993-01-01

    Extracellular solute-binding proteins of bacteria serve as chemoreceptors, recognition constituents of transport systems, and initiators of signal transduction pathways. Over 50 sequenced periplasmic solute-binding proteins of gram-negative bacteria and homologous extracytoplasmic lipoproteins of gram-positive bacteria have been analyzed for sequence similarities, and their degrees of relatedness have been determined. Some of these proteins are homologous to cytoplasmic transcriptional regulatory proteins of bacteria; however, with the sole exception of the vitamin B12-binding protein of Escherichia coli, which is homologous to human glutathione peroxidase, they are not demonstrably homologous to any of the several thousand sequenced eukaryotic proteins. Most of these proteins fall into eight distinct clusters as follows. Cluster 1 solute-binding proteins are specific for malto-oligosaccharides, multiple oligosaccharides, glycerol 3-phosphate, and iron. Cluster 2 proteins are specific for galactose, ribose, arabinose, and multiple monosaccharides, and they are homologous to a number of transcriptional regulatory proteins including the lactose, galactose, and fructose repressors of E. coli. Cluster 3 proteins are specific for histidine, lysine-arginine-ornithine, glutamine, octopine, nopaline, and basic amino acids. Cluster 4 proteins are specific for leucine and leucine-isoleucine-valine, and they are homologous to the aliphatic amidase transcriptional repressor, AmiC, of Pseudomonas aeruginosa. Cluster 5 proteins are specific for dipeptides and oligopeptides as well as nickel. Cluster 6 proteins are specific for sulfate, thiosulfate, and possibly phosphate. Cluster 7 proteins are specific for dicarboxylates and tricarboxylates, but these two proteins exhibit insufficient sequence similarity to establish homology. Finally, cluster 8 proteins are specific for iron complexes and possibly vitamin B12. Members of each cluster of binding proteins exhibit greater sequence conservation in their N-terminal domains than in their C-terminal domains. Signature sequences for these eight protein families are presented. The results reveal that binding proteins specific for the same solute from different bacteria are generally more closely related to each other than are binding proteins specific for different solutes from the same organism, although exceptions exist. They also suggest that a requirement for high-affinity solute binding imposes severe structural constraints on a protein. The occurrence of two distinct classes of bacterial cytoplasmic repressor proteins which are homologous to two different clusters of periplasmic binding proteins suggests that the gene-splicing events which allowed functional conversion of these proteins with retention of domain structure have occurred repeatedly during evolutionary history.(ABSTRACT TRUNCATED AT 400 WORDS) PMID:8336670

  18. Structural, functional, and evolutionary relationships among extracellular solute-binding receptors of bacteria.

    PubMed

    Tam, R; Saier, M H

    1993-06-01

    Extracellular solute-binding proteins of bacteria serve as chemoreceptors, recognition constituents of transport systems, and initiators of signal transduction pathways. Over 50 sequenced periplasmic solute-binding proteins of gram-negative bacteria and homologous extracytoplasmic lipoproteins of gram-positive bacteria have been analyzed for sequence similarities, and their degrees of relatedness have been determined. Some of these proteins are homologous to cytoplasmic transcriptional regulatory proteins of bacteria; however, with the sole exception of the vitamin B12-binding protein of Escherichia coli, which is homologous to human glutathione peroxidase, they are not demonstrably homologous to any of the several thousand sequenced eukaryotic proteins. Most of these proteins fall into eight distinct clusters as follows. Cluster 1 solute-binding proteins are specific for malto-oligosaccharides, multiple oligosaccharides, glycerol 3-phosphate, and iron. Cluster 2 proteins are specific for galactose, ribose, arabinose, and multiple monosaccharides, and they are homologous to a number of transcriptional regulatory proteins including the lactose, galactose, and fructose repressors of E. coli. Cluster 3 proteins are specific for histidine, lysine-arginine-ornithine, glutamine, octopine, nopaline, and basic amino acids. Cluster 4 proteins are specific for leucine and leucine-isoleucine-valine, and they are homologous to the aliphatic amidase transcriptional repressor, AmiC, of Pseudomonas aeruginosa. Cluster 5 proteins are specific for dipeptides and oligopeptides as well as nickel. Cluster 6 proteins are specific for sulfate, thiosulfate, and possibly phosphate. Cluster 7 proteins are specific for dicarboxylates and tricarboxylates, but these two proteins exhibit insufficient sequence similarity to establish homology. Finally, cluster 8 proteins are specific for iron complexes and possibly vitamin B12. Members of each cluster of binding proteins exhibit greater sequence conservation in their N-terminal domains than in their C-terminal domains. Signature sequences for these eight protein families are presented. The results reveal that binding proteins specific for the same solute from different bacteria are generally more closely related to each other than are binding proteins specific for different solutes from the same organism, although exceptions exist. They also suggest that a requirement for high-affinity solute binding imposes severe structural constraints on a protein. The occurrence of two distinct classes of bacterial cytoplasmic repressor proteins which are homologous to two different clusters of periplasmic binding proteins suggests that the gene-splicing events which allowed functional conversion of these proteins with retention of domain structure have occurred repeatedly during evolutionary history.(ABSTRACT TRUNCATED AT 400 WORDS) PMID:8336670

  19. Synthesis and NMR solution structure of an alpha-helical hairpin stapled with two disulfide bridges.

    PubMed Central

    Barthe, P.; Rochette, S.; Vita, C.; Roumestand, C.

    2000-01-01

    Helical coiled-coils and bundles are some of the most common structural motifs found in proteins. Design and synthesis of alpha-helical motifs may provide interesting scaffolds that can be useful as host structures to display functional sites, thus allowing the engineering of novel functional miniproteins. We have synthesized a 38-amino acid peptide, alpha2p8, encompassing the alpha-helical hairpin present in the structure of p8MTCP1, as an alpha-helical scaffold particularly promising for its stability and permissiveness of sequence mutations. The three-dimensional structure of this peptide has been solved using homonuclear two-dimensional NMR techniques at 600 MHz. After sequence specific assignment, a total of 285 distance and 29 dihedral restraints were collected. The solution structure of alpha2p8 is presented as a set of 30 DIANA structures, further refined by restrained molecular dynamics, using simulated annealing protocol with the AMBER force field. The RMSD values for the backbone and all heavy atoms are 0.65+/-0.25 and 1.51+/-0.21 A, respectively. Excised from its protein context, the alpha-hairpin keeps its native structure: an alpha-helical coiled-coil, similar to that found in superhelical structures, with two helices spanning residues 4-16 and 25-36, and linked by a short loop. This motif is stabilized by two interhelical disulfide bridges and several hydrophobic interactions at the helix interface, leaving most of its solvent-exposed surface available for mutation. This alpha-helical hairpin, easily amenable to synthetic chemistry and biological expression system, may represent a stable and versatile scaffold to display new functional sites and peptide libraries. PMID:10850804

  20. Structure and Dynamics of Full Length HIV-1 Capsid Protein in Solution

    PubMed Central

    Deshmukh, Lalit; Schwieters, Charles D.; Grishaev, Alexander; Ghirlando, Rodolfo; Baber, James L.; Clore, G. Marius

    2013-01-01

    The HIV-1 capsid protein plays a crucial role in viral infectivity, assembling into a cone that encloses the viral RNA. In the mature virion, the N-terminal domain of the capsid protein forms hexameric and pentameric rings, while C-terminal domain homodimers connect adjacent N-terminal domain rings to one another. Structures of disulfide-linked hexamer and pentamer assemblies, as well as structures of the isolated domains have been solved previously. The dimer configuration in C-terminal domain constructs differs in solution (residues 144–231) and crystal (residues 146–231) structures by ~30°, and it has been postulated that the former connects the hexamers while the latter links pentamers to hexamers. Here we study the structure and dynamics of full-length capsid protein in solution, comprising a mixture of monomeric and dimeric forms in dynamic equilibrium, using ensemble simulated annealing driven by experimental NMR residual dipolar couplings and X-ray scattering data. The complexity of the system necessitated the development of a novel computational framework that should be generally applicable to many other challenging systems that currently escape structural characterization by standard application of mainstream techniques of structural biology. We show that the orientation of the C-terminal domains in dimeric full-length capsid and isolated C-terminal domain constructs is the same in solution, and obtain a quantitative description of the conformational space sampled by the N-terminal domain relative to the C-terminal domain on the nano- to millisecond time-scale. The positional distribution of the N-terminal domain relative to the C-terminal domain is large and modulated by the oligomerization state of the C-terminal domain. We also show that a model of the hexamer/pentamer assembly can be readily generated with a single configuration of the C-terminal domain dimer, and that capsid assembly likely proceeds via conformational selection of sparsely-populated configurations of the N-terminal domain within the capsid protein dimer. PMID:24066695