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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. Phenix - a comprehensive python-based system for macromolecular structure solution

    SciTech Connect

    Terwilliger, Thomas C; Hung, Li - Wei; Adams, Paul D; Afonine, Pavel V; Bunkoczi, Gabor; Chen, Vincent B; Davis, Ian; Echols, Nathaniel; Headd, Jeffrey J; Grosse Kunstleve, Ralf W; Mccoy, Airlie J; Moriarty, Nigel W; Oeffner, Robert; Read, Randy J; Richardson, David C; Richardson, Jane S; Zwarta, Peter H

    2009-01-01

    Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many of these structures because of the need for manual interpretation of complex numerical data using many software packages, and the repeated use of interactive three-dimensional graphics. Phenix has been developed to provide a comprehensive system for crystallographic structure solution with an emphasis on automation of all procedures. This has relied on the development of algorithms that minimize or eliminate subjective input, the development of algorithms that automate procedures that are traditionally performed by hand, and finally the development of a framework that allows a tight integration between the algorithms.

  3. Data Mining of Macromolecular Structures.

    PubMed

    van Beusekom, Bart; Perrakis, Anastassis; Joosten, Robbie P

    2016-01-01

    The use of macromolecular structures is widespread for a variety of applications, from teaching protein structure principles all the way to ligand optimization in drug development. Applying data mining techniques on these experimentally determined structures requires a highly uniform, standardized structural data source. The Protein Data Bank (PDB) has evolved over the years toward becoming the standard resource for macromolecular structures. However, the process selecting the data most suitable for specific applications is still very much based on personal preferences and understanding of the experimental techniques used to obtain these models. In this chapter, we will first explain the challenges with data standardization, annotation, and uniformity in the PDB entries determined by X-ray crystallography. We then discuss the specific effect that crystallographic data quality and model optimization methods have on structural models and how validation tools can be used to make informed choices. We also discuss specific advantages of using the PDB_REDO databank as a resource for structural data. Finally, we will provide guidelines on how to select the most suitable protein structure models for detailed analysis and how to select a set of structure models suitable for data mining. PMID:27115630

  4. Macromolecular complexes in crystals and solutions

    PubMed Central

    Krissinel, Evgeny

    2011-01-01

    This paper presents a discussion of existing methods for the analysis of macromolecular interactions and complexes in crystal packing. Typical situations and conditions where wrong answers may be obtained in the course of ordinary procedures are presented and discussed. The more general question of what the relationship is between natural (in-solvent) and crystallized assemblies is discussed and researched. A computational analysis suggests that weak interactions with K d ≥ 100 µM have a considerable chance of being lost during the course of crystallization. In such instances, crystal packing misrepresents macromolecular complexes and interactions. For as many as 20% of protein dimers in the PDB the likelihood of misrepresentation is estimated to be higher than 50%. Given that weak macromolecular interactions play an important role in many biochemical processes, these results suggest that a complementary noncrystallographic study should be always conducted when inferring structural aspects of weakly bound complexes. PMID:21460456

  5. 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

  6. 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.

  7. 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

  8. 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

  9. The Phenix Software for Automated Determination of Macromolecular Structures

    PubMed Central

    Adams, Paul D.; Afonine, Pavel V.; Bunkczi, Gbor; Chen, Vincent B.; Echols, Nathaniel; Headd, Jeffrey J.; Hung, Li-Wei; Jain, Swati; Kapral, Gary J.; Grosse Kunstleve, Ralf W.; McCoy, Airlie J.; Moriarty, Nigel W.; Oeffner, Robert D.; Read, Randy J.; Richardson, David C.; Richardson, Jane S.; Terwilliger, Thomas C.; Zwart, Peter H.

    2011-01-01

    X-ray crystallography is a critical tool in the study of biological systems. It is able to provide information that has been a prerequisite to understanding the fundamentals of life. It is also a method that is central to the development of new therapeutics for human disease. Significant time and effort are required to determine and optimize many macromolecular structures because of the need for manual interpretation of complex numerical data, often using many different software packages, and the repeated use of interactive three-dimensional graphics. The Phenix software package has been developed to provide a comprehensive system for macromolecular crystallographic structure solution with an emphasis on automation. This has required the development of new algorithms that minimize or eliminate subjective input in favour of built-in expert-systems knowledge, the automation of procedures that are traditionally performed by hand, and the development of a computational framework that allows a tight integration between the algorithms. The application of automated methods is particularly appropriate in the field of structural proteomics, where high throughput is desired. Features in Phenix for the automation of experimental phasing with subsequent model building, molecular replacement, structure refinement and validation are described and examples given of running Phenix from both the command line and graphical user interface. PMID:21821126

  10. Homogenization Theory for the Prediction of Obstructed Solute Diffusivity in Macromolecular Solutions

    PubMed Central

    Donovan, Preston; Chehreghanianzabi, Yasaman; Rathinam, Muruhan; Zustiak, Silviya Petrova

    2016-01-01

    The study of diffusion in macromolecular solutions is important in many biomedical applications such as separations, drug delivery, and cell encapsulation, and key for many biological processes such as protein assembly and interstitial transport. Not surprisingly, multiple models for the a-priori prediction of diffusion in macromolecular environments have been proposed. However, most models include parameters that are not readily measurable, are specific to the polymer-solute-solvent system, or are fitted and do not have a physical meaning. Here, for the first time, we develop a homogenization theory framework for the prediction of effective solute diffusivity in macromolecular environments based on physical parameters that are easily measurable and not specific to the macromolecule-solute-solvent system. Homogenization theory is useful for situations where knowledge of fine-scale parameters is used to predict bulk system behavior. As a first approximation, we focus on a model where the solute is subjected to obstructed diffusion via stationary spherical obstacles. We find that the homogenization theory results agree well with computationally more expensive Monte Carlo simulations. Moreover, the homogenization theory agrees with effective diffusivities of a solute in dilute and semi-dilute polymer solutions measured using fluorescence correlation spectroscopy. Lastly, we provide a mathematical formula for the effective diffusivity in terms of a non-dimensional and easily measurable geometric system parameter. PMID:26731550

  11. Fast native-SAD phasing for routine macromolecular structure determination.

    PubMed

    Weinert, Tobias; Olieric, Vincent; Waltersperger, Sandro; Panepucci, Ezequiel; Chen, Lirong; Zhang, Hua; Zhou, Dayong; Rose, John; Ebihara, Akio; Kuramitsu, Seiki; Li, Dianfan; Howe, Nicole; Schnapp, Gisela; Pautsch, Alexander; Bargsten, Katja; Prota, Andrea E; Surana, Parag; Kottur, Jithesh; Nair, Deepak T; Basilico, Federica; Cecatiello, Valentina; Pasqualato, Sebastiano; Boland, Andreas; Weichenrieder, Oliver; Wang, Bi-Cheng; Steinmetz, Michel O; Caffrey, Martin; Wang, Meitian

    2015-02-01

    We describe a data collection method that uses a single crystal to solve X-ray structures by native SAD (single-wavelength anomalous diffraction). We solved the structures of 11 real-life examples, including a human membrane protein, a protein-DNA complex and a 266-kDa multiprotein-ligand complex, using this method. The data collection strategy is suitable for routine structure determination and can be implemented at most macromolecular crystallography synchrotron beamlines. PMID:25506719

  12. Structural changes in the ordering processes of macromolecular compounds

    NASA Astrophysics Data System (ADS)

    Kobayashi, M.; Tashiro, K.

    1998-06-01

    In order to clarify the microscopically-viewed relationship between the conformational ordering process and the aggregation process of the macromolecular chains in the phase transitions from melt to solid or from solution to gel, the time-resolved Fourier-transform infrared spectra and small-angle X-ray or neutron scattering data have been analyzed in an organized manner. Two concrete examples were presented. (1) In the gelation phenomenon of syndiotactic polystyrene-organic solvent system, the ordered TTGG conformation is formed and develops with time. This conformational ordering is accelerated by the aggregation of these chain segments, resulting in the formation of macroscopic gel network. (2) In the isothermal crystallization process from the melt of polyethylene, the following ordering mechanism was revealed. The conformationally-disordered short trans conformers appear at first in the random coils of the melt. These disordered trans sequences grow to longer and more regular trans sequences of the orthorhombic-type crystal and then the isolated lamellae are formed. Afterwards, the stacked lamellar structure is developed without change of lamellar thickness but with small decrease in the long period, indicating an insertion of new lamellae between the already produced lamellar layers.

  13. MMDB: 3D structures and macromolecular interactions

    PubMed Central

    Madej, Thomas; Addess, Kenneth J.; Fong, Jessica H.; Geer, Lewis Y.; Geer, Renata C.; Lanczycki, Christopher J.; Liu, Chunlei; Lu, Shennan; Marchler-Bauer, Aron; Panchenko, Anna R.; Chen, Jie; Thiessen, Paul A.; Wang, Yanli; Zhang, Dachuan; Bryant, Stephen H.

    2012-01-01

    Close to 60% of protein sequences tracked in comprehensive databases can be mapped to a known three-dimensional (3D) structure by standard sequence similarity searches. Potentially, a great deal can be learned about proteins or protein families of interest from considering 3D structure, and to this day 3D structure data may remain an underutilized resource. Here we present enhancements in the Molecular Modeling Database (MMDB) and its data presentation, specifically pertaining to biologically relevant complexes and molecular interactions. MMDB is tightly integrated with NCBI's Entrez search and retrieval system, and mirrors the contents of the Protein Data Bank. It links protein 3D structure data with sequence data, sequence classification resources and PubChem, a repository of small-molecule chemical structures and their biological activities, facilitating access to 3D structure data not only for structural biologists, but also for molecular biologists and chemists. MMDB provides a complete set of detailed and pre-computed structural alignments obtained with the VAST algorithm, and provides visualization tools for 3D structure and structure/sequence alignment via the molecular graphics viewer Cn3D. MMDB can be accessed at http://www.ncbi.nlm.nih.gov/structure. PMID:22135289

  14. Cryo-Electron Tomography for Structural Characterization of Macromolecular Complexes

    PubMed Central

    Cope, Julia; Heumann, John; Hoenger, Andreas

    2011-01-01

    Cryo-electron tomography (cryo-ET) is an emerging 3-D reconstruction technology that combines the principles of tomographic 3-D reconstruction with the unmatched structural preservation of biological material embedded in vitreous ice. Cryo-ET is particularly suited to investigating cell-biological samples and large macromolecular structures that are too polymorphic to be reconstructed by classical averaging-based 3-D reconstruction procedures. This unit aims to make cryo-ET accessible to newcomers and discusses the specialized equipment required, as well as the relevant advantages and hurdles associated with sample preparation by vitrification and cryo-ET. Protocols describe specimen preparation, data recording and 3-D data reconstruction for cryo-ET, with a special focus on macromolecular complexes. A step-by-step procedure for specimen vitrification by plunge freezing is provided, followed by the general practicalities of tilt-series acquisition for cryo-ET, including advice on how to select an area appropriate for acquiring a tilt series. A brief introduction to the underlying computational reconstruction principles applied in tomography is described, along with instructions for reconstructing a tomogram from cryo-tilt series data. Finally, a method is detailed for extracting small subvolumes containing identical macromolecular structures from tomograms for alignment and averaging as a means to increase the signal-to-noise ratio and eliminate missing wedge effects inherent in tomographic reconstructions. PMID:21842467

  15. 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.

  16. MMDB and VAST+: tracking structural similarities between macromolecular complexes.

    PubMed

    Madej, Thomas; Lanczycki, Christopher J; Zhang, Dachuan; Thiessen, Paul A; Geer, Renata C; Marchler-Bauer, Aron; Bryant, Stephen H

    2014-01-01

    The computational detection of similarities between protein 3D structures has become an indispensable tool for the detection of homologous relationships, the classification of protein families and functional inference. Consequently, numerous algorithms have been developed that facilitate structure comparison, including rapid searches against a steadily growing collection of protein structures. To this end, NCBI's Molecular Modeling Database (MMDB), which is based on the Protein Data Bank (PDB), maintains a comprehensive and up-to-date archive of protein structure similarities computed with the Vector Alignment Search Tool (VAST). These similarities have been recorded on the level of single proteins and protein domains, comprising in excess of 1.5 billion pairwise alignments. Here we present VAST+, an extension to the existing VAST service, which summarizes and presents structural similarity on the level of biological assemblies or macromolecular complexes. VAST+ simplifies structure neighboring results and shows, for macromolecular complexes tracked in MMDB, lists of similar complexes ranked by the extent of similarity. VAST+ replaces the previous VAST service as the default presentation of structure neighboring data in NCBI's Entrez query and retrieval system. MMDB and VAST+ can be accessed via http://www.ncbi.nlm.nih.gov/Structure. PMID:24319143

  17. REFMAC5 for the refinement of macromolecular crystal structures

    PubMed Central

    Murshudov, Garib N.; Skubák, Pavol; Lebedev, Andrey A.; Pannu, Navraj S.; Steiner, Roberto A.; Nicholls, Robert A.; Winn, Martyn D.; Long, Fei; Vagin, Alexei A.

    2011-01-01

    This paper describes various components of the macromolecular crystallographic refinement program REFMAC5, which is distributed as part of the CCP4 suite. REFMAC5 utilizes different likelihood functions depending on the diffraction data employed (amplitudes or intensities), the presence of twinning and the availability of SAD/SIRAS experimental diffraction data. To ensure chemical and structural integrity of the refined model, REFMAC5 offers several classes of restraints and choices of model parameterization. Reliable models at resolutions at least as low as 4 Å can be achieved thanks to low-resolution refinement tools such as secondary-structure restraints, restraints to known homologous structures, automatic global and local NCS restraints, ‘jelly-body’ restraints and the use of novel long-range restraints on atomic displacement parameters (ADPs) based on the Kullback–Leibler divergence. REFMAC5 additionally offers TLS parameterization and, when high-resolution data are available, fast refinement of anisotropic ADPs. Refinement in the presence of twinning is performed in a fully automated fashion. REFMAC5 is a flexible and highly optimized refinement package that is ideally suited for refinement across the entire resolution spectrum encountered in macromolecular crystallography. PMID:21460454

  18. 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.

  19. Automated identification of elemental ions in macromolecular crystal structures

    PubMed Central

    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.

    2014-01-01

    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

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

    SciTech Connect

    Foley, Patricia L.; Wilson, David B.; Shuler, Michael L.

    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.

  1. The effect of macromolecular crowding on the structure of the protein complex superoxide dismutase

    NASA Astrophysics Data System (ADS)

    Rajapaksha Mudalige, Ajith Rathnaweera

    Biological environments contain between 7 - 40% macromolecules by volume. This reduces the available volume for macromolecules and elevates the osmotic pressure relative to pure water. Consequently, biological macromolecules in their native environments tend to adopt more compact and dehydrated conformations than those in vitro. This effect is referred to as macromolecular crowding and constitutes an important physical difference between native biological environments and the simple solutions in which biomolecules are usually studied. We used small angle scattering (SAS) to measure the effects of macromolecular crowding on the size of a protein complex, superoxide dismutase (SOD). Crowding was induced using 400 MW polyethylene glycol (PEG), triethylene glycol (TEG), methyl-alpha-glucoside (alpha-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%. SAS coupled with osmotic pressure measurements allowed us to estimate a compressibility modulus for SOD. We believe this to be the first time the osmotic compressibility of a protein complex was measured. Molecular Dynamics (MD) simulations are widely used to obtain insights on biomolecular processes. However, it is not clear whether MD is capable of predicting subtle effects of macromolecular crowding. We used our experimentally observed compressibility of SOD to evaluate the ability of MD to predict macromolecular crowding. Effects of macromolecular crowding due to PEG on SOD were modeled using an all atom MD simulation with the CHARMM forcefield and the crystallographically resolved structures of SOD and PEG. Two parallel MD simulations were performed for SOD in water and SOD in 40% PEG for over 150~ns. Over the period of the simulation the SOD structure in 40% PEG did not change compared to the SOD structure in water. It therefore appears that under the conditions of our simulations MD could not describe the experimentally observed effects of macromolecular crowding. In a separate project, we measured the rate of diffusive transport in excised porcine corneal stroma using FCS for fluorescent labeled dextran molecules with hydrodynamic radii ranging from 1.3 to 34 nm. Dextran molecules diffuse more slowly in cornea as compared to buffer solution. The reduction in diffusion coefficient is modest however (67% smaller), and is uniform over the range of sizes that we measured. Diffusion coefficients measured parallel vs. perpendicular to the collagen lamellae were indistinguishable. This indicates that diffusion in the corneal stroma is not highly anisotropic. Delivery of therapeutic agents to the eye requires efficient transport through cellular and extracellular barriers. Our measurements bring important insights into how macromolecular and nanoparticle therapeutics might permeate through the eyes.

  2. Double-Lanthanide-Binding Tags for Macromolecular Crystallographic Structure Determination

    SciTech Connect

    Silvaggi,N.; Martin, L.; Schwalbe, H.; Imperiali, B.; Allen, K.

    2007-01-01

    A double-lanthanide-binding tag (dLBT), a small peptide sequence engineered to bind two lanthanide ions (e.g., Tb{sup 3+}) with high affinity, was used to solve the phase problem for the structure determination of ubiquitin by the single-wavelength anomalous diffraction (SAD) method. Since the dLBT is comprised exclusively of encoded amino acids, the necessity for the incorporation of unnatural amino acids or chemical modification of the protein as a prerequisite for X-ray structure determination is eliminated. A construct encoding the dLBT as an N-terminal fusion with ubiquitin provides for facile expression and purification using standard methods. Phasing of the single-wavelength X-ray data (at 2.6 {angstrom} resolution) using only the anomalous signal from the two tightly bound Tb{sup 3+} ions in the dLBT led to clear electron-density maps. Nearly 75% of the ubiquitin structure was built using automated model-building software without user intervention. It is anticipated that this technique will be broadly applicable, complementing existing macromolecular phasing methodologies. The dLBT should be particularly useful in cases where protein derivatization with heavy atoms proves to be problematic or synchrotron facilities are unavailable.

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

    SciTech Connect

    Joosten, Robbie P.; Soueidan, Hayssam; Wessels, Lodewyk F. A.; Perrakis, Anastassis

    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.

  4. Automated identification of elemental ions in macromolecular crystal structures

    SciTech Connect

    Echols, Nathaniel Morshed, Nader; Afonine, Pavel V.; McCoy, Airlie J.; Read, Randy J.; Terwilliger, Thomas C.; Adams, Paul D.

    2014-04-01

    The solvent-picking procedure in phenix.refine has been extended and combined with Phaser anomalous substructure completion and analysis of coordination geometry to identify and place elemental ions. 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.

  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 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 α-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 α-helices, other fragments can be exploited in an analogous way: libraries of helices with modelled side chains, β-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

  8. 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), α-MG (methyl-α-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

  9. Effects of macromolecular crowding on the structure of a protein complex: a small-angle scattering study of superoxide dismutase.

    PubMed

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

    2015-02-17

    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), α-MG (methyl-α-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

  10. PDBe: improved accessibility of macromolecular structure data from PDB and EMDB.

    PubMed

    Velankar, Sameer; van Ginkel, Glen; Alhroub, Younes; Battle, Gary M; Berrisford, John M; Conroy, Matthew J; Dana, Jose M; Gore, Swanand P; Gutmanas, Aleksandras; Haslam, Pauline; Hendrickx, Pieter M S; Lagerstedt, Ingvar; Mir, Saqib; Fernandez Montecelo, Manuel A; Mukhopadhyay, Abhik; Oldfield, Thomas J; Patwardhan, Ardan; Sanz-Garca, Eduardo; Sen, Sanchayita; Slowley, Robert A; Wainwright, Michael E; Deshpande, Mandar S; Iudin, Andrii; Sahni, Gaurav; Salavert Torres, Jose; Hirshberg, Miriam; Mak, Lora; Nadzirin, Nurul; Armstrong, David R; Clark, Alice R; Smart, Oliver S; Korir, Paul K; Kleywegt, Gerard J

    2016-01-01

    The Protein Data Bank in Europe (http://pdbe.org) accepts and annotates depositions of macromolecular structure data in the PDB and EMDB archives and enriches, integrates and disseminates structural information in a variety of ways. The PDBe website has been redesigned based on an analysis of user requirements, and now offers intuitive access to improved and value-added macromolecular structure information. Unique value-added information includes lists of reviews and research articles that cite or mention PDB entries as well as access to figures and legends from full-text open-access publications that describe PDB entries. A powerful new query system not only shows all the PDB entries that match a given query, but also shows the 'best structures' for a given macromolecule, ligand complex or sequence family using data-quality information from the wwPDB validation reports. A PDBe RESTful API has been developed to provide unified access to macromolecular structure data available in the PDB and EMDB archives as well as value-added annotations, e.g. regarding structure quality and up-to-date cross-reference information from the SIFTS resource. Taken together, these new developments facilitate unified access to macromolecular structure data in an intuitive way for non-expert users and support expert users in analysing macromolecular structure data. PMID:26476444

  11. PDBe: improved accessibility of macromolecular structure data from PDB and EMDB

    PubMed Central

    Velankar, Sameer; van Ginkel, Glen; Alhroub, Younes; Battle, Gary M.; Berrisford, John M.; Conroy, Matthew J.; Dana, Jose M.; Gore, Swanand P.; Gutmanas, Aleksandras; Haslam, Pauline; Hendrickx, Pieter M. S.; Lagerstedt, Ingvar; Mir, Saqib; Fernandez Montecelo, Manuel A.; Mukhopadhyay, Abhik; Oldfield, Thomas J.; Patwardhan, Ardan; Sanz-García, Eduardo; Sen, Sanchayita; Slowley, Robert A.; Wainwright, Michael E.; Deshpande, Mandar S.; Iudin, Andrii; Sahni, Gaurav; Salavert Torres, Jose; Hirshberg, Miriam; Mak, Lora; Nadzirin, Nurul; Armstrong, David R.; Clark, Alice R.; Smart, Oliver S.; Korir, Paul K.; Kleywegt, Gerard J.

    2016-01-01

    The Protein Data Bank in Europe (http://pdbe.org) accepts and annotates depositions of macromolecular structure data in the PDB and EMDB archives and enriches, integrates and disseminates structural information in a variety of ways. The PDBe website has been redesigned based on an analysis of user requirements, and now offers intuitive access to improved and value-added macromolecular structure information. Unique value-added information includes lists of reviews and research articles that cite or mention PDB entries as well as access to figures and legends from full-text open-access publications that describe PDB entries. A powerful new query system not only shows all the PDB entries that match a given query, but also shows the ‘best structures’ for a given macromolecule, ligand complex or sequence family using data-quality information from the wwPDB validation reports. A PDBe RESTful API has been developed to provide unified access to macromolecular structure data available in the PDB and EMDB archives as well as value-added annotations, e.g. regarding structure quality and up-to-date cross-reference information from the SIFTS resource. Taken together, these new developments facilitate unified access to macromolecular structure data in an intuitive way for non-expert users and support expert users in analysing macromolecular structure data. PMID:26476444

  12. DOMMINO 2.0: integrating structurally resolved protein-, RNA-, and DNA-mediated macromolecular interactions.

    PubMed

    Kuang, Xingyan; Dhroso, Andi; Han, Jing Ginger; Shyu, Chi-Ren; Korkin, Dmitry

    2016-01-01

    Macromolecular interactions are formed between proteins, DNA and RNA molecules. Being a principle building block in macromolecular assemblies and pathways, the interactions underlie most of cellular functions. Malfunctioning of macromolecular interactions is also linked to a number of diseases. Structural knowledge of the macromolecular interaction allows one to understand the interaction's mechanism, determine its functional implications and characterize the effects of genetic variations, such as single nucleotide polymorphisms, on the interaction. Unfortunately, until now the interactions mediated by different types of macromolecules, e.g. protein-protein interactions or protein-DNA interactions, are collected into individual and unrelated structural databases. This presents a significant obstacle in the analysis of macromolecular interactions. For instance, the homogeneous structural interaction databases prevent scientists from studying structural interactions of different types but occurring in the same macromolecular complex. Here, we introduce DOMMINO 2.0, a structural Database Of Macro-Molecular INteractiOns. Compared to DOMMINO 1.0, a comprehensive database on protein-protein interactions, DOMMINO 2.0 includes the interactions between all three basic types of macromolecules extracted from PDB files. DOMMINO 2.0 is automatically updated on a weekly basis. It currently includes ∼1 040 000 interactions between two polypeptide subunits (e.g. domains, peptides, termini and interdomain linkers), ∼43 000 RNA-mediated interactions, and ∼12 000 DNA-mediated interactions. All protein structures in the database are annotated using SCOP and SUPERFAMILY family annotation. As a result, protein-mediated interactions involving protein domains, interdomain linkers, C- and N- termini, and peptides are identified. Our database provides an intuitive web interface, allowing one to investigate interactions at three different resolution levels: whole subunit network, binary interaction and interaction interface.Database URL: http://dommino.org. PMID:26827237

  13. DOMMINO 2.0: integrating structurally resolved protein-, RNA-, and DNA-mediated macromolecular interactions

    PubMed Central

    Kuang, Xingyan; Dhroso, Andi; Han, Jing Ginger; Shyu, Chi-Ren; Korkin, Dmitry

    2016-01-01

    Macromolecular interactions are formed between proteins, DNA and RNA molecules. Being a principle building block in macromolecular assemblies and pathways, the interactions underlie most of cellular functions. Malfunctioning of macromolecular interactions is also linked to a number of diseases. Structural knowledge of the macromolecular interaction allows one to understand the interaction’s mechanism, determine its functional implications and characterize the effects of genetic variations, such as single nucleotide polymorphisms, on the interaction. Unfortunately, until now the interactions mediated by different types of macromolecules, e.g. protein–protein interactions or protein–DNA interactions, are collected into individual and unrelated structural databases. This presents a significant obstacle in the analysis of macromolecular interactions. For instance, the homogeneous structural interaction databases prevent scientists from studying structural interactions of different types but occurring in the same macromolecular complex. Here, we introduce DOMMINO 2.0, a structural Database Of Macro-Molecular INteractiOns. Compared to DOMMINO 1.0, a comprehensive database on protein-protein interactions, DOMMINO 2.0 includes the interactions between all three basic types of macromolecules extracted from PDB files. DOMMINO 2.0 is automatically updated on a weekly basis. It currently includes ∼1 040 000 interactions between two polypeptide subunits (e.g. domains, peptides, termini and interdomain linkers), ∼43 000 RNA-mediated interactions, and ∼12 000 DNA-mediated interactions. All protein structures in the database are annotated using SCOP and SUPERFAMILY family annotation. As a result, protein-mediated interactions involving protein domains, interdomain linkers, C- and N- termini, and peptides are identified. Our database provides an intuitive web interface, allowing one to investigate interactions at three different resolution levels: whole subunit network, binary interaction and interaction interface. Database URL: http://dommino.org PMID:26827237

  14. [FTIR spectroscopic study on the stress effect of compositions of macromolecular structure in tectonically deformed coals].

    PubMed

    Ju, Yi-wen; Jiang, Bo; Hou, Quan-lin; Wang, Gui-liang

    2005-08-01

    Fourier transform infrared spectroscopy (FTIR) was applied to the study of the stress effect of compositions of macromolecular structure in tectonically deformed coals. The results showed that in different kinds of tectonically deformed coals, the absorption band of aromatic structure, aliphatic structure and oxygen functional groups nearly consistent in the peak wave number, but the intensity of the peak is different which is justly influenced by different deformation degree and deformation mechanism of tectonically deformed coals under tectonic stress. In the metamorphic and deformed environments of the low, middle and high coal rank, for tectonically deformed coals, with the increasing stress, hydrogen-enriched degree and oxygen-enriched degree decrease, while the degree of ring condensation increases. But there are differences in the change of compositions contents of macromolecular structure. This might indicate that the FTIR could be used in the stress effect of compositions of macromolecular structure in tectonically deformed coals. PMID:16329484

  15. Macromolecular assembly structures by comparative modeling and electron microscopy.

    PubMed

    Lasker, Keren; Velázquez-Muriel, Javier A; Webb, Benjamin M; Yang, Zheng; Ferrin, Thomas E; Sali, Andrej

    2012-01-01

    Advances in electron microscopy allow for structure determination of large biological machines at increasingly higher resolutions. A key step in this process is fitting component structures into the electron microscopy-derived density map of their assembly. Comparative modeling can contribute by providing atomic models of the components, via fold assignment, sequence-structure alignment, model building, and model assessment. All four stages of comparative modeling can also benefit from consideration of the density map. In this chapter, we describe numerous types of modeling problems restrained by a density map and available protocols for finding solutions. In particular, we provide detailed instructions for density map-guided modeling using the Integrative Modeling Platform (IMP), MODELLER, and UCSF Chimera. PMID:22323229

  16. Mechanism of macromolecular structure evolution in self-assembled lipid nanoparticles for siRNA delivery.

    PubMed

    Gindy, Marian E; DiFelice, Katherine; Kumar, Varun; Prud'homme, Robert K; Celano, Robert; Haas, R Matthew; Smith, Jeffrey S; Boardman, David

    2014-04-29

    Lipid nanoparticles (LNPs) are a leading platform for therapeutic delivery of small interfering RNAs (siRNAs). Optimization of LNPs as therapeutic products is enabled by the development of structure-activity relationships (SAR) linking LNP physiochemical and macromolecular properties to bioperformance. Methods by which LNP properties can be rationally manipulated are thus critical enablers of this fundamental knowledge build. In this work, we present a mechanistic study of LNP self-assembly via a rapid antisolvent precipitation process and identify critical physiochemical and kinetic parameters governing the evolution of LNP three-dimensional macromolecular structure as a biorelevant SAR feature. Using small-angle X-ray scattering, LNPs are shown to undergo a temporal evolution in macromolecular structure during self-assembly, rearranging from initially disordered phases after precipitation into well-ordered structures following a necessary annealing stage of the assembly sequence. The ability of LNPs to undergo structural reorganization is shown to be effected by the chemical nature of the aqueous antisolvent used for precipitation. Antisolvents of varying buffering species differentially influence LNP macromolecular features, revealing a new participatory role of buffer ions in LNP self-assembly. Furthermore, the formation of macromolecular structure in LNPs is shown to improve the efficiency of siRNA encapsulation, thereby offering a simple, nonchemical route for preparation of high-payload LNPs that minimize the dose of lipid excipients. The developed LNP precipitation process and mechanistic understanding of self-assembly are shown to be generalizable, enabling the production of LNPs with a tunable range of macromolecular features, as evidenced by the cubic, hexagonal, and oligo-lamellar phase LNPs exemplarily generated. PMID:24684657

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

    NASA Astrophysics Data System (ADS)

    Ando, Tadashi; Chow, Edmond; Skolnick, Jeffrey

    2013-09-01

    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.

  18. 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

  19. 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…

  20. 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

  1. 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

  2. Quantification of Complex Topologies in Macromolecular and Nanoscale Structures using Small-Angle Scattering

    NASA Astrophysics Data System (ADS)

    Pradhan, Siddharth; Ramachandran, Ramanth; Rai, Durgesh; Beaucage, Gregory

    2012-02-01

    Polymers are characterized by molecular weight distribution, tacticity, block copolymer content and branch content and chain topology. The branch structure and particularly the topology of branched chains has remained a difficult characterization problem. Recently we have developed a scaling model that can be coupled with small-angle scattering to measure the average branch length, number of branches and branch-on-branch structure in macromolecules of complex topology. This method has been extended to understand the structure of two dimensional structures and crumpling in these macromolecular systems. We have explored a wide range of materials in this regard. This poster will give an overview of the current uses for the scaling model for macromolecular topology. References pertaining to this poster can be found at http://www.eng.uc.edu/˜gbeaucag/BranchingPapers.html.

  3. 3DEM Loupe: analysis of macromolecular dynamics using structures from electron microscopy

    PubMed Central

    Nogales-Cadenas, R.; Jonic, S.; Tama, F.; Arteni, A. A.; Tabas-Madrid, D.; Vázquez, M.; Pascual-Montano, A.; Sorzano, C. O. S.

    2013-01-01

    Electron microscopy (EM) provides access to structural information of macromolecular complexes in the 3–20 Å resolution range. Normal mode analysis has been extensively used with atomic resolution structures and successfully applied to EM structures. The major application of normal modes is the identification of possible conformational changes in proteins. The analysis can throw light on the mechanism following ligand binding, protein–protein interactions, channel opening and other functional macromolecular movements. In this article, we present a new web server, 3DEM Loupe, which allows normal mode analysis of any uploaded EM volume using a user-friendly interface and an intuitive workflow. Results can be fully explored in 3D through animations and movies generated by the server. The application is freely available at http://3demloupe.cnb.csic.es. PMID:23671335

  4. Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics

    PubMed Central

    Moffatt, Ryan; Ma, Buyong; Nussinov, Ruth

    2016-01-01

    Investigation of macromolecular structure and dynamics is fundamental to understanding how macromolecules carry out their functions in the cell. Significant advances have been made toward this end in silico, with a growing number of computational methods proposed yearly to study and simulate various aspects of macromolecular structure and dynamics. This review aims to provide an overview of recent advances, focusing primarily on methods proposed for exploring the structure space of macromolecules in isolation and in assemblies for the purpose of characterizing equilibrium structure and dynamics. In addition to surveying recent applications that showcase current capabilities of computational methods, this review highlights state-of-the-art algorithmic techniques proposed to overcome challenges posed in silico by the disparate spatial and time scales accessed by dynamic macromolecules. This review is not meant to be exhaustive, as such an endeavor is impossible, but rather aims to balance breadth and depth of strategies for modeling macromolecular structure and dynamics for a broad audience of novices and experts. PMID:27124275

  5. Architecture of macromolecular network of soft functional materials: from structure to function.

    PubMed

    Xiong, Jun-Ying; Liu, Xiang-Yang; Li, Jing-Liang; Vallon, Martin Wilhelm

    2007-05-24

    An enhanced macromolecular nanofiber network and its implications have been developed by employing the understanding of its formation with an emphasis on its topological aspect. Using agarose aqueous solution as a typical example, the macromolecular nanofiber network of soft functional materials has been clearly visualized for the first time using the developed technique of field emission scanning electronic microscopy coupled with flash-freeze-drying. Both the systematic kinetic study and the image evidence indicates that the nanofiber network in soft functional materials such as agarose turns out to form through a self-expitaxial nucleation-controlled process. This new understanding enables us to engineer ultra functions of soft materials via nanofiber network architecture, which in turn opens up a new direction in nano fabrication. PMID:17472367

  6. 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.

  7. 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

  8. The R-factor gap in macromolecular crystallography: an untapped potential for insights on accurate structures

    PubMed Central

    Holton, James M; Classen, Scott; Frankel, Kenneth A; Tainer, John A

    2014-01-01

    In macromolecular crystallography, the agreement between observed and predicted structure factors (Rcryst and Rfree) is seldom better than 20%. This is much larger than the estimate of experimental error (Rmerge). The difference between Rcryst and Rmerge is the R-factor gap. There is no such gap in small-molecule crystallography, for which calculated structure factors are generally considered more accurate than the experimental measurements. Perhaps the true noise level of macromolecular data is higher than expected? Or is the gap caused by inaccurate phases that trap refined models in local minima? By generating simulated diffraction patterns using the program MLFSOM, and including every conceivable source of experimental error, we show that neither is the case. Processing our simulated data yielded values that were indistinguishable from those of real data for all crystallographic statistics except the final Rcryst and Rfree. These values decreased to 3.8% and 5.5% for simulated data, suggesting that the reason for high R-factors in macromolecular crystallography is neither experimental error nor phase bias, but rather an underlying inadequacy in the models used to explain our observations. The present inability to accurately represent the entire macromolecule with both its flexibility and its protein-solvent interface may be improved by synergies between small-angle X-ray scattering, computational chemistry and crystallography. The exciting implication of our finding is that macromolecular data contain substantial hidden and untapped potential to resolve ambiguities in the true nature of the nanoscale, a task that the second century of crystallography promises to fulfill. Database Coordinates and structure factors for the real data have been submitted to the Protein Data Bank under accession 4tws. PMID:25040949

  9. The PDB_REDO server for macromolecular structure model optimization

    PubMed Central

    Joosten, Robbie P.; Long, Fei; Murshudov, Garib N.; Perrakis, Anastassis

    2014-01-01

    The refinement and validation of a crystallographic structure model is the last step before the coordinates and the associated data are submitted to the Protein Data Bank (PDB). The success of the refinement procedure is typically assessed by validating the models against geometrical criteria and the diffraction data, and is an important step in ensuring the quality of the PDB public archive [Read et al. (2011 ▶), Structure, 19, 1395–1412]. The PDB_REDO procedure aims for ‘constructive validation’, aspiring to consistent and optimal refinement parameterization and pro-active model rebuilding, not only correcting errors but striving for optimal interpretation of the electron density. A web server for PDB_REDO has been implemented, allowing thorough, consistent and fully automated optimization of the refinement procedure in REFMAC and partial model rebuilding. The goal of the web server is to help practicing crystallo­graphers to improve their model prior to submission to the PDB. For this, additional steps were implemented in the PDB_REDO pipeline, both in the refinement procedure, e.g. testing of resolution limits and k-fold cross-validation for small test sets, and as new validation criteria, e.g. the density-fit metrics implemented in EDSTATS and ligand validation as implemented in YASARA. Innovative ways to present the refinement and validation results to the user are also described, which together with auto-generated Coot scripts can guide users to subsequent model inspection and improvement. It is demonstrated that using the server can lead to substantial improvement of structure models before they are submitted to the PDB. PMID:25075342

  10. New methods for sedimentation and diffusion analysis of macromolecular structure

    SciTech Connect

    Demeler, B.

    1992-01-01

    Methods are presented to acquire data from analytical ultracentrifugation experiments by computer using the absorption optical scanning system of the Beckman Model-E ultracentrifuge. A computer program was written which analyzes sedimentation velocity experiments by the van Holde-Weischet method and the second moment method. The van Holde-Weischet method allows a high resolution analysis of sedimentation velocity data by eliminating the effects of diffusion on the shape of the moving boundary to provide sedimentation coefficients for a heterogeneous composition of a sample. The second moment method obtains the sedimentation coefficient by calculating the second moment point, by which the sedimentation coefficient is defined. A program was written for the acquisition of data to measure diffusion coefficients from quasi elastic light scattering experiments with a Langely Ford correlator. The analysis of autocorrelation spectra from light scattering experiments is performed by the Levenberg-Marquardt method, which allows fitting of data to nonlinear models. The development of the PPOL-1 208-n series of plasmids and of the miniplasmid pMX is described. These plasmids were designed to allow studies of in vitro transcription and chromatin structure after reconstitution with histones. Sedimentation data are presented which suggests a new method for rapid estimation of the sedimentation coefficient at zero concentration for molecules which show a concentration dependency of the sedimentation coefficient. This is accomplished by linearly extrapolating van Holde-Weischet distributions to zero concentration. Diffusion data for this plasmid DNA is used to demonstrate the feasibility of the multicomponent analysis. Sedimentation measurements were carried out on reconstituted chromatin. The programs were used to demonstrate significant changes in chromatin structure upon ethidium bromide binding.

  11. Denatured State Structural Property Determines Protein Stabilization by Macromolecular Crowding: A Thermodynamic and Structural Approach

    PubMed Central

    Mittal, Shruti; Singh, Laishram Rajendrakumar

    2013-01-01

    Understanding of protein structure and stability gained to date has been acquired through investigations made under dilute conditions where total macromolecular concentration never surpasses 10 g l−1. However, biological macromolecules are known to evolve and function under crowded intracellular environments that comprises of proteins, nucleic acids, ribosomes and carbohydrates etc. Crowded environment is known to result in altered biological properties including thermodynamic, structural and functional aspect of macromolecules as compared to the macromolecules present in our commonly used experimental dilute buffers (for example, Tris HCl or phosphate buffer). In this study, we have investigated the thermodynamic and structural consequences of synthetic crowding agent (Ficoll 70) on three different proteins (Ribonuclease-A, lysozyme and holo α-lactalbumin) at different pH values. We report here that the effect of crowding is protein dependent in terms of protein thermal stability and structure. We also observed that the structural characteristics of the denatured state determines if crowding will have an effect or not on the protein stability. PMID:24265729

  12. Evolution of the macromolecular structure of sporopollenin during thermal degradation

    SciTech Connect

    Bernard, S.; Benzerara, K.; Beyssac, O.; Balan, E.; G. E. Brown, Jr.

    2015-10-01

    Reconstructing the original biogeochemistry of organic microfossils requires quantifying the extent of the chemical transformations they experienced during burial and maturation processes. In the present study, fossilization experiments have been performed using modern sporopollenin chosen as an analogue for the resistant biocompounds possibly constituting the wall of many organic microfossils. Sporopollenin powder has been processed thermally under argon atmosphere at different temperatures (up to 1000 °C) for varying durations (up to 900 min). Solid residues of each experiment have been characterized using infrared, Raman and synchrotron-based XANES spectroscopies. Results indicate that significant defunctionalisation and aromatization affect the molecular structure of sporopollenin with increasing temperature. Two distinct stages of evolution with temperature are observed: in a first stage, sporopollenin experiences dehydrogenation and deoxygenation simultaneously (below 500 °C); in a second stage (above 500 °C) an increasing concentration in aromatic groups and a lateral growth of aromatic layers are observed. With increasing heating duration (up to 900 min) at a constant temperature (360 °C), oxygen is progressively lost and conjugated carbon–carbon chains or domains grow progressively, following a log-linear kinetic behavior. Based on the comparison with natural spores fossilized within metasediments which experienced intense metamorphism, we show that the present experimental simulations may not perfectly mimic natural diagenesis and metamorphism. Moreover, performing such laboratory experiments provides key insights on the processes transforming biogenic molecules into molecular fossils.

  13. Evolution of the macromolecular structure of sporopollenin during thermal degradation

    DOE PAGESBeta

    Bernard, S.; Benzerara, K.; Beyssac, O.; Balan, E.; G. E. Brown, Jr.

    2015-10-01

    Reconstructing the original biogeochemistry of organic microfossils requires quantifying the extent of the chemical transformations they experienced during burial and maturation processes. In the present study, fossilization experiments have been performed using modern sporopollenin chosen as an analogue for the resistant biocompounds possibly constituting the wall of many organic microfossils. Sporopollenin powder has been processed thermally under argon atmosphere at different temperatures (up to 1000 °C) for varying durations (up to 900 min). Solid residues of each experiment have been characterized using infrared, Raman and synchrotron-based XANES spectroscopies. Results indicate that significant defunctionalisation and aromatization affect the molecular structure ofmore » sporopollenin with increasing temperature. Two distinct stages of evolution with temperature are observed: in a first stage, sporopollenin experiences dehydrogenation and deoxygenation simultaneously (below 500 °C); in a second stage (above 500 °C) an increasing concentration in aromatic groups and a lateral growth of aromatic layers are observed. With increasing heating duration (up to 900 min) at a constant temperature (360 °C), oxygen is progressively lost and conjugated carbon–carbon chains or domains grow progressively, following a log-linear kinetic behavior. Based on the comparison with natural spores fossilized within metasediments which experienced intense metamorphism, we show that the present experimental simulations may not perfectly mimic natural diagenesis and metamorphism. Moreover, performing such laboratory experiments provides key insights on the processes transforming biogenic molecules into molecular fossils.« less

  14. Evolution of the macromolecular structure of sporopollenin during thermal degradation

    PubMed Central

    Bernard, S.; Benzerara, K.; Beyssac, O.; Balan, E.; Brown Jr., G.E.

    2015-01-01

    Reconstructing the original biogeochemistry of organic microfossils requires quantifying the extent of the chemical transformations they experienced during burial and maturation processes. In the present study, fossilization experiments have been performed using modern sporopollenin chosen as an analogue for the resistant biocompounds possibly constituting the wall of many organic microfossils. Sporopollenin powder has been processed thermally under argon atmosphere at different temperatures (up to 1000 °C) for varying durations (up to 900 min). Solid residues of each experiment have been characterized using infrared, Raman and synchrotron-based XANES spectroscopies. Results indicate that significant defunctionalisation and aromatization affect the molecular structure of sporopollenin with increasing temperature. Two distinct stages of evolution with temperature are observed: in a first stage, sporopollenin experiences dehydrogenation and deoxygenation simultaneously (below 500 °C); in a second stage (above 500 °C) an increasing concentration in aromatic groups and a lateral growth of aromatic layers are observed. With increasing heating duration (up to 900 min) at a constant temperature (360 °C), oxygen is progressively lost and conjugated carbon–carbon chains or domains grow progressively, following a log-linear kinetic behavior. Based on the comparison with natural spores fossilized within metasediments which experienced intense metamorphism, we show that the present experimental simulations may not perfectly mimic natural diagenesis and metamorphism. Yet, performing such laboratory experiments provides key insights on the processes transforming biogenic molecules into molecular fossils. PMID:27123494

  15. 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

  16. Cryo-EM and the elucidation of new macromolecular structures: Random Conical Tilt revisited

    PubMed Central

    Sorzano, C. O. S.; Alcorlo, M.; de la Rosa-Trevn, J. M.; Melero, R.; Foche, I.; Zaldvar-Peraza, A.; del Cano, L.; Vargas, J.; Abrishami, V.; Otn, J.; Marabini, R.; Carazo, J. M.

    2015-01-01

    Cryo-Electron Microscopy (cryo-EM) of macromolecular complexes is a fundamental structural biology technique which is expanding at a very fast pace. Key to its success in elucidating the three-dimensional structure of a macromolecular complex, especially of small and non-symmetric ones, is the ability to start from a low resolution map, which is subsequently refined with the actual images collected at the microscope. There are several methods to produce this first structure. Among them, Random Conical Tilt (RCT) plays a prominent role due to its unbiased nature (it can create an initial model based on experimental measurements). In this article, we revise the fundamental mathematical expressions supporting RCT, providing new expressions handling all key geometrical parameters without the need of intermediate operations, leading to improved automation and overall reliability, essential for the success of cryo-EM when analyzing new complexes. We show that the here proposed RCT workflow based on the new formulation performs very well in practical cases, requiring very few image pairs (as low as 13 image pairs in one of our examples) to obtain relevant 3D maps. PMID:26390853

  17. Determining macromolecular assembly structures by molecular docking and fitting into an electron density map

    PubMed Central

    Lasker, Keren; Sali, Andrej; Wolfson, Haim J.

    2010-01-01

    Structural models of macromolecular assemblies are instrumental for gaining a mechanistic understanding of cellular processes. Determining these structures is a major challenge for experimental techniques, such as X-ray crystallography, NMR spectroscopy and electron microscopy. Thus, computational modeling techniques, including molecular docking, are required. The development of most molecular docking methods has so far been focused on modeling of binary complexes. We have recently introduced the MultiFit method for modeling the structure of a multi-subunit complex by simultaneously optimizing the fit of the model into an electron microscopy density map of the entire complex and the shape complementarity between interacting subunits. Here, we report algorithmic advances of the MultiFit method that result in an efficient and accurate assembly of the input subunits into their density map. The successful predictions and the increasing number of complexes being characterized by electron microscopy suggests that the CAPRI challenge could be extended to include docking-based modeling of macromolecular assemblies guided by electron microscopy. PMID:20827723

  18. Automated structure solution with the PHENIX suite

    SciTech Connect

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

    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 determination that can rapidly arrive at an initial partial model of a structure without significant human intervention, given moderate resolution, and good quality data. This achievement has been made possible by the development of new algorithms for structure determination, maximum-likelihood molecular replacement (PHASER), heavy-atom search (HySS), template- and pattern-based automated model-building (RESOLVE, TEXTAL), automated macromolecular refinement (phenix. refine), and iterative model-building, density modification and refinement that can operate at moderate resolution (RESOLVE, AutoBuild). These algorithms are based on a highly integrated and comprehensive set of crystallographic libraries that have been built and made available to the community. The algorithms are tightly linked and made easily accessible to users through the PHENIX Wizards and the PHENIX GUI.

  19. Automated Structure Solution with the PHENIX Suite

    SciTech Connect

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

    2008-06-09

    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 determination that can rapidly arrive at an initial partial model of a structure without significant human intervention, given moderate resolution and good quality data. This achievement has been made possible by the development of new algorithms for structure determination, maximum-likelihood molecular replacement (PHASER), heavy-atom search (HySS), template and pattern-based automated model-building (RESOLVE, TEXTAL), automated macromolecular refinement (phenix.refine), and iterative model-building, density modification and refinement that can operate at moderate resolution (RESOLVE, AutoBuild). These algorithms are based on a highly integrated and comprehensive set of crystallographic libraries that have been built and made available to the community. The algorithms are tightly linked and made easily accessible to users through the PHENIX Wizards and the PHENIX GUI.

  20. A 3D Image Filter for Parameter-Free Segmentation of Macromolecular Structures from Electron Tomograms

    PubMed Central

    Ali, Rubbiya A.; Landsberg, Michael J.; Knauth, Emily; Morgan, Garry P.; Marsh, Brad J.; Hankamer, Ben

    2012-01-01

    3D image reconstruction of large cellular volumes by electron tomography (ET) at high (≤5 nm) resolution can now routinely resolve organellar and compartmental membrane structures, protein coats, cytoskeletal filaments, and macromolecules. However, current image analysis methods for identifying in situ macromolecular structures within the crowded 3D ultrastructural landscape of a cell remain labor-intensive, time-consuming, and prone to user-bias and/or error. This paper demonstrates the development and application of a parameter-free, 3D implementation of the bilateral edge-detection (BLE) algorithm for the rapid and accurate segmentation of cellular tomograms. The performance of the 3D BLE filter has been tested on a range of synthetic and real biological data sets and validated against current leading filters—the pseudo 3D recursive and Canny filters. The performance of the 3D BLE filter was found to be comparable to or better than that of both the 3D recursive and Canny filters while offering the significant advantage that it requires no parameter input or optimisation. Edge widths as little as 2 pixels are reproducibly detected with signal intensity and grey scale values as low as 0.72% above the mean of the background noise. The 3D BLE thus provides an efficient method for the automated segmentation of complex cellular structures across multiple scales for further downstream processing, such as cellular annotation and sub-tomogram averaging, and provides a valuable tool for the accurate and high-throughput identification and annotation of 3D structural complexity at the subcellular level, as well as for mapping the spatial and temporal rearrangement of macromolecular assemblies in situ within cellular tomograms. PMID:22479430

  1. Macromolecular conformation in solution. Study of carbonic anhydrase by the positron annihilation technique.

    PubMed Central

    Handel, E D; Graf, G; Glass, J C

    1980-01-01

    The structural features of carbonic anhydrase (carbonate hydro-lyase; EC 4.2.1.1) in aqueous solution were probed by the positron annihilation technique. The data obtained under varying conditions of temperature, pH, and enzyme concentration were interpreted in terms of the free volume model. The change of enzymic activity with temperature is accompanied by a change in free volume of the protein. Upon thermal denaturation an irreversible change in free volume of the molecule occurred. At low temperatures the protein-water interactions were investigated. These results are discussed in terms of current concepts of structure-function relationships in proteins. This study shows the sensitivity of the positron annihilation method toward the structure of proteins related to their overall conformation and to the nature of bound water. PMID:6789901

  2. 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

  3. Analytical ultracentrifugation: A versatile tool for the characterisation of macromolecular complexes in solution.

    PubMed

    Patel, Trushar R; Winzor, Donald J; Scott, David J

    2016-02-15

    Analytical ultracentrifugation, an early technique developed for characterizing quantitatively the solution properties of macromolecules, remains a powerful aid to structural biologists in their quest to understand the formation of biologically important protein complexes at the molecular level. Treatment of the basic tenets of the sedimentation velocity and sedimentation equilibrium variants of analytical ultracentrifugation is followed by considerations of the roles that it, in conjunction with other physicochemical procedures, has played in resolving problems encountered in the delineation of complex formation for three biological systems - the cytoplasmic dynein complex, mitogen-activated protein kinase (ERK2) self-interaction, and the terminal catalytic complex in selenocysteine synthesis. PMID:26555086

  4. Using support vector machines to improve elemental ion identification in macromolecular crystal structures

    SciTech Connect

    Morshed, Nader; Echols, Nathaniel; Adams, Paul D.

    2015-05-01

    A method to automatically identify possible elemental ions in X-ray crystal structures has been extended to use support vector machine (SVM) classifiers trained on selected structures in the PDB, with significantly improved sensitivity over manually encoded heuristics. In the process of macromolecular model building, crystallographers must examine electron density for isolated atoms and differentiate sites containing structured solvent molecules from those containing elemental ions. This task requires specific knowledge of metal-binding chemistry and scattering properties and is prone to error. A method has previously been described to identify ions based on manually chosen criteria for a number of elements. Here, the use of support vector machines (SVMs) to automatically classify isolated atoms as either solvent or one of various ions is described. Two data sets of protein crystal structures, one containing manually curated structures deposited with anomalous diffraction data and another with automatically filtered, high-resolution structures, were constructed. On the manually curated data set, an SVM classifier was able to distinguish calcium from manganese, zinc, iron and nickel, as well as all five of these ions from water molecules, with a high degree of accuracy. Additionally, SVMs trained on the automatically curated set of high-resolution structures were able to successfully classify most common elemental ions in an independent validation test set. This method is readily extensible to other elemental ions and can also be used in conjunction with previous methods based on a priori expectations of the chemical environment and X-ray scattering.

  5. 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.

  6. Divergence in macromolecular assembly: X-ray crystallographic structure analysis of lumazine synthase from Brucella abortus.

    PubMed

    Braden, B C; Velikovsky, C A; Cauerhff, A A; Polikarpov, I; Goldbaum, F A

    2000-04-14

    We have determined the three-dimensional structure of 6, 7-dimethyl-8-ribityllumazine synthase (lumazine synthase) from Brucella abortus, the infectious organism of the disease brucellosis in animals. This enzyme catalyses the formation of 6, 7-dimethyl-8-ribityllumazine, the penultimate product in the synthesis of riboflavin. The three-dimensional X-ray crystal structure of the enzyme from B. abortus has been solved and refined at 2.7 A resolution to a final R-value of 0.18 (R(free)=0.23). The macromolecular assembly of the enzyme differs from that of the enzyme from Bacillus subtilis, the only other lumazine synthase structure known. While the protein from B. subtilis assembles into a 60 subunit icosahedral capsid built from 12 pentameric units, the enzyme from B. abortus is pentameric in its crystalline form. Nonetheless, the active sites of the two enzymes are virtually identical indicating inhibitors to theses enzymes could be effective pharmaceuticals across a broad species range. Furthermore, we compare the structures of the enzyme from B. subtilis and B. abortus and describe the C teminus structure which accounts for the differences in quaternary structure. PMID:10764570

  7. Using support vector machines to improve elemental ion identification in macromolecular crystal structures

    SciTech Connect

    Morshed, Nader; Echols, Nathaniel; Adams, Paul D.

    2015-04-25

    In the process of macromolecular model building, crystallographers must examine electron density for isolated atoms and differentiate sites containing structured solvent molecules from those containing elemental ions. This task requires specific knowledge of metal-binding chemistry and scattering properties and is prone to error. A method has previously been described to identify ions based on manually chosen criteria for a number of elements. Here, the use of support vector machines (SVMs) to automatically classify isolated atoms as either solvent or one of various ions is described. Two data sets of protein crystal structures, one containing manually curated structures deposited with anomalous diffraction data and another with automatically filtered, high-resolution structures, were constructed. On the manually curated data set, an SVM classifier was able to distinguish calcium from manganese, zinc, iron and nickel, as well as all five of these ions from water molecules, with a high degree of accuracy. Additionally, SVMs trained on the automatically curated set of high-resolution structures were able to successfully classify most common elemental ions in an independent validation test set. This method is readily extensible to other elemental ions and can also be used in conjunction with previous methods based on a priori expectations of the chemical environment and X-ray scattering.

  8. Using support vector machines to improve elemental ion identification in macromolecular crystal structures

    DOE PAGESBeta

    Morshed, Nader; Echols, Nathaniel; Adams, Paul D.

    2015-04-25

    In the process of macromolecular model building, crystallographers must examine electron density for isolated atoms and differentiate sites containing structured solvent molecules from those containing elemental ions. This task requires specific knowledge of metal-binding chemistry and scattering properties and is prone to error. A method has previously been described to identify ions based on manually chosen criteria for a number of elements. Here, the use of support vector machines (SVMs) to automatically classify isolated atoms as either solvent or one of various ions is described. Two data sets of protein crystal structures, one containing manually curated structures deposited with anomalousmore » diffraction data and another with automatically filtered, high-resolution structures, were constructed. On the manually curated data set, an SVM classifier was able to distinguish calcium from manganese, zinc, iron and nickel, as well as all five of these ions from water molecules, with a high degree of accuracy. Additionally, SVMs trained on the automatically curated set of high-resolution structures were able to successfully classify most common elemental ions in an independent validation test set. This method is readily extensible to other elemental ions and can also be used in conjunction with previous methods based on a priori expectations of the chemical environment and X-ray scattering.« less

  9. X-ray Footprinting at Beamline X28C: A National Resource for Studying Macromolecular Structure and Dynamics

    SciTech Connect

    D'Mello, R.; Gupta, S; Bohen, J; Abel, D; Toomey, J; Sullivan, M; Chance, M

    2009-01-01

    X-ray footprinting employs intense X-rays produced by synchrotron radiation to generate hydroxyl radicals in solution on microseconds-milliseconds timescales. These hydroxyls radicals undergo stable reaction with solvent accessible sites of macromolecule and produce covalent modifications, which are appropriate to probing macromolecule dynamics under physiological condition. For nucleic acids, one analyzes the pattern of fragments after X-ray exposure by gel electrophoresis; the protected sections that are not cleaved yield a 'footprint'. For proteins, the exposed samples are digested with proteases and analyzed by liquid chromatography- and tandem-mass spectrometry to determine the extent and sites of modification. The data provide detailed structural information to map tertiary contacts of macromolecular interactions, which can subsequently be used as constraints for molecular modeling to generate high-resolution structures. This method is unique in providing 'local' structural information in solution for gaining insight into dynamic processes involving, large RNA-protein and protein-protein assemblies on biologically relevant timescales. The method also can uniquely probe the 'local' structure of large complexes poised at equilibrium for functional states of interest, and has been extended to in vivo studies. Beamline X28C is located at the National Synchrotron Light Source of Brookhaven National Laboratory. An expanding set of user groups utilize this national resource funded by the National Institute of Biomedical Imaging and Bioengineering of the National Institutes of Health. The facility is operated by the Center for Synchrotron Biosciences and the Center for Proteomics and Bioinformatics of Case Western Reserve University. The facility supports both onsite and offsite user access. Beam time is allocated online through peer reviewed user proposal system. Examples of recent research projects are provided.

  10. 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

  11. IMAGINE: first neutron protein structure and new capabilities for neutron macromolecular crystallography

    SciTech Connect

    Munshi, Parthapratim; Myles, Dean A A; Robertson, Lee; Stoica, Alexandru Dan; Crow, Lowell; Kovalevskyi, Andrii Y; Koritsanszky, Tibor S; Chakoumakos, Bryan C; Blessing, Robert; Meilleur, Flora

    2013-01-01

    We report the first high resolution neutron protein structure of perdeuterated rubredoxin from Pyrococcus furiosus (PfRd) determined using the new IMAGINE macromolecular neutron crystallography instrument at the Oak Ridge National Laboratory. Neutron diffraction data extending to 1.65 resolution were collected from a relatively small 0.7 mm3 PfRd crystal using 2.5 days (60 h) of beam time. The refined structure contains 371 out of 391, or 95%, of the deuterium atoms of the protein, and 58 solvent molecules. The IMAGINE instrument is designed to provide neutron data at or near atomic resolutions (1.5 ) from crystals with volume < 1.0 mm3 and with unit cell edges < 100 . Beam line features include elliptical focusing mirrors that deliver 3x107 n s-1 cm-2 into a 3.5 x 2.0 mm2 focal spot at the sample position, and variable short and long wavelength cutoff optics that provide automated exchange between multiple wavelength configurations ( min=2.0 , 2.8 , 3.3 - max =3.0 , 4.0 , 4.5 , ~20 ). Notably, the crystal used to collect this PfRd data is 5-10 times smaller than has been previously reported.

  12. MACROMOLECULAR THERAPEUTICS

    PubMed Central

    Yang, Jiyuan; Kopeček, Jindřich

    2014-01-01

    This review covers water-soluble polymer-drug conjugates and macromolecules that possess biological activity without attached low molecular weight drugs. The main design principles of traditional and backbone degradable polymer-drug conjugates as well as the development of a new paradigm in nanomedicines – (low molecular weight) drug-free macromolecular therapeutics are discussed. To address the biological features of cancer, macromolecular therapeutics directed to stem/progenitor cells and the tumor microenvironment are deliberated. Finally, the future perspectives of the field are briefly debated. PMID:24747162

  13. In situ macromolecular crystallography using microbeams

    PubMed Central

    Axford, Danny; Owen, Robin L.; Aishima, Jun; Foadi, James; Morgan, Ann W.; Robinson, James I.; Nettleship, Joanne E.; Owens, Raymond J.; Moraes, Isabel; Fry, Elizabeth E.; Grimes, Jonathan M.; Harlos, Karl; Kotecha, Abhay; Ren, Jingshan; Sutton, Geoff; Walter, Thomas S.; Stuart, David I.; Evans, Gwyndaf

    2012-01-01

    Despite significant progress in high-throughput methods in macromolecular crystallography, the production of diffraction-quality crystals remains a major bottleneck. By recording diffraction in situ from crystals in their crystallization plates at room temperature, a number of problems associated with crystal handling and cryoprotection can be side-stepped. Using a dedicated goniometer installed on the microfocus macromolecular crystallography beamline I24 at Diamond Light Source, crystals have been studied in situ with an intense and flexible microfocus beam, allowing weakly diffracting samples to be assessed without a manual crystal-handling step but with good signal to noise, despite the background scatter from the plate. A number of case studies are reported: the structure solution of bovine enterovirus 2, crystallization screening of membrane proteins and complexes, and structure solution from crystallization hits produced via a high-throughput pipeline. These demonstrate the potential for in situ data collection and structure solution with microbeams. PMID:22525757

  14. Novel 3D bio-macromolecular bilinear descriptors for protein science: Predicting protein structural classes.

    PubMed

    Marrero-Ponce, Yovani; Contreras-Torres, Ernesto; García-Jacas, César R; Barigye, Stephen J; Cubillán, Néstor; Alvarado, Ysaías J

    2015-06-01

    In the present study, we introduce novel 3D protein descriptors based on the bilinear algebraic form in the ℝ(n) space on the coulombic matrix. For the calculation of these descriptors, macromolecular vectors belonging to ℝ(n) space, whose components represent certain amino acid side-chain properties, were used as weighting schemes. Generalization approaches for the calculation of inter-amino acidic residue spatial distances based on Minkowski metrics are proposed. The simple- and double-stochastic schemes were defined as approaches to normalize the coulombic matrix. The local-fragment indices for both amino acid-types and amino acid-groups are presented in order to permit characterizing fragments of interest in proteins. On the other hand, with the objective of taking into account specific interactions among amino acids in global or local indices, geometric and topological cut-offs are defined. To assess the utility of global and local indices a classification model for the prediction of the major four protein structural classes, was built with the Linear Discriminant Analysis (LDA) technique. The developed LDA-model correctly classifies the 92.6% and 92.7% of the proteins on the training and test sets, respectively. The obtained model showed high values of the generalized square correlation coefficient (GC(2)) on both the training and test series. The statistical parameters derived from the internal and external validation procedures demonstrate the robustness, stability and the high predictive power of the proposed model. The performance of the LDA-model demonstrates the capability of the proposed indices not only to codify relevant biochemical information related to the structural classes of proteins, but also to yield suitable interpretability. It is anticipated that the current method will benefit the prediction of other protein attributes or functions. PMID:25843214

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

    SciTech Connect

    Pražnikar, Jure; Turk, Dušan

    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.

  16. Complexation of Statins with β-Cyclodextrin in Solutions of Small Molecular Additives and Macromolecular Colloids

    NASA Astrophysics Data System (ADS)

    Süle, András; Csempesz, Ferenc

    The solubility of lovastatin and simvastatin (inevitable drugs in the management of cardiovascular diseases) was studied by phase-solubility measurements in multicomponent colloidal and non-colloidal media. Complexation in aqueous solutions of the highly lipophilic statins with β-cyclodextrin (β-CD) in the absence and the presence of dissolved polyvinyl pyrrolidone, its monomeric compound, tartaric acid and urea, respectively, were investigated. For the characterization of the CD-statin inclusion complexes, stability constants for the associates have been calculated.

  17. Predictive Mechanical Characterization of Macro-Molecular Material Chemistry Structures of Cement Paste at Nano Scale - Two-phase Macro-Molecular Structures of Calcium Silicate Hydrate, Tri-Calcium Silicate, Di-Calcium Silicate and Calcium Hydroxide

    NASA Astrophysics Data System (ADS)

    Padilla Espinosa, Ingrid Marcela

    Concrete is a hierarchical composite material with a random structure over a wide range of length scales. At submicron length scale the main component of concrete is cement paste, formed by the reaction of Portland cement clinkers and water. Cement paste acts as a binding matrix for the other components and is responsible for the strength of concrete. Cement paste microstructure contains voids, hydrated and unhydrated cement phases. The main crystalline phases of unhydrated cement are tri-calcium silicate (C3S) and di-calcium silicate (C2S), and of hydrated cement are calcium silicate hydrate (CSH) and calcium hydroxide (CH). Although efforts have been made to comprehend the chemical and physical nature of cement paste, studies at molecular level have primarily been focused on individual components. Present research focuses on the development of a method to model, at molecular level, and analysis of the two-phase combination of hydrated and unhydrated phases of cement paste as macromolecular systems. Computational molecular modeling could help in understanding the influence of the phase interactions on the material properties, and mechanical performance of cement paste. Present work also strives to create a framework for molecular level models suitable for potential better comparisons with low length scale experimental methods, in which the sizes of the samples involve the mixture of different hydrated and unhydrated crystalline phases of cement paste. Two approaches based on two-phase cement paste macromolecular structures, one involving admixed molecular phases, and the second involving cluster of two molecular phases are investigated. The mechanical properties of two-phase macromolecular systems of cement paste consisting of key hydrated phase CSH and unhydrated phases C3S or C2S, as well as CSH with the second hydrated phase CH were calculated. It was found that these cement paste two-phase macromolecular systems predicted an isotropic material behavior. Also, these systems exhibited a high bulk modulus, compared to the elastic modulus. These results are an indication and concur with the high compression strength of cement paste seen at engineering length scale. In addition, the bulk modulus of two-phase systems consisting of hydrated CSH and unhydrated C3S or C2S was found to increase with higher levels of unhydrated components. The interaction energies of two-phase cement paste molecular structures studied in the present work were calculated, showing that a higher interaction is attained when the two phases are admixed as small components instead of cluster of phases. Finally, the mechanical behavior under shear deformation was predicted by using a quasi-static deformation method and analyzed for a representative two-phase (CSH and C2S) macromolecular structure of cement paste.

  18. NMR (Nuclear Magnetic Resonance) and macromolecular migration in a melt or in concentrated solutions

    NASA Technical Reports Server (NTRS)

    Addad, J. P. C.

    1983-01-01

    The purpose of this paper is to analyze the migration process of long polymer molecules in a melt or in concentrated solutions as it may be observed from the dynamics of the transverse magnetization of nuclear spins linked to these chains. The low frequency viscoelastic relaxation of polymer systems is known to be mainly controlled by the mechanism of dissociation of topological constraints excited on chains and which are called entanglements. This mechanism exhibits a strong dependence upon the chain molecular weight. These topological constraints also govern the diffusion process of polymer chains. So, the accurate description of the diffusion motion of a chain may be a convenient way to characterize disentanglement processes necessarily involved in any model proposed to explain viscoelastic effects.

  19. Hydropyrolysis of insoluble carbonaceous matter in the Murchison meteorite: new insights into its macromolecular structure

    NASA Astrophysics Data System (ADS)

    Sephton, M. A.; Love, G. D.; Watson, J. S.; Verchovsky, A. B.; Wright, I. P.; Snape, C. E.; Gilmour, I.

    2004-03-01

    The major organic component of carbonaceous chondrites is a solvent-insoluble, high molecular weight macromolecular material that constitutes at least 70% of the total organic content in these meteorites. Analytical pyrolysis is often used to thermally decompose macromolecular organic matter in an inert atmosphere into lower molecular weight fragments that are more amenable to conventional organic analytical techniques. Hydropyrolysis refers to pyrolysis assisted by high hydrogen gas pressures and a dispersed catalytically-active molybdenum sulfide phase. Hydropyrolysis of meteorites has not been attempted previously although it is ideally suited to such studies due to its relatively high yields. Hydropyrolysis of the Murchison macromolecular material successfully releases significant amounts of high molecular weight PAH including phenanthrene, carbazole, fluoranthene, pyrene, chrysene, perylene, benzoperylene and coronene units with varying degrees of alklyation. Analysis of both the products and residue from hydropyrolysis reveals that the meteoritic organic network contains both labile (pyrolysable) and refractory (nonpyrolysable) fractions. Comparisons of hydropyrolysis yields of Murchison macromolecular materials with those from terrestrial coals indicate that the refractory component probably consists of a network dominated by at least five- or six-ring PAH units cross-linked together.

  20. Sample preparation of biological macromolecular assemblies for the determination of high-resolution structures by cryo-electron microscopy.

    PubMed

    Stark, Holger; Chari, Ashwin

    2016-02-01

    Single particle cryo-EM has recently developed into a powerful tool to determine the 3D structure of macromolecular complexes at near-atomic resolution, which allows structural biologists to build atomic models of proteins. All technical aspects of cryo-EM technology have been considerably improved over the last two decades, including electron microscopic hardware, image processing software and the ever growing speed of computers. This leads to a more widespread use of the technique, and it can be anticipated that further automation of electron microscopes and image processing tools will soon fully shift the focus away from the technological aspects, onto biological questions that can be answered. In single particle cryo-EM, no crystals of a macromolecule are required. In contrast to X-ray crystallography, this significantly facilitates structure determination by cryo-EM. Nevertheless, a relatively high level of biochemical control is still essential to obtain high-resolution structures by cryo-EM, and it can be anticipated that the success of the cryo-EM technology goes hand in hand with further developments of sample purification and preparation techniques. This will allow routine high-resolution structure determination of the many macromolecular complexes of the cell that until now represent evasive targets for X-ray crystallographers. Here we discuss the various biochemical tools that are currently available and the existing sample purification and preparation techniques for cryo-EM grid preparation that are needed to obtain high-resolution images for structure determination. PMID:26671943

  1. Macromolecular Crystallization in Microgravity

    NASA Technical Reports Server (NTRS)

    Snell, Edward H.; Helliwell, John R.

    2004-01-01

    The key concepts that attracted crystal growers, macromolecular or solid state, to microgravity research is that density difference fluid flows and sedimentation of the growing crystals are greatly reduced. Thus, defects and flaws in the crystals can be reduced, even eliminated, and crystal volume can be increased. Macromolecular crystallography differs from the field of crystalline semiconductors. For the latter, crystals are harnessed for their electrical behaviors. A crystal of a biological macromolecule is used instead for diffraction experiments (X-ray or neutron) to determine the three-dimensional structure of the macromolecule. The better the internal order of the crystal of a biological macromolecule then the more molecular structure detail that can be extracted. This structural information that enables an understanding of how the molecule functions. This knowledge is changing the biological and chemical sciences with major potential in understanding disease pathologies. Macromolecular structural crystallography in general is a remarkable field where physics, biology, chemistry, and mathematics meet to enable insight to the basic fundamentals of life. In this review, we examine the use of microgravity as an environment to grow macromolecular crystals. We describe the crystallization procedures used on the ground, how the resulting crystals are studied and the knowledge obtained from those crystals. We address the features desired in an ordered crystal and the techniques used to evaluate those features in detail. We then introduce the microgravity environment, the techniques to access that environment, and the theory and evidence behind the use of microgravity for crystallization experiments. We describe how ground-based laboratory techniques have been adapted to microgravity flights and look at some of the methods used to analyze the resulting data. Several case studies illustrate the physical crystal quality improvements and the macromolecular structural advances. Finally, limitations and alternatives to microgravity and future directions for this research are covered.

  2. 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

  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. Effects of macromolecular crowding on nuclear size.

    PubMed

    Rosania, G R; Swanson, J A

    1995-05-01

    The concentration of macromolecules inside cells is high, and the resultant crowding of cytoplasm can be expected to affect many interactions involving macromolecular assemblies. Here, we have examined the effect of solute size and concentration on nuclear volume in saponin-permeabilized macrophages. Nuclei swelled in the presence of small solutes and shrank reversibly in the presence of larger permeant solutes. Remarkably, the smallest solutes capable of shrinking the nucleus were not excluded by the pores in the nuclear envelope. Indeed, nuclei shrank in the presence of such solutes even after the nuclear envelope had been sheared mechanically or permeabilized with detergent. Nuclei extracted with 1% Triton X-100 shrank in the presence of very high concentrations of small solute molecules (30% w/v) as well as in lower concentrations of larger solutes. Consistent with a macromolecular crowding effect, changes in nuclear volume were dependent on solute size and not simply dependent on the colligative properties of solutes or the exclusion of solutes by the nuclear envelope. Solute size-dependent changes in nuclear volume were independent of the chemical nature of the solutes and of the activity of the ions in the buffer. Together, these observations indicate that high concentrations of macromolecules such as those found inside cells can influence the size of the nucleus by directly affecting nuclear structure. PMID:7537686

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

    NASA Astrophysics Data System (ADS)

    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

    2014-05-01

    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.

  6. Radiation damage and derivatization in macromolecular crystallography: a structure factor’s perspective

    PubMed Central

    Owen, Robin L.; Sherrell, Darren A.

    2016-01-01

    During, or even after, data collection the presence and effects of radiation damage in macromolecular crystallography may not always be immediately obvious. Despite this, radiation damage is almost always present, with site-specific damage occurring on very short time (dose) scales well before global damage becomes apparent. A result of both site-specific radiation damage and derivatization is a change in the relative intensity of reflections. The size and approximate rate of onset of X-ray-induced transformations is compared with the changes expected from derivatization, and strategies for minimizing radiation damage are discussed. PMID:26960125

  7. Radiation damage and derivatization in macromolecular crystallography: a structure factor's perspective.

    PubMed

    Owen, Robin L; Sherrell, Darren A

    2016-03-01

    During, or even after, data collection the presence and effects of radiation damage in macromolecular crystallography may not always be immediately obvious. Despite this, radiation damage is almost always present, with site-specific damage occurring on very short time (dose) scales well before global damage becomes apparent. A result of both site-specific radiation damage and derivatization is a change in the relative intensity of reflections. The size and approximate rate of onset of X-ray-induced transformations is compared with the changes expected from derivatization, and strategies for minimizing radiation damage are discussed. PMID:26960125

  8. Collagen macromolecular drug delivery systems

    SciTech Connect

    Gilbert, D.L.

    1988-01-01

    The objective of this study was to examine collagen for use as a macromolecular drug delivery system by determining the mechanism of release through a matrix. Collagen membranes varying in porosity, crosslinking density, structure and crosslinker were fabricated. Collagen characterized by infrared spectroscopy and solution viscosity was determined to be pure and native. The collagen membranes were determined to possess native vs. non-native quaternary structure and porous vs. dense aggregate membranes by electron microscopy. Collagen monolithic devices containing a model macromolecule (inulin) were fabricated. In vitro release rates were found to be linear with respect to t{sup {1/2}} and were affected by crosslinking density, crosslinker and structure. The biodegradation of the collagen matrix was also examined. In vivo biocompatibility, degradation and {sup 14}C-inulin release rates were evaluated subcutaneously in rats.

  9. The First Crystal Structure of a Macromolecular Assembly under High Pressure: CpMV at 330 MPa

    PubMed Central

    Girard, Eric; Kahn, Richard; Mezouar, Mohamed; Dhaussy, Anne-Claire; Lin, Tianwei; Johnson, John E.; Fourme, Roger

    2005-01-01

    The structure of cubic Cowpea mosaic virus crystals, compressed at 330 MPa in a diamond anvil cell, was refined at 2.8 Å from data collected using ultrashort-wavelength (0.331 Å) synchrotron radiation. With respect to the structure at atmospheric pressure, order is increased with lower Debye Waller factors and a larger number of ordered water molecules. Hydrogen-bond lengths are on average shorter and the cavity volume is strongly reduced. A tentative mechanistic explanation is given for the coexistence of disordered and ordered cubic crystals in crystallization drops and for the disorder-order transition observed in disordered crystals submitted to high pressure. Based on such explanation, it can be concluded that pressure would in general improve, albeit to a variable extent, the order in macromolecular crystals. PMID:15731378

  10. Macromolecular structure of the organic framework of nacre in Haliotis rufescens: implications for growth and mechanical behavior.

    PubMed

    Bezares, Jiddu; Asaro, Robert J; Hawley, Marilyn

    2008-07-01

    We have performed a macromolecular structural analysis of the interlamellar and intertabular parts of the organic framework of the nacreous part of the shell of Haliotis rufescens, including the identification of structural chitin. Using histochemical optical microscopy we have mapped the locations of carboxylates and sulfates of proteins and chitin on the surfaces and within the core of the interlamellar layers and the intertabular matrix that together form the external organic matrix of composite nacre. This extends the earlier work of Nudelmann et al. [Nudelman, F., Gotliv, B.A., Addadi, L. and Weiner, S. 2006. Mollusk shell formation: mapping the distribution of organic matrix components underlying a single aragonite tablet in nacre. J. Struct. Biol. 153, 176-187] and Crenshaw and Ristedt [Crenshaw, M.A., Ristedt, H. 1976. The histochemical localization of reactive groups in septal nacre from Nautilus pompilius. In: Omori, M., Watabe, N. (Eds.) The Mechanisms of Biomineralization in Animals and Plants. Tokai University Press, Toyko] on Nautilus pompilius. Our mapping identifies distinct regions, defined by the macromolecular groups, including what is proposed to be the sites of CaCO(3) nucleation and that play a key role in nacre growth. Using AFM scanning probe microscopy we have identified a fibrous core within the framework that we associate with chitin. The structural picture that is evolved is then used to develop a simple structural model for the organic framework which is shown to be consistent with mechanical property measurements. The role of the intracrystalline matrix within the nacre tablets in mediating nacre's mechanical response is noted within the framework of our model. PMID:18538582

  11. 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

  12. Macromolecular Crowding Effects on Two Homologs of Ribosomal Protein S16: Protein-Dependent Structural Changes and Local Interactions

    PubMed Central

    Mikaelsson, Therese; Ådén, Jörgen; Wittung-Stafshede, Pernilla; Johansson, Lennart B.-Å.

    2014-01-01

    Proteins function in cellular environments that are crowded with biomolecules, and in this reduced available space, their biophysical properties may differ from those observed in dilute solutions in vitro. Here, we investigated the effects of a synthetic macromolecular crowding agent, dextran 20, on the folded states of hyperthermophilic (S16Thermo) and mesophilic (S16Meso) homologs of the ribosomal protein S16. As expected for an excluded-volume effect, the resistance of the mesophilic protein to heat-induced unfolding increased in the presence of dextran 20, and chemical denaturation experiments at different fixed temperatures showed the macromolecular crowding effect to be temperature-independent. Förster resonance energy transfer experiments show that intramolecular distances between an intrinsic Trp residue and BODIPY-labeled S16Meso depend on the level of the crowding agent. The BODIPY group was attached at three specific positions in S16Meso, allowing measurements of three intraprotein distances. All S16Meso variants exhibited a decrease in the average Trp-BODIPY distance at up to 100 mg/mL dextran 20, whereas the changes in distance became anisotropic (one distance increased, two distances decreased) at higher dextran concentrations. In contrast, the two S16Thermo mutants did not show any changes in Trp-BODIPY distances upon increase of dextran 20 concentrations. It should be noted that the fluorescence quantum yields and lifetimes of BODIPY attached to the two S16 homologs decreased gradually in the presence of dextran 20. To investigate the origin of this decrease, we studied the BODIPY quantum yield in three protein variants in the presence of a tyrosine-labeled dextran. The experiments revealed distinct tyrosine quenching behaviors of BODIPY in the three variants, suggesting a dynamic local interaction between dextran and one particular S16 variant. PMID:25028882

  13. Single-step Antibody-based Affinity Cryo-Electron Microscopy for Imaging and Structural Analysis of Macromolecular Assemblies

    PubMed Central

    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

    2014-01-01

    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 (nonpurified His-tagged bacteriophage T7, His-tagged E. coli 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

  14. Macromolecular changes and nano-structural arrangements in gliadin and glutenin films upon chemical modification: Relation to functionality.

    PubMed

    Rasheed, Faiza; Newson, William R; Plivelic, Tomás S; Kuktaite, Ramune; Hedenqvist, Mikael S; Gällstedt, Mikael; Johansson, Eva

    2015-08-01

    Protein macromolecules adopted for biological and bio-based material functions are known to develop a structured protein network upon chemical modification. In this study, we aimed to evaluate the impact of chemical additives such as, NaOH, NH4OH and salicylic acid (SA), on the secondary and nano-structural transitions of wheat proteins. Further, the effect of chemically induced modifications in protein macromolecular structure was anticipated in relation to functional properties. The gliadin-NH4OH-SA film showed a supramolecular protein organization into hexagonal structures with 65 Å lattice parameter, and other not previously observed structural entities having a characteristic distance of 50 Å. Proteins in gliadin-NH4OH-SA films were highly polymerized, with increased amount of disulfide crosslinks and β-sheets, causing improved strength and stiffness. Glutenin and WG proteins with NH4OH-SA showed extensive aggregation and an increase in β-sheet content together with irreversible crosslinks. Irreversible crosslinks hindered a high order structure formation in glutenins, and this resulted in films with only moderately improved stiffness. Thus, formation of nano-hierarchical structures based on β-sheets and disulfide crosslinks are the major reasons of high strength and stiffness in wheat protein based films. PMID:25936284

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

    PubMed Central

    Hassan, Sergio A.

    2012-01-01

    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. PMID:22920098

  16. 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.

  17. Macromolecular structure analysis and effective liquefaction pretreatment. Quarterly technical progress report, 1 April 1992--30 June 1992

    SciTech Connect

    Suuberg, E.M.; Yun, Y.; Lilly, W.D.

    1992-12-31

    Experiments show that combined DSC-solvent swelling provide insight into heat- and solvent-induced macromolecular structural changes in coal. In Pittsburgh No. 8 bitu. coal, there is a structural transition at 250 to 400 C. There are thermally induced (prepyrolysis) structural relaxations in bituminous coals at 270-430 C that make them more easily penetrable, swellable, and extractable in solvents. These relaxations are not observed in subbituminous and lignite; in these low-rank coals, gradual crosslinking with temperature was dominant. In medium and low volatile bituminous rank, the relaxation was much more pronounced. As in polymers, the relaxation transitions in coals depend strongly on heating rate. No relaxation was caused by pyridine preswelling of coals of rank higher than high volatile bituminous. Heat appears to disrupt the structure more than pyridine can; CS{sub 2}/pyridine however, relaxes the structure of Upper Freeport coal. Even strong solvents cannot swell high-rank coals more than 10% at <250 C, whereas heat treatment above 300 C and mixed solvents enhance the swellability. Origin of efficacy in swelling of a medium volatile rank coal by mixed solvents of CS{sub 2} appears to be physical; similar bonding interactions are disrupted by this synergistic solvent action and by heat.

  18. Role of the XPA protein in the NER pathway: A perspective on the function of structural disorder in macromolecular assembly

    PubMed Central

    Fadda, Elisa

    2015-01-01

    Lack of structure is often an essential functional feature of protein domains. The coordination of macromolecular assemblies in DNA repair pathways is yet another task disordered protein regions are highly implicated in. Here I review the available experimental and computational data and within this context discuss the functional role of structure and disorder in one of the essential scaffolding proteins in the nucleotide excision repair (NER) pathway, namely Xeroderma pigmentosum complementation group A (XPA). From the analysis of the current knowledge, in addition to protein–protein docking and secondary structure prediction results presented for the first time herein, a mechanistic framework emerges, where XPA builds the NER pre-incision complex in a modular fashion, as “beads on a string”, where the protein–protein interaction “beads”, or modules, are interconnected by disordered link regions. This architecture is ideal to avoid the expected steric hindrance constraints of the DNA expanded bubble. Finally, the role of the XPA structural disorder in binding affinity modulation and in the sequential binding of NER core factors in the pre-incision complex is also discussed. PMID:26865925

  19. Role of the XPA protein in the NER pathway: A perspective on the function of structural disorder in macromolecular assembly.

    PubMed

    Fadda, Elisa

    2016-01-01

    Lack of structure is often an essential functional feature of protein domains. The coordination of macromolecular assemblies in DNA repair pathways is yet another task disordered protein regions are highly implicated in. Here I review the available experimental and computational data and within this context discuss the functional role of structure and disorder in one of the essential scaffolding proteins in the nucleotide excision repair (NER) pathway, namely Xeroderma pigmentosum complementation group A (XPA). From the analysis of the current knowledge, in addition to protein-protein docking and secondary structure prediction results presented for the first time herein, a mechanistic framework emerges, where XPA builds the NER pre-incision complex in a modular fashion, as "beads on a string", where the protein-protein interaction "beads", or modules, are interconnected by disordered link regions. This architecture is ideal to avoid the expected steric hindrance constraints of the DNA expanded bubble. Finally, the role of the XPA structural disorder in binding affinity modulation and in the sequential binding of NER core factors in the pre-incision complex is also discussed. PMID:26865925

  20. Space-group and origin ambiguity in macromolecular structures with pseudo-symmetry and its treatment with the program Zanuda.

    PubMed

    Lebedev, Andrey A; Isupov, Michail N

    2014-09-01

    The presence of pseudo-symmetry in a macromolecular crystal and its interplay with twinning may lead to an incorrect space-group (SG) assignment. Moreover, if the pseudo-symmetry is very close to an exact crystallographic symmetry, the structure can be solved and partially refined in the wrong SG. Typically, in such incorrectly determined structures all or some of the pseudo-symmetry operations are, in effect, taken for crystallographic symmetry operations and vice versa. A mistake only becomes apparent when the R(free) ceases to decrease below 0.39 and further model rebuilding and refinement cannot improve the refinement statistics. If pseudo-symmetry includes pseudo-translation, the uncertainty in SG assignment may be associated with an incorrect choice of origin, as demonstrated by the series of examples provided here. The program Zanuda presented in this article was developed for the automation of SG validation. Zanuda runs a series of refinements in SGs compatible with the observed unit-cell parameters and chooses the model with the highest symmetry SG from a subset of models that have the best refinement statistics. PMID:25195756

  1. Proteomic characterization of a triton-insoluble fraction from chloroplasts defines a novel group of proteins associated with macromolecular structures.

    PubMed

    Phinney, Brett S; Thelen, Jay J

    2005-01-01

    Proteomic analysis of a Triton X-100 insoluble, 30,000 x g pellet from purified pea chloroplasts resulted in the identification of 179 nonredundant proteins. This chloroplast fraction was mostly depleted of chloroplast membranes since only 23% and 9% of the identified proteins were also observed in envelope and thylakoid membranes, respectively. One of the most abundant proteins in this fraction was sulfite reductase, a dual function protein previously shown to act as a plastid DNA condensing protein. Approximately 35 other proteins known (or predicted) to be associated with high-density protein-nucleic acid particles (nucleoids) were also identified including a family of DNA gyrases, as well as proteins involved in plastid transcription and translation. Although nucleoids appeared to be the predominant component of 30k x g Triton-insoluble chloroplast preparations, multi-enzyme protein complexes were also present including each subunit to the pyruvate dehydrogenase and acetyl-CoA carboxylase multi-enzyme complexes, as well as a proposed assembly of the first three enzymes of the Calvin cycle. Approximately 18% of the proteins identified were annonated as unknown or hypothetical proteins and another 20% contained "putative" or "like" in the identifier tag. This is the first proteomic characterization of a membrane-depleted, high-density fraction from plastids and demonstrates the utility of this simple procedure to isolate intact macromolecular structures from purified organelles for analysis of protein-protein and protein-nucleic acid interactions. PMID:15822927

  2. Statistical mechanics of macromolecular complexation

    NASA Astrophysics Data System (ADS)

    Nakamura, Issei

    The self-assembly of macromolecules through molecular association has attracted long-standing attention in soft-condensed matter physics. The hierarchical formation from small-scale building blocks into larger-scale complex structures often leads to very rich phase behavior controlled by various ambient conditions. The understanding and control of the phase behavior of self-assembling systems require detailed knowledge about the entropy and enthalpy contributions to the free energy of the system. However, this knowledge is limited at the present time because a comprehensive theoretical description of molecular association is still lacking. In this thesis, four tales of achievements in developing theories of macromolecular complexation are presented. (1) We begin with an analytically solvable model of the self-assembly of rigid macromolecules with surface adsorption. A generic understanding of the driving force and the role of entropy is obtained from the exact solutions. (2) We move on to further development of the theory in order to study the complexation between polymers and ionic molecules. The extension of the first model to chain-like molecules is performed using a well-established method in polymer physics, the self-consistent field theory (SCFT) of polymers. We also discuss gelation in this system within the scope of mean-filed approximations. (3) Then, a ladder-like polymer-polymer complexation is studied. Unconventional phase diagrams are predicted from the modified SCFT, indicating a large effect of variations in entropy due to the complexation on bulk properties. (4) Finally, the kinetic aspect of macromolecular binding reactions is discussed.

  3. Three dimensional electron microscopy and in silico tools for macromolecular structure determination

    PubMed Central

    Borkotoky, Subhomoi; Meena, Chetan Kumar; Khan, Mohammad Wahab; Murali, Ayaluru

    2013-01-01

    Recently, structural biology witnessed a major tool - electron microscopy - in solving the structures of macromolecules in addition to the conventional techniques, X-ray crystallography and nuclear magnetic resonance (NMR). Three dimensional transmission electron microscopy (3DTEM) is one of the most sophisticated techniques for structure determination of molecular machines. Known to give the 3-dimensional structures in its native form with literally no upper limit on size of the macromolecule, this tool does not need the crystallization of the protein. Combining the 3DTEM data with in silico tools, one can have better refined structure of a desired complex. In this review we are discussing about the recent advancements in three dimensional electron microscopy and tools associated with it.

  4. [Application of molecular absorption spectrophotometric method to the determination of biologic macromolecular structures].

    PubMed

    Cao, Shu-xia; Zhao, Yu-fen

    2004-10-01

    A review on recent applications of molecular absorption spectrophotometric method to the identification of the structures of biologic macromolecules, such as protein and nucleic acid, is presented. Molecular absorption spectrophotometric method is widely used in the structure determination of biologic macromolecules for its convenience and speed. Ultraviolet absorption spectrum (UV) can be used in the research on the mechanism of the interaction of anticancer drugs and DNA. UV can also be used to study the interaction of spectroscopic probe with biologic molecule and their binding mechanism. Protein secondary structure and conformation can be investigated by Fourier infrared spectroscopy (FTIR) deconvolution analysis. Molecular absorption spectrophotometric method is an important tool for structure study of biologic macromolecules. PMID:15760019

  5. 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

  6. 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

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

    PubMed

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

    2014-05-01

    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

  8. Hydroxyl radical footprinting in vivo: mapping macromolecular structures with synchrotron radiation

    PubMed Central

    Adilakshmi, Tadepalli; Lease, Richard A.; Woodson, Sarah A.

    2006-01-01

    We used a high flux synchrotron X-ray beam to map the structure of 16S rRNA and RNase P in viable bacteria in situ. A 300 ms exposure to the X-ray beam was sufficient for optimal cleavage of the phosphodiester backbone. The in vivo footprints of the 16S rRNA in frozen cells were similar to those obtained in vitro and were consistent with the predicted accessibility of the RNA backbone to hydroxyl radical. Protection or enhanced cleavage of certain nucleotides in vivo can be explained by interactions with tRNA and perturbation of the subunit interface. Thus, short exposures to a synchrotron X-ray beam can footprint the tertiary structure and protein contacts of RNA–protein complexes with nucleotide resolution in living cells. PMID:16682443

  9. Cooperative macromolecular device revealed by meta-analysis of static and time-resolved structures

    SciTech Connect

    Ren, Zhong; Šrajer, Vukica; Knapp, James E.; Royer, Jr., William E.

    2013-04-08

    Here we present a meta-analysis of a large collection of static structures of a protein in the Protein Data Bank in order to extract the progression of structural events during protein function. We apply this strategy to the homodimeric hemoglobin HbI from Scapharca inaequivalvis. We derive a simple dynamic model describing how binding of the first ligand in one of the two chemically identical subunits facilitates a second binding event in the other partner subunit. The results of our ultrafast time-resolved crystallographic studies support this model. We demonstrate that HbI functions like a homodimeric mechanical device, such as pliers or scissors. Ligand-induced motion originating in one subunit is transmitted to the other via conserved pivot points, where the E and F' helices from two partner subunits are 'bolted' together to form a stable dimer interface permitting slight relative rotation but preventing sliding.

  10. Hydroxyl Radical Footprinting in vivo: Mapping Macromolecular Structures with Synchrotron Radiation

    SciTech Connect

    Adilakshmi,T.; Lease, R.; Woodson, S.

    2006-01-01

    We used a high flux synchrotron X-ray beam to map the structure of 16S rRNA and RNase P in viable bacteria in situ. A 300 ms exposure to the X-ray beam was sufficient for optimal cleavage of the phosphodiester backbone. The in vivo footprints of the 16S rRNA in frozen cells were similar to those obtained in vitro and were consistent with the predicted accessibility of the RNA backbone to hydroxyl radical. Protection or enhanced cleavage of certain nucleotides in vivo can be explained by interactions with tRNA and perturbation of the subunit interface. Thus, short exposures to a synchrotron X-ray beam can footprint the tertiary structure and protein contacts of RNA-protein complexes with nucleotide resolution in living cells.

  11. Macromolecular recognition: Structural aspects of the origin of the genetic system

    NASA Technical Reports Server (NTRS)

    Rein, Robert; Sokalski, W. Andrzej; Barak, Dov; Luo, Ning; Zielinski, Theresa Julia; Shibata, Masayuki

    1991-01-01

    Theoretical simulation of prebiotic chemical processes is an invaluable tool for probing the phenomenon of the evolution of life. Using computational and modeling techniques and guided by analogies from present day systems, we seek to understand the emergence of the genetic apparatus, enzymatic catalysis and protein synthesis under prebiotic conditions. Modeling of the ancestral aminoacyl-tRNA-synthetases (aRS) may provide important clues to the emergence of the genetic code and the protein synthetic machinery. The minimal structural requirements for the catalysis of tRNA aminoacylation are being explored. A formation of an aminoacyl adenylate was studied in the framework of ab initio molecular orbital theory. The role of individual residues in the vicinity of the TyrRS active site was examined, and the effect of all possible amino acids substitutions near the active site was examined. A formation of aminoacyl tRNA was studied by the molecular modeling system SYBYL with the high resolution crystallographic structures of the present day tRNA, aRS's complexes. The ultimate goal is to propose a simple RNA segment that is small enough to be build in the primordial chemical environment but maintains the specificity and catalytic activity of the contemporary RNA enzyme. To understand the mechanism of ribozyme catalyzed reactions, ab initio and semi-empirical (ZINDO) programs were used to investigate the reaction path of transphosphorylation. A special emphasis was placed on the possible catalytic and structural roles played by the coordinated magnesium cation. Both the inline and adjacent mechanisms of transphosphorylation were studied. The structural characteristics of the target helices, particularly a possible role for the G-T pair, is also studied by a molecular dynamics (MD) simulation technique.

  12. NaOH treatment of chitosan films: Impact on macromolecular structure and film properties.

    PubMed

    Takara, E A; Marchese, J; Ochoa, N A

    2015-11-01

    In this paper, we examine the significance of treatment with NaOH on chitosan (CH) film structure to obtain biodegradable materials for several applications. In order to determine the structure of the films, an analysis based on SEM, FTIR spectroscopy and X-ray diffraction data was performed. In addition, the consequences of this treatment were evaluated by swelling index measurements and mechanical testing. As result of FTIR and X-ray analysis, three effects were identified: the deprotonation and phosphate extraction, which allowed new hydrogen bonds to form, and a higher CH deacetylation. These studies also revealed that two hydrated and anhydrous polymorphs were present in the CH-NaOH films. Moreover, the new hydrogen bond and the reduction of N-acetyl groups produced films with a more compact and disordered structure, reducing their swelling characteristics and increasing their brittleness. The introduction of a mild NaOH treatment is a versatile tool to obtain chitosan films with interesting and tunable properties. PMID:26256320

  13. Macromolecular recognition: Structural aspects of the origin of the genetic system

    NASA Technical Reports Server (NTRS)

    Rein, Robert; Barak, Dov; Luo, Ning; Zielinski, Theresa Julia; Shibata, Masayuki

    1991-01-01

    Theoretical simulation of prebiotic chemical processes is an invaluable tool for probing the phenomenon of evolution of life. Using computational and modeling techniques and guided by analogies from present day systems we, seek to understand the emergence of genetic apparatus, enzymatic catalysis and protein synthesis under prebiotic conditions. In one possible scenario, the RNA enzymatic reaction plays a key role in the emergence of the self-replicating and offers a clue to the onset of enzymatic catalysis prior to the existence of the protein biosynthetic machinery. Our ultimate goal is to propose a simple RNA segment which contains the specificity and catalytic activity of the contemporary RNA enzyme and which could emerge in a primordial chemical environment. To understand the mechanism of ribozyme catalyzed reactions, ab initio and semi-empirical (ZINDO) programs were used to investigate the reaction path of transphosphorylation. A special emphasis was placed on the possible catalytic and structural roles played by the coordinated magnesium cation. Both the inline and adjacent mechanisms of transphosphorylation have been studied. Another important aspect of this reaction is the identity of the functional groups which are essential for the acid base catalysis. The structural characteristics of the target helices, particularly a possible role of G center dot T pair, is under examination by molecular dynamics (MD) simulation technique. Modeling of the ancestral aminoacyl-tRNA synthetases (aRS) may provide important clues to the emergence of the genetic code and the protein synthetic machinery. Assuming that the catalytic function evolved before the elements of specific recognition of a particular amino acid, we are exploring the minimal structural requirements for the catalysis of tRNA aminoacylation. The molecular modeling system SYBYL was used for this study based on the high resolution crystallographic structures of the present day tyrosyl-adenylate:tyrRS and tRNA(Gln): ATP:glnRS complexes. The trinucleotide CCA of the 3'-end tRNA is placed into the active site pocket of tyrRS, based on the scheme of interaction between tRNA(Gln) and glnRS, and upon the stereochemistry of the tyrRS:tRNA:Tyr-AMP transition state. This provides a model of the non-specific recognition of a tRNA's 3'-end by an aRS, which might be similar to that of the ancestral aRS's. In the next step, modeling of the rest of the acceptor stem of tRNA (Tyr) with tyrRS is carried out.

  14. Facilitating best practices in collecting anomalous scattering data for de novo structure solution at the ESRF Structural Biology Beamlines

    PubMed Central

    de Sanctis, Daniele; Oscarsson, Marcus; Popov, Alexander; Svensson, Olof; Leonard, Gordon

    2016-01-01

    The constant evolution of synchrotron structural biology beamlines, the viability of screening protein crystals for a wide range of heavy-atom derivatives, the advent of efficient protein labelling and the availability of automatic data-processing and structure-solution pipelines have combined to make de novo structure solution in macromolecular crystallography a less arduous task. Nevertheless, the collection of diffraction data of sufficient quality for experimental phasing is still a difficult and crucial step. Here, some examples of good data-collection practice for projects requiring experimental phasing are presented and recent developments at the ESRF Structural Biology beamlines that have facilitated these are illustrated. PMID:26960128

  15. Facilitating best practices in collecting anomalous scattering data for de novo structure solution at the ESRF Structural Biology Beamlines.

    PubMed

    de Sanctis, Daniele; Oscarsson, Marcus; Popov, Alexander; Svensson, Olof; Leonard, Gordon

    2016-03-01

    The constant evolution of synchrotron structural biology beamlines, the viability of screening protein crystals for a wide range of heavy-atom derivatives, the advent of efficient protein labelling and the availability of automatic data-processing and structure-solution pipelines have combined to make de novo structure solution in macromolecular crystallography a less arduous task. Nevertheless, the collection of diffraction data of sufficient quality for experimental phasing is still a difficult and crucial step. Here, some examples of good data-collection practice for projects requiring experimental phasing are presented and recent developments at the ESRF Structural Biology beamlines that have facilitated these are illustrated. PMID:26960128

  16. Structure and property relations of macromolecular self-assemblies at interfaces

    NASA Astrophysics Data System (ADS)

    Yang, Zhihao

    Hydrophilic polymer chains, poly(ethylene glycol) (PEG), are attached to glass surfaces by silylation of the silanol groups on glass surfaces with the omega-(methoxyl terminated PEG) trimethoxysilanes. These tethered polymer chains resemble the self-assembled monolayers (SAMs) of PEG, which exhibit excellent biocompatibility and provide a model system for studying the interactions of proteins with polymer surfaces. The low molecular weight PEGs tend to extend, forming a brush-like monolayer, whereas the longer polymer chains tend to interpenetrate each other, forming a mushroom-like PEG monolayer at the interface. Interactions between a plasma protein, bovine serum albumin, and the PEG-SAMs are investigated in terms of protein adsorption and diffusion on the surfaces by the technique of fluorescence recovery after photobleaching (FRAP). The diffusion and aggregation behaviors of the protein on the two monolayers are found to be quite different despite the similarities in adsorption and desorption behaviors. The results are analyzed with a hypothesis of the hydrated surface dynamics. A method of covalently bonding phospholipid molecules to silica substrates followed by loading with free phospholipids is demonstrated to form well organized and stable phospholipid self-assembled monolayers. Surfaces of such SAMs structurally mimic the aqueous sides of phospholipid bilayer membranes. The dynamics of phospholipids and an adsorbed protein, lipase, in the SAMs are probed with FRAP, in terms of lateral diffusion of both phospholipids and protein molecules. The esterase activity of lipase on the SAM surfaces is confirmed by the hydrolysis reaction of a substrate, umbelliferone stearate, showing such lipid SAMs posess biomembrane functionality in terms of interfacial activation of the membranous enzymes. Dynamics of polyethylene oxide and polypropylene oxide tri-block copolymers, PEO-PPO-PEO and PPO-PEO-PPO, at the air/water interface upon thermal stimulation is studied by surface light scattering, in terms of the dynamic surface tension changes in response to a temperature jump. The characteristic of the surface tension relaxation is found to be highly related to the molecular structure and concentration of the copolymers at the interface.

  17. 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.

  18. Emerging applications of small angle solution scattering in structural biology

    PubMed Central

    Chaudhuri, Barnali N

    2015-01-01

    Small angle solution X-ray and neutron scattering recently resurfaced as powerful tools to address an array of biological problems including folding, intrinsic disorder, conformational transitions, macromolecular crowding, and self or hetero-assembling of biomacromolecules. In addition, small angle solution scattering complements crystallography, nuclear magnetic resonance spectroscopy, and other structural methods to aid in the structure determinations of multidomain or multicomponent proteins or nucleoprotein assemblies. Neutron scattering with hydrogen/deuterium contrast variation, or X-ray scattering with sucrose contrast variation to a certain extent, is a convenient tool for characterizing the organizations of two-component systems such as a nucleoprotein or a lipid-protein assembly. Time-resolved small and wide-angle solution scattering to study biological processes in real time, and the use of localized heavy-atom labeling and anomalous solution scattering for applications as FRET-like molecular rulers, are amongst promising newer developments. Despite the challenges in data analysis and interpretation, these X-ray/neutron solution scattering based approaches hold great promise for understanding a wide variety of complex processes prevalent in the biological milieu. PMID:25516491

  19. The nature and fate of natural resins in the geosphere. Part X{sup +ovr-}. Structural characteristics of the macromolecular constituents of modern Dammar resin and class II ambers.

    SciTech Connect

    Anderson, K. B.; Muntean, J. V.; Chemistry

    2000-01-01

    As part of a larger study of the structure and behavior of polyterpenoids in sedimentary systems, the structural characteristics of the macromolecular constituents of Dammar resin and a related Class II amber have been reinvestigated. The conclusions drawn from these analyses are inconsistent with the current widely held 'polycadinene' model for the macromolecular structure of these materials. Double bond characteristics observed by one and two dimensional NMR spectroscopy do not match those in the proposed 'polycadinene' structure. Based on these observations it is suggested that the proposed 'polycadinene' structure for these materials is inadequate and requires revision. Elemental and NMR data also suggest a significant contribution from functionalized monomers.

  20. Structural pathways for macromolecular and cellular transport across the blood-brain barrier during inflammatory conditions. Review.

    PubMed

    Lossinsky, A S; Shivers, R R

    2004-04-01

    This review presents an overview of the highlights of major concepts involving the anatomical routes for the transport of macromolecules and the transmigration of cellular elements across the blood-brain barrier (BBB) during inflammation. The particular focus will include inflammatory leukocytes, neoplastic cells and pathogenic microorganisms including specific types of viruses, bacteria and yeasts. The experimental animal models presented here have been employed successfully by the authors in several independent experiments during the past twenty-five years for investigations of pathologic alterations of the BBB after a variety of experimentally induced injuries and inflammatory conditions in mammalian and non-mammalian animal species. The initial descriptions of endothelial cell (EC) vesicles or caveolae serving as mini-transporters of fluid substances essentially served as a springboard for many subsequent discoveries during the past half century related to mechanisms of uptake of materials into ECs and whether or not pinocytosis is related to the transport of these materials across EC barriers under normal physiologic conditions and after tissue injury. In the mid-1970's, the authors of this review independently applied morphologic techniques (transmission electron microscopy-TEM), in conjunction with the plant protein tracer horseradish peroxidase (HRP) to investigate macromolecular transport structures that increased after the brain and spinal cord had been subjected to a variety of injuries. Based on morphologic evidence from these studies of BBB injury, the authors elaborated a unique EC system of modified caveolae that purportedly fused together forming transendothelial cell channels, and later similar EC profiles defined as vesiculo-canalicular or vesiculo-tubular structures (VTS, Lossinsky, et al., 1999). These EC structures were observed in association with increased BBB permeability of tracers including exogenously injected HRP, normally excluded from the intercellular milieu of the CNS. Subsequent studies of non-BBB-type tumor ECs determined that the EC VTS and other vesicular structures were defined by others as vesiculo-vacuolar organelles (VVOs, Kohn et al., 1992; Dvorak et al., 1996). Collectively, these structures appear to represent a type of anatomical gateway to the CNS likely serving as conduits. However, these CNS conduits become patent only in damaged ECs for the passage of macromolecules, and purportedly for inflammatory and neoplastic cells as well (Lossinsky et al., 1999). In this review, we focus attention on the similarities and differences between caveolae, fused racemic vesicular bundles, endothelial tubules and channels (VTS and the VVOs) that are manifest in normal, non-BBB-type blood vessels, and in the BBB after injury. This review will present evidence that the previous studies by the authors and other researchers established a framework for subsequent transmission (TEM), scanning (SEM) and high-voltage electron microscopic (HVEM) investigations concerning ultrastructural, ultracytochemical and immunoultra-structural alterations of the cerebral ECs and the mechanisms of the BBB transport that occurs after CNS injury. This review is not intended to include all of the many observations that might be included in a general historical overview of the development of the EC channel hypothesis, but it will discuss several of the major contributions. We have attempted to present some of the structural evidence that supports our early contributions and those made by other investigators by highlighting major features of these EC structures that are manifest in the injured BBB. We have focused on currently established concepts and principles related to mechanisms for the transendothelial transport of macromolecules after CNS injury and also offer a critical appraisal of some of this literature. Finally, we describe more recent concepts of transBBB avenues for viruses, including HIV-1, bacterial and mycotic organisms, as well as inflammatory and neoplastic cell adhesion and migration across the injured mammalian BBB. Data from studies of EC-related adhesion molecules, both from the literature and from the author's experimental results and observations made in other laboratories, as well as from personal communications underscore the importance of the adhesion molecules in facilitating the movement of leukocytic, neoplastic cell and human pathogens across the BBB during inflammatory and neoplastic events. Exciting, ongoing clinical trials are addressing possible therapeutic intervention in neuroinflammatory diseases, including multiple sclerosis, by blocking certain glycoprotein adhesion molecules before cells have the ability to adhere to the ECs and migrate across the BBB. Approaches whereby inflammation may be reduced or arrested using anti-adhesion molecules, by restructuring EC cytoskeletal, filamentous proteins, as well as remodeling cholesterol components of the modified VTS are discussed in the context of developing future therapies for BBB injury and inflammation. Understanding new concepts about the mechanism(s) by which inflammatory cells and a variety of pathogenic microorganisms are transported across the BBB can be expected to advance our understanding of fundamental disease processes. Taken together, the literature and the author's experiences during the past quarter of a century, will hopefully provide new clues related to the mechanisms of transendothelial cell adhesion and emigration across the injured BBB, issues that have been receiving considerable attention in the clinical arena. Learning how to chemically modulate the opening and/or closure of EC VTS and VVO structural pathways, or junctional complexes prior to cellular or microorganism adhesion and breaching the BBB presents challenging new questions in modern medicine. Future studies will be critically important for the development of therapeutic intervention in several human afflictions including traumatic brain and spinal cord injuries, stroke, cancer, multiple sclerosis and conditions where the immune system may be compromised including HIV infection, infantile and adult meningitis. PMID:15024715

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

    PubMed

    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 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

  2. 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

  3. 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.

  4. Controlling the phase structures of polymer/surfactant complexes by changing macromolecular architecture and adding n-alcohols.

    PubMed

    Percebom, Ana Maria; Loh, Watson

    2016-03-15

    Phase behavior of complex salts formed by a cationic surfactant and different ethoxylated polyions was investigated in water and with addition of two n-alcohols of different chain lengths: n-butanol and n-decanol. The polyion possesses a main chain of methacrylic acid randomly grafted with oligo(ethylene oxide) chains. Strong electrostatic interaction between the anionic main chain and the cationic surfactant hexadecyltrimethylammonium (C16TA) leads to the formation of C16TAP(MA-MAEOn) x:y complex salts. Modifications in polyion structure, such as changes in the proportion of grafted comonomers and in the side chain length caused differences in the overall balance of interactions with water and n-alcohols, altering the complex salt solubility and, consequently, the formed liquid-crystalline structures. The role of n-decanol as a cosurfactant was verified, but the hydrophilic side chains expanded the capacity of the formed liquid crystalline phases to incorporate water. Additionally, a novel structure, probably cubic bicontinuous (Pn3m), was observed coexisting with lamellar phases at low water concentration. Because n-butanol is known for being a good solvent for poly(ethylene oxide), these side chains intensified the role of this short chain n-alcohol as cosolvent for C16TAP(MA-MAEOn) x:y complex salts, favoring the formation of disordered solutions, including a bicontinuous microemulsion. PMID:26752433

  5. 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.; Bricogne, Gerard

    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.

  6. Structure of supersaturated zincate solutions

    SciTech Connect

    Dmitrenko, V.E.; Balyakina, N.N.; Baulov, V.I.; Kotov, A.V.; Zubov, M.S.

    1985-09-01

    During the discharge of chemical power sources with zinc electrodes, supersaturated zincate solution (SZS) is formed from which zinc oxide or hydroxide precipitates as a function of time. The deposit detracts from the functioning of these power sources. In view of the model suggested for the structure of SZS, it is expected that a stabilizing effect would be exerted on SZS by compounds having proton-donating groups which do not give off the protons in the strongly alkaline medium and are not discharged in this medium. For a check of this, the authors chose to use xylitol and molasses in their experiments. The SZS were produced with a mock-up silver-zinc battery using the procedure previously described.

  7. Automated macromolecular crystallization screening

    DOEpatents

    Segelke, Brent W.; Rupp, Bernhard; Krupka, Heike I.

    2005-03-01

    An automated macromolecular crystallization screening system wherein a multiplicity of reagent mixes are produced. A multiplicity of analysis plates is produced utilizing the reagent mixes combined with a sample. The analysis plates are incubated to promote growth of crystals. Images of the crystals are made. The images are analyzed with regard to suitability of the crystals for analysis by x-ray crystallography. A design of reagent mixes is produced based upon the expected suitability of the crystals for analysis by x-ray crystallography. A second multiplicity of mixes of the reagent components is produced utilizing the design and a second multiplicity of reagent mixes is used for a second round of automated macromolecular crystallization screening. In one embodiment the multiplicity of reagent mixes are produced by a random selection of reagent components.

  8. Practical macromolecular cryocrystallography

    SciTech Connect

    Pflugrath, J. W.

    2015-05-27

    Current methods, reagents and experimental hardware for successfully and reproducibly flash-cooling macromolecular crystals to cryogenic temperatures for X-ray diffraction data collection are reviewed. 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.

  9. The design of macromolecular crystallography diffraction experiments

    SciTech Connect

    Evans, Gwyndaf Axford, Danny; Owen, Robin L.

    2011-04-01

    Thoughts about the decisions made in designing macromolecular X-ray crystallography experiments at synchrotron beamlines are presented. The measurement of X-ray diffraction data from macromolecular crystals for the purpose of structure determination is the convergence of two processes: the preparation of diffraction-quality crystal samples on the one hand and the construction and optimization of an X-ray beamline and end station on the other. Like sample preparation, a macromolecular crystallography beamline is geared to obtaining the best possible diffraction measurements from crystals provided by the synchrotron user. This paper describes the thoughts behind an experiment that fully exploits both the sample and the beamline and how these map into everyday decisions that users can and should make when visiting a beamline with their most precious crystals.

  10. Solution Accounts for Structural Damping

    NASA Technical Reports Server (NTRS)

    Roussos, L. A.; Hyer, M. W.; Thornton, E. A.

    1982-01-01

    New analytical technique determines dynamic response of damped structures dominated by internal structural damping mechanisms. Though structural damping is often negligible compared with damping due to air friction and friction in joints, structural damping can be of major importance in structures having heavy damping treatments or in outer-space structures. Finite-element model includes nonlinear, nonviscous internal damping.

  11. 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.; Bricogne, Gerard

    2014-09-30

    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.

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

    PubMed Central

    Terwilliger, Thomas C.; Bricogne, Gerard

    2014-01-01

    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. PMID:25286839

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

    DOE PAGESBeta

    Terwilliger, Thomas C.; Bricogne, Gerard

    2014-09-30

    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 itmore » 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.« less

  14. Macromolecular bases of antischistosomal therapy.

    PubMed

    Angelucci, Francesco; Miele, Adriana Erica; Boumis, Giovanna; Brunori, Maurizio; Dimastrogiovanni, Daniela; Bellelli, Andrea

    2011-01-01

    Schistosomiasis is a widespread tropical parasitic disease, currently treated with Praziquantel, whose precise molecular target is actually unknown. Several other drugs are known to kill the schistosomes in vivo and in vitro, but these are seldom employed because of toxicity, high cost, complex administration or other reasons. The improvement of known drugs or the development of entirely new ones is a desirable goal, in view of the fact that strains of Schistosoma mansoni with reduced sensitivity to Praziquantel have appeared. In this review, we tried to collect the information available on known or putative macromolecular targets of schistosomicidal drugs; thus we focused on the biochemistry of the parasite, rather than the clinical properties of the drugs. The rationale of this approach is that drug design may become realistic if the mechanism of action of each known drug were known at atomic detail, ideally as the 3D structure of each drug in complex with its target. Important macromolecular targets of known drugs reviewed below are: Thioredoxin Glutathione Reductase; Cyclophilin; Acetyl Cholinesterase; Proteases and Purine Nucleoside Phosphorylase. Moreover, a few enzymes of the parasite are known, or thought, to be "druggable", and therefore interesting, even though no specific drugs are available as yet: examples of such enzymes are Glutathione Peroxidase and Peroxiredoxins. PMID:21619508

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

    SciTech Connect

    Foadi, James; Aller, Pierre; Alguel, Yilmaz; Cameron, Alex; Axford, Danny; Owen, Robin L.; Armour, Wes; Waterman, David G.; Iwata, So; Evans, Gwyndaf

    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 m 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.

  16. Macromolecular character of amber

    SciTech Connect

    Wert, C.A.; Weller, M.; Schlee, D.; Ledbetter, H.

    1989-03-15

    Measurements are reported of anelastic and dielectric loss of various ambers and copals. They show spectra typical of synthetic polymers. This similarity permits description of the macromolecular character of amber which was not possible from previous studies of chemical composition. Measurements on amber of several origins and geological ages show generally similar character, but also differences in detail. These may be caused by differences in chemistry of the original resin and the geological age and history of the amber, reflecting differences in degree of polymerization. Also reported are elastic constants measured at high frequency.

  17. 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

  18. Practical macromolecular cryocrystallography.

    PubMed

    Pflugrath, J W

    2015-06-01

    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

  19. 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.

  20. Magnetic macromolecular cross linked enzyme aggregates (CLEAs) of glucoamylase.

    PubMed

    Nadar, Shamraja S; Rathod, Virendra K

    2016-02-01

    This work illustrates the preparation of magnetic macromolecular glucoamylase CLEAs using dialdehydic pectin, as a cross linker instead of traditional glutaraldehyde. The effect of precipitators type and amount, cross linker concentration, cross linking time and amount of amino functionalized magnetic nanoparticles (AFMNs) on glucoamylase activity was studied. Glucoamylase magnetic macromolecular CLEAs prepared by precipitation in presence of AFMNs by ammonium sulfate were subsequently cross linked by dialdehydic pectin. After cross-linked by pectin, 95.4% activity recovery was achieved in magnetic macromolecular CLEAs, whereas in case of glutaraldehyde cross linker, 85.3% activity recovery was achieved. Magnetic macromolecular CLEAs showed 2.91 and 1.27 folds higher thermal stability as compared to free and magnetic glutaraldehyde CLEAs. In kinetics study, magnetic macromolecular CLEAs retained same Km values, whereas magnetic glutaraldehyde CLEAs showed higher Km value than free enzyme. The porous structure of magnetic macromolecular CLEAs was not only enhanced mass transfer toward macromolecular substrates, but also showed compression resistance for 5 consecutive cycles which was checked in terms of effectiveness factor. At the end, in reusability study; magnetic macromolecular CLEAs were retained 84% activity after 10(th) cycle without leaching of enzyme which is 22% higher than traditional magnetic CLEAs. PMID:26777253

  1. In-vacuum long-wavelength macromolecular crystallography.

    PubMed

    Wagner, Armin; Duman, Ramona; Henderson, Keith; Mykhaylyk, Vitaliy

    2016-03-01

    Structure solution based on the weak anomalous signal from native (protein and DNA) crystals is increasingly being attempted as part of synchrotron experiments. Maximizing the measurable anomalous signal by collecting diffraction data at longer wavelengths presents a series of technical challenges caused by the increased absorption of X-rays and larger diffraction angles. A new beamline at Diamond Light Source has been built specifically for collecting data at wavelengths beyond the capability of other synchrotron macromolecular crystallography beamlines. Here, the theoretical considerations in support of the long-wavelength beamline are outlined and the in-vacuum design of the endstation is discussed, as well as other hardware features aimed at enhancing the accuracy of the diffraction data. The first commissioning results, representing the first in-vacuum protein structure solution, demonstrate the promising potential of the beamline. PMID:26960130

  2. In-vacuum long-wavelength macromolecular crystallography

    PubMed Central

    Wagner, Armin; Duman, Ramona; Henderson, Keith; Mykhaylyk, Vitaliy

    2016-01-01

    Structure solution based on the weak anomalous signal from native (protein and DNA) crystals is increasingly being attempted as part of synchrotron experiments. Maximizing the measurable anomalous signal by collecting diffraction data at longer wavelengths presents a series of technical challenges caused by the increased absorption of X-rays and larger diffraction angles. A new beamline at Diamond Light Source has been built specifically for collecting data at wavelengths beyond the capability of other synchrotron macromolecular crystallography beamlines. Here, the theoretical considerations in support of the long-wavelength beamline are outlined and the in-vacuum design of the endstation is discussed, as well as other hardware features aimed at enhancing the accuracy of the diffraction data. The first commissioning results, representing the first in-vacuum protein structure solution, demonstrate the promising potential of the beamline. PMID:26960130

  3. Local Kinetic Measures of Macromolecular Structure Reveal Partitioning Among Multiple Parallel Pathways from the Earliest Steps in the Folding of a Large RNA Molecule

    SciTech Connect

    Laederach,A.; Shcherbakova, I.; Liang, M.; Brenowitz, M.; Altman, R.

    2006-01-01

    At the heart of the RNA folding problem is the number, structures, and relationships among the intermediates that populate the folding pathways of most large RNA molecules. Unique insight into the structural dynamics of these intermediates can be gleaned from the time-dependent changes in local probes of macromolecular conformation (e.g. reports on individual nucleotide solvent accessibility offered by hydroxyl radical ({center_dot}OH) footprinting). Local measures distributed around a macromolecule individually illuminate the ensemble of separate changes that constitute a folding reaction. Folding pathway reconstruction from a multitude of these individual measures is daunting due to the combinatorial explosion of possible kinetic models as the number of independent local measures increases. Fortunately, clustering of time progress curves sufficiently reduces the dimensionality of the data so as to make reconstruction computationally tractable. The most likely folding topology and intermediates can then be identified by exhaustively enumerating all possible kinetic models on a super-computer grid. The folding pathways and measures of the relative flux through them were determined for Mg{sup 2+} and Na{sup +}-mediated folding of the Tetrahymena thermophila group I intron using this combined experimental and computational approach. The flux during Mg{sup 2+}-mediated folding is divided among numerous parallel pathways. In contrast, the flux during the Na{sup +}-mediated reaction is predominantly restricted through three pathways, one of which is without detectable passage through intermediates. Under both conditions, the folding reaction is highly parallel with no single pathway accounting for more than 50% of the molecular flux. This suggests that RNA folding is non-sequential under a variety of different experimental conditions even at the earliest stages of folding. This study provides a template for the systematic analysis of the time-evolution of RNA structure from ensembles of local measures that will illuminate the chemical and physical characteristics of each step in the process. The applicability of this analysis approach to other macromolecules is discussed.

  4. Computing the origin and evolution of the ribosome from its structure — Uncovering processes of macromolecular accretion benefiting synthetic biology

    PubMed Central

    Caetano-Anollés, Gustavo; Caetano-Anollés, Derek

    2015-01-01

    Accretion occurs pervasively in nature at widely different timeframes. The process also manifests in the evolution of macromolecules. Here we review recent computational and structural biology studies of evolutionary accretion that make use of the ideographic (historical, retrodictive) and nomothetic (universal, predictive) scientific frameworks. Computational studies uncover explicit timelines of accretion of structural parts in molecular repertoires and molecules. Phylogenetic trees of protein structural domains and proteomes and their molecular functions were built from a genomic census of millions of encoded proteins and associated terminal Gene Ontology terms. Trees reveal a ‘metabolic-first’ origin of proteins, the late development of translation, and a patchwork distribution of proteins in biological networks mediated by molecular recruitment. Similarly, the natural history of ancient RNA molecules inferred from trees of molecular substructures built from a census of molecular features shows patchwork-like accretion patterns. Ideographic analyses of ribosomal history uncover the early appearance of structures supporting mRNA decoding and tRNA translocation, the coevolution of ribosomal proteins and RNA, and a first evolutionary transition that brings ribosomal subunits together into a processive protein biosynthetic complex. Nomothetic structural biology studies of tertiary interactions and ancient insertions in rRNA complement these findings, once concentric layering assumptions are removed. Patterns of coaxial helical stacking reveal a frustrated dynamics of outward and inward ribosomal growth possibly mediated by structural grafting. The early rise of the ribosomal ‘turnstile’ suggests an evolutionary transition in natural biological computation. Results make explicit the need to understand processes of molecular growth and information transfer of macromolecules. PMID:27096056

  5. Significance of wall structure, macromolecular composition, and surface polymers to the survival and transport of Cryptosporidium parvum Oocysts

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The structure and composition of the oocyst wall are primary factors determining the survival of Cryptosporidium parvum oocysts outside the host. An external polymer matrix (glycocalyx) may mediate interactions with environmental surfaces and, thus, affect the transport of oocysts in water, soil, an...

  6. 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 α-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

  7. 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.

  8. 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.

  9. Effect of structural alteration on the macromolecular properties of brown and bituminous coals, quantitative relationships to the hydrogenation reactivity with tetralin

    SciTech Connect

    Kuznetsov, P.N.; Kuznetsova, L.I.; Bimer, J.; Salbut, P.D.; Gruber, R.

    1996-12-31

    The mobility of macromolecular network has been found to be the fundamental property of both brown and bituminous coals governing the reactivity for hydrogenation with tetralin. In Kansk-Achinsk brown coal, this was primarily affected by carboxylate cross-linking via polyvalent cations like Ca.

  10. Mechanisms, kinetics, impurities and defects: consequences in macromolecular crystallization

    PubMed Central

    McPherson, Alexander; Kuznetsov, Yurii G.

    2014-01-01

    The nucleation and growth of protein, nucleic acid and virus crystals from solution are functions of underlying kinetic and thermodynamic parameters that govern the process, and these are all supersaturation-dependent. While the mechanisms of macromolecular crystal growth are essentially the same as for conventional crystals, the underlying parameters are vastly different, in some cases orders of magnitude lower, and this produces very different crystallization processes. Numerous physical features of macromolecular crystals are of serious interest to X-ray diffractionists; the resolution limit and mosaicity, for example, reflect the degree of molecular and lattice order. The defect structure of crystals has an impact on their response to flash-cooling, and terminal crystal size is dependent on impurity absorption and incorporation. The variety and extent of these issues are further unique to crystals of biological macromolecules. All of these features are amenable to study using atomic force microscopy, which provides direct images at the nanoscale level. Some of those images are presented here. PMID:24699728

  11. 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.

  12. Fractionation and characterization of soy β-conglycinin-dextran conjugates via macromolecular crowding environment and dry heating.

    PubMed

    Weng, Jingyi; Qi, Junru; Yin, Shouwei; Wang, Jinmei; Guo, Jian; Feng, Jilu; Liu, Qianru; Zhu, Jianhua; Yang, Xiaoquan

    2016-04-01

    Conjugates of β-conglycinin and dextran were prepared by heating in solution under macromolecular crowding environment and dry-heating methods, and then fractionated by solubility at pH 4.8 and pH 6.5 and characterized. The results showed that the degree of glycation of the conjugates extracted from pH 4.8 were higher than the conjugates extracted from pH 6.5. Corresponding to the higher degree of glycation, it was supposed that the β-conglycinin of groups 4.8 of macromolecular crowding environment was completely surrounded by the dextran molecular while that of groups 6.5 were encircled partially with a lower degree of glycation. Compared to β-conglycinin, groups 4.8 demonstrated a decreasing surface hydrophobicity and sulfhydryl group content while groups 6.5 increased. The secondary structure of β-conglycinin soluble at pH 4.8 after conjugating under macromolecular crowding environment tended to stretch out and the highly ordered structure turn to random structures. The differences between the extraction of pH 4.8 and pH 6.5 conjugated by dry-heating methods were not as remarkable as the difference between the extraction conjugated by macromolecular crowding environment. PMID:26593615

  13. Stochastic dynamics of macromolecular-assembly networks.

    NASA Astrophysics Data System (ADS)

    Saiz, Leonor; Vilar, Jose

    2006-03-01

    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 [1]. 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 λ induction switches, which rely on the formation of DNA loops by proteins [2] 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. [1] L. Saiz and J.M.G. Vilar, submitted (2005). [2] J.M.G. Vilar and L. Saiz, Current Opinion in Genetics & Development, 15, 136-144 (2005).

  14. REdiii: a pipeline for automated structure solution.

    PubMed

    Bohn, Markus Frederik; Schiffer, Celia A

    2015-05-01

    High-throughput crystallographic approaches require integrated software solutions to minimize the need for manual effort. REdiii is a system that allows fully automated crystallographic structure solution by integrating existing crystallographic software into an adaptive and partly autonomous workflow engine. The program can be initiated after collecting the first frame of diffraction data and is able to perform processing, molecular-replacement phasing, chain tracing, ligand fitting and refinement without further user intervention. Preset values for each software component allow efficient progress with high-quality data and known parameters. The adaptive workflow engine can determine whether some parameters require modifications and choose alternative software strategies in case the preconfigured solution is inadequate. This integrated pipeline is targeted at providing a comprehensive and efficient approach to screening for ligand-bound co-crystal structures while minimizing repetitiveness and allowing a high-throughput scientific discovery process. PMID:25945571

  15. A database of macromolecular motions.

    PubMed Central

    Gerstein, M; Krebs, W

    1998-01-01

    We describe a database of macromolecular motions meant to be of general use to the structural community. The database, which is accessible on the World Wide Web with an entry point at http://bioinfo.mbb.yale.edu/MolMovDB , attempts to systematize all instances of protein and nucleic acid movement for which there is at least some structural information. At present it contains >120 motions, most of which are of proteins. Protein motions are further classified hierarchically into a limited number of categories, first on the basis of size (distinguishing between fragment, domain and subunit motions) and then on the basis of packing. Our packing classification divides motions into various categories (shear, hinge, other) depending on whether or not they involve sliding over a continuously maintained and tightly packed interface. In addition, the database provides some indication about the evidence behind each motion (i.e. the type of experimental information or whether the motion is inferred based on structural similarity) and attempts to describe many aspects of a motion in terms of a standardized nomenclature (e.g. the maximum rotation, the residue selection of a fixed core, etc.). Currently, we use a standard relational design to implement the database. However, the complexity and heterogeneity of the information kept in the database makes it an ideal application for an object-relational approach, and we are moving it in this direction. Specifically, in terms of storing complex information, the database contains plausible representations for motion pathways, derived from restrained 3D interpolation between known endpoint conformations. These pathways can be viewed in a variety of movie formats, and the database is associated with a server that can automatically generate these movies from submitted coordinates. PMID:9722650

  16. 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.

  17. The use of a mini-κ goniometer head in macromolecular crystallography diffraction experiments

    SciTech Connect

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

    2013-07-01

    Hardware and software solutions for MX data-collection strategies using the EMBL/ESRF miniaturized multi-axis goniometer head are presented. 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 κ-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.

  18. Revealing the Macromolecular Targets of Fragment-Like Natural Products.

    PubMed

    Rodrigues, Tiago; Reker, Daniel; Kunze, Jens; Schneider, Petra; Schneider, Gisbert

    2015-09-01

    Fragment-like natural products were identified as ligand-efficient chemical matter for hit-to-lead development and chemical-probe discovery. Relying on a computational method using a topological pharmacophore descriptor and a drug database, several macromolecular targets from distinct protein families were expeditiously retrieved for structurally unrelated chemotypes. The selected fragments feature structural dissimilarity to the reference compounds and suitable target affinity, and they offer opportunities for chemical optimization. Experimental confirmation of hitherto unknown macromolecular targets for the selected molecules corroborate the usefulness of the computational approach and suggests broad applicability to chemical biology and molecular medicine. PMID:26202212

  19. 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

  20. Folding dynamics of Trp-cage in the presence of chemical interference and macromolecular crowding. I

    NASA Astrophysics Data System (ADS)

    Samiotakis, Antonios; Cheung, Margaret S.

    2011-11-01

    Proteins fold and function in the crowded environment of the cell's interior. In the recent years it has been well established that the so-called "macromolecular crowding" effect enhances the folding stability of proteins by destabilizing their unfolded states for selected proteins. On the other hand, chemical and thermal denaturation is often used in experiments as a tool to destabilize a protein by populating the unfolded states when probing its folding landscape and thermodynamic properties. However, little is known about the complicated effects of these synergistic perturbations acting on the kinetic properties of proteins, particularly when large structural fluctuations, such as protein folding, have been involved. In this study, we have first investigated the folding mechanism of Trp-cage dependent on urea concentration by coarse-grained molecular simulations where the impact of urea is implemented into an energy function of the side chain and/or backbone interactions derived from the all-atomistic molecular dynamics simulations with urea through a Boltzmann inversion method. In urea solution, the folding rates of a model miniprotein Trp-cage decrease and the folded state slightly swells due to a lack of contact formation between side chains at the terminal regions. In addition, the equilibrium m-values of Trp-cage from the computer simulations are in agreement with experimental measurements. We have further investigated the combined effects of urea denaturation and macromolecular crowding on Trp-cage's folding mechanism where crowding agents are modeled as hard-spheres. The enhancement of folding rates of Trp-cage is most pronounced by macromolecular crowding effect when the extended conformations of Trp-cast dominate at high urea concentration. Our study makes quantitatively testable predictions on protein folding dynamics in a complex environment involving both chemical denaturation and macromolecular crowding effects.

  1. Macromolecular Materials and Engineering

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Cover: The image shows electrospun fibers based on poly(lactic acid)/polyaniline blends with diameters from 90 to 1000 nm. The structural characteristics of the fibers are compared to cast films by scanning electron microscopy, small-angle X-ray scattering, differential scanning calorimetry, and ato...

  2. Structuring of polymer solutions upon solvent evaporation.

    PubMed

    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. PMID:25768523

  3. Structure and aggregation in model tetramethylurea solutions.

    PubMed

    Gupta, Rini; Patey, G N

    2014-08-14

    The structure of model aqueous tetramethylurea (TMU) solutions is investigated employing large-scale (32,000, 64,000 particles) molecular dynamics simulations. Results are reported for TMU mole fractions, X(t), ranging from infinite dilution up to 0.07, and for two temperatures, 300 and 330 K. Two existing force fields for TMU-water solutions are considered. These are the GROMOS 53A6 united-atom TMU model combined with SPC/E water [TMU(GROMOS-UA)/W(SPC/E)], and the more frequently employed AMBER03 all-atom force field for TMU combined with the TIP3P water model [TMU(AMBER-AA)/W(TIP3P)]. It is shown that TMU has a tendency towards aggregation for both models considered, but the tendency is significantly stronger for the [TMU(AMBER-AA)/W(TIP3P)] force field. For this model signs of aggregation are detected at X(t) = 0.005, aggregation is a well established feature of the solution at X(t) = 0.02, and the aggregates increase further in size with increasing concentration. This is in agreement with at least some experimental studies, which report signals of aggregation in the low concentration regime. The TMU aggregates exhibit little structure and are simply loosely ordered, TMU-rich regions of solution. The [TMU(GROMOS-UA)/W(SPC/E)] model shows strong signs of aggregation only at higher concentrations (X(t) ≳ 0.04), and the aggregates appear more loosely ordered, and less well-defined than those occurring in the [TMU(AMBER-AA)/W(TIP3P)] system. For both models, TMU aggregation increases when the temperature is increased from 300 to 330 K, consistent with an underlying entropy driven, hydrophobic interaction mechanism. At X(t) = 0.07, the extra-molecular correlation length expected for microheterogeneous solutions has become comparable with the size of the simulation cell for both models considered, indicating that even the systems simulated here are sufficiently large only at low concentrations. PMID:25134583

  4. Structure and aggregation in model tetramethylurea solutions

    SciTech Connect

    Gupta, Rini; Patey, G. N.

    2014-08-14

    The structure of model aqueous tetramethylurea (TMU) solutions is investigated employing large-scale (32 000, 64 000 particles) molecular dynamics simulations. Results are reported for TMU mole fractions, X{sub t}, ranging from infinite dilution up to 0.07, and for two temperatures, 300 and 330 K. Two existing force fields for TMU-water solutions are considered. These are the GROMOS 53A6 united-atom TMU model combined with SPC/E water [TMU(GROMOS-UA)/W(SPC/E)], and the more frequently employed AMBER03 all-atom force field for TMU combined with the TIP3P water model [TMU(AMBER-AA)/W(TIP3P)]. It is shown that TMU has a tendency towards aggregation for both models considered, but the tendency is significantly stronger for the [TMU(AMBER-AA)/W(TIP3P)] force field. For this model signs of aggregation are detected at X{sub t} = 0.005, aggregation is a well established feature of the solution at X{sub t} = 0.02, and the aggregates increase further in size with increasing concentration. This is in agreement with at least some experimental studies, which report signals of aggregation in the low concentration regime. The TMU aggregates exhibit little structure and are simply loosely ordered, TMU-rich regions of solution. The [TMU(GROMOS-UA)/W(SPC/E)] model shows strong signs of aggregation only at higher concentrations (X{sub t} ≳ 0.04), and the aggregates appear more loosely ordered, and less well-defined than those occurring in the [TMU(AMBER-AA)/W(TIP3P)] system. For both models, TMU aggregation increases when the temperature is increased from 300 to 330 K, consistent with an underlying entropy driven, hydrophobic interaction mechanism. At X{sub t} = 0.07, the extra-molecular correlation length expected for microheterogeneous solutions has become comparable with the size of the simulation cell for both models considered, indicating that even the systems simulated here are sufficiently large only at low concentrations.

  5. Structure and aggregation in model tetramethylurea solutions

    NASA Astrophysics Data System (ADS)

    Gupta, Rini; Patey, G. N.

    2014-08-01

    The structure of model aqueous tetramethylurea (TMU) solutions is investigated employing large-scale (32 000, 64 000 particles) molecular dynamics simulations. Results are reported for TMU mole fractions, Xt, ranging from infinite dilution up to 0.07, and for two temperatures, 300 and 330 K. Two existing force fields for TMU-water solutions are considered. These are the GROMOS 53A6 united-atom TMU model combined with SPC/E water [TMU(GROMOS-UA)/W(SPC/E)], and the more frequently employed AMBER03 all-atom force field for TMU combined with the TIP3P water model [TMU(AMBER-AA)/W(TIP3P)]. It is shown that TMU has a tendency towards aggregation for both models considered, but the tendency is significantly stronger for the [TMU(AMBER-AA)/W(TIP3P)] force field. For this model signs of aggregation are detected at Xt = 0.005, aggregation is a well established feature of the solution at Xt = 0.02, and the aggregates increase further in size with increasing concentration. This is in agreement with at least some experimental studies, which report signals of aggregation in the low concentration regime. The TMU aggregates exhibit little structure and are simply loosely ordered, TMU-rich regions of solution. The [TMU(GROMOS-UA)/W(SPC/E)] model shows strong signs of aggregation only at higher concentrations (Xt ≳ 0.04), and the aggregates appear more loosely ordered, and less well-defined than those occurring in the [TMU(AMBER-AA)/W(TIP3P)] system. For both models, TMU aggregation increases when the temperature is increased from 300 to 330 K, consistent with an underlying entropy driven, hydrophobic interaction mechanism. At Xt = 0.07, the extra-molecular correlation length expected for microheterogeneous solutions has become comparable with the size of the simulation cell for both models considered, indicating that even the systems simulated here are sufficiently large only at low concentrations.

  6. Macromolecular recognition in the Protein Data Bank

    SciTech Connect

    Janin, Joël; Rodier, Francis; Chakrabarti, Pinak

    2007-01-01

    X-ray structures in the PDB illustrate both the specific recognition of two polypeptide chains in protein–protein complexes and dimeric proteins and their nonspecific interaction at crystal contacts. Crystal structures deposited in the Protein Data Bank illustrate the diversity of biological macromolecular recognition: transient interactions in protein–protein and protein–DNA complexes and permanent assemblies in homodimeric proteins. The geometric and physical chemical properties of the macromolecular interfaces that may govern the stability and specificity of recognition are explored in complexes and homodimers compared with crystal-packing interactions. It is found that crystal-packing interfaces are usually much smaller; they bury fewer atoms and are less tightly packed than in specific assemblies. Standard-size interfaces burying 1200–2000 Å{sup 2} of protein surface occur in protease–inhibitor and antigen–antibody complexes that assemble with little or no conformation changes. Short-lived electron-transfer complexes have small interfaces; the larger size of the interfaces observed in complexes involved in signal transduction and homodimers correlates with the presence of conformation changes, often implicated in biological function. Results of the CAPRI (critical assessment of predicted interactions) blind prediction experiment show that docking algorithms efficiently and accurately predict the mode of assembly of proteins that do not change conformation when they associate. They perform less well in the presence of large conformation changes and the experiment stimulates the development of novel procedures that can handle such changes.

  7. 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.

  8. Interfacial inhibitors: targeting macromolecular complexes.

    PubMed

    Pommier, Yves; Marchand, Christophe

    2012-01-01

    Interfacial inhibitors belong to a broad class of natural products and synthetic drugs that are commonly used to treat cancers as well as bacterial and HIV infections. They bind selectively to interfaces as macromolecular machines assemble and are set in motion. The bound drugs transiently arrest the targeted molecular machines, which can initiate allosteric effects, or desynchronize macromolecular machines that normally function in concert. Here, we review five archetypical examples of interfacial inhibitors: the camptothecins, etoposide, the quinolone antibiotics, the vinca alkaloids and the novel anti-HIV inhibitor raltegravir. We discuss the common and diverging elements between interfacial and allosteric inhibitors and give a perspective for the rationale and methods used to discover novel interfacial inhibitors. PMID:22173432

  9. Structure-thermodynamics relation of electrolyte solutions

    NASA Astrophysics Data System (ADS)

    Kalcher, Immanuel; Dzubiella, Joachim

    2009-04-01

    The structure of aqueous LiCl, NaCl, KCl, CsCl, KF, and NaI solutions is calculated by molecular dynamics (MD) simulations of the frequently employed Dang force-field in SPC/E water. By using liquid state theory, we integrate the structure to obtain the electrolytes' osmotic coefficient ϕ and systematically investigate force-field quality and structural consequences to ion-specific bulk thermodynamics. The osmotic coefficients ϕχ calculated from the exact compressibility route for the cation-Cl- force-fields match experiments for concentrations ρ ≲2M, while NaI and KF parameters fail. Comparison of ϕχ with ϕv from the virial route, which relies on the pair potential approximation, shows that many-body effects become important for all salts above ρ ≃0.5M. They can be efficiently corrected, however, by employing a salt-type and ρ-dependent dielectric constant ɛ(ρ ), generalizing previous observations on NaCl only. For physiological concentrations, ρ ≲0.5M, the specific osmotic behavior is found to be determined by the short-ranged cation-anion pair potential only and is strongly related to the second virial coefficient of the latter. Presented methods and findings, based on simple integrations over the electrolyte structure, enable efficient MD force-field refinement by direct benchmarking to the sensitive electrolyte thermodynamics, instead to noncollective, single ion properties.

  10. Probing the Macromolecular Organization of Cells by Electron Tomography

    PubMed Central

    Hoenger, Andreas; McIntosh, J. Richard

    2010-01-01

    Summary A major goal in cell biology is to understand the functional organization of macromolecular complexes in vivo. Electron microscopy is helping cell biologists to achieve this goal, thanks to its ability to resolve structural details in the nanometer range. While issues related to specimen preparation, imaging, and image interpretation make this approach to cell architecture difficult, recent improvements in methods, equipment, and software have facilitated the study of both important macromolecular complexes and comparatively large volumes from cellular specimens. Here, we describe recent progress in electron microscopy of cells and the ways in which the relevant methodologies are helping to elucidate cell architecture. PMID:19185480

  11. Fluid Physics and Macromolecular Crystal Growth in Microgravity

    NASA Technical Reports Server (NTRS)

    Helliwell, John R.; Snell, Edward H.; Chayen, Naomi E.; Judge, Russell A.; Boggon, Titus J.; Pusey, M. L.; Rose, M. Franklin (Technical Monitor)

    2000-01-01

    The first protein crystallization experiment in microgravity was launched in April, 1981 and used Germany's Technologische Experimente unter Schwerelosigkeit (TEXUS 3) sounding rocket. The protein P-galactosidase (molecular weight 465Kda) was chosen as the sample with a liquid-liquid diffusion growth method. A sliding device brought the protein, buffer and salt solution into contact when microgravity was reached. The sounding rocket gave six minutes of microgravity time with a cine camera and schlieren optics used to monitor the experiment, a single growth cell. In microgravity a strictly laminar diffusion process was observed in contrast to the turbulent convection seen on the ground. Several single crystals, approx 100micron in length, were formed in the flight which were of inferior but of comparable visual quality to those grown on the ground over several days. A second experiment using the same protocol but with solutions cooled to -8C (kept liquid with glycerol antifreeze) again showed laminar diffusion. The science of macromolecular structural crystallography involves crystallization of the macromolecule followed by use of the crystal for X-ray diffraction experiments to determine the three dimensional structure of the macromolecule. Neutron protein crystallography is employed for elucidation of H/D exchange and for improved definition of the bound solvent (D20). The structural information enables an understanding of how the molecule functions with important potential for rational drug design, improved efficiency of industrial enzymes and agricultural chemical development. The removal of turbulent convection and sedimentation in microgravity, and the assumption that higher quality crystals will be produced, has given rise to the growing number of crystallization experiments now flown. Many experiments can be flown in a small volume with simple, largely automated, equipment - an ideal combination for a microgravity experiment. The term "protein crystal growth" is often historically used to describe these microgravity experiments. This is somewhat inaccurate as the field involves the study of many varied biological molecules including viruses, proteins, DNA, RNA and complexes of those structures. For this reason we use the term macromolecular crystal growth. In this chapter we review a series of diagnostic microgravity crystal growth experiments carried out principally using the European Space Agency (ESA) Advanced Protein Crystallization Facility (APCF). We also review related research, both experimental and theoretical, on the aspects of microgravity fluid physics that affect microgravity protein crystal growth. Our experiments have revealed some surprises that were not initially expected. We discuss them here in the context of practical lessons learnt and how to maximize the limited microgravity opportunities available.

  12. Multiscale macromolecular simulation: role of evolving ensembles.

    PubMed

    Singharoy, A; Joshi, H; Ortoleva, P J

    2012-10-22

    Multiscale analysis provides an algorithm for the efficient simulation of macromolecular assemblies. This algorithm involves the coevolution of a quasiequilibrium probability density of atomic configurations and the Langevin dynamics of spatial coarse-grained variables denoted order parameters (OPs) characterizing nanoscale system features. In practice, implementation of the probability density involves the generation of constant OP ensembles of atomic configurations. Such ensembles are used to construct thermal forces and diffusion factors that mediate the stochastic OP dynamics. Generation of all-atom ensembles at every Langevin time step is computationally expensive. Here, multiscale computation for macromolecular systems is made more efficient by a method that self-consistently folds in ensembles of all-atom configurations constructed in an earlier step, history, of the Langevin evolution. This procedure accounts for the temporal evolution of these ensembles, accurately providing thermal forces and diffusions. It is shown that efficiency and accuracy of the OP-based simulations is increased via the integration of this historical information. Accuracy improves with the square root of the number of historical timesteps included in the calculation. As a result, CPU usage can be decreased by a factor of 3-8 without loss of accuracy. The algorithm is implemented into our existing force-field based multiscale simulation platform and demonstrated via the structural dynamics of viral capsomers. PMID:22978601

  13. 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.

  14. A strategy for dissecting the architectures of native macromolecular assemblies.

    PubMed

    Shi, Yi; Pellarin, Riccardo; Fridy, Peter C; Fernandez-Martinez, Javier; Thompson, Mary K; Li, Yinyin; Wang, Qing Jun; Sali, Andrej; Rout, Michael P; Chait, Brian T

    2015-12-01

    It remains particularly problematic to define the structures of native macromolecular assemblies, which are often of low abundance. Here we present a strategy for isolating complexes at endogenous levels from GFP-tagged transgenic cell lines. Using cross-linking mass spectrometry, we extracted distance restraints that allowed us to model the complexes' molecular architectures. PMID:26436480

  15. Concentration Dependent Structure of Block Copolymer Solutions

    NASA Astrophysics Data System (ADS)

    Choi, Soohyung; Bates, Frank S.; Lodge, Timothy P.

    2015-03-01

    Addition of solvent molecules into block copolymer can induce additional interactions between the solvent and both blocks, and therefore expands the range of accessible self-assembled morphologies. In particular, the distribution of solvent molecules plays a key role in determining the microstructure and its characteristic domain spacing. In this study, concentration dependent structures formed by poly(styrene-b-ethylene-alt-propylene) (PS-PEP) solution in squalane are investigated using small-angle X-ray scattering. This reveals that squalane is essentially completely segregated into the PEP domains. In addition, the conformation of the PS block changes from stretched to nearly fully relaxed (i.e., Gaussian conformation) as amounts of squalane increases. NRF

  16. How can macromolecular crowding inhibit biological reactions? The enhanced formation of DNA nanoparticles

    PubMed Central

    Hou, Sen; Trochimczyk, Piotr; Sun, Lili; Wisniewska, Agnieszka; Kalwarczyk, Tomasz; Zhang, Xuzhu; Wielgus-Kutrowska, Beata; Bzowska, Agnieszka; Holyst, Robert

    2016-01-01

    In contrast to the already known effect that macromolecular crowding usually promotes biological reactions, solutions of PEG 6k at high concentrations stop the cleavage of DNA by HindIII enzyme, due to the formation of DNA nanoparticles. We characterized the DNA nanoparticles and probed the prerequisites for their formation using multiple techniques such as fluorescence correlation spectroscopy, dynamic light scattering, fluorescence analytical ultracentrifugation etc. In >25% PEG 6k solution, macromolecular crowding promotes the formation of DNA nanoparticles with dimensions of several hundreds of nanometers. The formation of DNA nanoparticles is a fast and reversible process. Both plasmid DNA (2686 bp) and double-stranded/single-stranded DNA fragment (66bp/nt) can form nanoparticles. We attribute the enhanced nanoparticle formation to the depletion effect of macromolecular crowding. This study presents our idea to enhance the formation of DNA nanoparticles by macromolecular crowding, providing the first step towards a final solution to efficient gene therapy. PMID:26903405

  17. Structure of aqueous sodium perchlorate solutions.

    PubMed

    General, Ignacio J; Asciutto, Eliana K; Madura, Jeffry D

    2008-12-01

    Salt solutions have been the object of study of many scientists through history, but one of the most important findings came along when the Hofmeister series were discovered. Their importance arises from the fact that they influence the relative solubility of proteins, and solubility is directly related to one of today's holy grails: protein folding. In this work we characterize one of the more-destabilizing salts in the series, sodium perchlorate, by studying it as an aqueous solution at various concentrations ranging from 0.08 to 1.60 mol/L. Molecular dynamics simulations at room temperature permitted a detailed study of the organization of solvent and cosolvent, in terms of its radial distribution functions, along with the study of the structure of hydrogen bonds in the ions' solvation shells. We found that the distribution functions have some variations in their shape as concentration changes, but the position of their peaks is mostly unaffected. Regarding water, the most salient fact is the noticeable (although small) change in the second hydration shell and even beyond, especially for g(O(w)***O(w)), showing that the locality of salt effects should not be restricted to considerations of only the first solvation shell. The perturbation of the second shell also appears in the study of the HB network, where the difference between the number of HBs around a water molecule and around the Na(+) cation gets much smaller as one goes from the first to the second solvation shell, yet the difference is not negligible. Nevertheless, the effect of the ions past their first hydration shell is not enough to make a noticeable change in the global HB network. The Kirkwood-Buff theory of liquids was applied to our system, in order to calculate the activity derivative of the cosolvent. This coefficient, along with a previously calculated preferential binding, allowed us to establish that if a folded AP peptide is immersed in the studied solution, becoming the solute, then increasing the salt concentration will make the helix more stable. PMID:18991374

  18. The macromolecular character of amber

    NASA Astrophysics Data System (ADS)

    Wert, Charles A.; Weller, Manfred; Schlee, Dieter; Ledbetter, Hassel

    1989-03-01

    Measurements are reported of anelastic and dielectric loss of various ambers and copals. They show spectra typical of synthetic polymers. This similarity permits description of the macromolecular character of amber which was not possible from previous studies of chemical composition. Measurements on amber of several origins and geological ages show generally similar character, but also differences in detail. These may be caused by differences in chemistry of the original resin and the geological age and history of the amber, reflecting differences in degree of polymerization. Also reported are elastic constants measured at high frequency.

  19. Macromolecular diffractive imaging using imperfect crystals.

    PubMed

    Ayyer, Kartik; Yefanov, Oleksandr M; Oberthür, Dominik; Roy-Chowdhury, Shatabdi; Galli, Lorenzo; Mariani, Valerio; Basu, Shibom; Coe, Jesse; Conrad, Chelsie E; Fromme, Raimund; Schaffer, Alexander; Dörner, Katerina; James, Daniel; Kupitz, Christopher; Metz, Markus; Nelson, Garrett; Xavier, Paulraj Lourdu; Beyerlein, Kenneth R; Schmidt, Marius; Sarrou, Iosifina; Spence, John C H; Weierstall, Uwe; White, Thomas A; Yang, Jay-How; Zhao, Yun; Liang, Mengning; Aquila, Andrew; Hunter, Mark S; Robinson, Joseph S; Koglin, Jason E; Boutet, Sébastien; Fromme, Petra; Barty, Anton; Chapman, Henry N

    2016-02-11

    The three-dimensional structures of macromolecules and their complexes are mainly elucidated by X-ray protein crystallography. A major limitation of this method is access to high-quality crystals, which is necessary to ensure X-ray diffraction extends to sufficiently large scattering angles and hence yields information of sufficiently high resolution with which to solve the crystal structure. The observation that crystals with reduced unit-cell volumes and tighter macromolecular packing often produce higher-resolution Bragg peaks suggests that crystallographic resolution for some macromolecules may be limited not by their heterogeneity, but by a deviation of strict positional ordering of the crystalline lattice. Such displacements of molecules from the ideal lattice give rise to a continuous diffraction pattern that is equal to the incoherent sum of diffraction from rigid individual molecular complexes aligned along several discrete crystallographic orientations and that, consequently, contains more information than Bragg peaks alone. Although such continuous diffraction patterns have long been observed--and are of interest as a source of information about the dynamics of proteins--they have not been used for structure determination. Here we show for crystals of the integral membrane protein complex photosystem II that lattice disorder increases the information content and the resolution of the diffraction pattern well beyond the 4.5-ångström limit of measurable Bragg peaks, which allows us to phase the pattern directly. Using the molecular envelope conventionally determined at 4.5 ångströms as a constraint, we obtain a static image of the photosystem II dimer at a resolution of 3.5 ångströms. This result shows that continuous diffraction can be used to overcome what have long been supposed to be the resolution limits of macromolecular crystallography, using a method that exploits commonly encountered imperfect crystals and enables model-free phasing. PMID:26863980

  20. Macromolecular diffractive imaging using imperfect crystals

    NASA Astrophysics Data System (ADS)

    Ayyer, Kartik; Yefanov, Oleksandr M.; Oberthür, Dominik; Roy-Chowdhury, Shatabdi; Galli, Lorenzo; Mariani, Valerio; Basu, Shibom; Coe, Jesse; Conrad, Chelsie E.; Fromme, Raimund; Schaffer, Alexander; Dörner, Katerina; James, Daniel; Kupitz, Christopher; Metz, Markus; Nelson, Garrett; Xavier, Paulraj Lourdu; Beyerlein, Kenneth R.; Schmidt, Marius; Sarrou, Iosifina; Spence, John C. H.; Weierstall, Uwe; White, Thomas A.; Yang, Jay-How; Zhao, Yun; Liang, Mengning; Aquila, Andrew; Hunter, Mark S.; Robinson, Joseph S.; Koglin, Jason E.; Boutet, Sébastien; Fromme, Petra; Barty, Anton; Chapman, Henry N.

    2016-02-01

    The three-dimensional structures of macromolecules and their complexes are mainly elucidated by X-ray protein crystallography. A major limitation of this method is access to high-quality crystals, which is necessary to ensure X-ray diffraction extends to sufficiently large scattering angles and hence yields information of sufficiently high resolution with which to solve the crystal structure. The observation that crystals with reduced unit-cell volumes and tighter macromolecular packing often produce higher-resolution Bragg peaks suggests that crystallographic resolution for some macromolecules may be limited not by their heterogeneity, but by a deviation of strict positional ordering of the crystalline lattice. Such displacements of molecules from the ideal lattice give rise to a continuous diffraction pattern that is equal to the incoherent sum of diffraction from rigid individual molecular complexes aligned along several discrete crystallographic orientations and that, consequently, contains more information than Bragg peaks alone. Although such continuous diffraction patterns have long been observed—and are of interest as a source of information about the dynamics of proteins—they have not been used for structure determination. Here we show for crystals of the integral membrane protein complex photosystem II that lattice disorder increases the information content and the resolution of the diffraction pattern well beyond the 4.5-ångström limit of measurable Bragg peaks, which allows us to phase the pattern directly. Using the molecular envelope conventionally determined at 4.5 ångströms as a constraint, we obtain a static image of the photosystem II dimer at a resolution of 3.5 ångströms. This result shows that continuous diffraction can be used to overcome what have long been supposed to be the resolution limits of macromolecular crystallography, using a method that exploits commonly encountered imperfect crystals and enables model-free phasing.

  1. 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.

  2. A strategy for dissecting the architectures of native macromolecular assemblies

    PubMed Central

    Shi, Yi; Pellarin, Riccardo; Fridy, Peter C.; Fernandez-Martinez, Javier; Thompson, Mary K.; Li, Yinyin; Wang, Qing Jun; Sali, Andrej; Rout, Michael P.; Chait, Brian T.

    2015-01-01

    Despite the central role of large multi-protein complexes in many biological processes, it remains challenging to elucidate their structures and particularly problematic to define the structures of native macromolecular assemblies, which are often of low abundance. Here, we present a strategy for isolating such complexes and for extracting distance restraints that allow the determination of their molecular architectures. The method was optimized to allow facile use of the extensive global resources of GFP-tagged transgenic cells and animals. PMID:26436480

  3. Macromolecular Crystal Growth by Means of Microfluidics

    NASA Technical Reports Server (NTRS)

    vanderWoerd, Mark; Ferree, Darren; Spearing, Scott; Monaco, Lisa; Molho, Josh; Spaid, Michael; Brasseur, Mike; Curreri, Peter A. (Technical Monitor)

    2002-01-01

    We have performed a feasibility study in which we show that chip-based, microfluidic (LabChip(TM)) technology is suitable for protein crystal growth. This technology allows for accurate and reliable dispensing and mixing of very small volumes while minimizing bubble formation in the crystallization mixture. The amount of (protein) solution remaining after completion of an experiment is minimal, which makes this technique efficient and attractive for use with proteins, which are difficult or expensive to obtain. The nature of LabChip(TM) technology renders it highly amenable to automation. Protein crystals obtained in our initial feasibility studies were of excellent quality as determined by X-ray diffraction. Subsequent to the feasibility study, we designed and produced the first LabChip(TM) device specifically for protein crystallization in batch mode. It can reliably dispense and mix from a range of solution constituents into two independent growth wells. We are currently testing this design to prove its efficacy for protein crystallization optimization experiments. In the near future we will expand our design to incorporate up to 10 growth wells per LabChip(TM) device. Upon completion, additional crystallization techniques such as vapor diffusion and liquid-liquid diffusion will be accommodated. Macromolecular crystallization using microfluidic technology is envisioned as a fully automated system, which will use the 'tele-science' concept of remote operation and will be developed into a research facility for the International Space Station as well as on the ground.

  4. Combined Effects of Agitation, Macromolecular Crowding, and Interfaces on Amyloidogenesis*

    PubMed Central

    Lee, Chiu Fan; Bird, Sarah; Shaw, Michael; Jean, Létitia; Vaux, David J.

    2012-01-01

    Amyloid formation and accumulation is a hallmark of protein misfolding diseases and is associated with diverse pathologies including type II diabetes and Alzheimer's disease (AD). In vitro, amyloidogenesis is widely studied in conditions that do not simulate the crowded and viscous in vivo environment. A high volume fraction of most biological fluids is occupied by various macromolecules, a phenomenon known as macromolecular crowding. For some amyloid systems (e.g. α-synuclein) and under shaking condition, the excluded volume effect of macromolecular crowding favors aggregation, whereas increased viscosity reduces the kinetics of these reactions. Amyloidogenesis can also be catalyzed by hydrophobic-hydrophilic interfaces, represented by the air-water interface in vitro and diverse heterogeneous interfaces in vivo (e.g. membranes). In this study, we investigated the effects of two different crowding polymers (dextran and Ficoll) and two different experimental conditions (with and without shaking) on the fibrilization of amyloid-β peptide, a major player in AD pathogenesis. Specifically, we demonstrate that, during macromolecular crowding, viscosity dominates over the excluded volume effect only when the system is spatially non homogeneous (i.e. an air-water interface is present). We also show that the surfactant activity of the crowding agents can critically influence the outcome of macromolecular crowding and that the structure of the amyloid species formed may depend on the polymer used. This suggests that, in vivo, the outcome of amyloidogenesis may be affected by both macromolecular crowding and spatial heterogeneity (e.g. membrane turn-over). More generally, our work suggests that any factors causing changes in crowding may be susceptibility factors in AD. PMID:22988239

  5. Theory for Surface Structure of Electrolyte Solutions.

    NASA Astrophysics Data System (ADS)

    Nichols, Albert Loyd, III

    A theory is developed for the salt concentration profile and ion-ion correlations near surfaces of electrolyte solutions. We use the random phase approximation to study the primitive surface model employed by Onsager and Samaras, and others. In this model the chief technical complication is the correct treatment of image forces. We invent an exact rearrangement of the mathematical formulation of the problem which makes especially transparent the special case solutions (infinite dielectric constant mismatch) previously found. This reformulation guides an analytical solution for arbitrary dielectric constant mismatch between the two phases, subject to other assumptions adopted by previous workers. Similarly general results are derived for mixtures of ionic and dipolar solutes. These general results form the basis for extending our theoretical studies in several new directions. First, higher concentration corrections are investigated. It is shown that over an experimentally significant range of low concentrations for aqueous solutions the initial concentration correction to the Onsager-Samaras absorption has a negative definite sign. The theory, including concentration corrections, is compared to available computer simulation data, and close agreement is found for aqueous solutions below a few tenths molar. Second, the theory is developed to treat asymmetric electrolytes, and applied to ionic surfactants spread on water-hydrocarbon interfaces. Again, the theory accurately describes available experimental data. Third, the theory is broadened to acknowledge the solubility of the salt in both phases. It is found that this generalization changes the qualitative nature of the low concentration limiting law for the excess surface tension: the limiting behavior is changed from the (rho)ln(rho) dependence predicted by Onsager and Samaras to a more generally correct (rho)(' 1/2) dependence. Experimental data which might test this (rho)(' 1/2) behavior are not presently available. It is suggested that experimental studies of the limiting law behavior as a liquid-vapor critical point is approached, where substantial salt concentration in both phases is expected, would clearly establish the general limiting law.

  6. Temperature-dependent macromolecular X-ray crystallography

    SciTech Connect

    Weik, Martin Colletier, Jacques-Philippe

    2010-04-01

    The dynamical behaviour of crystalline macromolecules and their surrounding solvent as a function of cryo-temperature is reviewed. 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.

  7. Regular branched Macromolecules: Structure of Bottlebrush Polymers in Solution

    NASA Astrophysics Data System (ADS)

    Pakula, T.; Rathgeber, S.; Matyjaszewski, K.

    2001-03-01

    The shape and internal structure of bottlebrush (comb) macromolecules under good solvent conditions have been studied using small angle neutron scattering and computer simulations. The form factor S(Q) was measured at low concentrations in toluene for comb polymers consisting of a p(BPEM) backbone with p(nBA) side chains. The following intramolecular parameters were varied: (1) backbone length, (2) grafting density and (3) length of the side chains. Using models which have been successfully applied to other regular branched polymers we derive the range of the hydrodynamic interaction within the polymer and the particle dimension from which we can conclude on the overall shape of the macromolecular brush. In addition we determined the radius of the gyration of the backbone R_g^bb and of the side chains R_g^sc. These parameters give information about the stiffness of the polymer. Experimental findings are compared with computer simulation results performed for a single bottlebrush macromolecule using the cooperative motion algorithm. The simulation gives direct access to R_g^bb and R_g^sc and allows an independent determination of S(Q). Good agreement between experiment and simulation has been found.

  8. WAXS studies of the structural diversity of hemoglobin in solution.

    SciTech Connect

    Makowski, L.; Bardhan, J.; Gore, D.; Lal, J.; Mandava, S.; Park, S.; Rodi, D. J.; Ho, N. T.; Ho, C.; Fischetti, R. F.

    2011-01-01

    Specific ligation states of hemoglobin are, when crystallized, capable of taking on multiple quaternary structures. The relationship between these structures, captured in crystal lattices, and hemoglobin structure in solution remains uncertain. Wide-angle X-ray solution scattering (WAXS) is a sensitive probe of protein structure in solution that can distinguish among similar structures and has the potential to contribute to these issues. We used WAXS to assess the relationships among the structures of human and bovine hemoglobins in different liganded forms in solution. WAXS data readily distinguished among the various forms of hemoglobins. WAXS patterns confirm some of the relationships among hemoglobin structures that have been defined through crystallography and NMR and extend others. For instance, methemoglobin A in solution is, as expected, nearly indistinguishable from HbCO A. Interestingly, for bovine hemoglobin, the differences between deoxy-Hb, methemoglobin and HbCO are smaller than the corresponding differences in human hemoglobin. WAXS data were also used to assess the spatial extent of structural fluctuations of various hemoglobins in solution. Dynamics has been implicated in allosteric control of hemoglobin, and increased dynamics has been associated with lowered oxygen affinity. Consistent with that notion, WAXS patterns indicate that deoxy-Hb A exhibits substantially larger structural fluctuations than HbCO A. Comparisons between the observed WAXS patterns and those predicted on the basis of atomic coordinate sets suggest that the structures of Hb in different liganded forms exhibit clear differences from known crystal structure.

  9. WAXS studies of the structural diversity of hemoglobin in solution

    PubMed Central

    Makowski, L.; Bardhan, J.; Gore, D.; Lal, J.; Mandava, S.; Park, S.; Rodi, D.J.; Ho, N.T.; Ho, C.; Fischetti, R. F.

    2011-01-01

    Specific ligation states of hemoglobin are, when crystallized, capable of taking on multiple quaternary structures. The relationship between these structures, captured in crystal lattices, and hemoglobin structure in solution remains uncertain. Wide-angle x-ray solution scattering (WAXS) is a sensitive probe of protein structure in solution that can distinguish among similar structures and has the potential to contribute to these issues. We used WAXS to assess the relationships among the structures of human and bovine hemoglobins in different liganded forms in solution. WAXS data readily distinguished among the various forms of hemoglobins. WAXS patterns confirm some of the relationships among hemoglobin structures that have been defined through crystallography and NMR and extend others. For instance, metHb A in solution is, as expected, nearly indistinguishable from HbCO A. Interestingly, for bovine hemoglobin, the differences between deoxyHb, metHb and HbCO are smaller than the corresponding differences in human hemoglobin. WAXS data was also used to assess the spatial extent of structural fluctuations of various hemoglobins in solution. Dynamics has been implicated in allosteric control of hemoglobin and increased dynamics has been associated with lowered oxygen affinity. Consistent with that notion, WAXS patterns indicate that deoxyHb A exhibits substantially larger structural fluctuations than HbCO A. Comparisons between the observed WAXS patterns and those predicted on the basis of atomic coordinate sets suggest that the structures of Hb in different liganded forms exhibit clear differences from known crystal structures. PMID:21420976

  10. International summer school on macromolecular crystallographic computing. Final report

    SciTech Connect

    1998-08-01

    The School was the seventh in a series of International Union of Crystallography (IUCr) Crystallographic Symposia. The format of the School was formal lectures in the morning, tutorials in the afternoon, and software demonstrations and more lectures in the evening. The full program which left both the organizers and attendees exhausted, reflects the current state of excitement in the field of macromolecular structure determination using the technique of X-ray crystallography. The new and improved technologies and techniques described in these Proceedings are contributing to that growth and at the same time, as pointed out in the paper given by Sussman, creating challenges for the Protein Data Bank (PDB). As the School progressed, the authors were struck by the similarities to events which took place in small molecule crystallography beginning some 20 to 25 years ago. Growth then was fueled by the advent of new algorithms, affordable computer hardware, and good software. So it is today for macromolecular crystallography, but with the added bonus of the Internet which is changing how scientist conduct their research. Flack presented this view as part of his on-going contribution to how crystallographers use the Internet. After presentations discussing structures en masse they returned to the more traditional mode of presentation which parallels the determination of a single macromolecular structure: data collection -- phasing -- model building and visualization -- refinement.

  11. 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.

  12. Quantifying macromolecular conformational transition pathways

    NASA Astrophysics Data System (ADS)

    Seyler, Sean; Kumar, Avishek; Thorpe, Michael; Beckstein, Oliver

    2015-03-01

    Diverse classes of proteins function through large-scale conformational changes that are challenging for computer simulations. A range of fast path-sampling techniques have been used to generate transitions, but it has been difficult to compare paths from (and assess the relative strengths of) different methods. We introduce a comprehensive method (pathway similarity analysis, PSA) for quantitatively characterizing and comparing macromolecular pathways. The Hausdorff and Fréchet metrics (known from computational geometry) are used to quantify the degree of similarity between polygonal curves in configuration space. A strength of PSA is its use of the full information available from the 3 N-dimensional configuration space trajectory without requiring additional specific knowledge about the system. We compare a sample of eleven different methods for the closed-to-open transitions of the apo enzyme adenylate kinase (AdK) and also apply PSA to an ensemble of 400 AdK trajectories produced by dynamic importance sampling MD and the Geometrical Pathways algorithm. We discuss the method's potential to enhance our understanding of transition path sampling methods, validate them, and help guide future research toward deeper physical insights into conformational transitions.

  13. Recent Advances in Structure Solution from Powder Diffraction Data

    NASA Astrophysics Data System (ADS)

    Neumann, M. A.; Leusen, F. J. J.; Engel, G. E.; Wilke, S.; Conesa-Moratilla, C.

    Crystal structure determination frequently is a prerequisite for the rational understanding of the solid state properties of new materials. Even though single crystal diffractometry is the method of choice when it comes to crystal structure determination, this approach is often impractical because of the difficulties involved in growing single crystals of appropriate size. High quality powder samples, on the other hand, are much easier to obtain. Using direct-space structure solution techniques, increasingly complex crystal structures can nowadays be solved directly from powder diffraction data. Combined with easy-to-use tools for model building and visualization as well as molecular mechanics and first principles Density Functional Theory (DFT) calculations, crystal structure solution from powder diffraction data is becoming a routine task. To illustrate the applicability of direct-space Monte Carlo techniques to the crystal structure solution of organic and inorganic compounds, a variety of structure solutions with the Powder Solve algorithm are presented. Recent advances include the determination of a preferred orientation correction during the structure solution search and the use of parallel tempering, a newly implemented global search algorithm. As a complementary technique, first principles DFT calculations have been used successfully to validate structure solutions and to aid the subsequent Rietveld refinement.

  14. 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 firstexcitement 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

  15. On the Origin of Macromolecular Sequences

    PubMed Central

    Pattee, Howard H.

    1961-01-01

    The origin of the degree and type of order found in biological macromolecules is not adequately explained solely as an accumulation of genetic restrictions acquired through natural selection from otherwise unrestricted primeval sequences capable of self-replication, since the biological process of replication is itself dependent on the pre-existence of such order, and since the number of sequences that could have ever been tested by selection on the earth is an insignificant fraction of the number of unrestricted sequences which would be possible. Therefore the hypothesis is considered that replication and selection began from well ordered sequences, rather than random sequences. It is shown how the Turing concept of computation in fed-back, discrete-state automata can lead to the generation of order withour pre-existing instructions, and how this computation can result in self-repeating, random-like, but well ordered sequences of great length. Macromolecular models of such computers are suggested on the basis of mechanisms proposed for the growth of eutactic polymers. Such self-replicating, mutable sequences may then evolve genetic control which is sufficient to accommodate the information accumulated by natural selection. The structure and function of enzymes and structural proteins is related to this model, and statistical evidence from known amino acid sequences is shown to be consistent with some degree of non-genetic ordering. PMID:14484391

  16. A macromolecular model for the endothelial surface layer

    NASA Astrophysics Data System (ADS)

    Harden, James; Danova-Okpetu, Darina; Grest, Gary

    2006-03-01

    The endothelial surface layer (ESL) is a micron-scale macromolecular lining of the luminal side of blood vessels composed of proteoglycans, glycoproteins, polysaccharides and associated plasma proteins all in dynamic equilibrium. It has numerous physiological roles including the regulation of blood flow and microvascular permeability, and active participation in mechanotransduction and stress regulation, coagulation, cell adhesion, and inflammatory response. The dynamic structure and the mechanical properties of the ESL are crucial for many of its physiological properties. We present a topological model for the ESL composed of three basic macromolecular elements: branched proteoglycans, linear polysaccharide chains, and small plasma proteins. The model was studied using non-equilibrium molecular dynamics simulations and compared with scaling theories for associating tethered polymers. We discuss the observed dynamical and mechanical properties of the ESL captured by this model, and the possible physical insight it provides into the physiological behavior of the ESL.

  17. Structure of serum amyloid A suggests a mechanism for selective lipoprotein binding and functions: SAA as a hub in macromolecular interaction networks.

    PubMed

    Frame, Nicholas M; Gursky, Olga

    2016-03-01

    Serum amyloid A is a major acute-phase plasma protein that modulates innate immunity and cholesterol homeostasis. We combine sequence analysis with x-ray crystal structures to postulate that SAA acts as an intrinsically disordered hub mediating interactions among proteins, lipids and proteoglycans. A structural model of lipoprotein-bound SAA monomer is proposed wherein two α-helices from the N-domain form a concave hydrophobic surface that binds lipoproteins. A C-domain, connected to the N-domain via a flexible linker, binds polar/charged ligands including cell receptors, bridging them with lipoproteins and rerouting cholesterol transport. Our model is supported by the SAA cleavage in the interdomain linker to generate the 1-76 fragment deposited in reactive amyloidosis. This model sheds new light on functions of this enigmatic protein. PMID:26918388

  18. Taking X-ray Diffraction to the Limit: Macromolecular Structures from Femtosecond X-ray Pulses and Diffraction Microscopy of Cells with Synchrotron Radiation

    SciTech Connect

    Chapman, H N; Miao, J; Kirz, J; Sayre, D; Hodgson, K O

    2003-10-01

    The methodology of X-ray crystallography has recently been successfully extended to the structure determination of non-crystalline specimens. The phase problem was solved by using the oversampling method, which takes advantage of ''continuous'' diffraction pattern from non-crystalline specimens. Here we review the principle of this newly developed technique and discuss the ongoing experiments of imaging non-periodic objects, like cells and cellular structures using coherent and bright X-rays from the 3rd generation synchrotron radiation. In the longer run, the technique may be applied to image single biomolecules by using the anticipated X-ray free electron lasers. Computer simulations have so far demonstrated two important steps: (1) by using an extremely intense femtosecond X-ray pulse, a diffraction pattern can be recorded from a macromolecule before radiation damage manifests itself, and (2) the phase information can be ab initio retrieved from a set of calculated noisy diffraction patterns of single protein molecules.

  19. Viral capsomere structure, surface processes and growth kinetics in the crystallization of macromolecular crystals visualized by in situ atomic force microscopy

    NASA Astrophysics Data System (ADS)

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

    2001-11-01

    In situ atomic force microscopy (AFM) was used to investigate surface evolution during the growth of single crystals of turnip yellow mosaic virus (TYMV), cucumber mosaic virus (CMV) and glucose isomerase. Growth of these crystals proceeded by two-dimensional (2D) nucleation. For glucose isomerase, from supersaturation dependencies of tangential step rates and critical step length, the kinetic coefficients of the steps and the surface free energy of the step edge were calculated for different crystallographic directions. The molecular structure of the step edges, the adsorption of individual virus particles and their aggregates, and the initial stages of formation of 2D nuclei on the surfaces of TYMV and CMV crystals were recorded. The surfaces of individual TYMV virions within crystals were visualized, and hexameric and pentameric capsomers of the T=3 capsids were clearly resolved. This, so far as we are aware, is the first direct visualization of the capsomere structure of a virus by AFM. In the course of recording the in situ development of the TYMV crystals, a profound restructuring of the surface arrangement was observed. This transformation was highly cooperative in nature, but the transitions were unambiguous and readily explicable in terms of an organized loss of classes of virus particles from specific lattice positions.

  20. Complexation of Actinides in Solution: Thermodynamic Measurementsand Structural Characterization

    SciTech Connect

    Rao, L.

    2007-02-01

    This paper presents a brief introduction of the studies of actinide complexation in solution at Lawrence Berkeley National Laboratory. An integrated approach of thermodynamic measurements and structural characterization is taken to obtain fundamental understanding of actinide complexation in solution that is of importance in predicting the behavior of actinides in separation processes and environmental transport.

  1. Discovery of Water Structural Transitions near Interfaces of Polarizable Solutes

    NASA Astrophysics Data System (ADS)

    Dinpajooh, Mohammadhasan; Matyushov, Dmitry

    2015-03-01

    The standard harmonic approximation describing polarization around the solute is expected to break down with increasing solute polarizability. The focus of this study is to investigate the structure of water around dipolar-polarizable solutes by Monte Carlo (MC) simulations in the non-harmonic regime. We observe a structural transition in the water hydration shell and its condensation, which are driven by increasing the solute polarizability. There is also a crossover in the orientational structure near the point of breakdown of the harmonic approximation. At lower polarizabilities, waters in the hydration shell point their hydrogens toward the solute. The dipoles flip their orientations at the transition to the non-harmonic regime. Both the hydration shell compressibility and the electric field susceptibility display maxima in the transition region. Using the water electric field at the center of the polarizable solute as the order parameter, a Landau-type model is formulated. Its predictions are in reasonable agreement with MC simulations performed for hard sphere and Lennard Jones polarizable solutes in a TIP3P water model. The observed structural transition suggests a general crossover phenomenon driven by the stabilization energy required to polarize the solute. This research was supported by the National Science Foundation (CHE-1213288). CPU time was provided by the National Science Foundation through XSEDE resources (TG-MCB080116N).

  2. The promise of macromolecular crystallization in microfluidic chips

    NASA Technical Reports Server (NTRS)

    van der Woerd, Mark; Ferree, Darren; Pusey, Marc

    2003-01-01

    Microfluidics, or lab-on-a-chip technology, is proving to be a powerful, rapid, and efficient approach to a wide variety of bioanalytical and microscale biopreparative 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 a macromolecule solution with a standard set of premixed solutions, are relatively straightforward and have been successfully demonstrated in a microfluidics platform. Optimization methods, in which 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 microfluidics 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 and harvesting of crystals as they are grown.

  3. Energy Structure of Emission Centers in Solutions with Silver Impurity

    NASA Astrophysics Data System (ADS)

    Zashivailo, T. V.; Kushnirenko, V. I.

    The spectral properties of solutions of oxygen-containing salts and acids with admixture of Аg+ ions were studied. The spectra of absorption, photoluminescence, and photoluminescence excitation for such systems are measured in the temperature range of 4.2-290 K. The energy structure of absorption and emission centers in the solution was determined. It is shown that the spectra under study are caused by the electron transitions between the energy levels, whose structure is deformed as a result of the interaction of ions Ag+ with the environment. The experimental results are interpreted on the basis of an ionic model for complexes for investigated solutions.

  4. Design and application of PDBlib, a C++ macromolecular class library.

    PubMed

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

    1994-12-01

    PDBlib is an extensible object-oriented class library written in C++ for representing the three-dimensional structure of biological macromolecules. The software design strategy, features of many of the 129 classes currently distributed with the library, and two sample applications which use the library are described. Version 1.0 of the library represents the structural features of proteins, DNA, RNA and complexes thereof, at a level of detail on a par with that which can be parsed from a Protein Data Bank (PDB) entry. However, the memory-resident representation of the macromolecule is independent of the PDB entry and can be obtained from other sources, e.g. relational and object-oriented databases. PDBlib classes are organized into four categories: (i) classes that model the macromolecule; (ii) classes that enhance the extensibility of the library; (iii) classes that provide navigation facilities of the object-oriented macromolecular structure representation; and (iv) a class that loads a PDB file into the memory-resident object-oriented representation. A number of general-purpose procedures that return features of this representation and that are relevant to all biological disciplines are included in (i). The library has been used to develop PDBtool, a prototype structure verification tool, and PDBview, a structure rendering tool that requires no specialized graphics hardware and software. Current work centers on making the macromolecular structures represented by PDBlib persistent using a commercial object-oriented database and providing an additional class library, MMQLlib, to query those structures. PMID:7704656

  5. Molecular Ornstein-Zernike approach to the solvent effects on solute electronic structures in solution

    NASA Astrophysics Data System (ADS)

    Yoshida, Norio; Kato, Shigeki

    2000-09-01

    A new approach to ab initio electronic structure calculations of solute molecules in solution is presented. Combined with the molecular Ornstein-Zernike (MOZ) integral equation theory for polyatomic liquids, solute electronic wave function and solvent distribution around a solute are determined in a self-consistent manner. The hypernetted chain approximation is employed for solving the MOZ equation. In order to describe the short-range solute-solvent interactions, the effective potential operating solute electron is placed on a solute molecule, which is determined by a least-squares fitting to ab initio exchange repulsion/charge transfer energies. The present method, referred to as the MOZ self-consistent-field (SCF) method, is applied to a solute H2O molecule in water solvent. The solvent shift for the vertical excitation to the nπ* state of H2CO in aqueous solution is also examined. The results obtained by the MOZ-SCF calculations are compared with those by the reference interaction site model-SCF theory and the polarizable continuum model.

  6. Macromolecular crowding conditions enhance glycation and oxidation of whey proteins in ultrasound-induced Maillard reaction.

    PubMed

    Perusko, Marija; Al-Hanish, Ayah; Cirkovic Velickovic, Tanja; Stanic-Vucinic, Dragana

    2015-06-15

    High intensity ultrasound (HIUS) can promote Maillard reaction (MR). Macromolecular crowding conditions accelerate reactions and stabilise protein structure. The aim of this study was to investigate if combined application of ultrasound and macromolecular crowding can improve efficiency of MR. The presence of crowding agent (polyethylene glycol) significantly increased ultrasound-induced whey protein (WP) glycation by arabinose. An increase in glycation efficiency results only in slight change of WP structure. Macromolecular crowding intensifies oxidative modifications of WP, as well as formation of amyloid-like structures by enhancement of MR. Solubility at different pH, thermal stability and antioxidative capacity of glycated WP were increased, especially in the presence of crowding agent, compared to sonicated nonglycated proteins. The application of HIUS under crowding conditions can be a new approach for enhancement of reactions in general, enabling short processing time and mild conditions, while preserving protein structure and minimising protein aggregation. PMID:25660883

  7. Multi-crystal Anomalous Diffraction for Low-resolution Macromolecular Phasing

    SciTech Connect

    Q Liu; Z Zhang; W Hendrickson

    2011-12-31

    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{sub min} = 3.5 {angstrom}) 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.

  8. Water's structure around hydrophobic solutes and the iceberg model.

    PubMed

    Galamba, N

    2013-02-21

    The structure of water in the hydration shells of small hydrophobic solutes was investigated through molecular dynamics. The results show that a subset of water molecules in the first hydration shell of a nonpolar solute have a significantly enhanced tetrahedrality and a slightly larger number of hydrogen bonds, relative to the molecules in water at room temperature, consistent with the experimentally observed negative excess entropy and increased heat capacity of hydrophobic solutions at room temperature. This ordering results from the rearrangement of a small number of water molecules near the nonpolar solutes that occupy one to two vertices of the enhanced water tetrahedra. Although this structuring is not nearly like that often associated with a literal interpretation of the term "iceberg" in the Frank and Evans iceberg model, it does support a moderate interpretation of this model. Thus, the tetrahedral orientational order of this ensemble of water molecules is comparable to that of liquid water at ~10 °C, although not accompanied by the small contraction of the O-O distance observed in cold water. Further, we show that the structural changes of water in the vicinity of small nonpolar solutes cannot be inferred from the water radial distribution functions, explaining why this increased ordering is not observed through neutron diffraction experiments. The present results restore a molecular view where the slower translational and reorientational dynamics of water near hydrophobic groups has a structural equivalent resembling water at low temperatures. PMID:23360515

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

    SciTech Connect

    Botiz, I.; Schlaad, H.; Reiter, G.

    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.

  10. Bringing macromolecular machinery to life using 3D animation.

    PubMed

    Iwasa, Janet H

    2015-04-01

    Over the past decade, there has been a rapid rise in the use of three-dimensional (3D) animation to depict molecular and cellular processes. Much of the growth in molecular animation has been in the educational arena, but increasingly, 3D animation software is finding its way into research laboratories. In this review, I will discuss a number of ways in which 3d animation software can play a valuable role in visualizing and communicating macromolecular structures and dynamics. I will also consider the challenges of using animation tools within the research sphere. PMID:25889615

  11. Bringing single-molecule spectroscopy to macromolecular protein complexes

    PubMed Central

    Joo, Chirlmin; Fareh, Mohamed; Kim, V. Narry

    2013-01-01

    Single-molecule fluorescence spectroscopy offers real-time, nanometer-resolution information. Over the past two decades, this emerging single-molecule technique has been rapidly adopted to investigate the structural dynamics and biological functions of proteins. Despite this remarkable achievement, single-molecule fluorescence techniques must be extended to macromolecular protein complexes that are physiologically more relevant for functional studies. In this review, we present recent major breakthroughs for investigating protein complexes within cell extracts using single-molecule fluorescence. We outline the challenges, future prospects and potential applications of these new single-molecule fluorescence techniques in biological and clinical research. PMID:23200186

  12. The Contrasting Effect of Macromolecular Crowding on Amyloid Fibril Formation

    PubMed Central

    Zhou, Zheng; Zhou, Bing-Rui; Meng, Sheng-Rong; Hu, Ji-Ying; Chen, Jie; Liang, Yi

    2012-01-01

    Background Amyloid fibrils associated with neurodegenerative diseases can be considered biologically relevant failures of cellular quality control mechanisms. It is known that in vivo human Tau protein, human prion protein, and human copper, zinc superoxide dismutase (SOD1) have the tendency to form fibril deposits in a variety of tissues and they are associated with different neurodegenerative diseases, while rabbit prion protein and hen egg white lysozyme do not readily form fibrils and are unlikely to cause neurodegenerative diseases. In this study, we have investigated the contrasting effect of macromolecular crowding on fibril formation of different proteins. Methodology/Principal Findings As revealed by assays based on thioflavin T binding and turbidity, human Tau fragments, when phosphorylated by glycogen synthase kinase-3β, do not form filaments in the absence of a crowding agent but do form fibrils in the presence of a crowding agent, and the presence of a strong crowding agent dramatically promotes amyloid fibril formation of human prion protein and its two pathogenic mutants E196K and D178N. Such an enhancing effect of macromolecular crowding on fibril formation is also observed for a pathological human SOD1 mutant A4V. On the other hand, rabbit prion protein and hen lysozyme do not form amyloid fibrils when a crowding agent at 300 g/l is used but do form fibrils in the absence of a crowding agent. Furthermore, aggregation of these two proteins is remarkably inhibited by Ficoll 70 and dextran 70 at 200 g/l. Conclusions/Significance We suggest that proteins associated with neurodegenerative diseases are more likely to form amyloid fibrils under crowded conditions than in dilute solutions. By contrast, some of the proteins that are not neurodegenerative disease-associated are unlikely to misfold in crowded physiological environments. A possible explanation for the contrasting effect of macromolecular crowding on these two sets of proteins (amyloidogenic proteins and non-amyloidogenic proteins) has been proposed. PMID:22558423

  13. Enzymes as Green Catalysts for Precision Macromolecular Synthesis.

    PubMed

    Shoda, Shin-Ichiro; Uyama, Hiroshi; Kadokawa, Jun-Ichi; Kimura, Shunsaku; Kobayashi, Shiro

    2016-02-24

    The present article comprehensively reviews the macromolecular synthesis using enzymes as catalysts. Among the six main classes of enzymes, the three classes, oxidoreductases, transferases, and hydrolases, have been employed as catalysts for the in vitro macromolecular synthesis and modification reactions. Appropriate design of reaction including monomer and enzyme catalyst produces macromolecules with precisely controlled structure, similarly as in vivo enzymatic reactions. The reaction controls the product structure with respect to substrate selectivity, chemo-selectivity, regio-selectivity, stereoselectivity, and choro-selectivity. Oxidoreductases catalyze various oxidation polymerizations of aromatic compounds as well as vinyl polymerizations. Transferases are effective catalysts for producing polysaccharide having a variety of structure and polyesters. Hydrolases catalyzing the bond-cleaving of macromolecules in vivo, catalyze the reverse reaction for bond forming in vitro to give various polysaccharides and functionalized polyesters. The enzymatic polymerizations allowed the first in vitro synthesis of natural polysaccharides having complicated structures like cellulose, amylose, xylan, chitin, hyaluronan, and chondroitin. These polymerizations are "green" with several respects; nontoxicity of enzyme, high catalyst efficiency, selective reactions under mild conditions using green solvents and renewable starting materials, and producing minimal byproducts. Thus, the enzymatic polymerization is desirable for the environment and contributes to "green polymer chemistry" for maintaining sustainable society. PMID:26791937

  14. Structure and phase behavior of polyelectrolyte star solutions.

    PubMed

    Hoffmann, Norman; Likos, Christos N; Löwen, Hartmut

    2004-10-01

    Using the recently developed effective interaction potentials between polyelectrolyte stars, we examine the structure and phase behavior of solutions of the same. The effective interaction is ultrasoft and density dependent, owing to the integration of the counterionic degrees of freedom. The latter contribute extensive volume terms that must be taken into account in drawing the phase diagram of the system. The structural behavior of the uniform fluid is characterized by anomalous structure factors, akin to those found previously for solutions of uncharged star polymers. The phase diagram of the system is very rich, featuring a fluid phase at low arm numbers of the stars, two reentrant melting regions, as well as a variety of crystal structures with unusual symmetry. The physical origin of these features can be traced back to the ultrasoft nature of the effective interaction potential. PMID:15473762

  15. A theory of macromolecular chemotaxis.

    PubMed

    Schurr, J Michael; Fujimoto, Bryant S; Huynh, Leticia; Chiu, Daniel T

    2013-06-27

    A macromolecule in a gradient of a cosolute that is preferentially (relative to the solvent) either attracted to or excluded from the domain of the macromolecule should experience a thermodynamic force and move, respectively, up or down the gradient. A theory of chemotactic forces arising from such preferential interactions, especially short-range ligand binding and excluded volume interactions, is developed via an extension of Kirkwood-Buff theory. The ligand binding result is confirmed for both non-ionic and ionic cosolutes by standard solution thermodynamics. The effect of increasing the electrolyte concentration to diminish the electrostatic free energy of a charged macromolecule is also treated formally via an electrostatic macromolecule-electrolyte preferential interaction coefficient. For short-range interactions, the induced chemotactic velocity is attributed entirely to tangential tractions at the interface between the macromolecule and its surrounding solution. The velocity of a spherical macromolecule driven by such tractions is derived by a hydrodynamic calculation for steady-state creepy flow with a partial slip boundary condition. Qualitative comparisons of theoretical predictions with experimental observations of Zheng and Pollack pertaining to charged microspheres near the surfaces of non-ionic gels suggest that the reported exclusion zones are due to chemotaxis induced by gradients of base (NaOH) (or acid (HCl)) and salt. With a single adjustable parameter, namely, the ratio of slip length to area per surface carboxyl (or amidine) group, this theory yields nearly quantitative agreement with many observations. The estimated slip length for the microspheres is comparable to that obtained for bovine serum albumen by fitting the chemotactic theory to two reported cross-diffusion coefficients. When a solution with a gradient of NaOH is placed in contact with a smooth glass wall, chemotactic surface tractions are predicted to cause convection of the solution toward the acidic end of the gradient, as observed in preliminary experiments. PMID:23656252

  16. Strong solutions to a nonlinear fluid structure interaction system

    NASA Astrophysics Data System (ADS)

    Kukavica, Igor; Tuffaha, Amjad; Ziane, Mohammed

    In this paper, we prove the existence of local-in-time smooth solutions to the nonlinear fluid structure interaction model first introduced in [J.-L. Lions, Quelques méthodes de résolution des problèmes aux limites non linéaires, Dunod, 1969] and considered in [V. Barbu, Z. Grujić, I. Lasiecka, A. Tuffaha, Existence of the energy-level weak solutions for a nonlinear fluid-structure interaction model, in: Fluids and Waves, in: Contemp. Math., vol. 440, Amer. Math. Soc., Providence, RI, 2007, pp. 55-82; V. Barbu, Z. Grujić, I. Lasiecka, A. Tuffaha, Smoothness of weak solutions to a nonlinear fluid-structure interaction model, Indiana Univ. Math. J. 57 (3) (2008) 1173-1207]. In particular, the strong solutions here are obtained given initial datum for the Navier-Stokes equation in the space H, and initial data for the wave equation w and w in the spaces H(Ω) and H(Ω) respectively.

  17. A local-optimization refinement algorithm in single particle analysis for macromolecular complex with multiple rigid modules.

    PubMed

    Shan, Hong; Wang, Zihao; Zhang, Fa; Xiong, Yong; Yin, Chang-Cheng; Sun, Fei

    2016-01-01

    Single particle analysis, which can be regarded as an average of signals from thousands or even millions of particle projections, is an efficient method to study the three-dimensional structures of biological macromolecules. An intrinsic assumption in single particle analysis is that all the analyzed particles must have identical composition and conformation. Thus specimen heterogeneity in either composition or conformation has raised great challenges for high-resolution analysis. For particles with multiple conformations, inaccurate alignments and orientation parameters will yield an averaged map with diminished resolution and smeared density. Besides extensive classification approaches, here based on the assumption that the macromolecular complex is made up of multiple rigid modules whose relative orientations and positions are in slight fluctuation around equilibriums, we propose a new method called as local optimization refinement to address this conformational heterogeneity for an improved resolution. The key idea is to optimize the orientation and shift parameters of each rigid module and then reconstruct their three-dimensional structures individually. Using simulated data of 80S/70S ribosomes with relative fluctuations between the large (60S/50S) and the small (40S/30S) subunits, we tested this algorithm and found that the resolutions of both subunits are significantly improved. Our method provides a proof-of-principle solution for high-resolution single particle analysis of macromolecular complexes with dynamic conformations. PMID:26678751

  18. Systematic solution to homo-oligomeric structures determined by NMR

    PubMed Central

    Martin, Jeffrey W.; Zhou, Pei; Donald, Bruce R.

    2015-01-01

    Protein structure determination by NMR has predominantly relied on simulated annealing-based conformational search for a converged fold using primarily distance constraints, including constraints derived from nuclear Overhauser effects (NOEs), paramagnetic relaxation enhancement (PRE), and cysteine crosslinkings. Although there is no guarantee that the converged fold represents the global minimum of the conformational space, it is generally accepted that good convergence is synonymous to the global minimum. Here, we show such a criterion breaks down in the presence of large numbers of ambiguous constraints from NMR experiments on homo-oligomeric protein complexes. A systematic evaluation of the conformational solutions that satisfy the NMR constraints of a trimeric membrane protein, DAGK, reveals 9 distinct folds, including the reported NMR and crystal structures. This result highlights the fundamental limitation of global fold determination for homo-oligomeric proteins using ambiguous distance constraints and provides a systematic solution for exhaustive enumeration of all satisfying solutions. PMID:25620116

  19. Solution structures of nanoassemblies based on pyrogallol[4]arenes.

    PubMed

    Kumari, Harshita; Deakyne, Carol A; Atwood, Jerry L

    2014-10-21

    Nanoassemblies of hydrogen-bonded and metal-seamed pyrogallol[4]arenes have been shown to possess novel solution-phase geometries. Further, we have demonstrated that both guest encapsulation and structural rearrangements may be studied by solution-phase techniques such as small-angle neutron scattering (SANS) and diffusion NMR. Application of these techniques to pyrogallol[4]arene-based nanoassemblies has allowed (1) differentiation among spherical, ellipsoidal, toroidal, and tubular structures in solution, (2) determination of factors that control the preferred geometrical shape and size of the nanoassemblies, and (3) detection of small variations in metric dimensions distinguishing similarly and differently shaped nanoassemblies in a given solution. Indeed, we have shown that the solution-phase structure of such nanoassemblies is often quite different from what one would predict based on solid-state studies, a result in disagreement with the frequently made assumption that these assemblies have similar structures in the two phases. We instead have predicted solid-state architectures from solution-phase structures by combining the solution-phase analysis with solid-state magnetic and elemental analyses. Specifically, the iron-seamed C-methylpyrogallol[4]arene nanoassembly was found to be tubular in solution and predicted to be tubular in the solid state, but it was found to undergo a rearrangement from a tubular to spherical geometry in solution as a function of base concentration. The absence of metal within a tubular framework affects its stability in both solution and the solid state; however, this instability is not necessarily characteristic of hydrogen-bonded capsular entities. Even metal seaming of the capsules does not guarantee similar solid-state and solution-phase architectures. The rugby ball-shaped gallium-seamed C-butylpyrogallol[4]arene hexamer becomes toroidal on dissolution, as does the spherically shaped gallium/zinc-seamed C-butylpyrogallol[4]arene hexamer. However, the arenes are arranged differently in the two toroids, a variation that accounts for the differences in their sizes and guest encapsulation. Guest encapsulation of biotemplates, such as insulin, has demonstrated the feasibility of synthesizing nanocapsules with a volume three times that of a hexamer. The solution-phase studies have also demonstrated that the self-assembly of dimers versus hexamers can be controlled by the choice of metal, solvent, and temperature. Controlling the size of the host, nature of the metal, and identity of the guest will allow construction of targeted host-guest assemblies having potential uses as drug delivery agents, nanoscale reaction vessels, and radioimaging/radiotherapy agents. Overall, the present series of solid- and solution-phase studies has begun to pave the way toward a more complete understanding of the properties and behavior of complex supramolecular nanoassemblies. PMID:25198830

  20. Solution structure by site directed tryptophan fluorescence in tear lipocalin.

    PubMed

    Gasymov, O K; Abduragimov, A R; Yusifov, T N; Glasgow, B J

    1997-10-01

    The solution structure of the G strand of human tear lipocalin was deduced by site directed tryptophan fluorescence (SDTF). The fluorescent amino acid, tryptophan, was sequentially substituted for each native amino acid in the sequence of the G strand. The fluorescent properties resolved alternating periodicity as predicted for beta sheet structure, twists in the beta sheet, strand orientation in the lipocalin cavity, and the relative depth of residues in the cavity. A distribution of microstates with various orientations of dipoles in the side chain environments of the G strand revealed mobility on the nanosecond time scale. SDTF is broadly applicable to most proteins and will complement x-ray crystallography, site directed spin labeling by electron paramagnetic resonance (EPR), and nuclear magnetic resonance (NMR) in the determination of solution structure. PMID:9345294

  1. 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

  2. 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

  3. Preparation of phenylboronate affinity rigid monolith with macromolecular porogen.

    PubMed

    Li, Xiang-Jie; Jia, Man; Zhao, Yong-Xin; Liu, Zhao-Sheng; Akber Aisa, Haji

    2016-03-18

    Boronate-affinity monolithic column was first prepared via polystyrene (PS) as porogen in this work. The monolithic polymer was synthetized using 4-vinylphenylboronic acid (4-VPBA) as functional monomer, ethylene glycol dimethacrylate (EDMA) as crosslinker monomer, and a mixture of PS solution in tetrahydrofuran, the linear macromolecular porogen, and toluene as porogen. Isoquercitrin (ISO) and hyperoside (HYP), isomer diol flavonoid glycosides, can be baseline separated on the poly(VPBA-co-EDMA) monolith. The effect of polymerization variables on the selectivity factor, e.g., the ratio of monomer to crosslinker (M/C), the amount of PS and the molecular weight of macromolecular porogen was investigated. The surface properties of the monolithic polymer were characterized by scanning electron microscopy and nitrogen adsorption. The best polymerization condition was the M/C ratio of 7:3, and the PS concentration of 40mg/ml. The poly(VPBA-co-EDMA) polymer was also applied to extract cis-diol flavonoid glycosides from the crude extraction of cotton flower. After treated by poly(VPBA-co-EDMA) for solid phase extraction, high purity ISO and HYP (>99.96%) can be obtained with recovery of 83.7% and 78.6%, respectively. PMID:26896914

  4. Probing the hydration water diffusion of macromolecular surfaces and interfaces

    NASA Astrophysics Data System (ADS)

    Ortony, Julia H.; Cheng, Chi-Yuan; Franck, John M.; Kausik, Ravinath; Pavlova, Anna; Hunt, Jasmine; Han, Songi

    2011-01-01

    We probe the translational dynamics of the hydration water surrounding the macromolecular surfaces of selected polyelectrolytes, lipid vesicles and intrinsically disordered proteins with site specificity in aqueous solutions. These measurements are made possible by the recent development of a new instrumental and methodological approach based on Overhauser dynamic nuclear polarization (DNP)-enhanced nuclear magnetic resonance (NMR) spectroscopy. This technique selectively amplifies 1H NMR signals of hydration water around a spin label that is attached to a molecular site of interest. The selective 1H NMR amplification within molecular length scales of a spin label is achieved by utilizing short-distance range (~r-3) magnetic dipolar interactions between the 1H spin of water and the electron spin of a nitroxide radical-based label. Key features include the fact that only minute quantities (<10 μl) and dilute (>=100 μM) sample concentrations are needed. There is no size limit on the macromolecule or molecular assembly to be analyzed. Hydration water with translational correlation times between 10 and 800 ps is measured within ~10 Å distance of the spin label, encompassing the typical thickness of a hydration layer with three water molecules across. The hydration water moving within this time scale has significant implications, as this is what is modulated whenever macromolecules or molecular assemblies undergo interactions, binding or conformational changes. We demonstrate, with the examples of polymer complexation, protein aggregation and lipid-polymer interaction, that the measurements of interfacial hydration dynamics can sensitively and site specifically probe macromolecular interactions.

  5. Structure of graphene oxide membranes in solvents and solutions

    NASA Astrophysics Data System (ADS)

    Klechikov, Alexey; Yu, Junchun; Thomas, Diana; Sharifi, Tiva; Talyzin, Alexandr V.

    2015-09-01

    The change of distance between individual graphene oxide sheets due to swelling is the key parameter to explain and predict permeation of multilayered graphene oxide (GO) membranes by various solvents and solutions. In situ synchrotron X-ray diffraction study shows that swelling properties of GO membranes are distinctly different compared to precursor graphite oxide powder samples. Intercalation of liquid dioxolane, acetonitrile, acetone, and chloroform into the GO membrane structure occurs with maximum one monolayer insertion (Type I), in contrast with insertion of 2-3 layers of these solvents into the graphite oxide structure. However, the structure of GO membranes expands in liquid DMSO and DMF solvents similarly to precursor graphite oxide (Type II). It can be expected that Type II solvents will permeate GO membranes significantly faster compared to Type I solvents. The membranes are found to be stable in aqueous solutions of acidic and neutral salts, but dissolve slowly in some basic solutions of certain concentrations, e.g. in NaOH, NaHCO3 and LiF. Some larger organic molecules, alkylamines and alkylammonium cations are found to intercalate and expand the lattice of GO membranes significantly, e.g. up to ~35 Å in octadecylamine/methanol solution. Intercalation of solutes into the GO structure is one of the limiting factors for nano-filtration of certain molecules but it also allows modification of the inter-layer distance of GO membranes and tuning of their permeation properties. For example, GO membranes functionalized with alkylammonium cations are hydrophobized and they swell in non-polar solvents.The change of distance between individual graphene oxide sheets due to swelling is the key parameter to explain and predict permeation of multilayered graphene oxide (GO) membranes by various solvents and solutions. In situ synchrotron X-ray diffraction study shows that swelling properties of GO membranes are distinctly different compared to precursor graphite oxide powder samples. Intercalation of liquid dioxolane, acetonitrile, acetone, and chloroform into the GO membrane structure occurs with maximum one monolayer insertion (Type I), in contrast with insertion of 2-3 layers of these solvents into the graphite oxide structure. However, the structure of GO membranes expands in liquid DMSO and DMF solvents similarly to precursor graphite oxide (Type II). It can be expected that Type II solvents will permeate GO membranes significantly faster compared to Type I solvents. The membranes are found to be stable in aqueous solutions of acidic and neutral salts, but dissolve slowly in some basic solutions of certain concentrations, e.g. in NaOH, NaHCO3 and LiF. Some larger organic molecules, alkylamines and alkylammonium cations are found to intercalate and expand the lattice of GO membranes significantly, e.g. up to ~35 Å in octadecylamine/methanol solution. Intercalation of solutes into the GO structure is one of the limiting factors for nano-filtration of certain molecules but it also allows modification of the inter-layer distance of GO membranes and tuning of their permeation properties. For example, GO membranes functionalized with alkylammonium cations are hydrophobized and they swell in non-polar solvents. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr04096e

  6. Electronic structures of Ascaris trypsin inhibitor in solution

    NASA Astrophysics Data System (ADS)

    Zheng, Haoping

    2003-11-01

    The electronic structures of Ascaris trypsin inhibitor in solution are obtained by the first-principles, all-electron, ab initio calculation using the self-consistent cluster-embedding (SCCE) method. The inhibitor, made up of 62 amino acid residues with 912 atoms, has two three-dimensional solution structures: 1ata and 1atb. The calculated ground-state energy of structure 1atb is lower than that of structure 1ata by 6.12 eV. The active sites are determined and explained: only structure 1atb has a N terminal at residue ARG+31. This shows that the structure 1atb is the stable and active form of the inhibitor, which is in agreement with the experimental results. The calculation reveals that some parts of the inhibitor can be easily changed while the inhibitor’s biological activity may be kept. This kind of information may be helpful in fighting viruses such as AIDS, SARS, and flu, since these viruses have higher variability. The calculation offers an independent theoretical estimate of the precision of structure determination.

  7. Structure of graphene oxide membranes in solvents and solutions.

    PubMed

    Klechikov, Alexey; Yu, Junchun; Thomas, Diana; Sharifi, Tiva; Talyzin, Alexandr V

    2015-10-01

    The change of distance between individual graphene oxide sheets due to swelling is the key parameter to explain and predict permeation of multilayered graphene oxide (GO) membranes by various solvents and solutions. In situ synchrotron X-ray diffraction study shows that swelling properties of GO membranes are distinctly different compared to precursor graphite oxide powder samples. Intercalation of liquid dioxolane, acetonitrile, acetone, and chloroform into the GO membrane structure occurs with maximum one monolayer insertion (Type I), in contrast with insertion of 2-3 layers of these solvents into the graphite oxide structure. However, the structure of GO membranes expands in liquid DMSO and DMF solvents similarly to precursor graphite oxide (Type II). It can be expected that Type II solvents will permeate GO membranes significantly faster compared to Type I solvents. The membranes are found to be stable in aqueous solutions of acidic and neutral salts, but dissolve slowly in some basic solutions of certain concentrations, e.g. in NaOH, NaHCO3 and LiF. Some larger organic molecules, alkylamines and alkylammonium cations are found to intercalate and expand the lattice of GO membranes significantly, e.g. up to ∼35 Å in octadecylamine/methanol solution. Intercalation of solutes into the GO structure is one of the limiting factors for nano-filtration of certain molecules but it also allows modification of the inter-layer distance of GO membranes and tuning of their permeation properties. For example, GO membranes functionalized with alkylammonium cations are hydrophobized and they swell in non-polar solvents. PMID:26332400

  8. Macromolecular extraction based on contour evolution

    NASA Astrophysics Data System (ADS)

    Wang, Zhaobin; Guo, Miao; Zhu, Ying; Yang, Lizhen; Ma, Yi-de

    2013-03-01

    Detecting the region of interest plays an important role in the field of image processing and analysis. For the microscopic image of plant embryo slice, region of interest usually indicates various cells or macromolecules. Combining contour evolution theory and pulse coupled neural network, we propose a new method of macromolecular detection and extraction for biological microscopic image. Some existing methods are compared with the proposed method. Experimental results show the proposed method has the better performance than existing methods.

  9. Connecting the Dots: The Effects of Macromolecular Crowding on Cell Physiology

    PubMed Central

    Mourão, Márcio A.; Hakim, Joe B.; Schnell, Santiago

    2014-01-01

    The physicochemical properties of cellular environments with a high macromolecular content have been systematically characterized to explain differences observed in the diffusion coefficients, kinetics parameters, and thermodynamic properties of proteins inside and outside of cells. However, much less attention has been given to the effects of macromolecular crowding on cell physiology. Here, we review recent findings that shed some light on the role of crowding in various cellular processes, such as reduction of biochemical activities, structural reorganization of the cytoplasm, cytoplasm fluidity, and cellular dormancy. We conclude by presenting some unresolved problems that require the attention of biophysicists, biochemists, and cell physiologists. Although it is still underappreciated, macromolecular crowding plays a critical role in life as we know it. PMID:25517143

  10. Radiation damage in macromolecular crystallography: what is it and why should we care?

    SciTech Connect

    Garman, Elspeth F.

    2010-04-01

    The basic causes of the radiation damage inflicted on macromolecular crystals during diffraction experiments are summarized, as well as the current state of research which attempts to understand and to mitigate it. Radiation damage inflicted during diffraction data collection in macromolecular crystallography has re-emerged in the last decade as a major experimental and computational challenge, as even for crystals held at 100 K it can result in severe data-quality degradation and the appearance in solved structures of artefacts which affect biological interpretations. Here, the observable symptoms and basic physical processes involved in radiation damage are described and the concept of absorbed dose as the basic metric against which to monitor the experimentally observed changes is outlined. Investigations into radiation damage in macromolecular crystallography are ongoing and the number of studies is rapidly increasing. The current literature on the subject is compiled as a resource for the interested researcher.

  11. 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 ρ 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.

  12. On the solution of creep induced buckling in general structure

    NASA Technical Reports Server (NTRS)

    Padovan, J.; Tovichakchaikul, S.

    1982-01-01

    This paper considers the pre and post buckling behavior of general structures exposed to high temperature fields for long durations wherein creep effects become significant. The solution to this problem is made possible through the use of closed upper bounding constraint surfaces which enable the development of a new time stepping algorithm. This permits the stable and efficient solution of structural problems which exhibit indefinite tangent properties. Due to the manner of constraining/bounding successive iterates, the algorithm developed herein is largely self adaptive, inherently stable, sufficiently flexible to handle geometric material and boundary induced nonlinearity, and can be incorporated into either finite element or difference simulations. To illustrate the capability of the procedure, as well as, the physics of creep induced pre and post buckling behavior, the results of several numerical experiments are included.

  13. Understanding the defect structure of solution grown zinc oxide

    SciTech Connect

    Liew, Laura-Lynn; Sankar, Gopinathan; Handoko, Albertus D.; Goh, Gregory K.L.; Kohara, Shinji

    2012-05-15

    Zinc oxide (ZnO) is a wide bandgap semiconducting oxide with many potential applications in various optoelectronic devices such as light emitting diodes (LEDs) and field effect transistors (FETs). Much effort has been made to understand the ZnO structure and its defects. However, one major issue in determining whether it is Zn or O deficiency that provides ZnO its unique properties remains. X-ray absorption spectroscopy (XAS) is an ideal, atom specific characterization technique that is able to probe defect structure in many materials, including ZnO. In this paper, comparative studies of bulk and aqueous solution grown ({<=}90 Degree-Sign C) ZnO powders using XAS and x-ray pair distribution function (XPDF) techniques are described. The XAS Zn-Zn correlation and XPDF results undoubtedly point out that the solution grown ZnO contains Zn deficiency, rather than the O deficiency that were commonly reported. This understanding of ZnO short range order and structure will be invaluable for further development of solid state lighting and other optoelectronic device applications. - Graphical abstract: Highlights: Black-Right-Pointing-Pointer ZnO powders have been synthesized through an aqueous solution method. Black-Right-Pointing-Pointer Defect structure studied using XAS and XPDF. Black-Right-Pointing-Pointer Zn-Zn correlations are less in the ZnO powders synthesized in solution than bulk. Black-Right-Pointing-Pointer Zn vacancies are present in the powders synthesized. Black-Right-Pointing-Pointer EXAFS and XPDF, when used complementary, are useful characterization techniques.

  14. Crystallization of macromolecular complexes: combinatorial complex crystallization

    NASA Astrophysics Data System (ADS)

    Stura, Enrico A.; Graille, Marc; Charbonnier, Jean-Baptiste

    2001-11-01

    The usefulness of antibody complexation, as a way of increasing the chances of crystallization needs to be re-evaluated after many antibody complexes have been crystallized and their structure determined. It is somewhat striking that among these, only a small number is a complex with a large protein antigen. The problem is that the effort of raising, cleaving and purifying an Fab is rewarded only by an extra chance of getting crystals; depending on the relative likelihood of crystallization of the complexed and uncomplexed protein. The example of the complex between HIV gp120, CD4 and an Fab fragment from a neutralizing antibody suggests that further complexation of an antigen-antibody complex with a third protein could, by increasing the number of possible combinations, improve the likelihood of crystallization. We propose the use of Ig-binding proteins as a way of extending the method from HIV gp120 to all proteins for which there are monoclonal antibodies. We discuss this technique, combinatorial complex crystallization (CCC), as part of a multi-component system for the enhancement of crystallization of macromolecular complexes. The method makes use of single Ig-binding domains from Staphylococcus aureus protein A (SpA), Peptostreptococcus magnus protein L (PpL) and the streptococcal protein G (SpG). The generality of the method depends on the ability of these domains to interact with a large repertoire of antibodies without affecting antigen binding. There is strong evidence to suggest that these Ig-binding domains bind outside the antigen-combining site of the antibody without perturbing antigen binding. It is clear from the crystal structure of the single SpG domain complexed with an Fab that the interaction involves mainly the immunoglobulin CH1 domain, a region not involved in antigen recognition. We have recently determined the structure of the complex between a human Fab and the domain D from SpA and found that steric hindrance is unlikely even for large antigens. We find that such binding involves only the well conserved framework region of the variable domain of the antibody heavy chain (VH) and does not affect the conformation of the hypervariable loops that define the antigen recognition site. Thus this domain could be used to complex to Fab or Fv fragments derived from a wide variety of antibodies. While protein A complexes with the VH domain, protein L recognizes the VL region of immunoglobulins. Our recent study of the interaction between an Fab and a domain of protein L shows that the situation is very similar. Indeed this domain binds to the VL framework region outside the antigen binding site. Since individual domains from each of these three multi-domain proteins bind to well separated and independent locations on immunoglobulins, they can be combined to search for a suitable crystalline lattice. This allows us to propose a combinatorial method as a rational way to exploit antibody complexation for the crystallographic structure determination of proteins that are otherwise difficult to crystallize. The overall method has strong parallels with other combinatorial methods used elsewhere in biology and chemistry, and we propose that together with stoichiometry variation screening (SVS), it may further enhance the probability of crystallization.

  15. 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.

  16. Outrunning free radicals in room-temperature macromolecular crystallography

    PubMed Central

    Owen, Robin L.; Axford, Danny; Nettleship, Joanne E.; Owens, Raymond J.; Robinson, James I.; Morgan, Ann W.; Doré, Andrew S.; Lebon, Guillaume; Tate, Christopher G.; Fry, Elizabeth E.; Ren, Jingshan; Stuart, David I.; Evans, Gwyndaf

    2012-01-01

    A significant increase in the lifetime of room-temperature macromolecular crystals is reported through the use of a high-brilliance X-ray beam, reduced exposure times and a fast-readout detector. This is attributed to the ability to collect diffraction data before hydroxyl radicals can propagate through the crystal, fatally disrupting the lattice. Hydroxyl radicals are shown to be trapped in amorphous solutions at 100 K. The trend in crystal lifetime was observed in crystals of a soluble protein (immunoglobulin γ Fc receptor IIIa), a virus (bovine enterovirus serotype 2) and a membrane protein (human A2A adenosine G-protein coupled receptor). The observation of a similar effect in all three systems provides clear evidence for a common optimal strategy for room-temperature data collection and will inform the design of future synchrotron beamlines and detectors for macro­molecular crystallography. PMID:22751666

  17. Influence of the extraction time on macromolecular parameters of galactomannans.

    PubMed

    Salvalaggio, Marina de Oliveira; de Freitas, Rilton Alves; Franquetto, Elvis Marcelo; Koop, Heidegrid Siebert; Silveira, Joana Léa Meira

    2015-02-13

    This study evaluated the aqueous extraction of galactomannans from the seeds of Mimosa scabrella (GM), Stryphnodendron adstringens (GS) and Schizolobium parahybae (GG) for 1, 2, 3, 4, 6, 24 and 48 h. The efficiency of extraction processes was assessed in terms of yield, carbohydrate and protein content. The extraction process, as well as the source of the galactomananns generated molecules with differences in molar mass, viscosity and rigidity analyzed by HPSEC-MALLS/RI/VIS. The extraction time results for each species, based on minimum extraction time and HPSEC-MALLS/RI/VIS results, were 4 h (GM4h), 6 h (GS6h) and 2 h (GG2h) for GM, GS and GG, respectively. In most cases, the apparent persistence length, as determined by viscometry, indicated that aggregates remained in galactomannans after centrifugation and filtration. Results suggest an effective extraction time for each plant source of galactomannan based on its performance and its macromolecular behavior in solution. PMID:25458290

  18. Flavin adenine dinucleotide structural motifs: from solution to gas phase.

    PubMed

    Molano-Arevalo, Juan Camilo; Hernandez, Diana R; Gonzalez, Walter G; Miksovska, Jaroslava; Ridgeway, Mark E; Park, Melvin A; Fernandez-Lima, Francisco

    2014-10-21

    Flavin adenine dinucleotide (FAD) is involved in important metabolic reactions where the biological function is intrinsically related to changes in conformation. In the present work, FAD conformational changes were studied in solution and in gas phase by measuring the fluorescence decay time and ion-neutral collision cross sections (CCS, in a trapped ion mobility spectrometer, TIMS) as a function of the solvent conditions (i.e., organic content) and gas-phase collisional partner (i.e., N2 doped with organic molecules). Changes in the fluorescence decay suggest that FAD can exist in four conformations in solution, where the abundance of the extended conformations increases with the organic content. TIMS-MS experiments showed that FAD can exist in the gas phase as deprotonated (M = C27H31N9O15P2) and protonated forms (M = C27H33N9O15P2) and that multiple conformations (up to 12) can be observed as a function of the starting solution for the [M + H](+) and [M + Na](+)molecular ions. In addition, changes in the relative abundances of the gas-phase structures were observed from a "stack" to a "close" conformation when organic molecules were introduced in the TIMS cell as collision partners. Candidate structures optimized at the DFT/B3LYP/6-31G(d,p) were proposed for each IMS band, and results showed that the most abundant IMS band corresponds to the most stable candidate structure. Solution and gas-phase experiments suggest that the driving force that stabilizes the different conformations is based on the interaction of the adenine and isoalloxazine rings that can be tailored by the "solvation" effect created with the organic molecules. PMID:25222439

  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. 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)

  1. Solution structure of murine macrophage inflammatory protein-2.

    PubMed

    Shao, W; Jerva, L F; West, J; Lolis, E; Schweitzer, B I

    1998-06-01

    The solution structure of murine macrophage inflammatory protein-2 (MIP-2), a heparin-binding chemokine that is secreted in response to inflammatory stimuli, has been determined using two-dimensional homonuclear and heteronuclear NMR spectroscopy. Structure calculations were carried out by means of torsion-angle molecular dynamics using the program X-PLOR. The structure is based on a total of 2390 experimental restraints, comprising 2246 NOE-derived distance restraints, 44 distance restraints for 22 hydrogen bonds, and 100 torsion angle restraints. The structure is well-defined, with the backbone (N, Calpha, C) and heavy atom atomic rms distribution about the mean coordinates for residues 9-69 of the dimer being 0.57 +/- 0.16 A and 0.96 +/- 0.12 A, respectively. The N- and C-terminal residues (1-8 and 70-73, respectively) are disordered. The overall structure of the MIP-2 dimer is similar to that reported previously for the NMR structures of MGSA and IL-8 and consists of a six-stranded antiparallel beta-sheet (residue 25-29, 39-44, and 48-52) packed against two C-terminal antiparallel alpha-helices. A best fit superposition of the NMR structure of MIP-2 on the structures of MGSA, NAP-2, and the NMR and X-ray structures of IL-8 are 1.11, 1.02, 1.27, and 1.19 A, respectively, for the monomers, and 1.28, 1.10, 1.55, and 1.36 A, respectively, for the dimers (IL-8 residues 7-14 and 16-67, NAP-2 residues 25-84). At the tertiary level, the main differences between the MIP-2 solution structure and the IL-8, MGSA, and NAP-2 structures involve the N-terminal loop between residues 9-23 and the loops formed by residues 30-38 and residues 53-58. At the quaternary level, the difference between MIP-2 and IL-8, MGSA, or NAP-2 results from differing interhelical angles and separations. PMID:9622482

  2. NMR solution structure of a parallel LNA quadruplex

    PubMed Central

    Randazzo, Antonio; Esposito, Veronica; Ohlenschläger, Oliver; Ramachandran, Ramadurai; Mayol, Luciano

    2004-01-01

    The solution structure of a locked nucleic acid (LNA) quadruplex, formed by the oligomer d(TGGGT), containing only conformationally restricted LNA residues is reported. NMR and CD spectroscopy, as well as molecular dynamics and mechanic calculations, has been used to characterize the complex. The molecule adopts a parallel stranded conformation with a 4-fold rotational symmetry, showing a right-handed helicity and the guanine residues in an almost planar conformation with three well-defined G-tetrads. The thermal stability of Q-LNA has been found to be comparable with that of [r(UGGGU)]4, while a Tm increment of 20°C with respect to the corresponding DNA quadruplex structure [d(TGGGT)]4 has been observed. The structural features of the LNA quadruplex reported here may open new perspectives for the biological application of LNAs as novel versatile tools to design aptamer or catalyst oligonucleotides. PMID:15181173

  3. Solution structure and dynamics of bovine beta-lactoglobulin A.

    PubMed Central

    Kuwata, K.; Hoshino, M.; Forge, V.; Era, S.; Batt, C. A.; Goto, Y.

    1999-01-01

    Using heteronuclear NMR spectroscopy, we studied the solution structure and dynamics of bovine beta-lactoglobulin A at pH 2.0 and 45 degrees C, where the protein exists as a monomeric native state. The monomeric NMR structure, comprising an eight-stranded continuous antiparallel beta-barrel and one major alpha-helix, is similar to the X-ray dimeric structure obtained at pH 6.2, including betaI-strand that forms the dimer interface and loop EF that serves as a lid of the interior hydrophobic hole. [1H]-15N NOE revealed that betaF, betaG, and betaH strands buried under the major alpha-helix are rigid on a pico- to nanosecond time scale and also emphasized rapid fluctuations of loops and the N- and C-terminal regions. PMID:10595563

  4. 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.

  5. Macromolecular Crystallization with Microfluidic Free-Interface Diffusion

    SciTech Connect

    Segelke, B

    2005-02-24

    Fluidigm released the Topaz 1.96 and 4.96 crystallization chips in the fall of 2004. Topaz 1.96 and 4.96 are the latest evolution of Fluidigm's microfluidics crystallization technologies that enable ultra low volume rapid screening for macromolecular crystallization. Topaz 1.96 and 4.96 are similar to each other but represent a major redesign of the Topaz system and have of substantially improved ease of automation and ease of use, improved efficiency and even further reduced amount of material needed. With the release of the new Topaz system, Fluidigm continues to set the standard in low volume crystallization screening which is having an increasing impact in the field of structural genomics, and structural biology more generally. In to the future we are likely to see further optimization and increased utility of the Topaz crystallization system, but we are also likely to see further innovation and the emergence of competing technologies.

  6. Structural dynamics of surfactant solutions in planar extensional flow

    NASA Astrophysics Data System (ADS)

    Luo, Binbin; Burghardt, Wesley

    2015-03-01

    We report in situ x-ray scattering investigation of the structure of aqueous surfactant solutions in planar extensional flow. Samples were studied in a cross-slot stagnation flow cell fed by a syringe pump using a highly collimated synchrtron x-ray beam that provides for spatially resolved measurements of fluid structure in the stagnation region of the flow. Prior attempts to use planar stagnation flows for either x-ray or neutron scattering employed low-aspect ratio flow geometries in which the kinematics are dominated by parasitic velocity gradients along the incident beam direction. In contrast, our cross-slot flow cell employs an aspect ratio of 5:1, providing a much more ideal two-dimensional extensional flow field in the stagnation region. This device has been used to study two different surfactant systems, one a wormlike micelle solution at high salt concentration which exhibits rheology similar to that of entangled polymers. Here the focus is on the degree of micelle orientation produced as a function of extension rate. We have also studied a system that forms lamellar ordering. In addition to induced alignment of the mesophase structure, it is also possible to interrogate flow-induced changes in lamellar d-spacing in this material.

  7. 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.

  8. The interplay of intrinsic disorder and macromolecular crowding on α-synuclein fibril formation.

    PubMed

    Shirai, Nobu C; Kikuchi, Macoto

    2016-02-01

    α-synuclein (α-syn) is an intrinsically disordered protein which is considered to be one of the causes of Parkinson's disease. This protein forms amyloid fibrils when in a highly concentrated solution. The fibril formation of α-syn is induced not only by increases in α-syn concentration but also by macromolecular crowding. In order to investigate the coupled effect of the intrinsic disorder of α-syn and macromolecular crowding, we construct a lattice gas model of α-syn in contact with a crowding agent reservoir based on statistical mechanics. The main assumption is that α-syn can be expressed as coarse-grained particles with internal states coupled with effective volume; and disordered states are modeled by larger particles with larger internal entropy than other states. Thanks to the simplicity of the model, we can exactly calculate the number of conformations of crowding agents, and this enables us to prove that the original grand canonical ensemble with a crowding agent reservoir is mathematically equivalent to a canonical ensemble without crowding agents. In this expression, the effect of macromolecular crowding is absorbed in the internal entropy of disordered states; it is clearly shown that the crowding effect reduces the internal entropy. Based on Monte Carlo simulation, we provide scenarios of crowding-induced fibril formation. We also discuss the recent controversy over the existence of helically folded tetramers of α-syn, and suggest that macromolecular crowding is the key to resolving the controversy. PMID:26851933

  9. The interplay of intrinsic disorder and macromolecular crowding on α-synuclein fibril formation

    NASA Astrophysics Data System (ADS)

    Shirai, Nobu C.; Kikuchi, Macoto

    2016-02-01

    α-synuclein (α-syn) is an intrinsically disordered protein which is considered to be one of the causes of Parkinson's disease. This protein forms amyloid fibrils when in a highly concentrated solution. The fibril formation of α-syn is induced not only by increases in α-syn concentration but also by macromolecular crowding. In order to investigate the coupled effect of the intrinsic disorder of α-syn and macromolecular crowding, we construct a lattice gas model of α-syn in contact with a crowding agent reservoir based on statistical mechanics. The main assumption is that α-syn can be expressed as coarse-grained particles with internal states coupled with effective volume; and disordered states are modeled by larger particles with larger internal entropy than other states. Thanks to the simplicity of the model, we can exactly calculate the number of conformations of crowding agents, and this enables us to prove that the original grand canonical ensemble with a crowding agent reservoir is mathematically equivalent to a canonical ensemble without crowding agents. In this expression, the effect of macromolecular crowding is absorbed in the internal entropy of disordered states; it is clearly shown that the crowding effect reduces the internal entropy. Based on Monte Carlo simulation, we provide scenarios of crowding-induced fibril formation. We also discuss the recent controversy over the existence of helically folded tetramers of α-syn, and suggest that macromolecular crowding is the key to resolving the controversy.

  10. Macromolecular Crowding Modulates Folding Mechanism of α/β Protein Apoflavodoxin

    PubMed Central

    Homouz, Dirar; Stagg, Loren; Wittung-Stafshede, Pernilla; Cheung, Margaret S.

    2009-01-01

    Abstract Protein dynamics in cells may be different from those in dilute solutions in vitro, because the environment in cells is highly concentrated with other macromolecules. This volume exclusion because of macromolecular crowding is predicted to affect both equilibrium and kinetic processes involving protein conformational changes. To quantify macromolecular crowding effects on protein folding mechanisms, we investigated the folding energy landscape of an α/β protein, apoflavodoxin, in the presence of inert macromolecular crowding agents, using in silico and in vitro approaches. By means of coarse-grained molecular simulations and topology-based potential interactions, we probed the effects of increased volume fractions of crowding agents (ϕc) as well as of crowding agent geometry (sphere or spherocylinder) at high ϕc. Parallel kinetic folding experiments with purified Desulfovibro desulfuricans apoflavodoxin in vitro were performed in the presence of Ficoll (sphere) and Dextran (spherocylinder) synthetic crowding agents. In conclusion, we identified the in silico crowding conditions that best enhance protein stability, and discovered that upon manipulation of the crowding conditions, folding routes experiencing topological frustrations can be either enhanced or relieved. Our test-tube experiments confirmed that apoflavodoxin's time-resolved folding path is modulated by crowding agent geometry. Macromolecular crowding effects may be a tool for the manipulation of protein-folding and function in living cells. PMID:19167312

  11. 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.)

  12. Solution structure of the human signaling protein RACK1

    PubMed Central

    2010-01-01

    Background The adaptor protein RACK1 (receptor of activated kinase 1) was originally identified as an anchoring protein for protein kinase C. RACK1 is a 36 kDa protein, and is composed of seven WD repeats which mediate its protein-protein interactions. RACK1 is ubiquitously expressed and has been implicated in diverse cellular processes involving: protein translation regulation, neuropathological processes, cellular stress, and tissue development. Results In this study we performed a biophysical analysis of human RACK1 with the aim of obtaining low resolution structural information. Small angle X-ray scattering (SAXS) experiments demonstrated that human RACK1 is globular and monomeric in solution and its low resolution structure is strikingly similar to that of an homology model previously calculated by us and to the crystallographic structure of RACK1 isoform A from Arabidopsis thaliana. Both sedimentation velocity and sedimentation equilibrium analytical ultracentrifugation techniques showed that RACK1 is predominantly a monomer of around 37 kDa in solution, but also presents small amounts of oligomeric species. Moreover, hydrodynamic data suggested that RACK1 has a slightly asymmetric shape. The interaction of RACK1 and Ki-1/57 was tested by sedimentation equilibrium. The results suggested that the association between RACK1 and Ki-1/57(122-413) follows a stoichiometry of 1:1. The binding constant (KB) observed for RACK1-Ki-1/57(122-413) interaction was of around (1.5 0.2) 106 M-1 and resulted in a dissociation constant (KD) of (0.7 0.1) 10-6 M. Moreover, the fluorescence data also suggests that the interaction may occur in a cooperative fashion. Conclusion Our SAXS and analytical ultracentrifugation experiments indicated that RACK1 is predominantly a monomer in solution. RACK1 and Ki-1/57(122-413) interact strongly under the tested conditions. PMID:20529362

  13. Solution structure of the luzopeptin-DNA complex

    SciTech Connect

    Zhang, Xiaolu; Patel, D.J. )

    1991-04-23

    The luzopeptin-d(C-A-T-G) complex (1 drug/duplex) has been generated in aqueous solution and its structure characterized by a combined application of two-dimensional NMR experiments and molecular dynamics calculations. Once equivalent of luzopeptin binds to the self-complementary tetranucleotide duplex with the 2-fold symmetry of the antitumor agent and the DNA oligomer retained on complex formation. The authors have assigned the exchangeable and nonexchangeable proton resonances of luzopeptin and the d(C-A-T-G) duplex in the complex and identified the intermolecular proton-proton NOEs that define the alignment of the antitumor agent at its binding site in duplex DNA. The analysis was greatly aided by a large number of intermolecular NOEs involving exchangeable protons on both the luzopeptin and the DNA in the complex. The formation of cis peptide bonds for luzopeptin in the complex results in an increased separation of the long sides of the rectangular cyclic depsipeptide backbone and reorients in the glycine amide proton so that it can form an intermolecular hydrogen bond with the 2-carbonyl of T3 in the complex. This observation explains, in part, the requirement for Watson-Crick A{center dot}T pairs to be sandwiched between the quinolines at the bisintercalation site in the luzopeptin-DNA complex. The NMR studies on the luzopeptin-d(C-A-T-G) complex unequivocally establish that antitumor agents can undergo conformational transitions on complex formation with DNA, and it is the conformation of the drug in the complex that should serve as the starting point for drug design studies. The above structural details on the solution structure of the luzopeptin-DNA complex also explain the sequence selectivity of luzopeptin for bisintercalation at d(C-A){center dot}d(T-G) steps in the d(C-A-T-G) duplex in solution.

  14. Automated macromolecular crystal detection system and method

    DOEpatents

    Christian, Allen T.; Segelke, Brent; Rupp, Bernard; Toppani, Dominique

    2007-06-05

    An automated macromolecular method and system for detecting crystals in two-dimensional images, such as light microscopy images obtained from an array of crystallization screens. Edges are detected from the images by identifying local maxima of a phase congruency-based function associated with each image. The detected edges are segmented into discrete line segments, which are subsequently geometrically evaluated with respect to each other to identify any crystal-like qualities such as, for example, parallel lines, facing each other, similarity in length, and relative proximity. And from the evaluation a determination is made as to whether crystals are present in each image.

  15. The three-dimensional solution structure of RANTES.

    PubMed

    Chung, C W; Cooke, R M; Proudfoot, A E; Wells, T N

    1995-07-25

    The solution structure of the chemokine RANTES (regulated on activation, normal T-cell expressed and secreted) has been determined using NMR spectroscopy. Backbone and side-chain 1H and 15N assignments have been obtained using a combination of two-dimensional homonuclear and three-dimensional heteronuclear spectra. Regular elements of secondary structure have been identified on the basis of a qualitative interpretation of NOE data, J(NH-H alpha) coupling constants, and amide exchange rates. Three-dimensional structures were calculated from a total of 2146 experimental restraints using a combination of distance geometry and simulated annealing protocols. For the 13 best structures the average backbone (N, C alpha, C) atomic rmsd from the mean coordinates for residues 5-65 is 0.64 A (+/- 0.14 A) for the dimer and 0.50 A (+/- 0.08 A) for the individual monomers. Each monomer consists of a three-stranded antiparallel beta-sheet (residues 26-30, 38-43, 48-51) in a Greek key motif with a C-terminal helix (56-65) packed across the sheet, an arrangement similar to the monomeric structure of other members of this chemokine family (IL-8, PF4, MGSA/Gro alpha, and MIP-1 beta). Overall, the RANTES dimer resembles that previously reported for MIP-1 beta. PMID:7542919

  16. Interfacial structures of acidic and basic aqueous solutions

    SciTech Connect

    Tian, C.; Ji, N.; Waychunas, G.; Shen, Y.R.

    2008-10-20

    Phase-sensitive sum-frequency vibrational spectroscopy was used to study water/vapor interfaces of HCl, HI, and NaOH solutions. The measured imaginary part of the surface spectral responses provided direct characterization of OH stretch vibrations and information about net polar orientations of water species contributing to different regions of the spectrum. We found clear evidence that hydronium ions prefer to emerge at interfaces. Their OH stretches contribute to the 'ice-like' band in the spectrum. Their charges create a positive surface field that tends to reorient water molecules more loosely bonded to the topmost water layer with oxygen toward the interface, and thus enhances significantly the 'liquid-like' band in the spectrum. Iodine ions in solution also like to appear at the interface and alter the positive surface field by forming a narrow double-charge layer with hydronium ions. In NaOH solution, the observed weak change of the 'liquid-like' band and disappearance of the 'ice-like' band in the spectrum indicates that OH{sup -} ions must also have excess at the interface. How they are incorporated in the interfacial water structure is however not clear.

  17. Macromolecular cross-linked enzyme aggregates (M-CLEAs) of α-amylase.

    PubMed

    Nadar, Shamraja S; Muley, Abhijeet B; Ladole, Mayur R; Joshi, Pranoti U

    2016-03-01

    Macromolecular cross-linked enzyme aggregates (M-CLEAs) of α-amylase were prepared by precipitation and subsequent cross-linking. The non-toxic, biodegradable, biocompatible, renewable polysaccharide based macromolecular cross-linkers viz. agar, chitosan, dextran, and gum arabic were used as a substitute for traditional glutaraldehyde to augment activity recovery toward macromolecular substrate. Macromolecular cross-linkers were prepared by periodate mediated controlled oxidation of polysaccharides. The effects of precipitating agent, concentration and different cross-linkers on activity recovery of α-amylase CLEAs were investigated. α-Amylase aggregated with ammonium sulphate and cross-linked by dextran showed 91% activity recovery, whereas glutaraldehyde CLEAs (G-CLEAs) exhibited 42% activity recovery. M-CLEAs exhibited higher thermal stability in correlation with α-amylase and G-CLEAs. Moreover, dextran and chitosan M-CLEAs showed same affinity for starch hydrolysis as of free α-amylase. The changes in secondary structures revealed the enhancements in structural and conformational rigidity attributed by cross-linkers. Finally, after five consecutive cycles dextran M-CLEAs retained 1.25 times higher initial activity than G-CLEAs. PMID:26675136

  18. Stibathiolanes: Synthesis, solid-state structure, and solution behavior

    SciTech Connect

    Fisher, R.A.; Nielsen, R.B.; Davis, W.M.; Buchwald, S.L. )

    1991-01-02

    The first examples of a new class of main group metallacycles, stibathiolanes, have been synthesized via transmetalation from ziconocene metallacycles. The x-ray crystal structures of three 1-halostibathionaes have been determined and the compounds found to be polymeric in the crystalline state. Physical and spectroscopic data indicate that the compounds are monomeric in hydrocarbon solution but that they undergo rapid-reversible halide-exchange reactions. A consequence of one of these exchange reactions is the inversion of stereochemistry at antimony. The processes have been investigated by using a variety of NMR and crossover experiments. The proposed intermediate for the inversion of stereochemistry at the metal center is supported by the solid-state structures of the compounds in which the proposed connectivity of the intermediate is crystallographically established.

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

    SciTech Connect

    Schiltz, Marc; Bricogne, Gérard

    2010-04-01

    Site-specific radiation damage and anisotropy of anomalous scattering can induce intensity differences in symmetry-related reflections. If the data are kept unmerged, these symmetry-breaking effects can become a source of phase information. 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.

  20. Pi sampling: a methodical and flexible approach to initial macromolecular crystallization screening

    SciTech Connect

    Gorrec, Fabrice Palmer, Colin M.; Lebon, Guillaume; Warne, Tony

    2011-05-01

    Pi sampling, derived from the incomplete factorial approach, is an effort to maximize the diversity of macromolecular crystallization conditions and to facilitate the preparation of 96-condition initial screens. The Pi sampling method is derived from the incomplete factorial approach to macromolecular crystallization screen design. The resulting ‘Pi screens’ have a modular distribution of a given set of up to 36 stock solutions. Maximally diverse conditions can be produced by taking into account the properties of the chemicals used in the formulation and the concentrations of the corresponding solutions. The Pi sampling method has been implemented in a web-based application that generates screen formulations and recipes. It is particularly adapted to screens consisting of 96 different conditions. The flexibility and efficiency of Pi sampling is demonstrated by the crystallization of soluble proteins and of an integral membrane-protein sample.

  1. Refined solution structure and backbone dynamics of HIV-1 Nef.

    PubMed Central

    Grzesiek, S.; Bax, A.; Hu, J. S.; Kaufman, J.; Palmer, I.; Stahl, S. J.; Tjandra, N.; Wingfield, P. T.

    1997-01-01

    The tendency of HIV-1 Nef to form aggregates in solution, particularly at pH values below 8, together with its large fraction of highly mobile residues seriously complicated determination of its three-dimensional structure, both for heteronuclear solution NMR (Grzesiek et al., 1996a, Nat Struct Biol 3:340-345) and for X-ray crystallography (Lee et al., 1996, Cell 85:931-942). Methods used to determine the Nef structure by NMR at pH 8 and 0.6 mM concentration are presented, together with a detailed description of Nef's secondary and tertiary structure. The described techniques have general applicability for the NMR structure determination of proteins that are aggregating and/or have limited stability at low pH values. Extensive chemical shift assignments are reported for backbone and side chain 1H, 13C, and 15N resonances of the HIV-1 Nef deletion mutants NEF delta 2-39, NEF delta 2-39, delta 159-173, and of NEF delta 2-39, delta 159-173 in complex with the SH3 domain of the Hck tyrosine protein kinase. Besides a type II polyproline helix, Nef's structure consists of three alpha-helices, a 3(10) helix, and a five-stranded anti-parallel beta-sheet. The analysis of 15N relaxation parameters of the backbone amide sites reveals that all the secondary structure elements are non-mobile on the picosecond to nanosecond and on the millisecond time scale. A large number of slowly exchanging amide protons provides evidence for the stability of the Nef core even on the time scale of hours. Significant internal motions on the ps to ns time scale are detected for residues 60 to 71 and for residues 149 to 180, which form solvent-exposed loops. The residues of the HIV-1 protease cleavage site (W57/L58) do not exhibit large amplitude motions on the sub-nanosecond time scale, and their side chains insert themselves into a hydrophobic crevice formed between the C-terminus of helix 1 and the N-terminus of helix 2. A refined structure has been determined based on additional constraints for side-chain and backbone dihedral angles derived from a large number of three-bond J-coupling and ROE data. PMID:9194185

  2. Observation of carbon growth and interface structures in methanol solution

    NASA Astrophysics Data System (ADS)

    Okuno, Kimio

    2015-11-01

    In the deposition of carbon on the surface of a tungsten tip in methanol solution by electrolysis, the growth structure of the carbon films, the interface state, and the dissolution of carbon atoms into the tungsten matrix of the substrate have been investigated with the atomic events by field ion microscopy (FIM). The carbon films preferentially condense on the W{111} plane. The interfacial reaction at the carbon atom-tungsten substrate interface is vigorous and the carbon atoms also readily dissolve into the substrate matrix to form a tungsten-carbon complex. The reaction depth of the deposited carbon depends on the magnitude of electrolytic current and the treatment duration in the methanol solution. In this work, the resolution depth of carbon was found to be approximately 270 atomic layers below the top layer of the tungsten substrate by a field evaporation technique. In the case of a low electrolytic current, the tungsten substrate surface is entirely covered with carbon atoms having a pseudomorphic structure. The field-electron emission characteristics were also evaluated for various coverages of the carbon film formed on the substrate.

  3. 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’.

  4. Extracting trends from two decades of microgravity macromolecular crystallization history

    NASA Technical Reports Server (NTRS)

    Judge, Russell A.; Snell, Edward H.; van der Woerd, Mark J.

    2005-01-01

    Since the 1980s hundreds of macromolecular crystal growth experiments have been performed in the reduced acceleration environment of an orbiting spacecraft. Significant enhancements in structural knowledge have resulted from X-ray diffraction of the crystals grown. Similarly, many samples have shown no improvement or degradation in comparison to those grown on the ground. A complex series of interrelated factors affect these experiments and by building a comprehensive archive of the results it was aimed to identify factors that result in success and those that result in failure. Specifically, it was found that dedicated microgravity missions increase the chance of success when compared with those where crystallization took place as a parasitic aspect of the mission. It was also found that the chance of success could not be predicted based on any discernible property of the macromolecule available to us.

  5. Direct structure analysis of a paraffin solid solution.

    PubMed

    Dorset, D L

    1990-11-01

    Single microcrystals of a 1:1 solid solution of n-C32H66/n-C36H74 have been grown by epitaxial nucleation on benzoic acid, and 0kl electron diffraction patterns from them can be obtained with a lamellar spacing characteristic of the intermediate n-paraffin n-C34H70. This average structure is also indicated by indices (space group Pca21) for major intensities in this zone. Direct phasing of the intensity data is carried out by combined use of low-dose electron microscope lattice images (to assign values to the "lamellar" reflections) and three-phase structure invariant relationships (to find values for the "polyethylene" reflections). The computed electrostatic potential map closely resembles the crystal structure of n-C34H74, for which all 34 atom positions can be found. It is apparent, however, that lower atomic occupancies at the chain ends correspond to anticipated disorder at the lamellar interface. Structural refinement based on this occupancy results in a good match to the observed intensity data. PMID:11607113

  6. Direct structure analysis of a paraffin solid solution.

    PubMed Central

    Dorset, D L

    1990-01-01

    Single microcrystals of a 1:1 solid solution of n-C32H66/n-C36H74 have been grown by epitaxial nucleation on benzoic acid, and 0kl electron diffraction patterns from them can be obtained with a lamellar spacing characteristic of the intermediate n-paraffin n-C34H70. This average structure is also indicated by indices (space group Pca21) for major intensities in this zone. Direct phasing of the intensity data is carried out by combined use of low-dose electron microscope lattice images (to assign values to the "lamellar" reflections) and three-phase structure invariant relationships (to find values for the "polyethylene" reflections). The computed electrostatic potential map closely resembles the crystal structure of n-C34H74, for which all 34 atom positions can be found. It is apparent, however, that lower atomic occupancies at the chain ends correspond to anticipated disorder at the lamellar interface. Structural refinement based on this occupancy results in a good match to the observed intensity data. Images PMID:11607113

  7. 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 Φ. The relation h ≈ N^{0.8}Φ^{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 Φ. La relation h≈ N^{0.8}Φ^{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.

  8. Solution structure of a recombinant type I sculpin antifreeze protein.

    PubMed

    Kwan, Ann H-Y; Fairley, Kayesh; Anderberg, Pia I; Liew, Chu Wai; Harding, Margaret M; Mackay, Joel P

    2005-02-15

    We have determined the solution structure of rSS3, a recombinant form of the type I shorthorn sculpin antifreeze protein (AFP), at 278 and 268 K. This AFP contains an unusual sequence of N-terminal residues, together with two of the 11-residue repeats that are characteristic of the type I winter flounder AFP. The solution conformation of the N-terminal region of the sculpin AFP has been assumed to be the critical factor that results in recognition of different ice planes by the sculpin and flounder AFPs. At 278 K, the two repeats units (residues 11-20 and 21-32) in rSS3 form a continuous alpha-helix, with the residues 30-33 in the second repeat somewhat less well defined. Within the N-terminal region, residues 2-6 are well defined and helical and linked to the main helix by a more flexible region comprising residues A7-T11. At 268 K the AFP is overall more helical but retains the apparent hinge region. The helical conformation of the two repeats units is almost identical to the corresponding repeats in the type I winter flounder AFP. We also show that while tetracetylated rSS3 has antifreeze activity comparable to the natural AFP, its overall structure is the same as that of the unacetylated peptide. These data provide some insight into the structural determinants of antifreeze activity and should assist in the development of models that explain the recognition of different ice interfaces by the sculpin and flounder type I AFPs. PMID:15697223

  9. Type IV kerogens as analogues for organic macromolecular materials in aqueously altered carbonaceous chondrites.

    PubMed

    Matthewman, Richard; Martins, Zita; Sephton, Mark A

    2013-04-01

    Understanding the processes involved in the evolution of organic matter in the early Solar System requires extensive experimental work. The scientifically valuable carbonaceous chondrites are principal targets for organic analyses, but these meteorites are rare. Meteoritic analog materials available in larger quantities, on which experiments can be performed, would be highly beneficial. The bulk of the organic inventory of carbonaceous chondrites is made up of solvent-insoluble macromolecular material. This high-molecular-weight entity provides a record of thermal and aqueous parent-body alteration of precursor organic structures present at the birth of the Solar System. To identify an effective analogue for this macromolecular material, we analyzed a series of terrestrial kerogens by pyrolysis-gas chromatography-mass spectrometry. Type I and II kerogens are unsuitable analogues owing to their highly aliphatic nature. Type III kerogens show some similarities to meteoritic macromolecular materials but display a substantial biological heritage. Type IV kerogens, in this study derived from Mesozoic paleosols and produced by the reworking and oxidation of organic matter, represent an effective analogue. Some isomeric differences exist between meteoritic macromolecular materials and type IV kerogens, and stepped pyrolysis indicates variations in thermal stability. In addition to being a suitable material for novel experimentation, type IV kerogens also have the potential to aid in the optimization of instruments for deployment on Mars. PMID:23551239

  10. 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

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

    SciTech Connect

    Bankura, Arindam; Carnevale, Vincenzo; Klein, Michael L.

    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.

  12. Structure and dynamics of aqueous solution of uranyl ions

    SciTech Connect

    Chopra, Manish; Choudhury, Niharendu

    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.

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

    NASA Astrophysics Data System (ADS)

    Bankura, Arindam; Carnevale, Vincenzo; Klein, Michael L.

    2013-01-01

    The solvation structures of Na^+, K^+, and Cl^- 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^+, K^+, and Cl^-, 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.

  14. Structure and phase behavior of aqueous methylcellulose solutions

    NASA Astrophysics Data System (ADS)

    McAllister, John; Schmidt, Peter; Lodge, Timothy; Bates, Frank

    2015-03-01

    Cellulose ethers (CE) constitute a multi-billion dollar industry, and have found end uses in a broad array of applications from construction materials, food products, personal care products, and pharmaceuticals for more than 80 years. Methylcellulose (MC, with the trade name METHOCEL™) is a CE in which there is a partial substitution of -OH groups with -OCH3 groups. This results in a polymer that is water-soluble at low temperatures, and aqueous solutions of MC display gelation and phase separation at higher temperatures. The nature of MC gelation has been debated for many years, and this project has made significant advances in the understanding of the solution properties of CEs. We have characterized a fibrillar structure of MC gels by cryogenic transmission electron microscopy (cryo-TEM) and small angle neutron scattering (SANS). Using light scattering, turbidity measurements, and dynamic mechanical spectroscopy (DMS) we report that MC microphase separates by nucleation and growth of fibril aggregates, and is a different process from LCST phase separation.

  15. Characterization of Chitin and Chitosan Molecular Structure in Aqueous Solution

    SciTech Connect

    Franca, Eduardo D.; Lins, Roberto D.; Freitas, Luiz C.; Straatsma, t. P.

    2008-11-08

    Molecular dynamics simulations have been used to characterize the structure of chitin and chitosan fibers in aqueous solutions. Chitin fibers, whether isolated or in the form of a β-chitin nanoparticle, adopt the so-called 2-fold helix with Φ and φ values similar to its crystalline state. In solution, the intramolecular hydrogen bond HO3(n)•••O5(n+1) responsible for the 2-fold helical motif is stabilized by hydrogen bonds with water molecules in a well-defined orientation. On the other hand, chitosan can adopt five distinct helical motifs and its conformational equilibrium is highly dependent on pH. The hydrogen bond pattern and solvation around the O3 atom of insoluble chitosan (basic pH) are nearly identical to these quantities in chitin. Our findings suggest that the solubility and conformation of these polysaccharides are related to the stability of the intrachain HO3(n)•••O5(n+1) hydrogen bond, which is affect by the water exchange around the O3-HO3 hydroxyl group.

  16. Identifying duplicate crystal structures: XTALCOMP, an open-source solution

    NASA Astrophysics Data System (ADS)

    Lonie, David C.; Zurek, Eva

    2012-03-01

    We describe the implementation of XTALCOMP, an efficient, reliable, and open-source library that tests if two crystal descriptions describe the same underlying structure. The algorithm has been tested and found to correctly identify duplicate structures in spite of the "real-world" difficulties that arise from working with numeric crystal representations: degenerate unit cell lattices, numerical noise, periodic boundaries, and the lack of a canonical coordinate origin. The library is portable, open, and not dependent on any external packages. A web interface to the algorithm is publicly accessible at http://xtalopt.openmolecules.net/xtalcomp/xtalcomp.html. Program summaryProgram title: XtalComp Catalogue identifier: AEKV_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEKV_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: "New" (3-clause) BSD [1] No. of lines in distributed program, including test data, etc.: 3148 No. of bytes in distributed program, including test data, etc.: 21 860 Distribution format: tar.gz Programming language: C++ Computer: No restrictions Operating system: All operating systems with a compliant C++ compiler. Classification: 7.8 Nature of problem: Computationally identifying duplicate crystal structures taken from the output of modern solid state calculations is a non-trivial exercise for many reasons. The translation vectors in the description are not unique — they may be transformed into linear combinations of themselves and continue to describe the same extended structure. The coordinates and cell parameters contain numerical noise. The periodic boundary conditions at the unit cell faces, edges, and corners can cause very small displacements of atomic coordinates to result in very different representations. The positions of all atoms may be uniformly translated by an arbitrary vector without modifying the underlying structure. Additionally, certain applications may consider enantiomorphic structures to be identical. Solution method: The XtalComp algorithm overcomes these issues to detect duplicate structures regardless of differences in representation. It begins by performing a Niggli reduction on the inputs, standardizing the translation vectors and orientations. A transform search is performed to identify candidate sets of rotations, reflections, and translations that potentially map the description of one crystal onto the other, solving the problems of enantiomorphs and rotationally degenerate lattices. The atomic positions resulting from each candidate transform are then compared, using a cell-expansion technique to remove periodic boundary issues. Computational noise is treated by comparing non-integer quantities using a specified tolerance. Running time: The test run provided takes less than a second to complete.

  17. Simulation and display of macromolecular complexes

    NASA Technical Reports Server (NTRS)

    Nir, S.; Garduno, R.; Rein, R.; Macelroy, R. D.

    1977-01-01

    In association with an investigation of the interaction of proteins with DNA and RNA, an interactive computer program for building, manipulating, and displaying macromolecular complexes has been designed. The system provides perspective, planar, and stereoscopic views on the computer terminal display, as well as views for standard and nonstandard observer locations. The molecule or its parts may be rotated and/or translated in any direction; bond connections may be added or removed by the viewer. Molecular fragments may be juxtaposed in such a way that given bonds are aligned, and given planes and points coincide. Another subroutine provides for the duplication of a given unit such as a DNA or amino-acid base.

  18. Panorama of ancient metazoan macromolecular complexes.

    PubMed

    Wan, Cuihong; Borgeson, Blake; Phanse, Sadhna; Tu, Fan; Drew, Kevin; Clark, Greg; Xiong, Xuejian; Kagan, Olga; Kwan, Julian; Bezginov, Alexandr; Chessman, Kyle; Pal, Swati; Cromar, Graham; Papoulas, Ophelia; Ni, Zuyao; Boutz, Daniel R; Stoilova, Snejana; Havugimana, Pierre C; Guo, Xinghua; Malty, Ramy H; Sarov, Mihail; Greenblatt, Jack; Babu, Mohan; Derry, W Brent; Tillier, Elisabeth R; Wallingford, John B; Parkinson, John; Marcotte, Edward M; Emili, Andrew

    2015-09-17

    Macromolecular complexes are essential to conserved biological processes, but their prevalence across animals is unclear. By combining extensive biochemical fractionation with quantitative mass spectrometry, here we directly examined the composition of soluble multiprotein complexes among diverse metazoan models. Using an integrative approach, we generated a draft conservation map consisting of more than one million putative high-confidence co-complex interactions for species with fully sequenced genomes that encompasses functional modules present broadly across all extant animals. Clustering reveals a spectrum of conservation, ranging from ancient eukaryotic assemblies that have probably served cellular housekeeping roles for at least one billion years, ancestral complexes that have accrued contemporary components, and rarer metazoan innovations linked to multicellularity. We validated these projections by independent co-fractionation experiments in evolutionarily distant species, affinity purification and functional analyses. The comprehensiveness, centrality and modularity of these reconstructed interactomes reflect their fundamental mechanistic importance and adaptive value to animal cell systems. PMID:26344197

  19. Quantum diffusive dynamics of macromolecular transitions.

    PubMed

    a Beccara, S; Garberoglio, G; Faccioli, P

    2011-07-21

    We study the role of quantum fluctuations of atomic nuclei in the real-time dynamics of non-equilibrium macro-molecular transitions. To this goal we introduce an extension of the dominant reaction pathways formalism, in which the quantum corrections to the classical overdamped Langevin dynamics are rigorously taken into account to order ?(2). We first illustrate our approach in simple cases, and compare with the results of the instanton theory. Then we apply our method to study the C7(eq) ? C7(ax) transition of alanine dipeptide. We find that the inclusion of quantum fluctuations can significantly modify the reaction mechanism for peptides. For example, the energy difference which is overcome along the most probable pathway is reduced by as much as 50%. PMID:21786983

  20. Quantum diffusive dynamics of macromolecular transitions

    NASA Astrophysics Data System (ADS)

    Beccara, S. a.; Garberoglio, G.; Faccioli, P.

    2011-07-01

    We study the role of quantum fluctuations of atomic nuclei in the real-time dynamics of non-equilibrium macro-molecular transitions. To this goal we introduce an extension of the dominant reaction pathways formalism, in which the quantum corrections to the classical overdamped Langevin dynamics are rigorously taken into account to order ?2. We first illustrate our approach in simple cases, and compare with the results of the instanton theory. Then we apply our method to study the C7eq ? C7ax transition of alanine dipeptide. We find that the inclusion of quantum fluctuations can significantly modify the reaction mechanism for peptides. For example, the energy difference which is overcome along the most probable pathway is reduced by as much as 50%.

  1. Unveiling Contacts within Macromolecular Assemblies by Solving Minimum Weight Connectivity Inference (MWC) Problems.

    PubMed

    Agarwal, Deepesh; Caillouet, Christelle; Coudert, David; Cazals, Frederic

    2015-08-01

    Consider a set of oligomers listing the subunits involved in subcomplexes of a macromolecular assembly, obtained e.g. using native mass spectrometry or affinity purification. Given these oligomers, connectivity inference (CI) consists of finding the most plausible contacts between these subunits, and minimum connectivity inference (MCI) is the variant consisting of finding a set of contacts of smallest cardinality. MCI problems avoid speculating on the total number of contacts but yield a subset of all contacts and do not allow exploiting a priori information on the likelihood of individual contacts. In this context, we present two novel algorithms, MILP-W and MILP-WB. The former solves the minimum weight connectivity inference (MWCI), an optimization problem whose criterion mixes the number of contacts and their likelihood. The latter uses the former in a bootstrap fashion to improve the sensitivity and the specificity of solution sets.Experiments on three systems (yeast exosome, yeast proteasome lid, human eIF3), for which reference contacts are known (crystal structure, cryo electron microscopy, cross-linking), show that our algorithms predict contacts with high specificity and sensitivity, yielding a very significant improvement over previous work, typically a twofold increase in sensitivity.The software accompanying this paper is made available and should prove of ubiquitous interest whenever connectivity inference from oligomers is faced. PMID:25850436

  2. 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

  3. Influence of macromolecular precipitants on phase behavior of monoclonal antibodies.

    PubMed

    Rakel, Natalie; Galm, Lara; Bauer, Katharina Christin; Hubbuch, Juergen

    2015-01-01

    For the successful application of protein crystallization as a downstream step, a profound knowledge of protein phase behavior in solutions is needed. Therefore, a systematic screening was conducted to analyze the influence of macromolecular precipitants in the form of polyethylene glycol (PEG). First, the influence of molecular weight and concentration of PEG at different pH-values were investigated and analyzed in three-dimensional (3-D) phase diagrams to find appropriate conditions in terms of a fast kinetic and crystal size for downstream processing. In comparison to the use of salts as precipitant, PEG was more suitable to obtain compact 3-D crystals over a broad range of conditions, whereby the molecular weight of PEG is, besides the pH-value, the most important parameter. Second, osmotic second virial coefficients as parameters for protein interactions are experimentally determined with static light scattering to gain a deep insight view in the phase behavior on a molecular basis. The PEG-protein solutions were analyzed as a pseudo-one-compartment system. As the precipitant is also a macromolecule, the new approach of analyzing cross-interactions between the protein and the macromolecule PEG in form of the osmotic second cross-virial coefficient (B23 ) was applied. Both parameters help to understand the protein phase behavior. However, a predictive description of protein phase behavior for systems consisting of monoclonal antibodies and PEG as precipitant is not possible, as kinetic phenomena and concentration dependencies were not taken into account. PMID:25504581

  4. Solution structure of the strawberry allergen Fra a 1.

    PubMed

    Seutter von Loetzen, Christian; Schweimer, Kristian; Schwab, Wilfried; Rösch, Paul; Hartl-Spiegelhauer, Olivia

    2012-12-01

    The PR10 family protein Fra a 1E from strawberry (Fragaria x ananassa) is down-regulated in white strawberry mutants, and transient RNAi (RNA interference)-mediated silencing experiments confirmed that Fra a 1 is involved in fruit pigment synthesis. In the present study, we determined the solution structure of Fra a 1E. The protein fold is identical with that of other members of the PR10 protein family and consists of a seven-stranded antiparallel β-sheet, two short V-shaped α-helices and a long C-terminal α-helix that encompass a hydrophobic pocket. Whereas Fra a 1E contains the glycine-rich loop that is highly conserved throughout the protein family, the volume of the hydrophobic pocket and the size of its entrance are much larger than expected. The three-dimensional structure may shed some light on its physiological function and may help to further understand the role of PR10 proteins in plants. PMID:22913709

  5. Analytical solution of thermal magnetization on memory stabilizer structures

    SciTech Connect

    Tomita, Yu; Viteri, C. Ricardo; Brown, Kenneth R.

    2010-10-15

    We return to the question of how the choice of stabilizer generators affects the preservation of information on structures whose degenerate ground state encodes a classical redundancy code. Controlled-not gates are used to transform the stabilizer Hamiltonian into a Hamiltonian consisting of uncoupled single spins and/or pairs of spins. This transformation allows us to obtain an analytical partition function and derive closed-form equations for the relative magnetization and susceptibility. These equations are in agreement with the numerical results presented in Viteri et al. [Phys. Rev. A 80, 042313 (2009)] for finite size systems. Analytical solutions show that there is no finite critical temperature, T{sub c}=0, for all of the memory structures in the thermodynamic limit. This is in contrast to the previously predicted finite critical temperatures based on extrapolation. The mismatch is a result of the infinite system being a poor approximation even for astronomically large finite-size systems, where spontaneous magnetization still arises below an apparent finite critical temperature. We extend our analysis to the canonical stabilizer Hamiltonian. Interestingly, Hamiltonians with two-body interactions have a higher apparent critical temperature than the many-body Hamiltonian.

  6. Solution structures of the lantibiotics duramycin B and C.

    PubMed

    Zimmermann, N; Freund, S; Fredenhagen, A; Jung, G

    1993-09-01

    The solution structures of the lantibiotics duramycin B in H2O/2H2O (9:1) and duramycin C in (2H3)acetonitrile/H2O (1:1) have been determined by NMR followed by distance-geometry and restrained-molecular-mechanics calculations. The constitution and location of three thioether bridges and a lysinoalanine ring system could be established by unambiguously assigned NOE contacts between the bridging side chains. Model building based on NMR constraints resulted in a U-shaped topology of the tetracyclic 19-peptides with a turn around Pro9 and a kink along a virtual line from residues 5 to 13. This clamp-like conformation is stabilized by the thioether bridges and is additionally supported by an antiparallel beta-strand-like structure of the N-termini and C-termini and the inherent amphiphilicity of duramycin-type lantibiotics. The duramycins B and C differ mainly in the relative mobilities of their rings A, C and D. Duramycin B is closely related to cinnamycin with an exchange of Phe10 to leucine, whereas duramycin C differs from duramycin B by three conserved and two non-conserved amino-acid exchanges. PMID:8375380

  7. The NMR solution structure of recombinant RGD-hirudin

    SciTech Connect

    Song, Xia; Mo, Wei; Liu, Xingang; Zhu, Lina; Yan, Xiaomin; Song, Houyan . E-mail: hysong@shmu.edu.cn; Dai, Linsen . 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.

  8. Phylogenetic Diversity in the Macromolecular Composition of Microalgae.

    PubMed

    Finkel, Zoe V; Follows, Mick J; Liefer, Justin D; Brown, Chris M; Benner, Ina; Irwin, Andrew J

    2016-01-01

    The elemental stoichiometry of microalgae reflects their underlying macromolecular composition and influences competitive interactions among species and their role in the food web and biogeochemistry. Here we provide a new estimate of the macromolecular composition of microalgae using a hierarchical Bayesian analysis of data compiled from the literature. The median macromolecular composition of nutrient-sufficient exponentially growing microalgae is 32.2% protein, 17.3% lipid, 15.0% carbohydrate, 17.3% ash, 5.7% RNA, 1.1% chlorophyll-a and 1.0% DNA as percent dry weight. Our analysis identifies significant phylogenetic differences in macromolecular composition undetected by previous studies due to small sample sizes and the large inherent variability in macromolecular pools. The phylogenetic differences in macromolecular composition lead to variations in carbon-to-nitrogen ratios that are consistent with independent observations. These phylogenetic differences in macromolecular and elemental composition reflect adaptations in cellular architecture and biochemistry; specifically in the cell wall, the light harvesting apparatus, and storage pools. PMID:27228080

  9. Macromolecular Powder Diffraction: Ready for genuine biological problems.

    PubMed

    Karavassili, Fotini; Margiolaki, Irene

    2016-01-01

    Knowledge of 3D structures of biological molecules plays a major role in both understanding important processes of life and developing pharmaceuticals. Among several methods available for structure determination, macromolecular X-ray powder diffraction (XRPD) has transformed over the past decade from an impossible dream to a respectable method. XRPD can be employed in biosciences for various purposes such as observing phase transitions, characterizing bulk pharmaceuticals, determining structures via the molecular replacement method, detecting ligands in protein-ligand complexes, as well as combining micro-sized single crystal crystallographic data and powder diffraction data. Studies using synchrotron and laboratory sources in some standard configuration setups are reported in this review, including their respective advantages and disadvantages. Methods presented here provide an alternative, complementary set of tools to resolve structural problems. A variety of already existing software packages for powder diffraction data processing and analysis, some of which have been adapted to large unit cell studies, are briefly described. This review aims to provide necessary elements of theory and current methods, along with practical explanations, available software packages and highlighted case studies. PMID:26786768

  10. The structures underlying soliton solutions in integrable hierarchies

    SciTech Connect

    Ferreira, Luiz A.

    1997-03-15

    We point out that a common feature of integrable hierarchies presenting soliton solutions is the existence of some special 'vacuum solutions' such that the Lax operators evaluated on them, lie in some abelian subalgebra of the associated Kac-Moody algebra. The soliton solutions are constructed out of those 'vacuum solitons' by the dressing transformation procedure.

  11. Solution Structure of Heparin Pentasaccharide: NMR and DFT Analysis.

    PubMed

    Hricovni, Milo

    2015-09-24

    High-resolution NMR and density functional theory (DFT) calculations have been applied to analysis of heparin pentasaccharide 3D structure in aqueous solution. The fully optimized molecular geometry of two pentasaccharide conformations (differing from each other in the form, one (1)C4 and the other (2)S0, of the sulfated iduronic acid residue) were obtained using the B3LYP/6-311+G(d,p) level of theory in the presence of solvent, the latter included as explicit water molecules. The presented approach enabled insight into variations of the bond lengths, bond angles, and torsion angles, formations of intra- and intermolecular hydrogen bonds, and ionic interactions in the two pentasaccharide conformations. A rather complex hydrogen bond network is formed, including inter-residue and intraresidue bonds between the NH group in the GlcN,3,6S with oxygens linked to C-2 at the IdoA2S residue and the glycosidic O-1 and the neighboring OSO3(-) group linked to C-3 in the same residue. On the other hand, because the first hydration shell is strongly influenced by strong ion-ion and ion-dipole interactions between sodium ions, sulfates, carboxylates, and -OH groups, ionic interactions play an important role in the stabilization of the 3D structure. The DFT-computed three-bond proton-proton coupling constants also showed that best agreement with experiment was obtained with a weighted average of 15:85 ((1)C4/(2)S0) of the sulfated iduronic acid forms indicating that the ratio is even more shifted toward the (2)S0 form than previously supposed. The DFT-computed pentasaccharide conformation differs from the previously published data, with the main changes at the glycosidic linkages, namely, the ?1 torsion angles and the ?3 angle. The comparison of the glycosidic linkage torsion angle values in solution with the antithrombin-pentasaccharide complex also indicates that the pentasaccharide conformation changes upon binding to antithrombin III. The data supports the assumption that the protein selects the more populated (2)S0 conformer of heparin pentasaccharide and, consequently, the binding process of heparin pentasaccharide with antithrombin III is energetically more favorable than formerly expected. PMID:26340667

  12. PIMA: Protein-Protein interactions in Macromolecular Assembly - a web server for its Analysis and Visualization

    PubMed Central

    Kaleeckal Mathew, Oommen; Sowdhamini, Ramanathan

    2016-01-01

    Protein-protein interactions are essential for the basic biological machinery of the cell. This is important for processes like protein synthesis, enzyme kinetics, molecular assembly and signal transduction. A high number of macromolecular structural complexes are known due to recent advances in structure determination techniques. Therefore, it is of interest to develop an interactive tool to objectively analyze large protein complexes. Hence, we describe the development and utility of a web enabled application named ‘Protein-Protein Interaction in Macro-molecular Assembly’ (PIMA) for the analysis of large protein assemblies. The intricate details of physical interactions amongst protein subunits in a large complex are presented as simple user preferred interactive network diagrams PMID:27212837

  13. From Simple DNA-Protein Interactions to the Macromolecular Machines of Gene Expression

    PubMed Central

    von Hippel, Peter H.

    2008-01-01

    The physicochemical concepts that underlie our present ideas on the structure and assembly of the macromolecular machines of gene expression are developed, starting with the structure and folding of the individual protein and DNA components, the thermodynamics and kinetics of their conformational rearrangements during complex assembly, and the molecular basis of the sequence specificity and recognition interactions of the final assemblies that include the DNA genome. The role of diffusion in reduced dimensions in the kinetics of the assembly of macromolecular machines from their components is also considered, and diffusion-driven reactions are compared with those fueled by ATP binding and hydrolysis, as well as by the specific covalent chemical modifications involved in rearranging chromatin and modifying signal transduction networks in higher organisms. PMID:17477836

  14. Structure of Solutions of Multidimensional Conservation Laws with Discontinuous Flux and Applications to Uniqueness

    NASA Astrophysics Data System (ADS)

    Crasta, Graziano; De Cicco, Virginia; De Philippis, Guido; Ghiraldin, Francesco

    2016-02-01

    We investigate the structure of solutions of conservation laws with discontinuous flux under quite general assumption on the flux. We show that any entropy solution admits traces on the discontinuity set of the coefficients and we use this to prove the validity of a generalized Kato inequality for any pair of solutions. Applications to uniqueness of solutions are then given.

  15. 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.

  16. Structure and solution properties of enzymatically synthesized glycogen.

    PubMed

    Kajiura, Hideki; Takata, Hiroki; Kuriki, Takashi; Kitamura, Shinichi

    2010-04-19

    Recently, a new enzymatic process for glycogen production was developed. In this process, short-chain amylose is used as a substrate for branching enzymes (BE, EC 2.4.1.18). The molecular weight of the enzymatically synthesized glycogen (ESG) depends on the size and concentration of the substrate. Structural and physicochemical properties of ESG were compared to those of natural source glycogen (NSG). The average chain length, interior chain length, and exterior chain length of ESG were 8.2-11.6, 2.0-3.3, and 4.2-7.6, respectively. These values were within the range of variation of NSG. The appearances of both ESG and NSG in solution were opalescent (milky white and slightly bluish). Furthermore, transmission electron microscopy and atomic force microscopy showed that ESG molecules formed spherical particles, and that there were no differences between ESG and NSG. Viscometric analyses also showed the spherical nature of both glycogens. When ESG and NSG were treated with pullulanase, a glucan-hydrolyzing enzyme known to degrade glycogen only on its surface portion, both glycogens were similarly degraded. These analyses revealed that ESG shares similar molecular shapes and surface properties with NSG. PMID:20153852

  17. Solution state structures of human pancreatic amylin and pramlintide

    PubMed Central

    Cort, John R.; Liu, Zhihong; Lee, Gregory M.; Huggins, K.N.L.; Janes, Susan; Prickett, Kathryn; Andersen, Niels H.

    2009-01-01

    We have employed pramlintide (prAM) as a surrogate for hAM in CD and NMR studies of the conformational preferences of the N-terminal portion of the structure in media which do not provide long-lived monomeric solutions of hAM due to its rapid conversion to preamyloid β aggregate states. Direct comparison of hAM and prAM could be made under helix-formation-favoring conditions. On the basis of CD and NMR studies: (i) the Cys2–Cys7 loop conformation has a short-span of helix (Ala5–Cys7); (ii) the extent to which this helix propagates further into the sequence is medium-dependent; a helix from Ala5 through Ser20 (with end fraying from His18 onward) is observed in aqueous fluoroalcohol media; (iii) in 12+ vol.% HFIP, the amyloidogenic region of hAM forms a second helical domain (Phe23–Ser29); (iv) the two helical regions of hAM do not have any specific geometric relationship as they are connected by a flexible loop that takes different conformations and (v) although the extreme C-terminus is essential for bioactivity, it is found to be extensively randomized with conformer interconversions occurring at a much faster rate than that is observed in the remainder of the peptide sequence. Two NMR-derived structures of the 1–22 sequence fragment of hAM have been derived. The work also serves to illustrate improved methods for the NMR characterization of helices. A detailed quantitative analysis of the NOE intensities observed in aqueous HFIP revealed alternative conformations in the C-terminal portion of the common amylin helix, a region that is known to be involved in the biorecognition phenomena leading to amyloidogenesis. Even though the SNN sequence appears to be a flexible loop, the chemical shifts (and changes induced upon helix structuring) suggest some interactions between the loop and the amyloidogenic segment of hAM that occur on partial helix formation. PMID:19596697

  18. The influence of interchain coupling on intramolecular oscillation mobility in coupled macromolecular chains: The case of coplanar parallel chains

    NASA Astrophysics Data System (ADS)

    Čevizović, D.; Petković, S.; Galović, S.; Chizhov, A.; Reshetnyak, A.

    2015-10-01

    We enlarge our results from the study of the hopping mechanism of the oscillation excitation transport in 1D model of one biologica-likel macromolecular chain to the case of a system composed from two 1D parallel macromolecular chains with consideration of the properties of intramolecular oscillation excitations. We suppose, that due to the exciton interaction with thermal oscillation (generated by mechanical phonon subsystem) of structural elements (consisting of the peptide group) of the chains, the exciton becomes by self trapped and forms the polaron state. We suggest a model which generalizes the modified Holstein polaron model to the case of two macromolecular chains and find that because of the interchain coupling, the exciton energy band is splitted into two subbands. The hopping process of exciton migration along the macromolecular chains is studied in dependence of system parameters and temperature. We pay an special attention to the temperature range (near T = 300 K) in which living cells operate. It is found that for the certain values of the system parameters there exists the abrupt change of the exciton migration nature from practically free (light) exciton motion to an immobile (heavy, dressed by phonon cloud) quasiparticle We discuss an application of the obtained results to the exciton transport both within deoxyribonucleic acid molecule and in the 2D polymer films organized from such macromolecular chains.

  19. 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

  20. 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.

    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.

  1. Solution structure of the chromomycin-DNA complex

    SciTech Connect

    Gao, X.; Patel, D.J. )

    1989-01-24

    The structure of the chromomycin-DNA complex at the deoxyoctanucleotide duplex level has been determined from one- and two-dimensional proton NMR studies in Mg-containing aqueous solution. The NMR results demonstrate that the antitumor agent binds as a symmetrical dimer to the self-complementary d(T-T-G-G-C-C-A-A) duplex with retention of the 2-fold symmetry in the complex. A set of intermolecular nuclear Overhauser enhancements (NOEs) established that two chromomycin molecules in the dimer share the minor groove at the G-G-C-C{center dot}G-G-C-C segment in such a way that each hydrophilic edge of the chromophore is located next to the G-G{center dot}C-C half-site and each C-D-E trisaccharide chain extends toward the 3{prime}-direction of the octanucleotide duplex. In addition, the A-B disaccharide segment and the hydrophilic side chain of the antitumor agent are directed toward the phosphate backbone. The observed changes in nucleic acid NOEs and coupling patterns on complex formation establish a transition to a wider and shallower minor groove at the central G-G-C-C{center dot}G-G-C-C segment required for accommodating the chromomycin dimer. The present demonstration that chromomycin binds as a dimer and switches the conformation of the DNA at its G{center dot}C-rich minor groove binding site provides new insights into antitumor agent design and the sequence specificity of antitumor agent-DNA recognition.

  2. Formation mechanisms, structure, solution behavior, and reactivity of aminodiborane.

    PubMed

    Li, Huizhen; Ma, Nana; Meng, Wenjuan; Gallucci, Judith; Qiu, Yongqing; Li, Shujun; Zhao, Qianyi; Zhang, Jie; Zhao, Ji-Cheng; Chen, Xuenian

    2015-09-30

    A facile synthesis of cyclic aminodiborane (NH2B2H5, ADB) from ammonia borane (NH3·BH3, AB) and THF·BH3 has made it possible to determine its important characteristics. Ammonia diborane (NH3BH2(μ-H)BH3, AaDB) and aminoborane (NH2BH2, AoB) were identified as key intermediates in the formation of ADB. Elimination of molecular hydrogen occurred from an ion pair, [H2B(NH3) (THF)](+)[BH4](-). Protic-hydridic hydrogen scrambling was proved on the basis of analysis of the molecular hydrogen products, ADB and other reagents through (2)H NMR and MS, and it was proposed that the scrambling occurred as the ion pair reversibly formed a BH5-like intermediate, [(THF)BH2NH2](η(2)-H2)BH3. Loss of molecular hydrogen from the ion pair led to the formation of AoB, most of which was trapped by BH3 to form ADB with a small amount oligomerizing to (NH2BH2)n. Theoretical calculations showed the thermodynamic feasibility of the proposed intermediates and the activation processes. The structure of the ADB·THF complex was found from X-ray single crystal analysis to be a three-dimensional array of zigzag chains of ADB and THF, maintained by hydrogen and dihydrogen bonding. Room temperature exchange of terminal and bridge hydrogens in ADB was observed in THF solution, while such exchange was not observed in diethyl ether or toluene. Both experimental and theoretical results confirm that the B-H-B bridge in ADB is stronger than that in diborane (B2H6, DB). The B-H-B bridge is opened when ADB and NaH react to form sodium aminodiboronate, Na[NH2(BH3)2]. The structure of the sodium salt as its 18-crown-6 ether adduct was determined by X-ray single crystal analysis. PMID:26335760

  3. Valence Electronic Structure of Aqueous Solutions: Insights from Photoelectron Spectroscopy.

    PubMed

    Seidel, Robert; Winter, Bernd; Bradforth, Stephen E

    2016-05-27

    The valence orbital electron binding energies of water and of embedded solutes are crucial quantities for understanding chemical reactions taking place in aqueous solution, including oxidation/reduction, transition-metal coordination, and radiation chemistry. Their experimental determination based on liquid-photoelectron spectroscopy using soft X-rays is described, and we provide an overview of valence photoelectron spectroscopy studies reported to date. We discuss principal experimental aspects and several theoretical approaches to compute the measured binding energies of the least tightly bound molecular orbitals. Solutes studied are presented chronologically, from simple electrolytes, via transition-metal ion solutions and several organic and inorganic molecules, to biologically relevant molecules, including aqueous nucleotides and their components. In addition to the lowest vertical ionization energies, the measured valence photoelectron spectra also provide information on adiabatic ionization energies and reorganization energies for the oxidation (ionization) half-reaction. For solutes with low solubility, resonantly enhanced ionization provides a promising alternative pathway. PMID:27023757

  4. 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; Shimizu, Nobutaka; Baba, Seiki; Hasegawa, Kazuya; Makino, Masatomo; Mizuno, Nobuhiro; Hoshino, Takeshi; Ito, Ren; Wada, Izumi; Kumasaka, Takashi

    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.

  5. Polydisulfide Based Biodegradable Macromolecular Magnetic Resonance Imaging Contrast Agents

    PubMed Central

    Lu, Zheng-Rong; Wu, Xueming

    2011-01-01

    Macromolecular Gd(III) complexes are advantageous over small molecular Gd(III) complexes in contrast enhanced magnetic resonance imaging (MRI) because of their prolonged blood circulation and preferential tumor accumulation. However, macromolecular contrast agents have not been approved for clinical applications because of the safety concerns related to their slow body excretion. Polydisulfide Gd(III) complexes have been designed and developed as biodegradable macromolecular MRI contrast agents to alleviate the concerns by facilitating the clearance of Gd(III) complexes from the body. These agents initially behave as macromolecular agents and result in superior contrast enhancement in the vasculature and tumor tissues. They can then be readily degraded in vivo into small molecular chelates that can rapidly excrete from the body via renal filtration after the MRI examinations. Various polydisulfide Gd(III) complexes have been prepared as biodegradable macromolecular MRI contrast agents. These agents have resulted in strong contrast enhancement in the vasculature and tumor tissue in animal models with minimal long-term tissue accumulation comparable to small molecular contrast agents. Polydisulfide Gd(III) complexes are promising for further clinical development as safe and effective biodegradable macromolecular MRI contrast agents for cardiovascular and cancer imaging. The review summarizes the chemistry and properties of polydisulfide Gd(III) complexes. PMID:21331318

  6. 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 Сhandrayan-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 on the Moon’s surface, densities, as well as graphic representations of the received data. Description of the geophysical profile of the Moon is based on exact mass, radius and moment of inertia of the Moon. Work was supported by grants RFBR 14-02-92113 Russian - Japanese - a and 14-02-31296-mol-a

  7. In vitro properties of an in situ forming gel for the parenteral delivery of macromolecular drugs.

    PubMed

    Joshi, R; Robinson, D H; Himmelstein, K J

    1999-01-01

    The purpose of this research was to (i) formulate a solution of a water-insoluble interpolymeric complex (IPC) containing poly(methacrylic acid) (PMA), 15 kDa, and poly(ethylene glycol) (PEG), 20 kDa, in a biocompatible cosolvent system; (ii) demonstrate that the IPC solution can transform into a gel, in situ, at physiological pH; and (iii) determine the ability of the gel to entrap, protect, and control the release of macromolecular drugs such as proteins and oligonucleotides. Ternary phase diagrams were prepared to identify cosolvent composition containing N-methylpyrrolidone (NMP), ethanol, and water that dissolve the IPC. IPC solutions (40, 50, or 60% w/v) each containing 1 mg of either model proteins, fluorescein isothiocyanate (FITC)-insulin and FITC-albumin, or 24-mer phosphorothioate oligonucleotides, were placed in containers that were immersed in buffer, pH 7.4. Aliquots of the buffer were sampled periodically and analyzed for the macromolecular content. In addition, in vitro bioactivity of another model protein, alpha-amylase, contained in the IPC solution was also determined. The studies demonstrated that a cosolvent containing 1:1:2 ratio of NMP/ethanol/water was most suitable for dissolving the IPC. Concentrations > 30% w/v IPC were required to form the gel, however, those mixtures containing > 60% w/v IPC could not be easily injected via 18-22 gauge needle. The gel can entrap and control the release of the model macromolecules for up to 6 days, in vitro. In addition, the gel can maintain the bioactivity of the protein, alpha-amylase, for 6 days. Therefore, an IPC gel can entrap, protect, and control the release of macromolecular drugs over a period of 6 days, in vitro, and therefore can be considered for in vivo investigation. PMID:10578505

  8. Three Biomedical Beamlines at NSLS-II for Macromolecular Crystallography and Small-Angle Scattering

    NASA Astrophysics Data System (ADS)

    Schneider, D. K.; Berman, L. E.; Chubar, O.; Hendrickson, W. A.; Hulbert, S. L.; Lucas, M.; Sweet, R. M.; Yang, L.

    2013-03-01

    We report on the status of the development of three beamlines for the National Synchrotron Light Source-II (NSLS-II), two for macromolecular crystallography (MX), and one for wide- and small-angle x-ray scattering (SAXS). Funded by the National Institutes of Health, this suite of Advanced Beamlines for Biological Investigations with X-rays (ABBIX) is scheduled to begin operation by 2015. The two MX beamlines share a sector with identical canted in-vacuum undulators (IVU21). The microfocusing FMX beamline on the inboard branch employs a two-stage horizontal source demagnification scheme, will cover an energy range of 5 - 23 keV, and at 12.7 keV will focus a flux of up to 1013 ph/s into a spot of 1 μm width. The companion AMX beamline on the short outboard branch of the sector is tunable in the range of 5 - 18 keV and has a native focus of 4 μm (h) × 2 μm (v). This robust beamline will be highly automated, have high throughput capabilities, and with larger beams and low divergence will be well suited for structure determinations on large complexes. The high brightness SAXS beamline, LIX, will provide multiple dynamic and static experimental systems to support scientific programs in solution scattering, membrane structure determination, and tissue imaging. It will occupy a different sector, equipped with a single in-vacuum undulator (IVU23). It can produce beams as small as 1 μm across, and with a broad energy range of 2.1 - 18 keV it will support anomalous SAXS.

  9. JBlulce Data Acquisition Software for Macromolecular Crystallography

    SciTech Connect

    2010-06-01

    JBlulce (Java Beam Line Universal Integrated Configuration Environment is a data acquisition software for macromolecular crystallography conforming user interface of the SSRL Blulce that has become a de-factor standard in the field. Besides this interface conformity, JBlulce is a unique system in terms of architecture, speec, capability and osftware implementation. It features only two software layers, the JBlulce clients and the EPICS servers, as compared to three layers present in Blulc and most of similar systems. This layers reduction provides a faster communication with hardware and an easier access to advanced hardware capabilities like on-the-fly scanning. Then JBlulc clients are designed to operate in parallel with the other beamline controls which streamlines the tasks performed by staff such as beamline preparation, maitenance, audting and user assistance. Another distinction is the deployment of multiple plugins that can be written in any programming languag thus involving more staff into the development. further on, JBlulce makes use of unified motion controls allowing for easy scanning and optimizing of any beamline component. Finally, the graphic interface is implemented in Java making full use of rich Java libraries and Jave IDE for debugging. to compare, Blulce user interface is implemented with aging Tcl/tk language providing very restricted capabilities. JBlulce makes full use of the industrial power and wide drivers selection of EPICS in controlling hardware; all hardware commuication is routed via multiple EPICS servers residing on local area network. JBlulce also includes several EPICS State Notation servers aimed at making hardware communication more robust. Besides using EPICS for controlling hardware, JBlulce extensively uses EPICS databases for efficien communications between multiple instances of JBlulce clients and JBlulce pplugins that can run in parallel on different computers. All of the above makes JBlulce one of the biggest and most sophisticated EPICS client projects to date. JBlulce configuraion is stored in my SQL database which provides flexibility in tuning the system. The database is also accessible by the plugins. From the users perspective JBlulce provides all standard features of data acquisition software for macromolecular crystallography plus such unique capabilities as:one click beamline energy change that may involve switching undulator harmonics, mirrors lanes and beam realignment, automated diffraction rtastering for finding small crystals and swwet spots on poorly diffracting crystals with automated scoring of raster cells by the number of reflections; data collection along a vector; automated on-the-fly fluorescent tastering, a faster and lower-irradiation compliment to the diffraction raster; fully automated fluorescence measurements for MAD that include signal optimization, fast on the fly energy scanning and automated adapting of scan range to chemical shifts; fly-scan mimibeam realighment; automated loop and crystal centering, controls for sample automounter, automated screening, data collectin audting, remoate access and a lot more.

  10. JBlulce Data Acquisition Software for Macromolecular Crystallography

    Energy Science and Technology Software Center (ESTSC)

    2010-06-01

    JBlulce (Java Beam Line Universal Integrated Configuration Environment is a data acquisition software for macromolecular crystallography conforming user interface of the SSRL Blulce that has become a de-factor standard in the field. Besides this interface conformity, JBlulce is a unique system in terms of architecture, speec, capability and osftware implementation. It features only two software layers, the JBlulce clients and the EPICS servers, as compared to three layers present in Blulc and most of similarmore » systems. This layers reduction provides a faster communication with hardware and an easier access to advanced hardware capabilities like on-the-fly scanning. Then JBlulc clients are designed to operate in parallel with the other beamline controls which streamlines the tasks performed by staff such as beamline preparation, maitenance, audting and user assistance. Another distinction is the deployment of multiple plugins that can be written in any programming languag thus involving more staff into the development. further on, JBlulce makes use of unified motion controls allowing for easy scanning and optimizing of any beamline component. Finally, the graphic interface is implemented in Java making full use of rich Java libraries and Jave IDE for debugging. to compare, Blulce user interface is implemented with aging Tcl/tk language providing very restricted capabilities. JBlulce makes full use of the industrial power and wide drivers selection of EPICS in controlling hardware; all hardware commuication is routed via multiple EPICS servers residing on local area network. JBlulce also includes several EPICS State Notation servers aimed at making hardware communication more robust. Besides using EPICS for controlling hardware, JBlulce extensively uses EPICS databases for efficien communications between multiple instances of JBlulce clients and JBlulce pplugins that can run in parallel on different computers. All of the above makes JBlulce one of the biggest and most sophisticated EPICS client projects to date. JBlulce configuraion is stored in my SQL database which provides flexibility in tuning the system. The database is also accessible by the plugins. From the users perspective JBlulce provides all standard features of data acquisition software for macromolecular crystallography plus such unique capabilities as:one click beamline energy change that may involve switching undulator harmonics, mirrors lanes and beam realignment, automated diffraction rtastering for finding small crystals and swwet spots on poorly diffracting crystals with automated scoring of raster cells by the number of reflections; data collection along a vector; automated on-the-fly fluorescent tastering, a faster and lower-irradiation compliment to the diffraction raster; fully automated fluorescence measurements for MAD that include signal optimization, fast on the fly energy scanning and automated adapting of scan range to chemical shifts; fly-scan mimibeam realighment; automated loop and crystal centering, controls for sample automounter, automated screening, data collectin audting, remoate access and a lot more.« less

  11. Macromolecular networks and intelligence in microorganisms

    PubMed Central

    Westerhoff, Hans V.; Brooks, Aaron N.; Simeonidis, Evangelos; García-Contreras, Rodolfo; He, Fei; Boogerd, Fred C.; Jackson, Victoria J.; Goncharuk, Valeri; Kolodkin, Alexey

    2014-01-01

    Living organisms persist by virtue of complex interactions among many components organized into dynamic, environment-responsive networks that span multiple scales and dimensions. Biological networks constitute a type of information and communication technology (ICT): they receive information from the outside and inside of cells, integrate and interpret this information, and then activate a response. Biological networks enable molecules within cells, and even cells themselves, to communicate with each other and their environment. We have become accustomed to associating brain activity – particularly activity of the human brain – with a phenomenon we call “intelligence.” Yet, four billion years of evolution could have selected networks with topologies and dynamics that confer traits analogous to this intelligence, even though they were outside the intercellular networks of the brain. Here, we explore how macromolecular networks in microbes confer intelligent characteristics, such as memory, anticipation, adaptation and reflection and we review current understanding of how network organization reflects the type of intelligence required for the environments in which they were selected. We propose that, if we were to leave terms such as “human” and “brain” out of the defining features of “intelligence,” all forms of life – from microbes to humans – exhibit some or all characteristics consistent with “intelligence.” We then review advances in genome-wide data production and analysis, especially in microbes, that provide a lens into microbial intelligence and propose how the insights derived from quantitatively characterizing biomolecular networks may enable synthetic biologists to create intelligent molecular networks for biotechnology, possibly generating new forms of intelligence, first in silico and then in vivo. PMID:25101076

  12. Macromolecular Topography Leaps into the Digital Age

    NASA Technical Reports Server (NTRS)

    Lovelace, J.; Bellamy, H.; Snell, E. H.; Borgstahl, G.

    2003-01-01

    A low-cost, real-time digital topography system is under development which will replace x-ray film and nuclear emulsion plates. The imaging system is based on an inexpensive surveillance camera that offers a 1000x1000 array of 8 im square pixels, anti-blooming circuitry, and very quick read out. Currently, the system directly converts x-rays to an image with no phosphor. The system is small and light and can be easily adapted to work with other crystallographic equipment. Preliminary images have been acquired of cubic insulin at the NSLS x26c beam line. NSLS x26c was configured for unfocused monochromatic radiation. Six reflections were collected with stills spaced from 0.002 to 0.001 degrees apart across the entire oscillation range that the reflections were in diffracting condition. All of the reflections were rotated to the vertical to reduce Lorentz and beam related effects. This particular CCD is designed for short exposure applications (much less than 1 sec) and so has a relatively high dark current leading to noisy raw images. The images are processed to remove background and other system noise with a multi-step approach including the use of wavelets, histogram, and mean window filtering. After processing, animations were constructed with the corresponding reflection profile to show the diffraction of the crystal volume vs. the oscillation angle as well as composite images showing the parts of the crystal with the strongest diffraction for each reflection. The final goal is to correlate features seen in reflection profiles captured with fine phi slicing to those seen in the topography images. With this development macromolecular topography finally comes into the digital age.

  13. Macromolecular networks and intelligence in microorganisms.

    PubMed

    Westerhoff, Hans V; Brooks, Aaron N; Simeonidis, Evangelos; García-Contreras, Rodolfo; He, Fei; Boogerd, Fred C; Jackson, Victoria J; Goncharuk, Valeri; Kolodkin, Alexey

    2014-01-01

    Living organisms persist by virtue of complex interactions among many components organized into dynamic, environment-responsive networks that span multiple scales and dimensions. Biological networks constitute a type of information and communication technology (ICT): they receive information from the outside and inside of cells, integrate and interpret this information, and then activate a response. Biological networks enable molecules within cells, and even cells themselves, to communicate with each other and their environment. We have become accustomed to associating brain activity - particularly activity of the human brain - with a phenomenon we call "intelligence." Yet, four billion years of evolution could have selected networks with topologies and dynamics that confer traits analogous to this intelligence, even though they were outside the intercellular networks of the brain. Here, we explore how macromolecular networks in microbes confer intelligent characteristics, such as memory, anticipation, adaptation and reflection and we review current understanding of how network organization reflects the type of intelligence required for the environments in which they were selected. We propose that, if we were to leave terms such as "human" and "brain" out of the defining features of "intelligence," all forms of life - from microbes to humans - exhibit some or all characteristics consistent with "intelligence." We then review advances in genome-wide data production and analysis, especially in microbes, that provide a lens into microbial intelligence and propose how the insights derived from quantitatively characterizing biomolecular networks may enable synthetic biologists to create intelligent molecular networks for biotechnology, possibly generating new forms of intelligence, first in silico and then in vivo. PMID:25101076

  14. Intelligent aids for parallel experiment planning and macromolecular crystallization.

    PubMed

    Gopalakrishnan, V; Buchanan, B G; Rosenberg, J M

    2000-01-01

    This paper presents a framework called Parallel Experiment Planning (PEP) that is based on an abstraction of how experiments are performed in the domain of macromolecular crystallization. The goal in this domain is to obtain a good quality crystal of a protein or other macromolecule that can be X-ray diffracted to determine three-dimensional structure. This domain presents problems encountered in real-world situations, such as a parallel and dynamic environment, insufficient resources and expensive tasks. The PEP framework comprises of two types of components: (1) an information management system for keeping track of sets of experiments, resources and costs; and (2) knowledge-based methods for providing intelligent assistance to decision-making. The significance of the developed PEP framework is three-fold--(a) the framework can be used for PEP even without one of its major intelligent aids that simulates experiments, simply by collecting real experimental data; (b) the framework with a simulator can provide intelligent assistance for experiment design by utilizing existing domain theories; and (c) the framework can help provide strategic assessment of different types of parallel experimentation plans that involve different tradeoffs. PMID:10977078

  15. 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

  16. 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

  17. Roles of partly unfolded conformations in macromolecular self-assembly.

    PubMed

    Namba, K

    2001-01-01

    From genes to cells there are many steps of hierarchical increments in building up complex frameworks that provide intricate networks of macromolecular interactions, through which cellular activities such as gene expression, signal processing, energy transduction and material conversion are dynamically organized and regulated. The self-assembly of macromolecules into large complexes is one such important step, but this process is by no means a simple aggregation of macromolecules with predefined, rigid complementary structures. In many cases the component molecules undergo either domain rearrangements or folding of disordered portions, which occurs only following binding to their correct partners. The partial disorder is used in some cases to prevent spontaneous assembly at inappropriate times or locations. It is also often used for finely tuning the equilibrium and activation energy of reversible binding. In other cases, such as protein translocation across membranes, an unfolded terminus appears to be the prerequisite for the process as an initiation signal, as well as the physical necessity to be taken into narrow channels. Self-assembly processes of viruses and bacterial flagella are typical examples where the induced folding of disordered chains plays a key role in regulating the addition of new components to a growing assembly. Various aspects of mechanistic roles of natively unfolded conformations of proteins are overviewed and discussed in this short review. PMID:11168592

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

    PubMed Central

    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

  19. 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.

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

    PubMed Central

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

    2012-01-01

    Summary 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

  1. Solution structure of [d(GGTATACC)]2: wrinkled D structure of the TATA moiety.

    PubMed

    Zhou, N; Bianucci, A M; Pattabiraman, N; James, T L

    1987-12-01

    Phase-sensitive two-dimensional nuclear Overhauser effect spectra of [d(GGTATACC)]2 in aqueous deuterium oxide solution at four mixing times were quantified to give all nonoverlapping cross-peak intensities. A structural model for [d(GGTATACC)]2 was built in which the GG- and -CC moieties were in the B-DNA form, while the middle -TATA- moiety was in the wrinkled-D form (BDB model). This model was subjected to energy refinement by molecular mechanics calculations with the program AMBER. Counterions (Na+) were added to neutralize the charges, and water molecules were placed bridging across the minor groove. A complete relaxation matrix analysis was used to calculate two-dimensional nuclear Overhauser effect spectra of [d(GGTATACC)]2 from the above models (before and after energy refinement) and from four other [d(GGTATACC)]2 structural models: regular A, crystalline A, regular B, and energy-minimized B. Among them, the energy-minimized BDB model yielded a set of theoretical spectra that gave the best fit to the experimental spectra. It was also the energetically most stable. Therefore, it is a good representation of the ensemble- and time-averaged structure of the octamer in solution. This model has backbone torsion angles similar to those of B-form DNA in the GG- and -CC moieties and torsion angles similar to those of wrinkled D form DNA in the -TATA- moiety. The base stacking and base pairing are not interrupted at the junctions between the two structural moieties. Its minor groove is narrower than that of B DNA, and the solvent-accessible surface of the minor groove forms a closed hydration tunnel in the middle -TATA- segment. PMID:3427113

  2. Solution structure of (d(GGTATACC))/sub 2/: wrinkled D structure of the TATA moiety

    SciTech Connect

    Zhou, N.; Bianucci, A.M.; Pattabiraman, N.; James, T.L.

    1987-12-01

    Phase-sensitive two-dimensional nuclear Overhauser effect spectra of (dGGTATACC))/sub 2/ in aqueous deuterium oxide solution at four mixing times were quantified to give all nonoverlapping cross-peak intensities. A structural model for (d(GGTATACC))/sub 2/ was built in which the GG- and -CC moieties were in the B-DNA form, while the middle -TATA- moiety was in the wrinkled-D form (BDB model). This model was subjected to energy refinement by molecular mechanics calculations with the program AMBER. Counterions (Na/sup +/) were added to neutralize the charges, and water molecules were placed bridging across the minor groove. A complete relaxation matrix analysis was used to calculate two-dimensional nuclear Overhauser effect spectra of (d(GGTATACC))/sub 2/ from the above models (before and after energy refinement) and from four other (d(GGTATACC))/sub 2/ structural models: regular A, crystalline A, regular B, and energy-minimized B. Among them, the energy-minimized BDB model yielded a set of theoretical spectra that gave the best fit to the experimental spectra. It was also the energetically most stable. Therefore, it is a good representation of the ensemble- and time-averaged structure of the octamer in solution. This model has backbone torsion angles similar to those of B-form DNA in the GG- and -CC moieties and torsion angles similar to those of wrinkled D for DNA in the -TATA- moiety. The base stacking and base pairing are not interrupted at the junctions between the two structural moieties. Its minor groove is narrower than that of B DNA, and the solvent-accessible surface of the minor groove forms a closed hydration tunnel in the middle -TATA- segment.

  3. 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.

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

    NASA Technical Reports Server (NTRS)

    Arya, Vinod K.

    1991-01-01

    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 materials. The computational results qualitatively replicate deformation behavior observed in experiments on prototypical structural components.

  5. 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.

  6. 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

  7. NMR solution structure of the neurotrypsin Kringle domain.

    PubMed

    Ozhogina, Olga A; Grishaev, Alexander; Bominaar, Emile L; Patthy, László; Trexler, Maria; Llinás, Miguel

    2008-11-25

    Neurotrypsin is a multidomain protein that serves as a brain-specific serine protease. Here we report the NMR structure of its kringle domain, NT/K. The data analysis was performed with the BACUS (Bayesian analysis of coupled unassigned spins) algorithm. This study presents the first application of BACUS to the structure determination of a 13C unenriched protein for which no prior experimental 3D structure was available. NT/K adopts the kringle fold, consisting of an antiparallel beta-sheet bridged by an overlapping pair of disulfides. The structure reveals the presence of a surface-exposed left-handed polyproline II helix that is closely packed to the core beta-structure. This feature distinguishes NT/K from other members of the kringle fold and points toward a novel functional role for a kringle domain. Functional divergence among kringle domains is discussed on the basis of their surface and electrostatic characteristics. PMID:18956887

  8. 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.

  9. Structure and interaction among protein and nanoparticle mixture in solution: Effect of temperature

    NASA Astrophysics Data System (ADS)

    Kundu, Sarathi; Das, Kaushik; Mehan, S.; Aswal, V. K.; Kohlbrecher, Joachim

    2015-11-01

    Structure and interaction among globular protein bovine serum albumin (BSA) and silica nanoparticle mixtures in solutions have been studied using small angle neutron scattering technique by varying the solution temperature. Our study shows that in absence of nanoparticles and up to 70 °C, an intermediate range repulsive and one long range attractive interaction potential between the proteins exist. Above that temperature, fractal structure forms. In presence of nanoparticles, fractal structures form even at room temperature by both the protein and nanoparticles. Fractal dimension increases with the increase of BSA concentration and solution temperature, and this temperature induced structural transition is irreversible.

  10. Geometric structures on solutions of equations of 3-dimensional adiabatic gas motion

    NASA Astrophysics Data System (ADS)

    Yumaguzhin, Valeriy

    2014-11-01

    In this paper, we show that characteristic covectors of a system of equations of 3-dimensional adiabatic gas motion generate a geometric structure on every solution of this system. This structure consists of a hyperplane and a non degenerate cone in every cotangent space to a solution. These hyperplane and cone intersect in zero point only. We construct differential invariants of this structure: a vector field, a conformal structure, a Lorentzian metric, and a linear connection. In the case of polytropic gas motion, we calculate classes of explicit solutions possessing the linear connection with zero torsion.

  11. Remote Access to the PXRR Macromolecular Crystallography Facilities at the NSLS

    SciTech Connect

    A Soares; D Schneider; J Skinner; M Cowan; R Buono; H Robinson; A Heroux; M Carlucci-Dayton; A Saxena; R Sweet

    2011-12-31

    The most recent surge of innovations that have simplified and streamlined the process of determining macromolecular structures by crystallography owes much to the efforts of the structural genomics community. However, this was only the last step in a long evolution that saw the metamorphosis of crystallography from an heroic effort that involved years of dedication and skill into a straightforward measurement that is occasionally almost trivial. Many of the steps in this remarkable odyssey involved reducing the physical labor that is demanded of experimenters in the field. Other steps reduced the technical expertise required for conducting those experiments.

  12. Remote Access to the PXRR Macromolecular Crystallography Facilities at the NSLS

    SciTech Connect

    Soares, A.S.; Schneider, D. K.; Skinner, J. M.; Cowan, M.; Buono, R.; Robinson, H. H.; Heroux, A.; Carlucci-Dayton, M.; Saxena, A.; Sweet, R. M.

    2008-09-01

    The most recent surge of innovations that have simplified and streamlined the process of determining macromolecular structures by crystallography owes much to the efforts of the structural genomics community. However, this was only the last step in a long evolution that saw the metamorphosis of crystallography from an heroic effort that involved years of dedication and skill into a straightforward measurement that is occasionally almost trivial. Many of the steps in this remarkable odyssey involved reducing the physical labor that is demanded of experimenters in the field. Other steps reduced the technical expertise required for conducting those experiments.

  13. Structural monitoring system with fiber Bragg grating sensors: implementation and software solution

    NASA Astrophysics Data System (ADS)

    Fedorov, Aleksey; Lazarev, Vladimir; Makhrov, Ilya; Pozhar, Nikolay; Anufriev, Maxim; Pnev, Alexey; Karasik, Valeriy

    2015-03-01

    We present a structural health monitoring system for nondestructive testing of composite materials based on the fiber Bragg grating sensors and specialized software solution. Developed structural monitoring system has potential applications for preliminary tests of novel composite materials as well as real-time structural health monitoring of industrial objects. The software solution realizes control for the system, data processing and alert of an operator.

  14. 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

  15. Effect of Escherichia coli enterotoxins on macromolecular absorption.

    PubMed Central

    Verma, M; Majumdar, S; Ganguly, N K; Walia, B N

    1994-01-01

    Macromolecular absorption of gliadin, a wheat protein and alpha lactalbumin, a milk protein was evaluated in control and Escherichia coli enterotoxin (heat-stable, heat-labile, and both heat-stable and heat-labile enterotoxin) treated mice. The peak concentration of gliadin and lactalbumin was two hours and three hours after their ingestion, respectively. There was also a significant increase (p < 0.01) in the absorption of both the proteins in all the three toxin treated groups compared with the control group. These results suggest that intestinal permeability and macromolecular absorption changes after E coli infection. PMID:7828983

  16. Synthesis of a macromolecular ligand by the modification of polystyrene

    SciTech Connect

    Phillips, H.H.; Kinstle, J.F.; Adcock, J.L.

    1981-01-01

    Uncrosslinked atactic polystyrene was chemically modified first by acetylation then by a Claisen condensation with ethyl perfluoropropanoate to produce three crosslinked chelating polymers that contained a phenyl, perfluoroethyl, beta-diketone chelating group in 10, 20, and 63 mole % compositions. Cu(II), Ni(II), and uranyl chelates of the macromolecular ligands were prepared and analyzed. The macromolecular ligands and their chelates were compared with the model ligating species 4,4,5,5,5-pentafluoro-1-phenyl-1,3-pentanedione with infrared and mass spectroscopy and proton nuclear magnetic resonance.

  17. Macromolecular crystallography beamline X25 at the NSLS.

    PubMed

    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

    2014-05-01

    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

  18. Finite element solution of transient fluid-structure interaction problems

    NASA Technical Reports Server (NTRS)

    Everstine, Gordon C.; Cheng, Raymond S.; Hambric, Stephen A.

    1991-01-01

    A finite element approach using NASTRAN is developed for solving time-dependent fluid-structure interaction problems, with emphasis on the transient scattering of acoustic waves from submerged elastic structures. Finite elements are used for modeling both structure and fluid domains to facilitate the graphical display of the wave motion through both media. For the liquid, the use of velocity potential as the fundamental unknown results in a symmetric matrix equation. The approach is illustrated for the problem of transient scattering from a submerged elastic spherical shell subjected to an incident tone burst. The use of an analogy between the equations of elasticity and the wave equation of acoustics, a necessary ingredient to the procedure, is summarized.

  19. Solution softening in magnesium alloys: the effect of solid solutions on the dislocation core structure and nonbasal slip.

    PubMed

    Tsuru, T; Udagawa, Y; Yamaguchi, M; Itakura, M; Kaburaki, H; Kaji, Y

    2013-01-16

    There is a pressing need to improve the ductility of magnesium alloys so that they can be applied as lightweight structural materials. In this study, a mechanism for enhancing the ductility of magnesium alloys has been pursued using the atomistic method. The generalized stacking fault (GSF) energies for basal and prismatic planes in magnesium were calculated by using density functional theory, and the effect of the GSF energy on the dislocation core structures was examined using a semidiscrete variational Peierls-Nabarro model. Yttrium was found to have an anomalous influence on the solution softening owing to a reduction in the GSF energy gradient. PMID:23220883

  20. Element-by-element Solution Procedures for Nonlinear Structural Analysis

    NASA Technical Reports Server (NTRS)

    Hughes, T. J. R.; Winget, J. M.; Levit, I.

    1984-01-01

    Element-by-element approximate factorization procedures are proposed for solving the large finite element equation systems which arise in nonlinear structural mechanics. Architectural and data base advantages of the present algorithms over traditional direct elimination schemes are noted. Results of calculations suggest considerable potential for the methods described.

  1. Structure and photophysics in C 60-micellar solutions

    NASA Astrophysics Data System (ADS)

    Eastoe, Julian; Crooks, Esther R.; Beeby, Andrew; Heenan, Richard K.

    1995-11-01

    Routes to the preparation of monomeric and colloidal C 60 in micellar solutions of non-ionic surfactants are described. UV-visible spectra and small-angle neutron scattering provide clear evidence for these two different forms. The micelles serve to stabilise the excited triplet state 3C 60 and the lifetime τT is increased by a factor of 3 as compared to 3C 60 in toluene. Furthermore, with monomeric dispersions in the presence of the electron donor DABCO, the radical anion C 60- is formed, with an unusually long lifetime τA = 16 ms. This lifetime is approximately 270 times longer than for γ-cyclodextrin. stabilised systems.

  2. 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.

  3. 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.

  4. Macromolecular Crowding Studies of Amino Acids Using NMR Diffusion Measurements and Molecular Dynamics Simulations

    NASA Astrophysics Data System (ADS)

    Virk, Amninder; Stait-Gardner, Timothy; Willis, Scott; Torres, Allan; Price, William

    2015-02-01

    Molecular crowding occurs when the total concentration of macromolecular species in a solution is so high that a considerable proportion of the volume is physically occupied and therefore not accessible to other molecules. This results in significant changes in the solution properties of the molecules in such systems. Macromolecular crowding is ubiquitous in biological systems due to the generally high intracellular protein concentrations. The major hindrance to understanding crowding is the lack of direct comparison of experimental data with theoretical or simulated data. Self-diffusion is sensitive to changes in the molecular weight and shape of the diffusing species, and the available diffusion space (i.e., diffusive obstruction). Consequently, diffusion measurements are a direct means for probing crowded systems including the self-association of molecules. In this work, nuclear magnetic resonance measurements of the self-diffusion of four amino acids (glycine, alanine, valine and phenylalanine) up to their solubility limit in water were compared directly with molecular dynamics simulations. The experimental data were then analyzed using various models of aggregation and obstruction. Both experimental and simulated data revealed that the diffusion of both water and the amino acids were sensitive to the amino acid concentration. The direct comparison of the simulated and experimental data afforded greater insights into the aggregation and obstruction properties of each amino acid.

  5. Chemical name to structure: OPSIN, an open source solution.

    PubMed

    Lowe, Daniel M; Corbett, Peter T; Murray-Rust, Peter; Glen, Robert C

    2011-03-28

    We have produced an open source, freely available, algorithm (Open Parser for Systematic IUPAC Nomenclature, OPSIN) that interprets the majority of organic chemical nomenclature in a fast and precise manner. This has been achieved using an approach based on a regular grammar. This grammar is used to guide tokenization, a potentially difficult problem in chemical names. From the parsed chemical name, an XML parse tree is constructed that is operated on in a stepwise manner until the structure has been reconstructed from the name. Results from OPSIN on various computer generated name/structure pair sets are presented. These show exceptionally high precision (99.8%+) and, when using general organic chemical nomenclature, high recall (98.7-99.2%). This software can serve as the basis for future open source developments of chemical name interpretation. PMID:21384929

  6. Molecular solutes in ionic liquids: a structural perspective.

    PubMed

    Pádua, Agílio A H; Costa Gomes, Margarida F; Canongia Lopes, José N A

    2007-11-01

    Understanding physicochemical properties of ionic liquids is important for their rational use in extractions, reactions, and other applications. Ionic liquids are not simple fluids: their ions are generally asymetric, flexible, with delocalized electrostatic charges, and available in a wide variety. It is difficult to capture their subtle properties with models that are too simplistic. Molecular simulation using atomistic force fields, which describe structures and interactions in detail, is an excellent tool to gain insights into their liquid-state organization, how they solvate different compounds, and what molecular factors determine their properties. The identification of certain ionic liquids as self-organized phases, with aggregated nonpolar and charged domains, provides a new way to interpret the solvation and structure of their mixtures. Many advances are the result of a successful interplay between experiment and modeling, possible in this field where none of the two methodologies had a previous advance. PMID:17661440

  7. Supermolecular structure of cellulose/amylose blends prepared from aqueous NaOH solutions and effects of amylose on structural formation of cellulose from its solution.

    PubMed

    Miyamoto, Hitomi; Ago, Mariko; Yamane, Chihiro; Seguchi, Masaharu; Ueda, Kazuyoshi; Okajima, Kunihiko

    2011-05-01

    We previously proposed a mechanism for the structural formation of cellulose from its solution using a molecular dynamics (MD) simulation and suggested that the initial structure from its solution plays a critical role in determining its final structure. Structural changes in the van der Waals-associated cellulose molecular sheet as the initial structure were examined by MD simulation; the molecular sheet was found to be disordered due to maltohexaoses as an amylose model in terms of the hydrogen bonding system of cellulose. The structure and properties of cellulose/amylose blends prepared from an aqueous NaOH solution were examined experimentally by wide-angle X-ray diffraction and dynamic viscoelasticity measurements. The crystallinity of cellulose in the cellulose/amylose blend films was lower than that of cellulose film. The diffraction peaks of the cellulose/amylose blends were slightly shifted; specifically, (1 1 0) was shifted to a higher angle, and (1 1 0) and (0 2 0) were shifted to lower angles. These experimental results probably resulted from the disordered molecular sheet, as revealed by MD simulations. PMID:21392738

  8. ANOVA-HDMR structure of the higher order nodal diffusion solution

    SciTech Connect

    Bokov, P. M.; Prinsloo, R. H.; Tomasevic, D. I.

    2013-07-01

    Nodal diffusion methods still represent a standard in global reactor calculations, but employ some ad-hoc approximations (such as the quadratic leakage approximation) which limit their accuracy in cases where reference quality solutions are sought. In this work we solve the nodal diffusion equations utilizing the so-called higher-order nodal methods to generate reference quality solutions and to decompose the obtained solutions via a technique known as High Dimensional Model Representation (HDMR). This representation and associated decomposition of the solution provides a new formulation of the transverse leakage term. The HDMR structure is investigated via the technique of Analysis of Variance (ANOVA), which indicates why the existing class of transversely-integrated nodal methods prove to be so successful. Furthermore, the analysis leads to a potential solution method for generating reference quality solutions at a much reduced calculational cost, by applying the ANOVA technique to the full higher order solution. (authors)

  9. Solution Structure of the Conserved Hypothetical Protein Rv2302 from Mycobacterium tuberculosis.

    SciTech Connect

    Buchko, Garry W.; Kim, Chang Y.; Terwilliger, Thomas C.; Kennedy, Michael A.

    2006-08-01

    The hypothetical Mycobacterium tuberculosis protein RV2302 (80 residues, MW = 8.6 kDa) has been characterized using nuclear magnetic resonance (NMR) and circular dichroism (CD) spectroscopy. Size exclusion chromatography and NMR spectroscopy suggest that RV2302 is as a monomer is solution. Circular dichroism spectroscopy indicates the protein is structured in solution, but, irreversible unfolds upon heating with an inflection point of {approx}48 C. Using NMR based methods we determined the solution structure of RV2302. The protein contains a five strand, anti-parallel b-sheet core with one C-terminal a-helix (A65-A75) nestled against its side. Dali searches using the structure closest to the average structure did not identify any high similarities to any other known protein structure. Consequently, the structure of Rv2302 may potentially represent a novel protein fold.

  10. Phase sensitive x-ray diffraction imaging of defects in biological macromolecular crystals

    NASA Technical Reports Server (NTRS)

    Hu, Z. W.; Lai, B.; Chu, Y. S.; Cai, Z.; Mancini, D. C.; Thomas, B. R.; Chernov, A. A.

    2001-01-01

    Conventional x-ray diffraction topography is currently used to map defects in the bulk of protein crystals, but the lack of sufficient contrast is frequently a limiting factor. We experimentally demonstrate that this barrier can be circumvented using a method that combines phase sensitive and diffraction imaging principles. Details of defects revealed in tetragonal lysozyme and cubic ferritin crystals are presented and discussed. The approach enabling the detection of the phase changes of diffracted x rays should prove to be useful in the study of defect structures in a broad range of biological macromolecular crystals.

  11. 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

  12. Phase Behavior of a Single Structured Ionomer Chain in Solution

    SciTech Connect

    Aryal, Dipak; Etampawala, Thusitha; Perahia, Dvora; Grest, Gary S.

    2014-08-14

    Structured polymers offer a means to tailor transport pathways within mechanically stable manifolds. Here we examine the building block of such a membrane, namely a single large pentablock co-polymer that consist of a center block of a randomly sulfonated polystyrene, designed for transport, tethered to poly-ethylene-r-propylene and end-capped by poly-t-butyl styrene, for mechanical stability,using molecular dynamics simulations. The polymer structure in a cyclohexane-heptane mixture, a technologically viable solvent, and in water, a poor solvent for all segments and a ubiquitous substance is extracted. In all solvents the pentablock collapsed into nearly spherical aggregates where the ionic block is segregated. In hydrophobic solvents, the ionic block resides in the center, surrounded by swollen intermix of flexible and end blocks. In water all blocks are collapsed with the sulfonated block residing on the surface. Our results demonstrate that solvents drive different local nano-segregation, providing a gateway to assemble membranes with controlled topology.

  13. Phase Behavior of a Single Structured Ionomer Chain in Solution

    DOE PAGESBeta

    Aryal, Dipak; Etampawala, Thusitha; Perahia, Dvora; Grest, Gary S.

    2014-08-14

    Structured polymers offer a means to tailor transport pathways within mechanically stable manifolds. Here we examine the building block of such a membrane, namely a single large pentablock co-polymer that consist of a center block of a randomly sulfonated polystyrene, designed for transport, tethered to poly-ethylene-r-propylene and end-capped by poly-t-butyl styrene, for mechanical stability,using molecular dynamics simulations. The polymer structure in a cyclohexane-heptane mixture, a technologically viable solvent, and in water, a poor solvent for all segments and a ubiquitous substance is extracted. In all solvents the pentablock collapsed into nearly spherical aggregates where the ionic block is segregated. Inmore » hydrophobic solvents, the ionic block resides in the center, surrounded by swollen intermix of flexible and end blocks. In water all blocks are collapsed with the sulfonated block residing on the surface. Our results demonstrate that solvents drive different local nano-segregation, providing a gateway to assemble membranes with controlled topology.« less

  14. Structural characterization of human general transcription factor TFIIF in solution

    PubMed Central

    Akashi, Satoko; Nagakura, Shinjiro; Yamamoto, Seiji; Okuda, Masahiko; Ohkuma, Yoshiaki; Nishimura, Yoshifumi

    2008-01-01

    Human general transcription factor IIF (TFIIF), a component of the transcription pre-initiation complex (PIC) associated with RNA polymerase II (Pol II), was characterized by size-exclusion chromatography (SEC), electrospray ionization mass spectrometry (ESI-MS), and chemical cross-linking. Recombinant TFIIF, composed of an equimolar ratio of α and β subunits, was bacterially expressed, purified to homogeneity, and found to have a transcription activity similar to a natural one in the human in vitro transcription system. SEC of purified TFIIF, as previously reported, suggested that this protein has a size >200 kDa. In contrast, ESI-MS of the purified sample gave a molecular size of 87 kDa, indicating that TFIIF is an αβ heterodimer, which was confirmed by matrix-assisted laser desorption/ionization (MALDI) MS of the cross-linked TFIIF components. Recent electron microscopy (EM) and photo-cross-linking studies showed that the yeast TFIIF homolog containing Tfg1 and Tfg2, corresponding to the human α and β subunits, exists as a heterodimer in the PIC, so the human TFIIF is also likely to exist as a heterodimer even in the PIC. In the yeast PIC, EM and photo-cross-linking studies showed different results for the mutual location of TFIIE and TFIIF along DNA. We have examined the direct interaction between human TFIIF and TFIIE by ESI-MS, SEC, and chemical cross-linking; however, no direct interaction was observed, at least in solution. This is consistent with the previous photo-cross-linking observation that TFIIF and TFIIE flank DNA separately on both sides of the Pol II central cleft in the yeast PIC. PMID:18218714

  15. Molecular structures and protonation state of 2-Mercaptopyridine in aqueous solution

    NASA Astrophysics Data System (ADS)

    Eckert, S.; Miedema, P. S.; Quevedo, W.; O'Cinneide, B.; Fondell, M.; Beye, M.; Pietzsch, A.; Ross, M.; Khalil, M.; Föhlisch, A.

    2016-03-01

    The speciation of 2-Mercaptopyridine in aqueous solution has been investigated with nitrogen 1s Near Edge X-ray Absorption Fine Structure spectroscopy and time dependent Density Functional Theory. The prevalence of distinct species as a function of the solvent basicity is established. No indications of dimerization towards high concentrations are found. The determination of different molecular structures of 2-Mercaptopyridine in aqueous solution is put into the context of proton-transfer in keto-enol and thione-thiol tautomerisms.

  16. Imaging Macromolecular Interactions at an Interface

    PubMed Central

    Lampe, Joshua W.; Liao, Zhengzheng; Dmochowski, Ivan J.; Ayyaswamy, Portonovo S.; Eckmann, David M.

    2010-01-01

    Important physiological, pathological, and technological processes occur at continuous and dispersed phase interfaces. Understanding these processes is limited by inability to quantitate molecular events occurring at the interface. To provide a model-independent measurement of protein concentration and mobility at the interface, we employed confocal laser scanning microscopy (CLSM). Fluorescently labeled albumin and fibrinogen were studied singly, pairwise, and with a surfactant, Pluronic F-127, in aqueous droplets. CLSM enables measurement of molecular behaviors manifest as surface inhomogeneity and of biophysical quantities including partitioning between the bulk and the gas-liquid (GL) interface. We conclude that albumin and fibrinogen behave substantially differently at the GL interface, that adsorption from multi-species solutions is fundamentally different than adsorption from solutions of single species, and surfactants can inhibit proteins from occupying the interface. PMID:20085337

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

    PubMed Central

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

    2014-01-01

    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

  18. 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

  19. Solvent-dependent structure of molecular iodine probed by picosecond X-ray solution scattering.

    PubMed

    Kim, Kyung Hwan; Ki, Hosung; Lee, Jae Hyuk; Park, Sungjun; Kong, Qingyu; Kim, Jeongho; Kim, Joonghan; Wulff, Michael; Ihee, Hyotcherl

    2015-04-14

    The effect of solute-solvent interaction on molecular structure and reaction dynamics has been a target of intense studies in solution-phase chemistry, but it is often challenging to characterize the subtle effect of solute-solvent interaction even for the simplest diatomic molecules. Since the I2 molecule has only one structural parameter and exhibits solvatochromism, it is a good model system for investigating the solvent dependence of the solute structure. By using X-rays as a probe, time-resolved X-ray liquidography (TRXL) can directly elucidate the structures of reacting molecules in solution and can thus determine the solvent-dependent structural change with atomic resolution. Here, by applying TRXL, we characterized the molecular structure of I2 in methanol and cyclohexane with sub-angstrom accuracy. Specifically, we found that the I-I bond length of I2 is longer in the polar solvent (methanol) by ∼0.2 Å than in nonpolar solvents (cyclohexane and CCl4). Density functional theory (DFT) using 22 explicit methanol molecules well reproduces the longer I-I bond of molecular iodine in methanol and reveals that the larger bond length originates from partial negative charge filled in an antibonding σ* orbital through solvent-to-solute charge transfer. PMID:25760386

  20. Global structure of black hole and brane solutions in a multidimensional model with anisotropic fluid

    NASA Astrophysics Data System (ADS)

    Bolokhov, S. V.; Ivashchuk, V. D.

    We analyse the global causal structure of a family of multidimensional spherically-symmetric solutions with a horizon which appear in the model with 1-component anisotropic fluid. This family can be considered as a generalized analogs of the well-known black hole solutions (including the Reissner--Nordström one) and some black brane solutions. The structure of regular horizons and singular boundaries is studied, and the corresponding Carter--Penrose diagrams are constructed for various values of the parameters of the model.

  1. Solution structure of the cAMP-dependent protein kinase

    SciTech Connect

    Trewhella, J.; Olah, G.A.; Walsh, D.A.; Mitchell, R.D.

    1998-12-31

    This is the final report of a three-year, Laboratory Directed Research and Development (LDRD) project as Los Alamos National Laboratory (LANL). Protein phosphorylation is well established as one of the most important mechanisms of signal transduction and cellular regulation. Two of the key enzymes that catalyze these phosphorylation reactions are the cAMP- (PKA) and cGMP- (PKG) dependent protein kinases. PKA has served as the prototypic model of this class of enzymes that now comprises in excess of 300 phylogenetically related proteins. A large number of these protein kinases are critical for the regulation of cell function and a full analysis of their similarities and differences is essential to understand their diverse physiological roles. The cAMP-dependent protein kinase has the subunit structure R2C2, in which C and R refer to the catalytic and regulatory subunits, respectively. The cGMP-dependent protein kinase (PKG) is highly homologous to PKA but is distinguished from it by having the regulatory and catalytic domains on a contiguous polypeptide. The studies described here use small-angle scattering and Fourier Transform InfraRed (FTIR) spectroscopy to study domain movements and conformational changes in these enzymes in different functional states in order to elucidate the molecular bases for the regulation of their activities.

  2. Structure of electrolyte solutions sorbed in carbon nanospaces, studied by the replica RISM theory.

    PubMed

    Tanimura, A; Kovalenko, A; Hirata, F

    2007-01-30

    The replica RISM theory is used to investigate the structure of electrolyte solutions confined in carbonized polyvinylidene chloride (PVDC) nanoporous material, compared to bulk electrolyte solution. Comparisons are made between the models of electrolyte solution sorbed in the carbonized PVDC material and a single carbon nanosphere in bulk electrolyte solution. Particular attention is paid to the chemical potential balance between the species of the sorbed electrolyte solution and the bulk solution in contact with the nanoporous material. As a result of the strong hydrophobicity of the carbonized PVDC material in the absence of activating chemical groups, the densities of water and ions sorbed in the material are remarkably low compared to those in the ambient bulk solution. The interaction between water molecules and cations becomes strong in nanospaces. It turns out that, in carbon nanopores, a cation adsorbed at the carbon surface is fully surrounded by the hydration shell of water molecules which separates the cation and the surface. Distinctively, an anion is adsorbed in direct contact with the carbon surface, which squeezes a part of its hydration shell out. The tendency increases toward smaller cations, which are characterized as "positive hydration" ions. In the bulk, cations are not hydrated so strongly and behave similarly to anions. The results suggest that the specific capacitance of an electric double-layer supercapacitor with nanoporous electrodes is intimately related to the solvation structure of electrolyte solution sorbed in nanopores, which is affected by the microscopic structure of the nanoporous electrode. PMID:17241081

  3. Investigations on the structure of DMSO and acetone in aqueous solution

    SciTech Connect

    McLain, Sylvia E; Soper, Alan K

    2007-01-01

    Aqueous solutions of dimethyl sulfoxide (DMSO) and acetone have been investigated using neutron diffraction augmented with isotopic substitution and empirical potential structure refinement computer simulations. Each solute has been measured at two concentrations-1:20 and 1:2 solute:water mole ratios. At both concentrations for each solute, the tetrahedral hydrogen bonding network of water is largely unperturbed, though the total water molecule coordination number is reduced in the higher 1:2 concentrations. With higher concentrations of acetone, water tends to segregate into clusters, while in higher concentrations of DMSO the present study reconfirms that the structure of the liquid is dominated by DMSO-water interactions. This result may have implications for the highly nonideal behavior observed in the thermodynamic functions for 1:2 DMSO-water solutions.

  4. A structured multi-block solution-adaptive mesh algorithm with mesh quality assessment

    NASA Technical Reports Server (NTRS)

    Ingram, Clint L.; Laflin, Kelly R.; Mcrae, D. Scott

    1995-01-01

    The dynamic solution adaptive grid algorithm, DSAGA3D, is extended to automatically adapt 2-D structured multi-block grids, including adaption of the block boundaries. The extension is general, requiring only input data concerning block structure, connectivity, and boundary conditions. Imbedded grid singular points are permitted, but must be prevented from moving in space. Solutions for workshop cases 1 and 2 are obtained on multi-block grids and illustrate both increased resolution of and alignment with the solution. A mesh quality assessment criteria is proposed to determine how well a given mesh resolves and aligns with the solution obtained upon it. The criteria is used to evaluate the grid quality for solutions of workshop case 6 obtained on both static and dynamically adapted grids. The results indicate that this criteria shows promise as a means of evaluating resolution.

  5. The density, viscosity and structural properties of aqueous ethambutol hydrochloride solutions

    NASA Astrophysics Data System (ADS)

    Deosarkar, S. D.; Puyad, A. L.; Kalyankar, T. M.

    2012-05-01

    Ethambutol (EMB) is a bacteriostatic antimycobacterial drug prescribed to treat tuberculosis. It is bacteriostatic against actively growing TB bacilli. The density and viscosity of aqueous ethambutol hydrochloride solutions have been studied at 298.15, 301.15 and 304.15 K and at different concentrations (0.255, 0.168, 0.128, 0.087, 0.041, and 0.023 mol dm-3). The apparent molar volume of these solutions for different temperatures and concentrations was calculated from the density data. The relative viscosities of drug solutions have been analysed by Jones-Dole equation. The limiting apparent molar volumes have been evaluated for different temperatures. The different properties have been used to study structural properties, structure formation and breaking properties of drug and solute-solvent interactions in solutions.

  6. 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.

  7. An early look at macromolecular crowding.

    PubMed

    Laurent, T C

    1995-12-01

    Interest in the interaction between proteins and polysaccharides in semidilute systems developed in the late 1950's and early 1960's both in the field of matrix biology and in the construction of new separation techniques. The author gives an account of how his work in the 50's on the characterization of a connective tissue polysaccharide, hyaluronan, led him into studies on polysaccharide networks, sieve effects, molecular exclusion, a theory of gel filtration, solubility of proteins and chemical equilibria in polymer solutions, water and protein homeostatis in vivo, and ordered convectional flow in concentrated polymer systems. PMID:17023331

  8. 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.

  9. SASSIE: A program to study intrinsically disordered biological molecules and macromolecular ensembles using experimental scattering restraints

    NASA Astrophysics Data System (ADS)

    Curtis, Joseph E.; Raghunandan, Sindhu; Nanda, Hirsh; Krueger, Susan

    2012-02-01

    A program to construct ensembles of biomolecular structures that are consistent with experimental scattering data are described. Specifically, we generate an ensemble of biomolecular structures by varying sets of backbone dihedral angles that are then filtered using experimentally determined restraints to rapidly determine structures that have scattering profiles that are consistent with scattering data. We discuss an application of these tools to predict a set of structures for the HIV-1 Gag protein, an intrinsically disordered protein, that are consistent with small-angle neutron scattering experimental data. We have assembled these algorithms into a program called SASSIE for structure generation, visualization, and analysis of intrinsically disordered proteins and other macromolecular ensembles using neutron and X-ray scattering restraints. Program summaryProgram title: SASSIE Catalogue identifier: AEKL_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEKL_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License v3 No. of lines in distributed program, including test data, etc.: 3 991 624 No. of bytes in distributed program, including test data, etc.: 826 Distribution format: tar.gz Programming language: Python, C/C++, Fortran Computer: PC/Mac Operating system: 32- and 64-bit Linux (Ubuntu 10.04, Centos 5.6) and Mac OS X (10.6.6) RAM: 1 GB Classification: 3 External routines: Python 2.6.5, numpy 1.4.0, swig 1.3.40, scipy 0.8.0, Gnuplot-py-1.8, Tcl 8.5, Tk 8.5, Mac installation requires aquaterm 1.0 (or X window system) and Xcode 3 development tools. Nature of problem: Open source software to generate structures of disordered biological molecules that subsequently allow for the comparison of computational and experimental results is limiting the use of scattering resources. Solution method: Starting with an all atom model of a protein, for example, users can input regions to vary dihedral angles, ensembles of structures can be generated. Additionally, simple two-body rigid-body rotations are supported with and without disordered regions. Generated structures can then be used to calculate small-angle scattering profiles which can then be filtered against experimentally determined data. Filtered structures can be visualized individually or as an ensemble using density plots. In the modular and expandable program framework the user can easily access our subroutines and structural coordinates can be easily obtained for study using other computational physics methods. Additional comments: The distribution file for this program is over 159 Mbytes and therefore is not delivered directly when download or Email is requested. Instead an html file giving details of how the program can be obtained is sent. Running time: Varies depending on application. Typically 10 minutes to 24 hours depending on the number of generated structures.

  10. 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".

  11. 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.

  12. Localization of Protein Aggregation in Escherichia coli Is Governed by Diffusion and Nucleoid Macromolecular Crowding Effect

    PubMed Central

    Coquel, Anne-Sophie; Jacob, Jean-Pascal; Primet, Mael; Demarez, Alice; Dimiccoli, Mariella; Julou, Thomas; Moisan, Lionel

    2013-01-01

    Aggregates of misfolded proteins are a hallmark of many age-related diseases. Recently, they have been linked to aging of Escherichia coli (E. coli) where protein aggregates accumulate at the old pole region of the aging bacterium. Because of the potential of E. coli as a model organism, elucidating aging and protein aggregation in this bacterium may pave the way to significant advances in our global understanding of aging. A first obstacle along this path is to decipher the mechanisms by which protein aggregates are targeted to specific intercellular locations. Here, using an integrated approach based on individual-based modeling, time-lapse fluorescence microscopy and automated image analysis, we show that the movement of aging-related protein aggregates in E. coli is purely diffusive (Brownian). Using single-particle tracking of protein aggregates in live E. coli cells, we estimated the average size and diffusion constant of the aggregates. Our results provide evidence that the aggregates passively diffuse within the cell, with diffusion constants that depend on their size in agreement with the Stokes-Einstein law. However, the aggregate displacements along the cell long axis are confined to a region that roughly corresponds to the nucleoid-free space in the cell pole, thus confirming the importance of increased macromolecular crowding in the nucleoids. We thus used 3D individual-based modeling to show that these three ingredients (diffusion, aggregation and diffusion hindrance in the nucleoids) are sufficient and necessary to reproduce the available experimental data on aggregate localization in the cells. Taken together, our results strongly support the hypothesis that the localization of aging-related protein aggregates in the poles of E. coli results from the coupling of passive diffusion-aggregation with spatially non-homogeneous macromolecular crowding. They further support the importance of “soft” intracellular structuring (based on macromolecular crowding) in diffusion-based protein localization in E. coli. PMID:23633942

  13. A Web Resource for Standardized Benchmark Datasets, Metrics, and Rosetta Protocols for Macromolecular Modeling and Design

    PubMed Central

    Pache, Roland A.; Ollikainen, Noah; Kundert, Kale; O'Meara, Matthew J.; Smith, Colin A.; Kortemme, Tanja

    2015-01-01

    The development and validation of computational macromolecular modeling and design methods depend on suitable benchmark datasets and informative metrics for comparing protocols. In addition, if a method is intended to be adopted broadly in diverse biological applications, there needs to be information on appropriate parameters for each protocol, as well as metrics describing the expected accuracy compared to experimental data. In certain disciplines, there exist established benchmarks and public resources where experts in a particular methodology are encouraged to supply their most efficient implementation of each particular benchmark. We aim to provide such a resource for protocols in macromolecular modeling and design. We present a freely accessible web resource (https://kortemmelab.ucsf.edu/benchmarks) to guide the development of protocols for protein modeling and design. The site provides benchmark datasets and metrics to compare the performance of a variety of modeling protocols using different computational sampling methods and energy functions, providing a “best practice” set of parameters for each method. Each benchmark has an associated downloadable benchmark capture archive containing the input files, analysis scripts, and tutorials for running the benchmark. The captures may be run with any suitable modeling method; we supply command lines for running the benchmarks using the Rosetta software suite. We have compiled initial benchmarks for the resource spanning three key areas: prediction of energetic effects of mutations, protein design, and protein structure prediction, each with associated state-of-the-art modeling protocols. With the help of the wider macromolecular modeling community, we hope to expand the variety of benchmarks included on the website and continue to evaluate new iterations of current methods as they become available. PMID:26335248

  14. 3D structure of individual nanocrystals in solution by electron microscopy

    NASA Astrophysics Data System (ADS)

    Park, Jungwon; Elmlund, Hans; Ercius, Peter; Yuk, Jong Min; Limmer, David T.; Chen, Qian; Kim, Kwanpyo; Han, Sang Hoon; Weitz, David A.; Zettl, A.; Alivisatos, A. Paul

    2015-07-01

    Knowledge about the synthesis, growth mechanisms, and physical properties of colloidal nanoparticles has been limited by technical impediments. We introduce a method for determining three-dimensional (3D) structures of individual nanoparticles in solution. We combine a graphene liquid cell, high-resolution transmission electron microscopy, a direct electron detector, and an algorithm for single-particle 3D reconstruction originally developed for analysis of biological molecules. This method yielded two 3D structures of individual platinum nanocrystals at near-atomic resolution. Because our method derives the 3D structure from images of individual nanoparticles rotating freely in solution, it enables the analysis of heterogeneous populations of potentially unordered nanoparticles that are synthesized in solution, thereby providing a means to understand the structure and stability of defects at the nanoscale.

  15. Effect of solute atoms on dislocation motion in Mg: An electronic structure perspective

    PubMed Central

    Tsuru, T.; Chrzan, D. C.

    2015-01-01

    Solution strengthening is a well-known approach to tailoring the mechanical properties of structural alloys. Ultimately, the properties of the dislocation/solute interaction are rooted in the electronic structure of the alloy. Accordingly, we compute the electronic structure associated with, and the energy barriers to dislocation cross-slip. The energy barriers so obtained can be used in the development of multiscale models for dislocation mediated plasticity. The computed electronic structure can be used to identify substitutional solutes likely to interact strongly with the dislocation. Using the example of a-type screw dislocations in Mg, we compute accurately the Peierls barrier to prismatic plane slip and argue that Y, Ca, Ti, and Zr should interact strongly with the studied dislocation, and thereby decrease the dislocation slip anisotropy in the alloy. PMID:25740411

  16. 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.

  17. 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

  18. Exact solution to the problem of N bodies forming a multi-layer rotating structure.

    PubMed

    Smulsky, Joseph J

    2015-01-01

    Exact solutions to the problem of the Newtonian gravitational interaction of N material points moving around N 2 concentric circular orbits are considered. Each circular orbit contains N 3 axisymmetrically located bodies having identical masses. The structure as a whole rotates around its symmetry axis. Such structures are identical to the homographic-dynamics configurations, or planar central configurations, known from literature. Conceptually, those structures can be considered as structures formed by mutually embedded polygons with point bodies placed at polygon vortices. For structures involving less than 20 bodies, solutions were obtained using Hamiltonian-mechanics methods. In the study, the forces acting on each body in the rotating structure from the side of all other bodies were found. The differential motion equations of the bodies were reduced to a system of linear algebraic equations for the body masses. Solutions in various forms were obtained. For specifying the initial parameters and for calculating all other characteristics of the structures, a computer program RtCrcSt2.for has been developed. Structures comprising up to one million bodies have been calculated. Graphical images of obtained structures are presented, and their properties are described. Stability problems for examined structures are considered, and possible application of obtained results to celestial- and space-mechanics problems is discussed. PMID:26203407

  19. 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

  20. Solution structures of proteins from NMR data and modeling: Alternative folds for neutrophil peptide 5

    SciTech Connect

    Levy, R.M.; Bassolino, D.A.; Kitchen, D.B. ); Pardi, A. )

    1989-11-28

    The structure of neutrophil peptide 5 in solution has recently reported. The structure determination was accomplished by using a distance geometry algorithm and 107 interproton distances constrains obtained from 2D NMR data. In each of the eight independent solutions to the distance geometry equations, the overall fold of the polypeptide backbone was identical and the root mean square (rms) deviation between backbone atoms of the superimposed structures was small. In this paper the authors report additional NP-5 structures obtained by using a new structure generation algorithm: a Monte Carlo search in torsion angle space. These structures have a large rms backbone deviation from the distance geometry structures. The backbone topologies differ in significant respects from the distance geometry structures and from each other. Structures are found that are pseudo mirror images of part or all of the fold corresponding to that first obtained with the distance geometry procedure. The results demonstrate that the previously accepted criteria for defining the accuracy and precision of a peptide structure generated from NMR data are inadequate. An energetic analysis of structures corresponding to the different folding topologies has been carried out. The molecular mechanics energies obtained by minimization and molecular dynamics refinement provide sufficient information to eliminate certain alternative structures. On the basis of a careful comparison of the different trial structures with the experimental data, it is concluded that the NP-5 peptide fold which was originally reported is most consistent with the data.

  1. Diffusion accessibility as a method for visualizing macromolecular surface geometry.

    PubMed

    Tsai, Yingssu; Holton, Thomas; Yeates, Todd O

    2015-10-01

    Important three-dimensional spatial features such as depth and surface concavity can be difficult to convey clearly in the context of two-dimensional images. In the area of macromolecular visualization, the computer graphics technique of ray-tracing can be helpful, but further techniques for emphasizing surface concavity can give clearer perceptions of depth. The notion of diffusion accessibility is well-suited for emphasizing such features of macromolecular surfaces, but a method for calculating diffusion accessibility has not been made widely available. Here we make available a web-based platform that performs the necessary calculation by solving the Laplace equation for steady state diffusion, and produces scripts for visualization that emphasize surface depth by coloring according to diffusion accessibility. The URL is http://services.mbi.ucla.edu/DiffAcc/. PMID:26189444

  2. Discussions on equivalent solutions and localized structures via the mapping method based on Riccati equation

    NASA Astrophysics Data System (ADS)

    Xu, Ling; Cheng, Xuan; Dai, Chao-Qing

    2015-12-01

    Although the mapping method based on Riccati equation was proposed to obtain variable separation solutions many years ago, two important problems have not been studied: i) the equivalence of variable separation solutions by means of the mapping method based on Riccati equation with the radical sign combined ansatz; and ii) lack of physical meanings for some localized structures constructed by variable separation solutions. In this paper, we re-study the (2+1)-dimensional Boiti-Leon-Pempinelli equation via the mapping method based on Riccati equation and prove that nine types of variable separation solutions are actually equivalent to each other. Moreover, we also re-study localized structures constructed by variable separation solutions. Results indicate that some localized structures reported in the literature are lacking real values due to the appearance of the divergent and un-physical phenomenon for the initial field. Therefore, we must be careful with the initial field to avoid the appearance of some un-physical or even divergent structures in it when we construct localized structures for the potential field.

  3. 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

  4. Impact of synchrotron radiation on macromolecular crystallography: a personal view

    PubMed Central

    Dauter, Zbigniew; Jaskolski, Mariusz; Wlodawer, Alexander

    2010-01-01

    The introduction of synchrotron radiation sources almost four decades ago has led to a revolutionary change in the way that diffraction data from macromolecular crystals are being collected. Here a brief history of the development of methodologies that took advantage of the availability of synchrotron sources are presented, and some personal experiences with the utilization of synchrotrons in the early days are recalled. PMID:20567074

  5. Path Similarity Analysis: A Method for Quantifying Macromolecular Pathways.

    PubMed

    Seyler, Sean L; Kumar, Avishek; Thorpe, M F; Beckstein, Oliver

    2015-10-01

    Diverse classes of proteins function through large-scale conformational changes and various sophisticated computational algorithms have been proposed to enhance sampling of these macromolecular transition paths. Because such paths are curves in a high-dimensional space, it has been difficult to quantitatively compare multiple paths, a necessary prerequisite to, for instance, assess the quality of different algorithms. We introduce a method named Path Similarity Analysis (PSA) that enables us to quantify the similarity between two arbitrary paths and extract the atomic-scale determinants responsible for their differences. PSA utilizes the full information available in 3N-dimensional configuration space trajectories by employing the Hausdorff or Fréchet metrics (adopted from computational geometry) to quantify the degree of similarity between piecewise-linear curves. It thus completely avoids relying on projections into low dimensional spaces, as used in traditional approaches. To elucidate the principles of PSA, we quantified the effect of path roughness induced by thermal fluctuations using a toy model system. Using, as an example, the closed-to-open transitions of the enzyme adenylate kinase (AdK) in its substrate-free form, we compared a range of protein transition path-generating algorithms. Molecular dynamics-based dynamic importance sampling (DIMS) MD and targeted MD (TMD) and the purely geometric FRODA (Framework Rigidity Optimized Dynamics Algorithm) were tested along with seven other methods publicly available on servers, including several based on the popular elastic network model (ENM). PSA with clustering revealed that paths produced by a given method are more similar to each other than to those from another method and, for instance, that the ENM-based methods produced relatively similar paths. PSA applied to ensembles of DIMS MD and FRODA trajectories of the conformational transition of diphtheria toxin, a particularly challenging example, showed that the geometry-based FRODA occasionally sampled the pathway space of force field-based DIMS MD. For the AdK transition, the new concept of a Hausdorff-pair map enabled us to extract the molecular structural determinants responsible for differences in pathways, namely a set of conserved salt bridges whose charge-charge interactions are fully modelled in DIMS MD but not in FRODA. PSA has the potential to enhance our understanding of transition path sampling methods, validate them, and to provide a new approach to analyzing conformational transitions. PMID:26488417

  6. Path Similarity Analysis: A Method for Quantifying Macromolecular Pathways

    PubMed Central

    Seyler, Sean L.; Kumar, Avishek; Thorpe, M. F.; Beckstein, Oliver

    2015-01-01

    Diverse classes of proteins function through large-scale conformational changes and various sophisticated computational algorithms have been proposed to enhance sampling of these macromolecular transition paths. Because such paths are curves in a high-dimensional space, it has been difficult to quantitatively compare multiple paths, a necessary prerequisite to, for instance, assess the quality of different algorithms. We introduce a method named Path Similarity Analysis (PSA) that enables us to quantify the similarity between two arbitrary paths and extract the atomic-scale determinants responsible for their differences. PSA utilizes the full information available in 3N-dimensional configuration space trajectories by employing the Hausdorff or Fréchet metrics (adopted from computational geometry) to quantify the degree of similarity between piecewise-linear curves. It thus completely avoids relying on projections into low dimensional spaces, as used in traditional approaches. To elucidate the principles of PSA, we quantified the effect of path roughness induced by thermal fluctuations using a toy model system. Using, as an example, the closed-to-open transitions of the enzyme adenylate kinase (AdK) in its substrate-free form, we compared a range of protein transition path-generating algorithms. Molecular dynamics-based dynamic importance sampling (DIMS) MD and targeted MD (TMD) and the purely geometric FRODA (Framework Rigidity Optimized Dynamics Algorithm) were tested along with seven other methods publicly available on servers, including several based on the popular elastic network model (ENM). PSA with clustering revealed that paths produced by a given method are more similar to each other than to those from another method and, for instance, that the ENM-based methods produced relatively similar paths. PSA applied to ensembles of DIMS MD and FRODA trajectories of the conformational transition of diphtheria toxin, a particularly challenging example, showed that the geometry-based FRODA occasionally sampled the pathway space of force field-based DIMS MD. For the AdK transition, the new concept of a Hausdorff-pair map enabled us to extract the molecular structural determinants responsible for differences in pathways, namely a set of conserved salt bridges whose charge-charge interactions are fully modelled in DIMS MD but not in FRODA. PSA has the potential to enhance our understanding of transition path sampling methods, validate them, and to provide a new approach to analyzing conformational transitions. PMID:26488417

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

    SciTech Connect

    Pröpper, Kevin; Meindl, Kathrin; Sammito, Massimo; Dittrich, Birger; Sheldrick, George M.; Pohl, Ehmke; Usón, Isabel

    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 α-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.

  8. 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.

  9. Application of complex macromolecular architectures for advanced microelectronic materials.

    PubMed

    Hedrick, James L; Magbitang, Teddie; Connor, Eric F; Glauser, Thierry; Volksen, Willi; Hawker, Craig J; Lee, Victor Y; Miller, Robert D

    2002-08-01

    The distinctive features of well-defined, three-dimensional macromolecules with topologies designed to enhance solubility and amplify end-group functionality facilitated nanophase morphologies in mixtures with organosilicates and ultimately nanoporous organosilicate networks. Novel macromolecular architectures including dendritic and star-shaped polymers and organic nanoparticles were prepared by a modular approach from several libraries of building blocks including various generations of dendritic initiators and dendrons, selectively placed to amplify functionality and/or arm number, coupled with living polymerization techniques. Mixtures of an organosilicate and the macromolecular template were deposited, cured, and the phase separation of the organic component, organized the vitrifying organosilicate into nanostructures. Removal of the sacrificial macromolecular template, also denoted as porogen, by thermolysis, yielded the desired nanoporous organosilicate, and the size scale of phase separation was strongly dependent on the chain topology. These materials were designed for use as interlayer, ultra-low dielectric insulators for on-chip applications with dielectric constant values as low as 1.5. The porogen design, chemistry and role of polymer architecture on hybrid and pore morphology will be emphasized. PMID:12203311

  10. The solvent component of macromolecular crystals.

    PubMed

    Weichenberger, Christian X; Afonine, Pavel V; Kantardjieff, Katherine; Rupp, Bernhard

    2015-05-01

    The mother liquor from which a biomolecular crystal is grown will contain water, buffer molecules, native ligands and cofactors, crystallization precipitants and additives, various metal ions, and often small-molecule ligands or inhibitors. On average, about half the volume of a biomolecular crystal consists of this mother liquor, whose components form the disordered bulk solvent. Its scattering contributions can be exploited in initial phasing and must be included in crystal structure refinement as a bulk-solvent model. Concomitantly, distinct electron density originating from ordered solvent components must be correctly identified and represented as part of the atomic crystal structure model. Herein, are reviewed (i) probabilistic bulk-solvent content estimates, (ii) the use of bulk-solvent density modification in phase improvement, (iii) bulk-solvent models and refinement of bulk-solvent contributions and (iv) modelling and validation of ordered solvent constituents. A brief summary is provided of current tools for bulk-solvent analysis and refinement, as well as of modelling, refinement and analysis of ordered solvent components, including small-molecule ligands. PMID:25945568

  11. Finite element solution for the structural behavior of a scientific balloon

    NASA Technical Reports Server (NTRS)

    Schur, W. W.; Simpson, J. M.

    1993-01-01

    A finite element solution for the structural behavior of a scientific balloon has been obtained using a non-linear finite element code. The pneumatic skin is modelled by shell elements that are given a small artificial bending stiffness to overcome numerical problems yet the membrane solution remains unaffected. Validation of the analysis approach is provided through strain measurements on a small scale balloon that exhibits all essential features of a full scale balloon.

  12. Structure and dynamics of solutions of lithium salts relevant to battery construction

    NASA Astrophysics Data System (ADS)

    Solutions of lithium salts in media of low permittivity without or with addition of macrocycles have been characterized in their structural and dynamical behavior using various methods as infrared spectra, audio frequency electrical conductivity, microwave dielectric relaxation and ultrasonic relaxation techniques. The above electrolyte solutions and the criteria of their choice are highly relevant topics for the construction of secondary lithium batteries, the optimization of their use and of their recycling.

  13. Micro-scale NMR Experiments for Monitoring the Optimization of Membrane Protein Solutions for Structural Biology

    PubMed Central

    Horst, Reto; Wüthrich, Kurt

    2016-01-01

    Reconstitution of integral membrane proteins (IMP) in aqueous solutions of detergent micelles has been extensively used in structural biology, using either X-ray crystallography or NMR in solution. Further progress could be achieved by establishing a rational basis for the selection of detergent and buffer conditions, since the stringent bottleneck that slows down the structural biology of IMPs is the preparation of diffracting crystals or concentrated solutions of stable isotope labeled IMPs. Here, we describe procedures to monitor the quality of aqueous solutions of [2H, 15N]-labeled IMPs reconstituted in detergent micelles. This approach has been developed for studies of β-barrel IMPs, where it was successfully applied for numerous NMR structure determinations, and it has also been adapted for use with α-helical IMPs, in particular GPCRs, in guiding crystallization trials and optimizing samples for NMR studies (Horst et al., 2013). 2D [15N, 1H]-correlation maps are used as “fingerprints” to assess the foldedness of the IMP in solution. For promising samples, these “inexpensive” data are then supplemented with measurements of the translational and rotational diffusion coefficients, which give information on the shape and size of the IMP/detergent mixed micelles. Using microcoil equipment for these NMR experiments enables data collection with only micrograms of protein and detergent. This makes serial screens of variable solution conditions viable, enabling the optimization of parameters such as the detergent concentration, sample temperature, pH and the composition of the buffer. PMID:27077076

  14. Structural and nanomechanical comparison of epitaxially and solution-grown amyloid β25-35 fibrils.

    PubMed

    Murvai, Ünige; Somkuti, Judit; Smeller, László; Penke, Botond; Kellermayer, Miklós S Z

    2015-05-01

    Aβ25-35, the fibril-forming, biologically active toxic fragment of the full-length amyloid β-peptide also forms fibrils on mica by an epitaxial assembly mechanism. Here we investigated, by using atomic force microscopy, nanomechanical manipulation and FTIR spectroscopy, whether the epitaxially grown fibrils display structural and mechanical features similar to the ones evolving under equilibrium conditions in bulk solution. Unlike epitaxially grown fibrils, solution-grown fibrils displayed a heterogeneous morphology and an apparently helical structure. While fibril assembly in solution occurred on a time scale of hours, it appeared within a few minutes on mica surface fibrils. Both types of fibrils showed a similar plateau-like nanomechanical response characterized by the appearance of force staircases. The IR spectra of both fibril types contained an intense peak between 1620 and 1640 cm(-1), indicating that β-sheets dominate their structure. A shift in the amide I band towards greater wave numbers in epitaxially assembled fibrils suggests that their structure is less compact than that of solution-grown fibrils. Thus, equilibrium conditions are required for a full structural compaction. Epitaxial Aβ25-35 fibril assembly, while significantly accelerated, may trap the fibrils in less compact configurations. Considering that under in vivo conditions the assembly of amyloid fibrils is influenced by the presence of extracellular matrix components, the ultimate fibril structure is likely to be influenced by the features of underlying matrix elements. PMID:25600136

  15. 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

  16. Ice crystallization in ultrafine water-salt aerosols: nucleation, ice-solution equilibrium, and internal structure.

    PubMed

    Hudait, Arpa; Molinero, Valeria

    2014-06-01

    Atmospheric aerosols have a strong influence on Earth's climate. Elucidating the physical state and internal structure of atmospheric aqueous aerosols is essential to predict their gas and water uptake, and the locus and rate of atmospherically important heterogeneous reactions. Ultrafine aerosols with sizes between 3 and 15 nm have been detected in large numbers in the troposphere and tropopause. Nanoscopic aerosols arising from bubble bursting of natural and artificial seawater have been identified in laboratory and field experiments. The internal structure and phase state of these aerosols, however, cannot yet be determined in experiments. Here we use molecular simulations to investigate the phase behavior and internal structure of liquid, vitrified, and crystallized water-salt ultrafine aerosols with radii from 2.5 to 9.5 nm and with up to 10% moles of ions. We find that both ice crystallization and vitrification of the nanodroplets lead to demixing of pure water from the solutions. Vitrification of aqueous nanodroplets yields nanodomains of pure low-density amorphous ice in coexistence with vitrified solute rich aqueous glass. The melting temperature of ice in the aerosols decreases monotonically with an increase of solute fraction and decrease of radius. The simulations reveal that nucleation of ice occurs homogeneously at the subsurface of the water-salt nanoparticles. Subsequent ice growth yields phase-segregated, internally mixed, aerosols with two phases in equilibrium: a concentrated water-salt amorphous mixture and a spherical cap-like ice nanophase. The surface of the crystallized aerosols is heterogeneous, with ice and solution exposed to the vapor. Free energy calculations indicate that as the concentration of salt in the particles, the advance of the crystallization, or the size of the particles increase, the stability of the spherical cap structure increases with respect to the alternative structure in which a core of ice is fully surrounded by solution. We predict that micrometer-sized particles and nanoparticles have the same equilibrium internal structure. The variation of liquid-vapor surface tension with solute concentration is a key factor in determining whether a solution-embedded ice core or vapor-exposed ice cap is the equilibrium structure of the aerosols. In agreement with experiments, we predict that the structure of mixed-phase HNO3-water particles, representative of polar stratospheric clouds, consists of an ice core surrounded by freeze-concentrated solution. The results of this work are important to determine the phase state and internal structure of sea spray ultrafine aerosols and other mixed-phase particles under atmospherically relevant conditions. PMID:24820354

  17. Molecular dynamics simulations of large macromolecular complexes.

    PubMed

    Perilla, Juan R; Goh, Boon Chong; Cassidy, C Keith; Liu, Bo; Bernardi, Rafael C; Rudack, Till; Yu, Hang; Wu, Zhe; Schulten, Klaus

    2015-04-01

    Connecting dynamics to structural data from diverse experimental sources, molecular dynamics simulations permit the exploration of biological phenomena in unparalleled detail. Advances in simulations are moving the atomic resolution descriptions of biological systems into the million-to-billion atom regime, in which numerous cell functions reside. In this opinion, we review the progress, driven by large-scale molecular dynamics simulations, in the study of viruses, ribosomes, bioenergetic systems, and other diverse applications. These examples highlight the utility of molecular dynamics simulations in the critical task of relating atomic detail to the function of supramolecular complexes, a task that cannot be achieved by smaller-scale simulations or existing experimental approaches alone. PMID:25845770

  18. Molecular dynamics simulations of large macromolecular complexes

    PubMed Central

    Perilla, Juan R.; Goh, Boon Chong; Cassidy, C. Keith; Liu, Bo; Bernardi, Rafael C.; Rudack, Till; Yu, Hang; Wu, Zhe; Schulten, Klaus

    2015-01-01

    Connecting dynamics to structural data from diverse experimental sources, molecular dynamics simulations permit the exploration of biological phenomena in unparalleled detail. Advances in simulations are moving the atomic resolution descriptions of biological systems into the million-to-billion atom regime, in which numerous cell functions reside. In this opinion, we review the progress, driven by large-scale molecular dynamics simulations, in the study of viruses, ribosomes, bioenergetic systems, and other diverse applications. These examples highlight the utility of molecular dynamics simulations in the critical task of relating atomic detail to the function of supramolecular complexes, a task that cannot be achieved by smaller-scale simulations or existing experimental approaches alone. PMID:25845770

  19. New insights into structural alteration of enamel apatite induced by citric acid and sodium fluoride solutions.

    PubMed

    Wang, Xiaojie; Klocke, Arndt; Mihailova, Boriana; Tosheva, Lubomira; Bismayer, Ulrich

    2008-07-24

    Attenuated total reflectance infrared spectroscopy and complementary scanning electron microscopy were applied to analyze the surface structure of enamel apatite exposed to citric acid and to investigate the protective potential of fluorine-containing reagents against citric acid-induced erosion. Enamel and, for comparison, geological hydroxylapatite samples were treated with aqueous solutions of citric acid and sodium fluoride of different concentrations, ranging from 0.01 to 0.5 mol/L for citric acid solutions and from 0.5 to 2.0% for fluoride solutions. The two solutions were applied either simultaneously or consecutively. The citric acid-induced structural modification of apatite increases with the increase in the citric acid concentration and the number of treatments. The application of sodium fluoride alone does not suppress the atomic level changes in apatite exposed to acidic agents. The addition of sodium fluoride to citric acid solutions leads to formation of surface CaF2 and considerably reduces the changes in the apatite P-O-Ca framework. However, the CaF2 globules deposited on the enamel surface seem to be insufficient to prevent the alteration of the apatite structure upon further exposure to acidic agents. No evidence for fluorine-induced recovery of the apatite structure was found. PMID:18588337

  20. 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

  1. Effects of Multidimensional Description of the Spatial Structure of Hydraulic Conductivity on Solute Transport

    NASA Astrophysics Data System (ADS)

    Haslauer, C. P.; Rau, M.; Bárdossy, A.; Sudicky, E. A.

    2010-12-01

    Hydraulic conductivity (K) is a fundamental parameter that influences groundwater flow and solute transport. Measurements of K are limited and uncertain. Moreover, the spatial structure of K, which impacts the groundwater velocity field and hence directly influences the advective spreading of a solute migrating in the subsurface, is commonly described by approaches using second order moments. The objective of the presented work is to use multidimensional spatial copulas to describe and model the spatial dependence of the spatial structure of K and evaluate the effects of this multidimensional description on solute transport. It is shown how copulas can capture better than second order moments the structural uncertainty in spatially distributed fields. The copula models fit best to observed dependence structures at small separation distances, smaller than ~1/2 the range. The fit of copulas to this microstructure is so much improved compared to a multi-gaussian fit that it leads to significantly different dispersion coefficients - despite identical second order statistics of the K field. The effects of the spatial description of K on solute transport are analyzed using a series of numerical tracer experiments using a high-resolution groundwater flow and solute transport model (HydroGeoSphere). Flow and transport characteristics were derived, particularly the rate of change of the spatial moments of the evolving solute plume. These characteristics were compared between two types of dependence: a gaussian dependence structure of K, and a spatial dependence structure as modelled with non-gaussian copulas. Both types of spatial K-fields were constrained to have the same second order moments, but they do exhibit a different spatial dependence structure when modeled by copulas, and thus produce a different solute transport behavior. The dispersion tensor, which is proportional to the rate of change of the 2nd-order spatial moments of the evolving solute plume, is different for the Gaussian and non-Gaussian descriptions of spatial dependence. The outlined theory is applied to three-dimensional anisotropic K-data obtained from two of the most extensively studied aquifer test-sites. Each site comprises ~1200 or more samples taken along two cross-sections. One site is the aquifer at Borden, Ontario, a homogeneous aquifer with a low variance of K, and the other site, located near North Bay, Ontario, is comprised of a highly heterogeneous glacial deposit. In both of these settings, non-gaussian dependence structures of K and hence non-gaussian transport characteristics were identified.

  2. Frequency modelling and solution of fluid-structure interaction in complex pipelines

    NASA Astrophysics Data System (ADS)

    Xu, Yuanzhi; Johnston, D. Nigel; Jiao, Zongxia; Plummer, Andrew R.

    2014-05-01

    Complex pipelines may have various structural supports and boundary conditions, as well as branches. To analyse the vibrational characteristics of piping systems, frequency modelling and solution methods considering complex constraints are developed here. A fourteen-equation model and Transfer Matrix Method (TMM) are employed to describe Fluid-Structure Interaction (FSI) in liquid-filled pipes. A general solution for the multi-branch pipe is proposed in this paper, offering a methodology to predict frequency responses of the complex piping system. Some branched pipe systems are built for the purpose of validation, indicating good agreement with calculated results.

  3. 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.

  4. Biophotonic probing of macromolecular transformations during apoptosis

    PubMed Central

    Pliss, Artem; Kuzmin, Andrey N.; Kachynski, Aliaksandr V.; Prasad, Paras N.

    2010-01-01

    We introduce here multiplex nonlinear optical imaging as a powerful tool for studying the molecular organization and its transformation in cellular processes, with the specific example of apoptosis. Apoptosis is a process of self-initiated cell death, critically important for physiological regulation and elimination of genetic disorders. Nonlinear optical microscopy, combining the coherent anti-Stokes Raman scattering (CARS) microscopy and two-photon excited fluorescence (TPEF), has been used for analysis of spatial distribution of major types of biomolecules: proteins, lipids, and nucleic acids in the cells while monitoring their changes during apoptosis. CARS imaging revealed that in the nuclei of proliferating cells, the proteins are distributed nearly uniformly, with local accumulations in several nuclear structures. We have found that this distribution is abruptly disrupted at the onset of apoptosis and is transformed to a progressively irregular pattern. Fluorescence recovery after photobleaching (FRAP) studies indicate that pronounced aggregation of proteins in the nucleoplasm of apoptotic cells coincides with a gradual reduction in their mobility. PMID:20615987

  5. Backbone Solution Structures of Proteins Using Residual Dipolar Couplings: Application to a Novel Structural Genomics Target

    PubMed Central

    Valafar, H.; Mayer, K. L.; Bougault, C. M.; LeBlond, P. D.; Jenney, F. E.; Brereton, P. S.; Adams, M.W.W.; Prestegard, J.H.

    2006-01-01

    Structural genomics (or proteomics) activities are critically dependent on the availability of high-throughput structure determination methodology. Development of such methodology has been a particular challenge for NMR based structure determination because of the demands for isotopic labeling of proteins and the requirements for very long data acquisition times. We present here a methodology that gains efficiency from a focus on determination of backbone structures of proteins as opposed to full structures with all side chains in place. This focus is appropriate given the presumption that many protein structures in the future will be built using computational methods that start from representative fold family structures and replace as many as 70% of the side chains in the course of structure determination. The methodology we present is based primarily on residual dipolar couplings (RDCs), readily accessible NMR observables that constrain the orientation of backbone fragments irrespective of separation in space. A new software tool is described for the assembly of backbone fragments under RDC constraints and an application to a structural genomics target is presented. The target is an 8.7 kDa protein from Pyrococcus furiosus, PF1061, that was previously not well annotated, and had a nearest structurally characterized neighbor with only 33% sequence identity. The structure produced shows structural similarity to this sequence homologue, but also shows similarity to other proteins that suggests a functional role in sulfur transfer. Given the backbone structure and a possible functional link this should be an ideal target for development of modeling methods. PMID:15704012

  6. 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 μm 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

  7. Insulin involvement in intestinal macromolecular transmission and closure in neonatal pigs.

    PubMed

    Svendsen, L S; Weström, B R; Svendsen, J; Ohlsson, B G; Ekman, R; Karlsson, B W

    1986-01-01

    The involvement of insulin in the intestinal transmission of macromolecules to blood and the cessation of this transport (intestinal closure) was studied in neonatal pigs by measuring the serum levels of the markers bovine serum albumin and fluorescein isothiocyanate labelled dextran 70,000 (FITC-D) at 4 h after gavage feeding. In naturally suckled pigs, intestinal closure at 18 h was shown to be associated with an increase in serum immunoreactive insulin (IRI) levels. Similarly, intestinal closure obtained at 18 h, by gavage feeding unsuckled pigs a total of 48 g lactose/kg, was accompanied by an increase in serum IRI levels. Neither high serum IRI levels nor closure were observed in fasted pigs or in pigs gavage fed a total of 12 g lactose/kg. The effect of exogenous insulin on intestinal macromolecular transmission was studied by injecting 5 IU insulin/kg subcutaneously at 3 and 6 h, respectively, in newborn pigs gavage fed 10 ml sow colostrum/kg at 3 h intervals. This resulted in a reduction in the transmission of the markers when tested at 12 h, in comparison to littermates receiving the same amount of colostrum and littermates suckling the sow. It appears as if insulin, reflected as high serum levels over an extended period of time, is involved in the regulation of macromolecular transmission and intestinal closure in neonatal pigs. It was speculated that insulin may be involved in these processes by initiating the synthesis of membrane structural proteins in the enterocytes. PMID:3083082

  8. A theory for water and macromolecular transport in the pulmonary artery wall with a detailed comparison to the aorta

    PubMed Central

    Zeng, Zhongqing; Jan, Kung-Ming

    2012-01-01

    The pulmonary artery (PA) wall, which has much higher hydraulic conductivity and albumin void space and approximately one-sixth the normal transmural pressure of systemic arteries (e.g, aorta, carotid arteries), is rarely atherosclerotic, except under pulmonary hypertension. This study constructs a detailed, two-dimensional, wall-structure-based filtration and macromolecular transport model for the PA to investigate differences in prelesion transport processes between the disease-susceptible aorta and the relatively resistant PA. The PA and aorta models are similar in wall structure, but very different in parameter values, many of which have been measured (and therefore modified) since the original aorta model of Huang et al. (23). Both PA and aortic model simulations fit experimental data on transwall LDL concentration profiles and on the growth of isolated endothelial (horseradish peroxidase) tracer spots with circulation time very well. They reveal that lipid entering the aorta attains a much higher intima than media concentration but distributes better between these regions in the PA than aorta and that tracer in both regions contributes to observed tracer spots. Solutions show why both the overall transmural water flow and spot growth rates are similar in these vessels despite very different material transport parameters. Since early lipid accumulation occurs in the subendothelial intima and since (matrix binding) reaction kinetics depend on reactant concentrations, the lower intima lipid concentrations in the PA vs. aorta likely lead to slower accumulation of bound lipid in the PA. These findings may be relevant to understanding the different atherosusceptibilities of these vessels. PMID:22198178

  9. Nuclear magnetic resonance solution structure of dendrotoxin K from the venom of Dendroaspis polylepis polylepis.

    PubMed

    Berndt, K D; Güntert, P; Wüthrich, K

    1993-12-01

    The solution structure of dendrotoxin K (Toxin K), a protein consisting of one polypeptide chain with 57 residues purified from the venom of the black mamba, Dendroaspis polylepis polylepis, was determined by nuclear magnetic resonance (NMR) spectroscopy. On the basis of virtually complete sequence-specific 1H NMR assignments, including individual assignments for 38 pairs of diastereotopic substituents and side-chain amide protons, a total of 818 nuclear Overhauser effect distance constraints and 123 dihedral angle constraints were identified. Using this input, the solution structure of Toxin K was calculated with the program DIANA, and refined by restrained energy-minimization with a modified version of the program AMBER. The average root-mean-square deviation (r.m.s.d.) relative to the mean atomic co-ordinates of the 20 conformers selected to represent the solution structure is 0.31 A for all backbone atoms N, C alpha and C', and 0.90 A for all heavy-atoms of residues 2 to 56. The solution structure of Toxin K is very similar to the solution structure of the basic pancreatic trypsin inhibitor (BPTI) and the X-ray crystal structure of the alpha-dendrotoxin from Dendroaspis angusticeps (alpha-DTX), with r.m.s.d. values of 1.31 A and 0.92 A, respectively, for the backbone atoms of residues 2 to 56. Some local structural differences between Toxin K and BPTI are directly related to the fact that intermolecular interactions with two of the four internal molecules of hydration water in BPTI are replaced by intramolecular hydrogen bonds in Toxin K. PMID:8254670

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

    PubMed Central

    Prpper, Kevin; Meindl, Kathrin; Sammito, Massimo; Dittrich, Birger; Sheldrick, George M.; Pohl, Ehmke; Usn, Isabel

    2014-01-01

    ProteinDNA 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 proteinDNA 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 proteinDNA 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 proteinDNA 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. PMID:24914984

  11. Polarizable Atomic Multipole X-Ray Refinement: Particle Mesh Ewald Electrostatics for Macromolecular Crystals.

    PubMed

    Schnieders, Michael J; Fenn, Timothy D; Pande, Vijay S

    2011-04-12

    Refinement of macromolecular models from X-ray crystallography experiments benefits from prior chemical knowledge at all resolutions. As the quality of the prior chemical knowledge from quantum or classical molecular physics improves, in principle so will resulting structural models. Due to limitations in computer performance and electrostatic algorithms, commonly used macromolecules X-ray crystallography refinement protocols have had limited support for rigorous molecular physics in the past. For example, electrostatics is often neglected in favor of nonbonded interactions based on a purely repulsive van der Waals potential. In this work we present advanced algorithms for desktop workstations that open the door to X-ray refinement of even the most challenging macromolecular data sets using state-of-the-art classical molecular physics. First we describe theory for particle mesh Ewald (PME) summation that consistently handles the symmetry of all 230 space groups, replicates of the unit cell such that the minimum image convention can be used with a real space cutoff of any size and the combination of space group symmetry with replicates. An implementation of symmetry accelerated PME for the polarizable atomic multipole optimized energetics for biomolecular applications (AMOEBA) force field is presented. Relative to a single CPU core performing calculations on a P1 unit cell, our AMOEBA engine called Force Field X (FFX) accelerates energy evaluations by more than a factor of 24 on an 8-core workstation with a Tesla GPU coprocessor for 30 structures that contain 240 000 atoms on average in the unit cell. The benefit of AMOEBA electrostatics evaluated with PME for macromolecular X-ray crystallography refinement is demonstrated via rerefinement of 10 crystallographic data sets that range in resolution from 1.7 to 4.5 Å. Beginning from structures obtained by local optimization without electrostatics, further optimization using AMOEBA with PME electrostatics improved agreement of the model with the data (Rfree was lowered by 0.5%), improved geometric features such as favorable (ϕ, ψ) backbone conformations, and lowered the average potential energy per residue by over 10 kcal/mol. Furthermore, the MolProbity structure validation tool indicates that the geometry of these rerefined structures is consistent with X-ray crystallographic data collected up to 2.2 Å, which is 0.9 Å better than the actual mean quality (3.1 Å). We conclude that polarizable AMOEBA-assisted X-ray refinement offers advantages to methods that neglect electrostatics and is now efficient enough for routine use. PMID:26606362

  12. 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.

  13. Effects of Multidimensional Description of the Spatial Structure of Hydraulic Conductivity on Solute Transport

    NASA Astrophysics Data System (ADS)

    Haslauer, C. P.; Bardossy, A.; Sudicky, E. A.

    2011-12-01

    Hydraulic conductivity (K) is a fundamental parameter that influences groundwater flow and solute transport. Measurements of K are limited and uncertain. Moreover, the spatial structure of K, which impacts the groundwater velocity field and hence directly influences the advective spreading of a solute migrating in the subsurface, is commonly described by approaches using second order moments. The objective of the presented work is to use multidimensional spatial copulas to describe and model the spatial dependence of the spatial structure of K and evaluate the effects of this multidimensional description on solute transport. The spatial dependence structure of K at two field-sites is shown to be not Gaussian. The non-Gaussian spatial copula models that were fitted to field data model the spatial dependence of the field data significantly better than the fitted Gaussian copula model. The difference between the fitted Gaussian and the fitted non-Gaussian models leads to significantly different dispersion coefficients - despite identical second order statistics of the K field. The effects of the spatial description of K on solute transport are analyzed using a series of numerical tracer experiments using a high-resolution groundwater flow and solute transport model (HydroGeoSphere) in two- and in three dimensions. Flow and transport characteristics were derived, particularly the rate of change of the spatial moments of the evolving solute plume. These characteristics were compared between two types of dependence: a Gaussian dependence structure of K, and a spatial dependence structure as modelled with non-Gaussian copulas, both fitted to real-world data. Both types of spatial K-fields were constrained to have the same second order moments, but they do exhibit a different spatial dependence structure when modeled by copulas, and thus produce a different solute transport behavior. The dispersion tensor, which is proportional to the rate of change of the 2nd-order spatial moments of the evolving solute plume, is different for the Gaussian and non-Gaussian descriptions of spatial dependence. The outlined theory is applied to three-dimensional anisotropic K-data obtained from two of the most extensively studied aquifer test-sites. Each site comprises ~1500 samples taken along two cross-sections. One site is the aquifer at Borden, Ontario, a homogeneous aquifer with a low variance of K, and the other site, located near North Bay, Ontario, is comprised of a heterogeneous glacial deposit. In both of these settings, non-Gaussian dependence structures of K and hence non-Gaussian transport characteristics were identified.

  14. Solution structures of calcium regulating proteins: A small-angle scattering study

    SciTech Connect

    Trewhella, J.; Heidorn, D.B.; Seeger, P.A.

    1987-11-01

    Small-angle X-ray scattering (SAXS) experiments have shown that the solution structures of two calcium-binding regulatory proteins, calmodulin and troponin C, are significantly different from their crystal structure forms. The structural differences occur in a region of calmodulin that is thought to bind to target enzymes;the calmodulin-enzyme complex is an initiator for many important biochemical processes. Calcium binding to calmodulin induces a conformational change that is a prerequisite for calmodulin binding to a target enzyme. SAXS data can characterize this conformational change and give insight into the mechanism of enzyme binding. Neutron resonance scattering promises to determine accurately the distances between calcium binding sites, thus providing important constraints on the structure of calmodulin in solution. 24 refs., 5 figs., 1 tab.

  15. Comparison of shock structure solutions using independent continuum and kinetic theory approaches

    NASA Technical Reports Server (NTRS)

    Fiscko, Kurt A.; Chapman, Dean R.

    1988-01-01

    A vehicle traversing the atmosphere will experience flight regimes at high altitudes in which the thickness of a hypersonic shock wave is not small compared to the shock standoff distance from the hard body. When this occurs, it is essential to compute accurate flow field solutions within the shock structure. In this paper, one-dimensional shock structure is investigated for various monatomic gases from Mach 1.4 to Mach 35. Kinetic theory solutions are computed using the Direct Simulation Monte Carlo method. Steady-state solutions of the Navier-Stokes equations and of a slightly truncated form of the Burnett equations are determined by relaxation to a steady state of the time-dependent continuum equations. Monte Carlo results are in excellent agreement with published experimental data and are used as bases of comparison for continuum solutions. For a Maxwellian gas, the truncated Burnett equations are shown to produce far more accurate solutions of shock structure than the Navier-Stokes equations.

  16. An efficient solution procedure for the thermoelastic analysis of truss space structures

    NASA Technical Reports Server (NTRS)

    Givoli, D.; Rand, O.

    1992-01-01

    A solution procedure is proposed for the thermal and thermoelastic analysis of truss space structures in periodic motion. In this method, the spatial domain is first descretized using a consistent finite element formulation. Then the resulting semi-discrete equations in time are solved analytically by using Fourier decomposition. Geometrical symmetry is taken advantage of completely. An algorithm is presented for the calculation of heat flux distribution. The method is demonstrated via a numerical example of a cylindrically shaped space structure.

  17. Combining crystallography and EPR: crystal and solution structures of the multidomain cochaperone DnaJ

    SciTech Connect

    Barends, Thomas R. M.; Brosi, Richard W. W.; Steinmetz, Andrea; Scherer, Anna; Hartmann, Elisabeth; Eschenbach, Jessica; Lorenz, Thorsten; Seidel, Ralf; Shoeman, Robert L.; Zimmermann, Sabine; Bittl, Robert; Schlichting, Ilme; Reinstein, Jochen

    2013-08-01

    The crystal structure of the N-terminal part of T. thermophilus DnaJ unexpectedly showed an ordered GF domain and guided the design of a construct enabling the first structure determination of a complete DnaJ cochaperone molecule. By combining the crystal structures with spin-labelling EPR and cross-linking in solution, a dynamic view of this flexible molecule was developed. Hsp70 chaperones assist in a large variety of protein-folding processes in the cell. Crucial for these activities is the regulation of Hsp70 by Hsp40 cochaperones. DnaJ, the bacterial homologue of Hsp40, stimulates ATP hydrolysis by DnaK (Hsp70) and thus mediates capture of substrate protein, but is also known to possess chaperone activity of its own. The first structure of a complete functional dimeric DnaJ was determined and the mobility of its individual domains in solution was investigated. Crystal structures of the complete molecular cochaperone DnaJ from Thermus thermophilus comprising the J, GF and C-terminal domains and of the J and GF domains alone showed an ordered GF domain interacting with the J domain. Structure-based EPR spin-labelling studies as well as cross-linking results showed the existence of multiple states of DnaJ in solution with different arrangements of the various domains, which has implications for the function of DnaJ.

  18. Destruction of tissue, cells and organelles in type 1 diabetic rats presented at macromolecular resolution.

    PubMed

    Ravelli, Raimond B G; Kalicharan, Ruby D; Avramut, M Cristina; Sjollema, Klaas A; Pronk, Joachim W; Dijk, Freark; Koster, Abraham J; Visser, Jeroen T J; Faas, Frank G A; Giepmans, Ben N G

    2013-01-01

    Finding alternatives for insulin therapy and making advances in etiology of type 1 diabetes benefits from a full structural and functional insight into Islets of Langerhans. Electron microscopy (EM) can visualize Islet morphology at the highest possible resolution, however, conventional EM only provides biased snapshots and lacks context. We developed and employed large scale EM and compiled a resource of complete cross sections of rat Islets during immuno-destruction to provide unbiased structural insight of thousands of cells at macromolecular resolution. The resource includes six datasets, totalling 25.000 micrographs, annotated for cellular and ultrastructural changes during autoimmune diabetes. Granulocytes are attracted to the endocrine tissue, followed by extravasation of a pleiotrophy of leukocytes. Subcellullar changes in beta cells include endoplasmic reticulum stress, insulin degranulation and glycogen accumulation. Rare findings include erythrocyte extravasation and nuclear actin-like fibers. While we focus on a rat model of autoimmune diabetes, our approach is general applicable. PMID:23652855

  19. NMR and small-angle scattering-based structural analysis of protein complexes in solution.

    PubMed

    Madl, Tobias; Gabel, Frank; Sattler, Michael

    2011-03-01

    Structural analysis of multi-domain protein complexes is a key challenge in current biology and a prerequisite for understanding the molecular basis of essential cellular processes. The use of solution techniques is important for characterizing the quaternary arrangements and dynamics of domains and subunits of these complexes. In this respect solution NMR is the only technique that allows atomic- or residue-resolution structure determination and investigation of dynamic properties of multi-domain proteins and their complexes. As experimental NMR data for large protein complexes are sparse, it is advantageous to combine these data with additional information from other solution techniques. Here, the utility and computational approaches of combining solution state NMR with small-angle X-ray and Neutron scattering (SAXS/SANS) experiments for structural analysis of large protein complexes is reviewed. Recent progress in experimental and computational approaches of combining NMR and SAS are discussed and illustrated with recent examples from the literature. The complementary aspects of combining NMR and SAS data for studying multi-domain proteins, i.e. where weakly interacting domains are connected by flexible linkers, are illustrated with the structural analysis of the tandem RNA recognition motif (RRM) domains (RRM1-RRM2) of the human splicing factor U2AF65 bound to a nine-uridine (U9) RNA oligonucleotide. PMID:21074620

  20. Structure and Dynamics of NaCl Ion Pairing in Solutions of Water and Methanol.

    PubMed

    Kelley, Morgan; Donley, Amber; Clark, Sue; Clark, Aurora

    2015-12-24

    Ion pairing can have profound effects upon the ionic strength of electrolyte solutions but is poorly understood in solutions containing more than one solvent. Herein a combined density functional theory and molecular dynamics approach is used to examine the effect of both methanol concentration and interionic distance upon the structure and dynamics within successive solvation shells of Na(+) and Cl(-) in water/methanol binary solutions. The structure and dynamics of the first and second solvation shells were studied along a reaction coordinate associated with ion pair formation using potential of mean force simulations. The lifetimes of the solvent-solvent hydrogen bonds become perturbed when the second solvation shells of the ions begin to interact. In contrast, the structural properties within the first and second solvation shells of the ions were found to be largely independent of both methanol concentration and interionic distance until a contact ion pair is formed. Thus, as the ions are brought together, the effect of the opposing ion manifests itself in the solvation dynamics before any structural changes are observed. As anticipated based upon the decreased dielectric constant of the binary solution, ion pair formation becomes energetically more favorable as the concentration of methanol increases. PMID:26641882

  1. 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.

  2. Comparing Multiple Solutions in the Structured Problem Solving: Deconstructing Japanese Lessons from Learner's Perspective

    ERIC Educational Resources Information Center

    Hino, Keiko

    2015-01-01

    The purpose of this study is to enhance our understanding of how students listen and attend to multiple solutions proposed by their classmates during the activity of comparison. This study examines ten consecutive lessons in each of the two eighth-grade classrooms in Tokyo that are organized in the style of "structured problem solving".…

  3. Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX autosol wizard

    SciTech Connect

    Terwilliger, Thomas C; Adams, Paul D; Read, Randy J; Mccoy, Airlie J

    2008-01-01

    Ten measures of experimental electron-density-map quality are examined and the skewness of electron density is found to be the best indicator of actual map quality. A Bayesian approach to estimating map quality is developed and used in the PHENIX AutoSol wizard to make decisions during automated structure solution.

  4. Evidence for water structuring forces between surfaces

    SciTech Connect

    Stanley, Christopher B; Rau, Dr. Donald

    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.

  5. 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.

  6. Structural Analysis of Protein-RNA Complexes in Solution Using NMR Paramagnetic Relaxation Enhancements.

    PubMed

    Hennig, Janosch; Warner, Lisa R; Simon, Bernd; Geerlof, Arie; Mackereth, Cameron D; Sattler, Michael

    2015-01-01

    Biological activity in the cell is predominantly mediated by large multiprotein and protein-nucleic acid complexes that act together to ensure functional fidelity. Nuclear magnetic resonance (NMR) spectroscopy is the only method that can provide information for high-resolution three-dimensional structures and the conformational dynamics of these complexes in solution. Mapping of binding interfaces and molecular interactions along with the characterization of conformational dynamics is possible for very large protein complexes. In contrast, de novo structure determination by NMR becomes very time consuming and difficult for protein complexes larger than 30 kDa as data are noisy and sparse. Fortunately, high-resolution structures are often available for individual domains or subunits of a protein complex and thus sparse data can be used to define their arrangement and dynamics within the assembled complex. In these cases, NMR can therefore be efficiently combined with complementary solution techniques, such as small-angle X-ray or neutron scattering, to provide a comprehensive description of the structure and dynamics of protein complexes in solution. Particularly useful are NMR-derived paramagnetic relaxation enhancements (PREs), which provide long-range distance restraints (ca. 20Å) for structural analysis of large complexes and also report on conformational dynamics in solution. Here, we describe the use of PREs from sample production to structure calculation, focusing on protein-RNA complexes. On the basis of recent examples from our own research, we demonstrate the utility, present protocols, and discuss potential pitfalls when using PREs for studying the structure and dynamic features of protein-RNA complexes. PMID:26068746

  7. Pitfalls in assessing microvascular endothelial barrier function: impedance-based devices versus the classic macromolecular tracer assay.

    PubMed

    Bischoff, Iris; Hornburger, Michael C; Mayer, Bettina A; Beyerle, Andrea; Wegener, Joachim; Fürst, Robert

    2016-01-01

    The most frequently used parameters to describe the barrier properties of endothelial cells (ECs) in vitro are (i) the macromolecular permeability, indicating the flux of a macromolecular tracer across the endothelium, and (ii) electrical impedance of ECs grown on gold-film electrodes reporting on the cell layer's tightness for ion flow. Due to the experimental differences between these approaches, inconsistent observations have been described. Here, we present the first direct comparison of these assays applied to one single cell type (human microvascular ECs) under the same experimental conditions. The impact of different pharmacological tools (histamine, forskolin, Y-27632, blebbistatin, TRAP) on endothelial barrier function was analyzed by Transwell(®) tracer assays and two commercial impedance devices (xCELLigence(®), ECIS(®)). The two impedance techniques provided very similar results for all compounds, whereas macromolecular permeability readings were found to be partly inconsistent with impedance. Possible reasons for these discrepancies are discussed. We conclude that the complementary combination of both approaches is highly recommended to overcome the restrictions of each assay. Since the nature of the growth support may contribute to the observed differences, structure-function relationships should be based on cells that are consistently grown on either permeable or impermeable growth supports in all experiments. PMID:27025965

  8. A decade of user operation on the macromolecular crystallography MAD beamline ID14-4 at the ESRF

    PubMed Central

    McCarthy, Andrew A.; Brockhauser, Sandor; Nurizzo, Didier; Theveneau, Pascal; Mairs, Trevor; Spruce, Darren; Guijarro, Matias; Lesourd, Marc; Ravelli, Raimond B. G.; McSweeney, Sean

    2009-01-01

    ID14-4 at the ESRF is the first tunable undulator-based macromolecular crystallography beamline that can celebrate a decade of user service. During this time ID14-4 has not only been instrumental in the determination of the structures of biologically important molecules but has also contributed significantly to the development of various instruments, novel data collection schemes and pioneering radiation damage studies on biological samples. Here, the evolution of ID14-4 over the last decade is presented, and some of the major improvements that were carried out in order to maintain its status as one of the most productive macromolecular crystallography beamlines are highlighted. The experimental hutch has been upgraded to accommodate a high-precision diffractometer, a sample changer and a large CCD detector. More recently, the optical hutch has been refurbished in order to improve the X-ray beam quality on ID14-4 and to incorporate the most modern and robust optical elements used at other ESRF beamlines. These new optical elements will be described and their effect on beam stability discussed. These studies may be useful in the design, construction and maintenance of future X-ray beamlines for macromolecular crystallography and indeed other applications, such as those planned for the ESRF upgrade. PMID:19844017

  9. Resonance assignments, secondary structure and topology of leukaemia inhibitory factor in solution.

    PubMed

    Hinds, M G; Maurer, T; Zhang, J G; Nicola, N A; Norton, R S

    1997-02-01

    The chemical shift assignments and secondary structure of a murine-human chimera, MH35, of leukaemia inhibitory factor (LIF), a 180-residue protein of molecular mass 20 kDa, have been determined from multidimensional heteronuclear NMR spectra acquired on a uniformly 13C, 15N-labelled sample. Secondary structure elements were defined on the basis of chemical shifts, NH-C alpha H coupling constants; medium-range NOEs and the location of slowly exchanging amide protons. The protein contains four alpha-helices, the relative orientations of which were determined on the basis of long-range, interhelical NOEs. The four helices are arranged in an up-up-down-down orientation, as found in other four-helical bundle cytokines. The overall topology of MH35-LIF is similar to that of the X-ray crystallographic structure for murine LIF [Robinson et al. (1994) Cell, 77, 1101-1116]. Differences between the X-ray structure and the solution structure are evident in the N-terminal tail, where the solution structure has a trans-Pro17 compared with the cis-Pro17 found in the crystal structure and the small antiparallel beta-sheet encompassing residues in the N-terminus and CD loop in the crystal structure is less stable. PMID:9090127

  10. Solution structure and internal dynamics of NSCP, a compact calcium-binding protein.

    PubMed

    Rabah, Ghada; Popescu, Razvan; Cox, Jos A; Engelborghs, Yves; Craescu, Constantin T

    2005-04-01

    The solution structure of Nereis diversicolor sarcoplasmic calcium-binding protein (NSCP) in the calcium-bound form was determined by NMR spectroscopy, distance geometry and simulated annealing. Based on 1859 NOE restraints and 262 angular restraints, 17 structures were generated with a rmsd of 0.87 A from the mean structure. The solution structure, which is highly similar to the structure obtained by X-ray crystallography, includes two open EF-hand domains, which are in close contact through their hydrophobic surfaces. The internal dynamics of the protein backbone were determined by studying amide hydrogen/deuterium exchange rates and 15N nuclear relaxation. The two methods revealed a highly compact and rigid structure, with greatly restricted mobility at the two termini. For most of the amide protons, the free energy of exchange-compatible structural opening is similar to the free energy of structural stability, suggesting that isotope exchange of these protons takes place through global unfolding of the protein. Enhanced conformational flexibility was noted in the unoccupied Ca2+-binding site II, as well as the neighbouring helices. Analysis of the experimental nuclear relaxation and the molecular dynamics simulations give very similar profiles for the backbone generalized order parameter (S2), a parameter related to the amplitude of fast (picosecond to nanosecond) movements of N(H)-H vectors. We also noted a significant correlation between this parameter, the exchange rate, and the crystallographic B factor along the sequence. PMID:15819893

  11. ZnO Nanoporous Structure Growth, Optical and Structural Characterization by Aqueous Solution Route

    NASA Astrophysics Data System (ADS)

    Kashif, M.; Ali, Syed M. Usman; Foo, K. L.; Hashim, U.; Willander, Magnus

    2011-05-01

    In this study, we have demonstrated the structural and optical characterization of ZnO nanoporous structure grown on gold coated plastic substrate using low temperature aqueous chemical growth (ACG) technique and the annealing temperature was kept at 150 C. ZnO nanoporous structures were fabricated using hydrolysis process by reacting zinc acetate dehydrate with anhydrous ethanol. The crystalline morphology of ZnO nanoporous structures were investigated by using X-ray diffraction (XRD), surface morphology was observed by field emission scanning electron microscope (FESEM). The optical characteristics of ZnO nanoporous structures were investigated at room temperature, PL was observed using UV-Vis Spectrophotometer and the chemical composition is analyzed using Fourier Transform Infra-Red spectrometer (FTIR).

  12. Macromolecular Monomers for the Synthesis of Hydrogel Niches and Their Application in Cell Encapsulation and Tissue Engineering

    PubMed Central

    Nuttelman, Charles R.; Rice, Mark A.; Rydholm, Amber E.; Salinas, Chelsea N.; Shah, Darshita N.

    2008-01-01

    Hydrogels formed from the photoinitiated, solution polymerization of macromolecular monomers present distinct advantages as cell delivery materials and are enabling researchers to three-dimensionally encapsulate cells within diverse materials that mimic the extracellular matrix and support cellular viability. Approaches to synthesize gels with biophysically and biochemically controlled microenvironments are becoming increasingly important, and require strategies to control gel properties (e.g., degradation rate and mechanism) on multiple time and size scales. Furthermore, biological responses of gel-encapsulated cells can be promoted by hydrogel degradation products, as well as by the release of tethered biologically relevant molecules. PMID:19461945

  13. Solution structure of CEH-37 homeodomain of the nematode Caenorhabditis elegans

    SciTech Connect

    Moon, Sunjin; Lee, Yong Woo; Kim, Woo Taek; Lee, Weontae

    2014-01-10

    Highlights: •We have determined solution structures of CEH-37 homedomain. •CEH-37 HD has a compact α-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 α-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. Macromolecular crowding and confinement: biochemical, biophysical, and potential physiological consequences*

    PubMed Central

    Zhou, Huan-Xiang; Rivas, Germn; Minton, Allen P.

    2009-01-01

    Expected and observed effects of volume exclusion on the free energy of rigid and flexible macromolecules in crowded and confined systems, and consequent effects of crowding and confinement on macromolecular reaction rates and equilibria are summarized. Findings from relevant theoretical/simulation and experimental literature published from 2004 onward are reviewed. Additional complexity arising from the heterogeneity of local environments in biological media, and the presence of nonspecific interactions between macromolecules over and above steric repulsion are discussed. Theoretical and experimental approaches to the characterization of crowding- and confinement-induced effects in systems approaching the complexity of living organisms are suggested. PMID:18573087

  15. Protein crystal growth studies at the Center for Macromolecular Crystallography

    NASA Astrophysics Data System (ADS)

    Delucas, Lawrence J.; Long, Marianna M.; Moore, Karen M.; Harrington, Michael; McDonald, William T.; Smith, Craig D.; Bray, Terry; Lewis, Johanna; Crysel, William B.; Weise, Lance D.

    2000-01-01

    The Center for Macromolecular Crystallography (CMC) has been involved in fundamental studies of protein crystal growth (PCG) in microgravity and in our earth-based laboratories. A large group of co-investigators from academia and industry participated in these experiments by providing protein samples and by performing the x-ray crystallographic analysis. These studies have clearly demonstrated the usefulness of a microgravity environment for enhancing the quality and size of protein crystals. Review of the vapor diffusion (VDA) PCG results from nineteen space shuttle missions is given in this paper. .

  16. 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.

  17. Structural and Electronic Properties of a Wide-Gap Quaternary Solid Solution: \\(Zn, Mg\\) \\(S, Se\\)

    NASA Astrophysics Data System (ADS)

    Saitta, A. M.; de Gironcoli, S.; Baroni, S.

    1998-06-01

    The structural properties of the (Zn, Mg) (S, Se) solid solutions are determined by a combination of the computational alchemy and the cluster expansion methods with Monte Carlo simulations. We determine the phase diagram of the alloy and show that the homogeneous phase is characterized by a large amount of short-range order occurring among first-nearest neighbors. Electronic-structure calculations performed using the special quasirandom structure approach indicate that the energy gap of the alloy is rather sensitive to this short-range order.

  18. 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

  19. 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.

  20. Structural Properties and Phase Behavior of Crosslinked Networks in Polymer Solutions

    PubMed Central

    Benmouna, Farida; Zemmour, Samira; Benmouna, Mustapha

    2016-01-01

    ABSTRACT Structural properties and phase behavior of crosslinked networks embedded in polymer solutions are theoretically investigated. The partial structure factor of the network is calculated using a matrix formulation of the random phase approximation and the forward scattering limit is correlated with the phase behavior. Swelling and deswelling processes are analyzed in terms of the polymer concentration, the mismatch of solvent quality with respect to polymer and network, the polymers incompatibility and their characteristic sizes. Most studies reported so far in the literature have focussed on the swelling of crosslinked networks and gels in pure solvents but the correlation of the structural properties with the phase behavior in the presence of high molecular weight polymers in solution has not been given sufficient attention. The present work is intended to fill this gap in view of the current efforts to develop novel drug encapsulating and targeted delivery devices. PMID:27134310

  1. 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) (α- N-acetyl-neuraminyl-(2,3)-β- D-galactopyranosyl-(1,4)-[α- L-fucopyranosyl-(1,3)-β- 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.

  2. Water structuring around complex solutes: theoretical modeling of α- D-glucopyranose

    NASA Astrophysics Data System (ADS)

    Leroux, B.; Bizot, H.; Brady, J. W.; Tran, V.

    1997-04-01

    The structuring of solvent water by sugar solutes is studied using a molecular dynamics (MD) simulation of α- D-glucopyranose in aqueous (SPC) solution. The distribution of water positions actually observed in the MD simulation is compared to the solvent positions expected from a locally-tetrahedral distribution of hydrogen-bonded water molecules around the oxygen atoms. A reasonable correspondence between the observed and predicted hydration sites was found, but with certain deviations resulting from the incommensurate solvation requirements of adjacent functional groups. No evidence was found to support previous theories about sugar hydration which are based upon a supposed coincidence of the sugar structure with an assumed lattice-like model of liquid water. Solvent pair distribution functions were also used to characterize the observed water structuring, and methods of eliminating artificial minima in these distributions resulting from spherical averaging were examined.

  3. Grain boundary structure and solute segregation in titanium-doped sapphire bicrystals

    SciTech Connect

    Taylor, Seth T.

    2002-05-17

    Solute segregation to ceramic grain boundaries governs material processing and microstructure evolution, and can strongly influence material properties critical to engineering performance. Understanding the evolution and implications of grain boundary chemistry is a vital component in the greater effort to engineer ceramics with controlled microstructures. This study examines solute segregation to engineered grain boundaries in titanium-doped sapphire (Al2O3) bicrystals, and explores relationships between grain boundary structure and chemistry at the nanometer scale using spectroscopic and imaging techniques in the transmission electron microscope (TEM). Results demonstrate dramatic changes in solute segregation stemming from small fluctuations in grain boundary plane and structure. Titanium and silicon solute species exhibit strong tendencies to segregate to non-basal and basal grain boundary planes, respectively. Evidence suggests that grain boundary faceting occurs in low-angle twis t boundaries to accommodate nonequilibrium solute segregation related to slow specimen cooling rates, while faceting of tilt grain boundaries often occurs to expose special planes of the coincidence site lattice (CSL). Moreover, quantitative analysis of grain boundary chemistry indicates preferential segregation of charged defects to grain boundary dislocations. These results offer direct proof that static dislocations in ionic materials can assume a net charge, and emphasize the importance of interactions between charged point, line, and planar defects in ionic materials. Efforts to understand grain boundary chemistry in terms of space charge theory, elastic misfit and nonequilibrium segregation are discussed for the Al2O3 system.

  4. New solutions of the Jacobi equations for three-dimensional Poisson structures

    NASA Astrophysics Data System (ADS)

    Hernández-Bermejo, Benito

    2001-10-01

    A systematic investigation of the skew-symmetric solutions of the three-dimensional Jacobi equations is presented. As a result, three disjoint and complementary new families of solutions are characterized. Such families are very general, thus unifying many different and well-known Poisson structures seemingly unrelated which now appear embraced as particular cases of a more general solution. This unification is not only conceptual but allows the development of algorithms for the explicit determination of important properties such as the symplectic structure, the Casimir invariants and the Darboux canonical form, which are known only for a limited sample of Poisson structures. These common procedures are thus simultaneously valid for all the particular cases which can now be analyzed in a unified and more economic framework, instead of using a case-by-case approach. In addition, the methods developed are valid globally in phase space, thus ameliorating the usual scope of Darboux' reduction which is only of local nature. Finally, the families of solutions found present some new nonlinear superposition principles which are characterized.

  5. Structural properties and adsorption capacity of holocellulose aerogels synthesized from an alkali hydroxide-urea solution

    NASA Astrophysics Data System (ADS)

    Kwon, Gu-Joong; Kim, Dae-Young; Hwang, Jae-Hyun; Kang, Joo-Hyon

    2014-05-01

    A tulip tree was used to synthesize a holocellulose aerogel from an aqueous alkali hydroxide-urea solution with the substitution of an organic solvent followed by freeze-drying. For comparison, the synthesized holocellulose aerogels were divided into two groups according to the source of the hydrogel, an upper suspended layer and a bottom concentrated layer of the centrifuged solution of cellulose and NaOH/urea solvents. We investigated the effects of the temperature of the pre-cooled NaOH/urea solution ( i.e., dissolution temperature) on the pore structure and the adsorption capacity of the holocellulose aerogel. A nano-fibrillar network structure of the holocellulose aerogel was observed, with little morphological difference in pore structure for different dissolution temperatures. Both micropores and mesopores were observed in the holocellulose aerogel. The specific surface area of the holocellulose aerogel was generally greater at lower dissolution temperatures. In a series of adsorption tests using methylene blue, the holocellulose aerogel showed the greatest adsorption capacity at the lowest dissolution temperature tested (-2°C). However, the dissolution temperature generally had little effect on the adsorption capacity. The holocellulose aerogel produced from the upper suspended layer of the centrifuged hydrogel solution showed a greater porosity and adsorption capacity than the one produced from the bottom concentrated layer. Overall, the aerogel made by utilizing a delignified tulip tree display a high surface area and a high adsorption property, indicating its possible application in eco-friendly adsorption materials.

  6. Structure and dimerization of translation initiation factor aIF5B in solution

    SciTech Connect

    Rasmussen, Louise Caroe Vohlander; Oliveira, Cristiano Luis Pinto; Byron, Olwyn; Jensen, Janni Mosgaard; Pedersen, Jan Skov; Sperling-Petersen, Hans Uffe; Mortensen, Kim Kusk

    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.

  7. Structure from solute-solvent interactions in supercritical polyatomic molecular mixtures

    SciTech Connect

    Lee, L.L.; Cochran, H.D.

    1994-12-31

    Solute-solvent and solute-solute microstructures at the sueprcritical state are important in elucidating chemical reaction and spectroscopic data. We can classify the range of pair correlations into two regions: a short range (r {le} r{sub min}) and a long range (r from r{sub min} to 20 {approximately} 50 molecular diameters). The often cited local density enhacement referes to the short range corelations and is shown not to be related to the critical behavior of the mixture. The long-range behavior of the pair correlations is responsible for the buildup of osmotic susceptibility and is related to the closeness to solvent`s critical point. In the class of attractive supercritical mixtures, the solute-solvent short-range pair correlation exhibits complicated bheavior: enhanced solvation (within the first neighborhood) at low to medium densities and peak attenuation followed by peak growth at higher densities. Earlier theor. studies (integral equations) dealt with idealized model of solute molecules as spheres (molecular size effects accounted for, but not molecular shape effects). This study examines behavioral change due to molecular shapes and orientations as the solutes take the shape of polyatomic molecules. For example the case of di-tert-butylnitroxide radicals in supercritical ethylene can be modeled as linear dimeric molecules. Reference interaction site model integral equation is used to produce site-site correlation functions. We map out the density ranges where structural changes take place and elucidate their practical implications.

  8. Towards solution and refinement of organic crystal structures by fitting to the atomic pair distribution function.

    PubMed

    Prill, Dragica; Juhás, Pavol; Billinge, Simon J L; Schmidt, Martin U

    2016-01-01

    A method towards the solution and refinement of organic crystal structures by fitting to the atomic pair distribution function (PDF) is developed. Approximate lattice parameters and molecular geometry must be given as input. The molecule is generally treated as a rigid body. The positions and orientations of the molecules inside the unit cell are optimized starting from random values. The PDF is obtained from carefully measured X-ray powder diffraction data. The method resembles `real-space' methods for structure solution from powder data, but works with PDF data instead of the diffraction pattern itself. As such it may be used in situations where the organic compounds are not long-range-ordered, are poorly crystalline, or nanocrystalline. The procedure was applied to solve and refine the crystal structures of quinacridone (β phase), naphthalene and allopurinol. In the case of allopurinol it was even possible to successfully solve and refine the structure in P1 with four independent molecules. As an example of a flexible molecule, the crystal structure of paracetamol was refined using restraints for bond lengths, bond angles and selected torsion angles. In all cases, the resulting structures are in excellent agreement with structures from single-crystal data. PMID:26697868

  9. Towards solution and refinement of organic crystal structures by fitting to the atomic pair distribution function

    SciTech Connect

    Prill, Dragica; Juhas, Pavol; Billinge, Simon J. L.; Schmidt, Martin U.

    2016-01-01

    In this study, a method towards the solution and refinement of organic crystal structures by fitting to the atomic pair distribution function (PDF) is developed. Approximate lattice parameters and molecular geometry must be given as input. The molecule is generally treated as a rigid body. The positions and orientations of the molecules inside the unit cell are optimized starting from random values. The PDF is obtained from carefully measured X-ray powder diffraction data. The method resembles `real-space' methods for structure solution from powder data, but works with PDF data instead of the diffraction pattern itself. As such it may be used in situations where the organic compounds are not long-range-ordered, are poorly crystalline, or nanocrystalline. The procedure was applied to solve and refine the crystal structures of quinacridone (β phase), naphthalene and allopurinol. In the case of allopurinol it was even possible to successfully solve and refine the structure in P1 with four independent molecules. As an example of a flexible molecule, the crystal structure of paracetamol was refined using restraints for bond lengths, bond angles and selected torsion angles. In all cases, the resulting structures are in excellent agreement with structures from single-crystal data.

  10. Towards solution and refinement of organic crystal structures by fitting to the atomic pair distribution function

    DOE PAGESBeta

    Prill, Dragica; Juhas, Pavol; Billinge, Simon J. L.; Schmidt, Martin U.

    2016-01-01

    In this study, a method towards the solution and refinement of organic crystal structures by fitting to the atomic pair distribution function (PDF) is developed. Approximate lattice parameters and molecular geometry must be given as input. The molecule is generally treated as a rigid body. The positions and orientations of the molecules inside the unit cell are optimized starting from random values. The PDF is obtained from carefully measured X-ray powder diffraction data. The method resembles `real-space' methods for structure solution from powder data, but works with PDF data instead of the diffraction pattern itself. As such it may bemore » used in situations where the organic compounds are not long-range-ordered, are poorly crystalline, or nanocrystalline. The procedure was applied to solve and refine the crystal structures of quinacridone (β phase), naphthalene and allopurinol. In the case of allopurinol it was even possible to successfully solve and refine the structure in P1 with four independent molecules. As an example of a flexible molecule, the crystal structure of paracetamol was refined using restraints for bond lengths, bond angles and selected torsion angles. In all cases, the resulting structures are in excellent agreement with structures from single-crystal data.« less

  11. Solution structure of a DNA duplex with a chiral alkyl phosphonate moiety

    PubMed Central

    Soliva, R.; Monaco, V.; Gómez-Pinto, I.; Meeuwenoord, N. J.; Marel, G. A. Van der; Boom, J. H. Van; González, C.; Orozco, M.

    2001-01-01

    The solution structures of two DNA decamers of sequence d(CCACCpxGGAAC)·(GTTCCGGTGG) with a chiral alkyl phosphonate moiety (px) have been determined using NMR and restrained molecular dynamics simulations and compared with the solution structure of the unmodified duplex. The 1H NMR spectra of two samples with pure stereochemistry in the modified phosphate have been assigned. The structures of both diastereoisomers, as well as the unmodified control duplex, have been determined from NMR-derived distance and torsion angle constraints. Accurate distance constraints were obtained from a complete relaxation matrix analysis of the NOE intensities. The structures have been refined with state of the art molecular dynamics methods, including explicit solvent and applying the particle mesh Ewald method to properly evaluate the long-range electrostatic interactions. In both cases, the calculations converge to well-defined structures, with RMSDs of ∼1 Å. The resulting structures belong to the general B family of DNA structures, even though the presence of the alkyl phosphonate moiety induces some slight displacement to the A-form in the neighborhood of the modified phosphate. Partial neutralization of this phosphate and the steric effect of the alkyl moiety provoke moderate bending in the DNA. This effect is more pronounced in the S diastereoisomer, where the alkyl group points inwards to the double helix. PMID:11452022

  12. Solution structure of peptide AG4 used to form silver nanoparticles

    SciTech Connect

    Lee, Eunjung; Kim, Dae-Hee; Woo, Yoonkyung; Hur, Ho-Gil; Lim, Yoongho

    2008-11-21

    The preparation of silver nanoparticles (AgNPs) is of great interest due to their various biological activities, such as observed in their antimicrobial and wound healing actions. Moreover, the formation of AgNPs using silver-binding peptide has certain advantages because they can be made in aqueous solution at ambient temperature. The solution structure of the silver-binding peptide AG4 was determined using nuclear magnetic resonance spectroscopy, and the site of the AG4 interaction with AgNPs was elucidated.

  13. Electrostatic Effect on the Solution Structure and Dynamics of PEDOT:PSS

    NASA Astrophysics Data System (ADS)

    Leaf, Michael; Muthukumar, Murugappan

    Poly(3,4-ethylenedioxythiophene):poly(styrene sulfonic acid) (PEDOT:PSS) is a popular material used in organic electronic devices as a conductor. It consists of PEDOT polycations complexed with PSS polyanions which are initially suspended in aqueous solution and eventually cast into a film. Various annealing and doping methods dramatically enhance PEDOT:PSS film conductivity. To understand the physical interactions at play, we explore structural and dynamic aspects of PEDOT:PSS solutions through scattering and rheology techniques. We highlight several aspects of the phase behavior of PEDOT:PSS, and the significance of electrostatic interactions.

  14. Families of solutions to the generalized Ginzburg-Landau equation and structural transitions between them

    SciTech Connect

    Ovchinnikov, Yu. N.

    2013-09-15

    Solutions to the generalized Ginzburg-Landau equations for superconductors are obtained for a Ginzburg-Landau parameter {kappa} close to unity. The families of solutions with arbitrary number n of flux quanta in a unit cell are analyzed. It is shown that under certain conditions, a cascade of phase transitions between different structures in a magnetic field appears near T{sub c}. Algebraic equations are derived for determining the boundaries of coexistence of different phases on the (T, H{sub 0}) plane.

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

    PubMed Central

    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 of 2 molar NaOH in aqueous solution from neutron diffraction and empirical potential structure refinement

    SciTech Connect

    McLain, Sylvia E.; Imberti, Silvia; Soper, Alan K.; Botti, Alberto; Bruni, Fabio; Ricci, Maria Antonietta

    2006-09-01

    Neutron diffraction with isotopic substitution has been used to investigate aqueous solutions of 2M NaOH in the liquid state. The data were modeled using empirical potential structure refinement which allows for the extraction of the ion-water and water-water correlations. The data show that the ion-water radial distribution functions are in accordance with those found by previous studies on NaOH solutions and follow a trend which is dependent on the concentration of the solute. In particular, the shape of the hydroxide hydration shell is found to be concentration independent, but the number of water molecules occupying this shell increases with dilution. Additionally, the water-water correlations show that there is still a measurable effect on water structure with the addition of ions at this concentration, as the second shell in the water oxygen radial distribution function is compressed relative to the first shell. The data are also used to discuss the recent claims that the published radial distribution functions of water are unreliable, showing that data taken at different neutron sources, with different diffraction geometry and systematic errors lead to the same structural information when analyzed via a realistic modeling regime.

  17. 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

  18. Elongation factor TFIIS contains three structural domains: solution structure of domain II.

    PubMed Central

    Morin, P E; Awrey, D E; Edwards, A M; Arrowsmith, C H

    1996-01-01

    Transcription elongation by RNA polymerase II is regulated by the general elongation factor TFIIS. This factor stimulates RNA polymerase II to transcribe through regions of DNA that promote the formation of stalled ternary complexes. Limited proteolytic digestion showed that yeast TFIIS is composed of three structural domains, termed I, II, and III. The two C-terminal domains (II and III) are required for transcription activity. The structure of domain III has been solved previously by using NMR spectroscopy. Here, we report the NMR-derived structure of domain II: a three-helix bundle built around a hydrophobic core composed largely of three tyrosines protruding from one face of the C-terminal helix. The arrangement of known inactivating mutations of TFIIS suggests that two surfaces of domain II are critical for transcription activity. Images Fig. 1 Fig. 2 Fig. 3 PMID:8855225

  19. Solution secondary structure of calcium-saturated troponin C monomer determined by multidimensional heteronuclear NMR spectroscopy.

    PubMed Central

    Slupsky, C. M.; Reinach, F. C.; Smillie, L. B.; Sykes, B. D.

    1995-01-01

    The solution secondary structure of calcium-saturated skeletal troponin C (TnC) in the presence of 15% (v/v) trifluoroethanol (TFE), which has been shown to exist predominantly as a monomer (Slupsky CM, Kay CM, Reinach FC, Smillie LB, Sykes BD, 1995, Biochemistry 34, forthcoming), has been investigated using multidimensional heteronuclear nuclear magnetic resonance spectroscopy. The 1H, 15N, and 13C NMR chemical shift values for TnC in the presence of TFE are very similar to values obtained for calcium-saturated NTnC (residues 1-90 of skeletal TnC), calmodulin, and synthetic peptide homodimers. Moreover, the secondary structure elements of TnC are virtually identical to those obtained for calcium-saturated NTnC, calmodulin, and the synthetic peptide homodimers, suggesting that 15% (v/v) TFE minimally perturbs the secondary and tertiary structure of this stably folded protein. Comparison of the solution structure of calcium-saturated TnC with the X-ray crystal structure of half-saturated TnC reveals differences in the phi/psi angles of residue Glu 41 and in the linker between the two domains. Glu 41 has irregular phi/psi angles in the crystal structure, producing a kink in the B helix, whereas in calcium-saturated TnC, Glu 41 has helical phi/psi angles, resulting in a straight B helix. The linker between the N and C domains of calcium-saturated TnC is flexible in the solution structure. PMID:7670371

  20. Variable effects of soman on macromolecular secretion by ferret trachea

    SciTech Connect

    McBride, R.K.; Zwierzynski, D.J.; Stone, K.K.; Culp, D.J.; Marin, M.G. )

    1991-01-01

    The purpose of this study was to examine the effect of the anticholinesterase agent, soman, on macromolecular secretion by ferret trachea, in vitro. We mounted pieces of ferret trachea in Ussing-type chambers. Secreted sulfated macromolecules were radiolabeled by adding 500 microCi of {sup 35}SO{sub 4} to the submucosal medium and incubating for 17 hr. Soman added to the submucosal side produced a concentration-dependent increase in radiolabeled macromolecular release with a maximal secretory response (mean +/- SD) of 202 +/- 125% (n = 8) relative to the basal secretion rate at a concentration of 10{sup {minus} 7} M. The addition of either 10{sup {minus}6} M pralidoxime (acetylcholinesterase reactivator) or 10{sup {minus}6} M atropine blocked the response to 10{sup {minus}7} M soman. At soman concentrations greater than 10{sup {minus}7} M, secretion rate decreased and was not significantly different from basal secretion. Additional experiments utilizing acetylcholine and the acetylcholinesterase inhibitor, physostigmine, suggest that inhibition of secretion by high concentrations of soman may be due to a secondary antagonistic effect of soman on muscarinic receptors.

  1. 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 ω and consists of four linear positioners working synchronously to achieve x, y, z translations and χ rotation (0–90°), followed by a ϕ 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 ω, χ and ϕ, 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

  2. 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.

  3. Mast cells and macromolecular leak in intestinal immunological reactions

    PubMed Central

    Murray, Max; Jarrett, W. F. H.; Jennings, F. W.

    1971-01-01

    The onset of the exponential expulsion of Nippostrongylus brasiliensis worms in the rat is associated with a sharp burst of intestinal mast cell activity and increased permeability of the bowel wall. It was found that the onset of maximum velocity of worm expulsion occurred earlier in female rats than in male rats and proceeded at a faster rate. There was a corresponding difference in the timing of the mast cell rise and macromolecular leak between the sexes. This suggested that there is a relationship between these events. Cortisone, a drug known to stop worm expulsion and to suppress the mast cell response, also prevented the macromolecular leak. Electron microscopy showed that during the period of increased permeability a pathway for protein tracers had opened up between the epithelial cells and it is suggested that this is the route for enhanced antibody transfer across mucous membranes. We suggest that a stimulus or stimuli from the parasite cause synchronous development of new populations of mast cells, IgE-producing plasma cells and plasma cells synthesizing antibodies of other classes possessing an anti-worm effect. It is also suggested that these mast cells discharge their pharmacological mediators by an allergen—reaginic antibody mediated system and that these mediators create a pathway through the intestinal mucosa for the translocation of antibody. ImagesFIG. 5FIG. 6FIG. 7 PMID:5105046

  4. 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

  5. A structural study of the intermolecular interactions of tyramine in the solid state and in solution

    NASA Astrophysics Data System (ADS)

    Quevedo, Rodolfo; Nuñez-Dallos, Nelson; Wurst, Klaus; Duarte-Ruiz, Álvaro

    2012-12-01

    The nature of the interactions between tyramine units was investigated in the solid state and in solution. Crystals of tyramine in its free base form were analyzed by Fourier transform infrared (FT-IR) spectroscopy and single-crystal X-ray diffraction (XRD). The crystal structure shows a linear molecular organization held together by "head-to-tail" intermolecular hydrogen bonds between the amino groups and the phenolic hydroxyl groups. These chains are arranged in double layers that can geometrically favor the formation of templates in solution, which may facilitate macrocyclization reactions to form azacyclophane-type compounds. Computational calculations using the PM6-DH+ method and electrospray ionization mass spectrometry (ESI-HRMS) reveal that the formation of a hydrogen-bonded tyramine dimer is favored in solution.

  6. The Method of Decomposition in Invariant Structures: Exact Solutions for N Internal Waves in Three Dimensions

    NASA Astrophysics Data System (ADS)

    Miroshnikov, Victor

    2015-11-01

    The Navier-Stokes system of PDEs is reduced to a system of the vorticity, continuity, Helmholtz, and Lamb-Helmholtz PDEs. The periodic Dirichlet problems are formulated for conservative internal waves vanishing at infinity in upper and lower domains. Stationary kinematic Fourier (SKF) structures, stationary kinematic Euler-Fourier (SKEF) structures, stationary dynamic Euler-Fourier (SDEF) structures, and SKEF-SDEF structures of three spatial variables and time are constructed to consider kinematic and dynamic problems of the three-dimensional theory of the Newtonian flows with harmonic velocity. Exact solutions for propagation and interaction of N internal waves in the upper and lower domains are developed by the method of decomposition in invariant structures and implemented through experimental and theoretical programming in Maple. Main results are summarized in a global existence theorem for the strong solutions. The SKEF, SDEF, and SKEF-SDEF structures of the cumulative flows are visualized by two-parametric surface plots for six fluid-dynamic variables.

  7. Phase transitions of macromolecular microsphere composite hydrogels based on the stochastic Cahn-Hilliard equation

    NASA Astrophysics Data System (ADS)

    Li, Xiao; Ji, Guanghua; Zhang, Hui

    2015-02-01

    We use the stochastic Cahn-Hilliard equation to simulate the phase transitions of the macromolecular microsphere composite (MMC) hydrogels under a random disturbance. Based on the Flory-Huggins lattice model and the Boltzmann entropy theorem, we develop a reticular free energy suit for the network structure of MMC hydrogels. Taking the random factor into account, with the time-dependent Ginzburg-Landau (TDGL) mesoscopic simulation method, we set up a stochastic Cahn-Hilliard equation, designated herein as the MMC-TDGL equation. The stochastic term in the equation is constructed appropriately to satisfy the fluctuation-dissipation theorem and is discretized on a spatial grid for the simulation. A semi-implicit difference scheme is adopted to numerically solve the MMC-TDGL equation. Some numerical experiments are performed with different parameters. The results are consistent with the physical phenomenon, which verifies the good simulation of the stochastic term.

  8. Phase transitions of macromolecular microsphere composite hydrogels based on the stochastic Cahn–Hilliard equation

    SciTech Connect

    Li, Xiao Ji, Guanghua Zhang, Hui

    2015-02-15

    We use the stochastic Cahn–Hilliard equation to simulate the phase transitions of the macromolecular microsphere composite (MMC) hydrogels under a random disturbance. Based on the Flory–Huggins lattice model and the Boltzmann entropy theorem, we develop a reticular free energy suit for the network structure of MMC hydrogels. Taking the random factor into account, with the time-dependent Ginzburg-Landau (TDGL) mesoscopic simulation method, we set up a stochastic Cahn–Hilliard equation, designated herein as the MMC-TDGL equation. The stochastic term in the equation is constructed appropriately to satisfy the fluctuation-dissipation theorem and is discretized on a spatial grid for the simulation. A semi-implicit difference scheme is adopted to numerically solve the MMC-TDGL equation. Some numerical experiments are performed with different parameters. The results are consistent with the physical phenomenon, which verifies the good simulation of the stochastic term.

  9. Engineering human immunodeficiency virus 1 protease heterodimers as macromolecular inhibitors of viral maturation.

    PubMed Central

    McPhee, F; Good, A C; Kuntz, I D; Craik, C S

    1996-01-01

    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. Images Fig. 1 Fig. 2 Fig. 3 Fig. 4 PMID:8876160

  10. Engineering Human Immunodeficiency Virus 1 Protease Heterodimers as Macromolecular Inhibitors of Viral Maturation

    NASA Astrophysics Data System (ADS)

    McPhee, Fiona; Good, Andrew C.; Kuntz, Irwin D.; Craik, Charles S.

    1996-10-01

    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.

  11. Site-selective electroless nickel plating on patterned thin films of macromolecular metal complexes.

    PubMed

    Kimura, Mutsumi; Yamagiwa, Hiroki; Asakawa, Daisuke; Noguchi, Makoto; Kurashina, Tadashi; Fukawa, Tadashi; Shirai, Hirofusa

    2010-12-01

    We demonstrate a simple route to depositing nickel layer patterns using photocross-linked polymer thin films containing palladium catalysts, which can be used as adhesive interlayers for fabrication of nickel patterns on glass and plastic substrates. Electroless nickel patterns can be obtained in three steps: (i) the pattern formation of partially quaterized poly(vinyl pyridine) by UV irradiation, (ii) the formation of macromolecular metal complex with palladium, and (iii) the nickel metallization using electroless plating bath. Metallization is site-selective and allows for a high resolution. And the resulting nickel layered structure shows good adhesion with glass and plastic substrates. The direct patterning of metallic layers onto insulating substrates indicates a great potential for fabricating micro/nano devices. PMID:21069972

  12. Localized reconstruction of subunits from electron cryomicroscopy images of macromolecular complexes.

    PubMed

    Ilca, Serban L; Kotecha, Abhay; Sun, Xiaoyu; Poranen, Minna M; Stuart, David I; Huiskonen, Juha T

    2015-01-01

    Electron cryomicroscopy can yield near-atomic resolution structures of highly ordered macromolecular complexes. Often however some subunits bind in a flexible manner, have different symmetry from the rest of the complex, or are present in sub-stoichiometric amounts, limiting the attainable resolution. Here we report a general method for the localized three-dimensional reconstruction of such subunits. After determining the particle orientations, local areas corresponding to the subunits can be extracted and treated as single particles. We demonstrate the method using three examples including a flexible assembly and complexes harbouring subunits with either partial occupancy or mismatched symmetry. Most notably, the method allows accurate fitting of the monomeric RNA-dependent RNA polymerase bound at the threefold axis of symmetry inside a viral capsid, revealing for the first time its exact orientation and interactions with the capsid proteins. Localized reconstruction is expected to provide novel biological insights in a range of challenging biological systems. PMID:26534841

  13. The kinetic dose limit in room-temperature time-resolved macromolecular crystallography

    SciTech Connect

    Schmidt, M.; Srajer, V.; Purwar, N.; Tripathi, S.

    2012-05-24

    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.

  14. Localized reconstruction of subunits from electron cryomicroscopy images of macromolecular complexes

    PubMed Central

    Ilca, Serban L.; Kotecha, Abhay; Sun, Xiaoyu; Poranen, Minna M.; Stuart, David I.; Huiskonen, Juha T.

    2015-01-01

    Electron cryomicroscopy can yield near-atomic resolution structures of highly ordered macromolecular complexes. Often however some subunits bind in a flexible manner, have different symmetry from the rest of the complex, or are present in sub-stoichiometric amounts, limiting the attainable resolution. Here we report a general method for the localized three-dimensional reconstruction of such subunits. After determining the particle orientations, local areas corresponding to the subunits can be extracted and treated as single particles. We demonstrate the method using three examples including a flexible assembly and complexes harbouring subunits with either partial occupancy or mismatched symmetry. Most notably, the method allows accurate fitting of the monomeric RNA-dependent RNA polymerase bound at the threefold axis of symmetry inside a viral capsid, revealing for the first time its exact orientation and interactions with the capsid proteins. Localized reconstruction is expected to provide novel biological insights in a range of challenging biological systems. PMID:26534841

  15. Pseudopeptides and beta folding: x-ray structures compared with structures in solution.

    PubMed

    Aubry, A; Marraud, M

    1989-01-01

    In order to restrain the flexibility of the peptide molecules and reduce their biodegradation, modifications of the main chain are now introduced in pseudopeptide analogues. Surprisingly, there is very little data on the conformational properties of these derivatives. We have examined pseudopeptide analogues of RCO-X-Y-NHR' model dipeptides in the depsi, N-methylated, reduced, retro, alpha, beta-dehydro, beta-amino acid, and hydrazino series, in the solid state by x-ray diffraction, and in solution by ir and 1H-nmr spectroscopy. This study provides us with accurate dimensions of the peptide surrogates, and gives some information on the conformational tendencies induced by these substitutions, with reference to those of the related dipeptide sequences. PMID:2720098

  16. Silica/alkali ratio dependence of the microscopic structure of sodium silicate solutions.

    PubMed

    Nordstrm, Jonas; Sundblom, Andreas; Jensen, Grethe Vestergaard; Pedersen, Jan Skov; Palmqvist, Anders; Matic, Aleksandar

    2013-05-01

    Alkaline sodium silicate solutions with SiO2:Na2O molar ratios in the range 4-10 are known to be colloidally unstable manifested in phase separation or gelation. The mechanistic understanding of this instability is generally poor. To improve this situation the microscopic structure of a series of solutions with ratios in the range 3.3-8.9 has been characterised using small-angle X-ray scattering, Dynamic light scattering, Fourier transformed infrared spectroscopy, and (29)Si Nuclear magnetic resonance spectroscopy to cover the relevant length scales related to silica clusters, aggregates, and particles present. In the starting solution, with ratio 3.3, there are silica present in three fractions. The main part is present as small silica clusters with a radius of 0.7 nm. There are also a significant portion of monomers/small oligomeric silica species as well as a minute amount of larger colloidal silica particles. At a higher SiO2:Na2O ratio, above approximately 4, smaller spherical colloidal particles are formed due to condensation reactions. However, as a result of a too high ionic strength the suspension is not stable and the particles aggregate to fractal structures with a size that depends on ratio and ageing time. At the highest SiO2:Na2O ratio, fractals are not formed because of the lower ionic strength and the smaller colloidal particles are stable in the solution. By carefully adding small amounts of NaCl to the high ratio solution it is possible to induce gelation of the solution confirming the hypothesis that the instability region is due to too high electrolyte concentration for the silica species present under those conditions. PMID:23484773

  17. Influence of the organized structure of 1-alkyl-3-methylimidazolium tetrafluoroborates on the rotational diffusion of structurally similar nondipolar solutes.

    PubMed

    Gangamallaiah, V; Dutt, G B

    2014-11-26

    To understand how the organized structure of the ionic liquids influences the location and mobility of nondipolar solutes, rotational diffusion of 2,5-dimethyl-1,4-dioxo-3,6-diphenylpyrrolo[3,4-c]pyrrole (DMDPP) and 1,4-dioxo-3,6-diphenylpyrrolo[3,4-c]pyrrole (DPP) has been examined in 1-alkyl-3-methylimidazolium (alkyl = ethyl, butyl, hexyl, and octyl) tetrafluoroborates. Both the solutes are structurally similar-the sole difference being the two NCH3 groups of DMDPP are replaced by two NH groups in DPP. The rotational diffusion of DPP is found to be significantly slower than DMDPP due to specific interactions between the NH groups of the solute and the anion of the ionic liquid. It has been observed that for a given viscosity and temperature, the rotational diffusion of DMDPP becomes progressively faster with an increase in the length of the alkyl chain on the imidazolium cation. DMDPP resides in the nonpolar domains of these ionic liquids whose sizes increase with an increase in the length of the alkyl chain, and as a result it experiences microviscosity that is lower than the bulk viscosity. However, an increase in the length of the alkyl chain has no apparent effect on the rotational diffusion of DPP because specific interactions with tetrafluoroborate necessitate the solute to be located in the vicinity of the anion. The results of this work exemplify that despite having similar size and shape, the rotational diffusion of DMDPP and DPP is quite contrasting as their sites of solubilization and the nature of interactions with the surroundings are vastly different owing to subtle variations in their chemical structures. PMID:25365536

  18. Chapter 21 Architecture of Hydrates and Local Structure of Acetic Acid Aqueous Solution

    NASA Astrophysics Data System (ADS)

    Pu, Liang; Wang, Qing; Zhang, Yong; Miao, Qiang; Kim, Yang-Soo; Zhang, Zhibing

    The protonation and deprotonation phenomena and molecular association of solute molecule with water via intermolecular hydrogen bonding forming various hydration compounds are very common in aqueous solution and in biological cell in nature. In the aqueous solution, more complicated type of hydrogen bond, hydrogen-bonding rings, various kinds of hydration compounds (hydrates), and even hydrogen-bonding network can be expected. The nature of hydrogen bonding, the bonds networking, the rule in architecture of larger hydration compounds, deprotonation of acetic acid in solution, stability of the hydrated proton, and the local structure of its aqueous solution are the most fundamental problems to understanding solute molecule living style in aqueous solution. Hydrogen-bonding rings and network in the multi-hydrates of acetic acid monomer have been investigated by ab initio calculations, and ab initio molecular dynamics (CPMD) simulations on acetic acid monomer-water system were also performed to explore the local structure of acetic acid aqueous solution. More than hundreds of multi-hydrates have been selected as candidates during our calculations. The structural optimizations and energy calculations have been performed at the MP2/6-31+g (d, p) and MP4/6-31+g (d, p) levels which are adequate for our large hydrates calculations with reliable results and reasonable cost as we stated in the Section 2. The most stable structure of the smallest hydration compound of acetic acid monomer, i.e., acetic acid water dimer, has a four-membered head-on ring with the smallest dipole moment. To verify the existence of it, the infrared spectra experiment data were collected in the dilute CCl4/HAc and CCl4/H2O ratio condition. The hydroxyl (O-H) stretching vibrations in molecules of water, acetic acid, and the dimer are distinguished, for the dissolved species are isolated from each other by surrounded solvent molecules CCl4. The calculated and measured vibration frequencies are almost lain in line with 0.872 scaling. The four-, five-, and six-membered head-on rings are the most favorable in the small multi-hydrates with a stable planar structure and the side-on ring with a weak hydrogen-bonding interaction of C-H...Ow-H. The six-membered ring is most important in the large multi-hydrates and in the local structure of dilute solution also verified by our CPMD simulations. A larger ring of or more than seven-membered could no longer maintain the planar structure. Larger multi-hydrates of acetic acid monomer could be constructed from these basic building blocks. The strength order for the five kinds of bonds is in the descending order as C-O-H...Ow-H>Ow-H...Ow-H>CO...H-Ow>Ow-H...Oa-H>>C-H...Ow-H. The three hydroxyl bonds O-H in the hydrated proton could be divided into two types: one of the hydroxyl bonds is hydrogen bonded to the deprotonated oxygen of the acetic acid, other two to waters in the hydrate. The larger the RO-H becomes, the smaller the RO...H and the stronger the associated hydrogen bond are. The hydrated proton is stable and liberated from the deprotonated acetic acid in the large multi-hydrate with more complicit head-on ring. In small hydrates, the protonating hydrogen is shared partly by the acetic acid.

  19. 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.

  20. Solution growth of metal-organic complex CuTCNQ in small dimension interconnect structures

    NASA Astrophysics Data System (ADS)

    Demolliens, A.; Muller, Ch.; Müller, R.; Turquat, Ch.; Goux, L.; Deleruyelle, D.; Wouters, D. J.

    2010-11-01

    In this paper, we report two different elaboration routes to grow metal-organic complex CuTCNQ in liquid phase within small interconnect structures (i.e. via holes opened in SiO 2/SiC stack). The basic common idea relies on the formation of CuTCNQ material from the partial corrosion of a Cu bottom electrode by a TCNQ-based solution. The two solution growth methods are compared in terms of (i) via holes filling; (ii) local microstructure of CuTCNQ complex and (iii) quality of interface between CuTCNQ and copper metallic electrode. In the first route, in the reaction of the substrate with a TCNQ/copper salt solution in acetonitrile/toluene, a rapid formation of porous CuTCNQ complex is observed with an over-growth outside interconnect structures and many voids within via holes and at the interface with Cu layer. In contrast to this "mushroom-like" growth, the reaction of the substrate with a TCNQ solution in acetonitrile/2-butanone results in a "crystal-like" dense CuTCNQ complex within via holes and a CuTCNQ/Cu interface free of voids. In the latter case, satisfactory electrical performances are expected for future resistive switching memory devices.

  1. 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, 20, and 40, 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 crowders result in only disordered oligomers and simulations with 40 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

  2. Mechanical degradation of porous titanium with entangled structure filled with biodegradable magnesium in Hanks' solution.

    PubMed

    Li, Qiuyan; Jiang, Guofeng; Wang, Cunlong; Dong, Jie; He, Guo

    2015-12-01

    The degradation behavior of the porous titanium with entangled structure filled with biodegradable magnesium (p-Ti/Mg) in Hanks' solution was investigated. It was found that the p-Ti/Mg composite had higher strength than pure magnesium and porous titanium with entangled structure (p-Ti). Although the magnesium in p-Ti/Mg was completely dissolved in Hanks' solution after immersion for 104 h, the rest of the sample still maintained strength of about 86 MPa. Moreover, the produced porousness (due to magnesium-degradation) could provide channels for the ingrowth and transportation of bone cells. However, the high corrosion rate of p-Ti/Mg is still a problem when used as a candidate biomedical material, which needs further improvement. PMID:26354275

  3. Rational rates of uniform decay for strong solutions to a fluid-structure PDE system

    NASA Astrophysics Data System (ADS)

    Avalos, George; Bucci, Francesca

    2015-06-01

    In this work we investigate the uniform stability properties of solutions to a well-established partial differential equation (PDE) model for a fluid-structure interaction. The PDE system under consideration comprises a Stokes flow which evolves within a three-dimensional cavity; moreover, a Kirchhoff plate equation is invoked to describe the displacements along a (fixed) portion - say, Ω - of the cavity wall. Contact between the respective fluid and structure dynamics occurs on the boundary interface Ω. The main result in the paper is as follows: the solutions to the composite PDE system, corresponding to smooth initial data, decay at the rate of O (1 / t). Our method of proof hinges upon the appropriate invocation of a relatively recent resolvent criterion for polynomial decays of C0-semigroups. While the characterization provided by said criterion originates in the context of operator theory and functional analysis, the work entailed here is wholly within the realm of PDE.