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1

Macromolecular powder diffraction : structure solution via molecular.  

SciTech Connect

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.

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

2009-01-01

2

PHENIX: a comprehensive Python-based system for macromolecular structure solution  

PubMed Central

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 macromolecular crystallo­graphic structure solution with an emphasis on the 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. PMID:20124702

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

2010-01-01

3

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

SciTech Connect

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.

Terwilliger, Thomas C [Los Alamos National Laboratory; Hung, Li - Wei [Los Alamos National Laboratory; Adams, Paul D [UC BERKELEY; Afonine, Pavel V [UC BERKELEY; Bunkoczi, Gabor [UNIV OF CAMBRIDGE; Chen, Vincent B [DUKE UNIV; Davis, Ian [DUKE UNIV; Echols, Nathaniel [LBNL; Headd, Jeffrey J [DUKE UNIV; Grosse Kunstleve, Ralf W [LBNL; Mccoy, Airlie J [UNIV OF CAMBRIDGE; Moriarty, Nigel W [LBNL; Oeffner, Robert [UNIV OF CAMBRIDGE; Read, Randy J [UNIV OF CAMBRIDGE; Richardson, David C [DUKE UNIV; Richardson, Jane S [DUKE UNIV; Zwarta, Peter H [LBNL

2009-01-01

4

A General Method for Modeling Macromolecular Shape in Solution  

PubMed Central

A general method for modeling macromolecular shape in solution is described involving measurements of viscosity, radius of gyration, and the second thermodynamic virial coefficient. The method, which should be relatively straightforward to apply, does not suffer from uniqueness problems, involves shape functions that are independent of hydration, and models the gross conformation of the macromolecule in solution as a general triaxial ellipsoid. The method is illustrated by application to myosin, and the relevance and applicability of ellipsoid modeling to biological structures is discussed. PMID:19431695

Harding, Stephen E.

1987-01-01

5

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

PubMed

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

Mezzasalma, Stefano A

2007-12-01

6

Solution-Phase Processes of Macromolecular Crystallization  

NASA Technical Reports Server (NTRS)

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.

Pusey, Marc L.; Minamitani, Elizabeth Forsythe

2004-01-01

7

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

NASA Astrophysics Data System (ADS)

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 architectures is controlled by processing methods that rely on 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.

Kelley, Elizabeth G.; Murphy, Ryan P.; Seppala, Jonathan E.; Smart, Thomas P.; Hann, Sarah D.; Sullivan, Millicent O.; Epps, Thomas H.

2014-04-01

8

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

PubMed Central

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

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

2014-01-01

9

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

Microsoft Academic Search

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

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

1998-01-01

10

Fast native-SAD phasing for routine macromolecular structure determination.  

PubMed

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

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

11

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

PubMed

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 architectures is controlled by processing methods that rely on 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

Kelley, Elizabeth G; Murphy, Ryan P; Seppala, Jonathan E; Smart, Thomas P; Hann, Sarah D; Sullivan, Millicent O; Epps, Thomas H

2014-01-01

12

Maintaining network security: how macromolecular structures cross the peptidoglycan layer.  

PubMed

Peptidoglycan plays a vital role in bacterial physiology, maintaining cell shape and resisting cellular lysis from high internal turgor pressures. Its integrity is carefully maintained by controlled remodeling during growth and division by the coordinated activities of penicillin-binding proteins, lytic transglycosylases, and N-acetylmuramyl-l-alanine amidases. However, its small pore size (?2 nm) and covalently closed structure make it a formidable barrier to the assembly of large macromolecular cell-envelope-spanning complexes involved in motility and secretion. Here, we review the strategies used by Gram-negative bacteria to assemble such macromolecular complexes across the peptidoglycan layer, while preserving its essential structural role. In addition, we discuss evidence that suggests that peptidoglycan can be integrated into cell-envelope-spanning complexes as a structural and functional extension of their architecture. PMID:21276045

Scheurwater, Edie M; Burrows, Lori L

2011-05-01

13

Modeling Symmetric Macromolecular Structures in Rosetta3  

PubMed Central

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

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

2011-01-01

14

Macromolecular Structure Database. Final Progress Report  

SciTech Connect

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.

Gilliland, Gary L.

2003-09-23

15

REFMAC5 for the refinement of macromolecular crystal structures  

PubMed Central

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

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

16

Crosslinked macromolecular structures in bituminous coals: Theoretical and experimental considerations  

NASA Astrophysics Data System (ADS)

Ample evidence from physicochemical experiments suggests that bituminous coals can be described as highly crosslinked and entangled networks of macromolecular chains of irregular structure. Theoretically these structures can be analyzed by statistical mechanical models considering non-Gaussian distribution of the macro-molecular chains along with departure from the Flory theories of crosslinked macromolecules. The models of Kovac (1978) and Peppas and Lucht (1979) have been developed in order to describe non-extractable coal matrices and their behavior during swelling in appropriate swelling agents. The molecular weight between cross-links Mc and the crosslinking density ?x can be determined for various solvents and equilibrium swelling ratios. Few experimental data are available to which these models can be applied. Thus, in view of these new theoretical models, experimental research must be directed towards the reexamination of extraction and swelling behavior of bituminous coals. Some of the important parameters to be determined for characterization of the physical structure of coals include the thermodynamic interaction parameter ?, the crosslinking parameters Mc and ?x and the molecular weight distribution of the extractable coal portion.

Lucht, Lucy M.; Peppas, Nicolaos A.

1981-02-01

17

Macromolecular structure analysis and effective liquefaction pretreatment. Final report  

SciTech Connect

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.

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

1994-07-01

18

Analysis of stability of macromolecular clusters in dilute heteropolymer solutions  

E-print Network

We study the formation of clusters consisting of several chains in dilute solutions of amphiphilic heteropolymers. By means of the Gaussian variational theory we show that in a region of the phase diagram within the conventional two-phase coexistence region mesoglobules of equal size possess the lowest free energy. Monte Carlo simulation confirms that the mesoglobules are stabilised due to micro-phase separation, which introduces a preferred length scale. The very existence of such mesoscopic structures is related to a delicate balance of the energetic and entropic terms under the connectivity constraints. The issue of size monodispersity and fluctuations for mesoglobules is investigated.

E. G. Timoshenko; Yu. A. Kuznetsov

2000-02-18

19

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

SciTech Connect

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.

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

2010-04-23

20

Macromolecular ab initio phasing enforcing secondary and tertiary structure.  

PubMed

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

Millán, Claudia; Sammito, Massimo; Usón, Isabel

2015-01-01

21

Macromolecular ab initio phasing enforcing secondary and tertiary structure  

PubMed Central

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

Millán, Claudia; Sammito, Massimo; Usón, Isabel

2015-01-01

22

Microelectrophoretic study of calcium oxalate monohydrate in macromolecular solutions  

NASA Technical Reports Server (NTRS)

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.

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

1987-01-01

23

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

PubMed

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

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

2015-02-17

24

The electrokinetic behavior of calcium oxalate monohydrate in macromolecular solutions  

NASA Technical Reports Server (NTRS)

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.

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

1988-01-01

25

Facilitating structure determination: workshop on robotics andautomation in macromolecular crystallography  

SciTech Connect

As part of the annual Advanced Light Source (ALS) andStanford Synchrotron Radiation Laboratory (SSRL) Users' Meeting inOctober of this year, the macromolecular crystallography staff at bothsynchrotrons held a joint hands-on workshop to address automation issuesin crystal mounting and data collection at the beamline. This paperdescribes the ALS portion of the workshop, while the accompanying paperreviews the SSRL workshop.

Ralston, Corie; Cork, C.W.; McDermott, G.; Earnest, T.N.

2006-03-28

26

MOLMOL: A program for display and analysis of macromolecular structures  

Microsoft Academic Search

MOLMOL is a molecular graphics program for display, analysis, and manipulation of three-dimensional structures of biological macromolecules, with special emphasis on nuclear magnetic resonance (NMR) solution structures of proteins and nucleic acids. MOLMOL has a graphical user interface with menus, dialog boxes, and on-line help. The display possibilities include conventional presentation, as well as novel schematic drawings, with the option

Reto Koradi; Martin Billeter; Kurt Wüthrich

1996-01-01

27

AmbiPack: A Systematic Algorithm for Packing of Macromolecular Structures With Ambiguous  

E-print Network

method to solve the packing and the assignment problems simultaneously given rigid monomer structuresAmbiPack: A Systematic Algorithm for Packing of Macromolecular Structures With Ambiguous Distance of multimers presents interesting new challenges. The structure(s) of the individual monomers must be found

Lozano-Perez, Tomas

28

Macromolecular properties and polymeric structure of canine tracheal mucins.  

PubMed Central

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

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

1991-01-01

29

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

PubMed Central

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

Minor, Daniel L.

2010-01-01

30

Structure, function, and folding of phosphoglycerate kinase are strongly perturbed by macromolecular crowding  

PubMed Central

We combine experiment and computer simulation to show how macromolecular crowding dramatically affects the structure, function, and folding landscape of phosphoglycerate kinase (PGK). Fluorescence labeling shows that compact states of yeast PGK are populated as the amount of crowding agents (Ficoll 70) increases. Coarse-grained molecular simulations reveal three compact ensembles: C (crystal structure), CC (collapsed crystal), and Sph (spherical compact). With an adjustment for viscosity, crowded wild-type PGK and fluorescent PGK are about 15 times or more active in 200 mg/ml Ficoll than in aqueous solution. Our results suggest a previously undescribed solution to the classic problem of how the ADP and diphosphoglycerate binding sites of PGK come together to make ATP: Rather than undergoing a hinge motion, the ADP and substrate sites are already located in proximity under crowded conditions that mimic the in vivo conditions under which the enzyme actually operates. We also examine T-jump unfolding of PGK as a function of crowding experimentally. We uncover a nonmonotonic folding relaxation time vs. Ficoll concentration. Theory and modeling explain why an optimum concentration exists for fastest folding. Below the optimum, folding slows down because the unfolded state is stabilized relative to the transition state. Above the optimum, folding slows down because of increased viscosity. PMID:20921368

Dhar, Apratim; Samiotakis, Antonios; Ebbinghaus, Simon; Nienhaus, Lea; Homouz, Dirar; Gruebele, Martin; Cheung, Margaret S.

2010-01-01

31

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

NASA Astrophysics Data System (ADS)

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.

Ando, Tadashi; Chow, Edmond; Skolnick, Jeffrey

2013-09-01

32

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

ERIC Educational Resources Information Center

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…

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

2010-01-01

33

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

PubMed Central

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

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

2014-01-01

34

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

PubMed

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

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

2013-07-01

35

A new dimension in structural biology: fully fledged high-pressure macromolecular crystallography  

Microsoft Academic Search

The amount of accurate crystallographic data currently available on macromolecular structures at high pressure is extremely limited, mainly due to the lack of appropriate instrumentation and X-ray sources. A technical breakthrough has been achieved with a set-up at the ESRF ID30 beamline equipped with a diamond anvil cell and a large imaging plate, and taking advantage from undulators providing a

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

2004-01-01

36

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

PubMed

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

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

2014-05-01

37

PSICO: Combining Constraint Programming and Optimisation to Solve Macromolecular Structures  

Microsoft Academic Search

Here we present PSICO (Processing Structural Information with Constraint propagation and Optimisation), a mixed approach to determine protein structures from experimental and theoretical data. We briefly focus the factors motivating this work, the results obtained so far and our perspectives for future developments and applications. An application of PSICO to solve structures compatible with distance constraints obtained from Nuclear Magnetic

Ludwig Krippahl; Pedro Barahona

38

The chemical structure of macromolecular fractions of a sulfur-rich oil  

NASA Astrophysics Data System (ADS)

A selective stepwise chemical degradation has been developed for structural studies of highmolecularweight (HMW) fractions of sulfur-rich oils. The degradation steps are: (i) desulfurization (ii) cleavage of oxygen-carbon bonds (iii) oxidation of aromatic structural units. After each step, the remaining macromolecular matter was subjected to the subsequent reaction. This degradation scheme was applied to the asphaltene, the resin and a macromolecular fraction of low polarity (LPMF) of the Rozel Point oil. Total amounts of degraded low-molecular-weight compounds increased progressively in the order asphaltene < resin < LPMF. Desulfurization yielded mainly phytane, steranes and triterpanes. Oxygen-carbon bond cleavage resulted in hydrocarbon fractions predominated by n-alkanes and acyclic isoprenoids. The oxidation step afforded high amounts of linear carboxylic acids in the range of C 11 to C 33. The released compounds provide a more complete picture of the molecular structure of the oil fractions than previously available. Labelling experiments with deuterium atoms allowed to characterize the site of bonding and the type of linkage for the released compounds. Evidence is presented that subunits of the macromolecular network are attached simultaneously by oxygen and sulfur (n-alkanes, hopanes) or by sulfur and aromatic units ( n-alkanes, steranes).

Richnow, Hans H.; Jenisch, Angela; Michaelis, Walter

1993-06-01

39

The chemical structure of macromolecular fractions of a sulfur-rich oil  

SciTech Connect

A selective stepwise chemical degradation has been developed for structural studies of high-molecular-weight (HMW) fractions of sulfur-rich oils. The degradation steps are: (i) desulfurization; (ii) cleavage of oxygen-carbon bonds; and (iii) oxidation of aromatic structural units. After each step, the remaining macromolecular matter was subjected to the subsequent reaction. This degradation scheme was applied to the asphaltene, the resin, and a macromolecular fraction of low polarity (LPMF) of Rozel Point oil. Total amounts of degraded low-molecular-weight compounds increased progressively in the order asphaltene < resin < LPMF. Desulfurization yielded mainly phytane, steranes, and triterpanes. Oxygen-carbon bond cleavage resulted in hydrocarbon fractions predominated by n-alkanes and acyclic isoprenoids. The oxidation step afforded high amounts of linear carboxylic acids in the range of C[sub 11] to C[sub 33]. The released compounds provide a more complete picture of the molecular structure of the oil fractions than previously available. Labelling experiments with deuterium atoms allowed characterization of the site of bonding and the type of linkage for compounds. Evidence is presented that subunits of the macromolecular network are attached simultaneously by oxygen and sulfur (n-alkanes, hopanes) or by sulfur and aromatic units (n-alkanes, steranes).

Richnow, H.H.; Jenisch, A.; Michaelis, W. (Universitaet Hamburg (Germany))

1993-06-01

40

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

PubMed Central

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

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

2014-01-01

41

MMDB: An ASN.1 specification for macromolecular structure  

SciTech Connect

We present an exchange specification for data describing the three-dimensional structure of biological macromolecules. The specification was designed for MMDB, a Molecular Modeling Database supported by the National Center for Biotechnology Information (NCBI), based on information from the Protein Data Bank (PDB). In the MMDB; specification, the chemical structures of molecules are described hierarchically as connectivity graphs, to directly support comparison by subgraph isomorphism or assignment algorithms. Three-dimensional coordinates are linked unambiguously to nodes in the chemical graph, so that homology-derived structures may be generated directly from alignment of chemically similar groups. In conversion to this form, data from PDB are extensively validated, so as to provide a description of chemical and spatial structure that is as accurate as possible. These changes in format and content of the known structure data are intended to support development of intelligent molecular modeling applications that make use of this invaluable information resource.

Ohkawa, Hitomi; Ostell, J.; Bryant, S. [National Inst. of Health, Bethesda, MD (United States)

1995-12-31

42

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

PubMed Central

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 ?-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

Mittal, Shruti; Singh, Laishram Rajendrakumar

2013-01-01

43

Multi-resolution Contour-based Fitting of Macromolecular Structures  

E-print Network

Wriggers Department of Molecular Biology, The Scripps Research Institute, 10550 N. Torrey Pines Road, La, a new pseudo-atomic model of a microtubule was constructed from a 20 AÃ? resolution EM map and from atomic structures of a and b tubulin subunits. # 2002 Elsevier Science Ltd. Keywords: low resolution

Wriggers, Willy

44

Recovering a representative conformational ensemble from underdetermined macromolecular structural data.  

PubMed

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

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

2013-11-01

45

Recovering a Representative Conformational Ensemble from Underdetermined Macromolecular Structural Data  

PubMed Central

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

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

2013-01-01

46

[18] improving structures using all-atom contacts 385 The methodology of macromolecular crystallography is mature, powerful,  

E-print Network

[18] improving structures using all-atom contacts 385 The methodology of macromolecular of protein and nucleic acid crystal structures. [18] New Tools and Data for Improving Structures, Using All-atom criteria for protein structure validation: (1) development of the all-atom contact method, which can

Richardson, David

47

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

PubMed Central

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

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

2014-01-01

48

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

PubMed

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

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

2015-02-01

49

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

PubMed Central

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

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

2010-01-01

50

Capillary Viscometer for Fully Automated Measurement of the Concentration and Shear Dependence of the Viscosity of Macromolecular Solutions  

PubMed Central

The construction and operation of a novel viscometer/rheometer are described. The instrument is designed to measure the viscosity of a macromolecular solution while automatically varying both solute concentration and shear rate. Viscosity is calculated directly from Poiseuille's Law, given the measured difference in pressure between two ends of a capillary tube through which the solution is flowing at a known rate. The instrument requires as little as 0.75 ml of a solution to provide a full profile of viscosity as a function of concentration and shear rate, and can measure viscosities as high as 500 cP and as low as 1 cP, at shear rates between 10 and 2 × 103 s-1. The results of control experiments are presented to document the accuracy and precision of measurement at both low and high concentration of synthetic polymers and proteins. PMID:23130673

Grupi, Asaf; Minton, Allen P.

2014-01-01

51

Automated structure solution with the PHENIX suite  

SciTech Connect

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.

Terwilliger, Thomas C [Los Alamos National Laboratory; Zwart, Peter H [LBNL; Afonine, Pavel V [LBNL; Grosse - Kunstleve, Ralf W [LBNL

2008-01-01

52

Automated Structure Solution with the PHENIX Suite  

SciTech Connect

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.

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

53

Function and dynamics of macromolecular complexes explored by integrative structural and computational biology.  

PubMed

Three vignettes exemplify the potential of combining EM and X-ray crystallographic data with molecular dynamics (MD) simulation to explore the architecture, dynamics and functional properties of multicomponent, macromolecular complexes. The first two describe how EM and X-ray crystallography were used to solve structures of the ribosome and the Arp2/3-actin complex, which enabled MD simulations that elucidated functional dynamics. The third describes how EM, X-ray crystallography, and microsecond MD simulations of a GPCR:G protein complex were used to explore transmembrane signaling by the ?-adrenergic receptor. Recent technical advancements in EM, X-ray crystallography and computational simulation create unprecedented synergies for integrative structural biology to reveal new insights into heretofore intractable biological systems. PMID:25238653

Purdy, Michael D; Bennett, Brad C; McIntire, William E; Khan, Ali K; Kasson, Peter M; Yeager, Mark

2014-08-01

54

A 3D image filter for parameter-free segmentation of macromolecular structures from electron tomograms.  

PubMed

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

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

2012-01-01

55

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

PubMed Central

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

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

2012-01-01

56

New computational tools for H/D determination in macromolecular structures from neutron data.  

PubMed

Two new computational methods dedicated to neutron crystallography, called n-FreeLunch and DNDM-NDM, have been developed and successfully tested. The aim in developing these methods is to determine hydrogen and deuterium positions in macromolecular structures by using information from neutron density maps. Of particular interest is resolving cases in which the geometrically predicted hydrogen or deuterium positions are ambiguous. The methods are an evolution of approaches that are already applied in X-ray crystallography: extrapolation beyond the observed resolution (known as the FreeLunch procedure) and a difference electron-density modification (DEDM) technique combined with the electron-density modification (EDM) tool (known as DEDM-EDM). It is shown that the two methods are complementary to each other and are effective in finding the positions of H and D atoms in neutron density maps. PMID:21041931

Siliqi, Dritan; Caliandro, Rocco; Carrozzini, Benedetta; Cascarano, Giovanni Luca; Mazzone, Annamaria

2010-11-01

57

Macromolecular structure of cellulose studied by second-harmonic generation imaging microscopy  

NASA Astrophysics Data System (ADS)

The macromolecular structure of purified cellulose samples is studied by second-harmonic generation (SHG) imaging microscopy. We show that the SHG contrast in both Valonia and Acetobacter cellulose strongly resembles that of collagen from animal tissues, both in terms of morphology and polarization anisotropy. Polarization analysis shows that microfibrils in each lamella are highly aligned and ordered and change directions by 90° in adjacent lamellae. The angular dependence of the SHG intensity fits well to a cos2 ? distribution, which is characteristic of the electric dipole interaction. Enzymatic degradation of Valonia fibers by cellulase is followed in real time by SHG imaging and results in exponential decay kinetics, showing that SHG imaging microscopy is ideal for monitoring dynamics in biological systems.

Brown, R. Malcom; Millard, Andrew C.; Campagnola, Paul J.

2003-11-01

58

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

PubMed Central

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

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

2014-01-01

59

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.

60

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

SciTech Connect

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.

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

2009-01-01

61

Effect of Macromolecular Crowding on Protein Folding Dynamics at the Secondary Structure Level  

PubMed Central

Macromolecular crowding is one of the key characteristics of the cellular environment and therefore, is intimately coupled to the process of protein folding in vivo. While previous studies have provided invaluable insight into the effect of crowding on the stability and folding rate of protein tertiary structures, very little is known about how crowding affects protein folding dynamics at the secondary structure level. Herein, we examine the thermal stability and folding-unfolding kinetics of three small folding motifs, i.e., a 34-residue ?-helix, a 34-residue cross-linked helix-turn-helix, and a 16-residue ? hairpin, in the presence of two commonly used crowding agents, Dextran 70 (200 g/L) and Ficoll 70 (200 g/L). We find that these polymers do not induce any appreciable changes in the folding kinetics of the two helical peptides, which is somewhat surprising as the helix-coil transition kinetics have been shown to depend on viscosity. Also to our surprise and in contrast to what has been observed for larger proteins, we find that crowding leads to an appreciable decrease in the folding rate of the shortest ?-hairpin peptide, indicating that besides the excluded volume effect, other factors also need to be considered when evaluating the net effect of crowding on protein folding kinetics. A model considering both the static and dynamic effects arising from the presence of the crowding agent is proposed to rationalize these results. PMID:19682997

Mukherjee, Smita; Waegele, Matthias M.; Chowdhury, Pramit; Guo, Lin; Gai, Feng

2009-01-01

62

Online Macromolecular Museum  

NSDL National Science Digital Library

The Online Macromolecular Museum (OMM) is a site for the display and study of macromolecules. Macromolecular structures, as discovered by crystallographic or NMR methods, are scientific objects in much the same sense as fossil bones or dried specimens: they can be archived, studied, and displayed in aesthetically pleasing, educational exhibits. Hence, a museum seems an appropriate designation for the collection of displays that we are assembling. The OMM's exhibits are interactive tutorials on individual molecules in which hypertextual explanations of important biochemical features are linked to illustrative renderings of the molecule at hand.

David Marcey (CLU; Biology)

2012-06-01

63

The Online Macromolecular Museum  

NSDL National Science Digital Library

The Online Macromolecular Museum (OMM) is a site for the display and study of macromolecules. Macromolecular structures, as discovered by crystallographic or NMR methods, are scientific objects in much the same sense as fossil bones or dried specimens: they can be archived, studied, and displayed in aesthetically pleasing, educational exhibits. Hence, a museum seems an appropriate designation for the collection of displays that we are assembling. The OMM's exhibits are interactive Jmol tutorials on individual molecules in which hypertextual explanations of important biochemical features are linked to illustrative renderings of the molecule at hand.

David Marcey (CLU; Biology)

2011-08-01

64

Extra-column dispersion of macromolecular solutes in aqueous-phase size-exclusion chromatography.  

PubMed

A set of dextran standards was used to study the extra-column dispersion in conventional chromatographic equipment at a broad range of molecular weights, different mobile phase flow rates and connecting tube lengths and diameters. All known correlations for the tube dispersion at laminar flow, including those for short tubes, overestimated the values of the variance of the outlet concentration signal. The difference increased with the solute molecular weight and the flow rate. It was assumed that the discrepancy was due to the effect of natural convection invoked by the density differences of the injected dextran solutions and water. A suitable approximation of the relative band spreading was suggested in a form of a power function of the Reynolds and Schmidt numbers. A significant decrease of the dispersion was observed when the chromatography tubing was coiled into a circle. This decrease was successfully predicted combining the existing correlations for long coiled tubes and short straight tubes. PMID:15248423

Grznárová, G; Polakovic, M; Acai, P; Görner, T

2004-06-18

65

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

NASA Technical Reports Server (NTRS)

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.

Addad, J. P. C.

1983-01-01

66

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

PubMed

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

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

2014-01-01

67

Solution structure and p43 binding of the p38 leucine zipper motif: coiled-coil interactions mediate the association between p38 and p43  

Microsoft Academic Search

p38, which has been suggested to be a scaffold protein for the assembly of a macromolecular tRNA synthetase complex, contains a leucine zipper-like motif. To understand the importance of the leucine zipper-like motif of p38 (p38LZ) in macromolecular assembly, the p38LZ solution structure was investigated by circular dichroism and nuclear magnetic resonance spectroscopy. The solution structure of p38LZ showed an

Hee-Chul Ahn; Sunghoon Kim; Bong-Jin Lee

2003-01-01

68

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

ERIC Educational Resources Information Center

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…

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

2013-01-01

69

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

NASA Astrophysics Data System (ADS)

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

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

1993-01-01

70

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

E-print Network

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

Sherrill, David

71

On the use of low-frequency normal modes to enforce collective movements in refining macromolecular structural models.  

PubMed

As more and more structures of macromolecular complexes get solved in different conditions, it has become apparent that flexibility is an inherent part of their biological function. Normal mode analysis using simplified models of proteins such as the elastic network model has proved very effective in showing that many of the structural transitions derived from a survey of the Protein Data Bank can be explained by just a few of the lowest-frequency normal modes. In this work, normal modes are used to carry out medium- or low-resolution structural refinement, enforcing collective and large-amplitude movements that are beyond the reach of existing methods. Refinement is carried out in reciprocal space with respect to the normal mode amplitudes, by using standard conjugate-gradient minimization. Several tests on synthetic diffraction data whose mode concentration follows the one of real movements observed in the Protein Data Bank have shown that the radius of convergence is larger than the one of rigid-body refinement. Tests with experimental diffraction data for the same protein in different environments also led to refined structural models showing drastic reduction of the rms deviation with the target model. Because the structural transition is described by very few parameters, over-fitting of real experimental data is easily detected by using a cross-validation test. The method has also been applied to the refinement of atomic models into molecular envelopes and could readily be used to fit large macromolecular complex rearrangements into cryo-electron microscopy-reconstructed images as well as small-angle x-ray scattering-derived envelopes. PMID:15096585

Delarue, Marc; Dumas, Philippe

2004-05-01

72

Neutron Spectroscopy as a Probe of Macromolecular Structure and Dynamics under Extreme Spatial Confinement  

NASA Astrophysics Data System (ADS)

We illustrate the use of high-resolution neutron spectroscopy to explore the extreme spatial confinement of soft matter in nanostructured materials. Two well-defined limits are considered, involving either intercalation or interfacial adsorption of the ubiquitous polymer poly(ethylene oxide) in graphite-oxide-based hosts. Vibrational modes associated with the confined macromolecular phase undergo dramatic changes over a broad range of energy transfers, from those associated with intermolecular modes in the Terahertz frequency range (1 THz = 33 cm?1), to those characteristic of strong chemical bonds above 2000 cm?1. We also consider the effects of polymer chain size and chemical composition of the host material. Variation of the degree of oxidation and exfoliation of graphite oxide leads to two distinct cases, namely: (i) subnanometer two-dimensional confinement; and (ii) surface immobilization. Case (i) is characterised by significant changes to conformational and collective vibrational modes of the polymer as a consequence of a preferentially planar trans-trans-trans chain conformation, whereas case (ii) leads to a substantial increase in the population of gauche conformers. Macroscopically, case (i) translates into the complete suppression of crystallization and glassy behaviour. In contrast, case (ii) exhibits well-defined glass and melting transitions associated with the confined phase, yet at significantly lower temperatures than those of the bulk.

Barroso-Bujans, F.; Fernandez-Alonso, F.; Colmenero, J.

2014-11-01

73

O the Phase Refinement and Extension of Macromolecular Structures Using both Real and Reciprocal Space Approaches  

NASA Astrophysics Data System (ADS)

Available from UMI in association with The British Library. By examining the solution to the phase problem of X-ray crystallography, it is established that the structure factor magnitudes and phases are linked through constraints on the electron density. There are real and reciprocal space approaches to the phase problem depending on the way the constraints on electron density are exploited. A constraint on the electron density--the correct density histogram--is added to the list of other constraints. A new density modification technique--histogram matching --was developed based on the matching of the density histogram to that of the correct one. Its application to 2Zn pig insulin successfully refined and extended the 1.9A MIR phases to 1.5A resolution. In order to obtain a molecular envelope with a detailed boundary, a molecular envelope refinement technique was designed which proved to be quite effective. A gradient technique of defining molecular boundary was also explored and was found to be better than the conventional convolution technique. The two dimensional histogram of density and gradient was examined. It was found that the matching of density histograms also matches that of the gradient histograms. The combination of Sayre's equation with solvent flattening and histogram matching led to a new phase refinement and extension technique--SQUASH. It proved to be a powerful technique by its successful refinement of 3.0A MIR phases of 2Zn pig insulin and subsequent extension to 2.0A resolution.

Zhang, Kam Yong Jian

74

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

Microsoft Academic Search

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

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

1996-01-01

75

A Specification for Defining andAnnotating-Regions of Macromolecular Structures  

E-print Network

without specializ&i equipment or software. The Protein Data Bank (PDB) (Abola aal. 1987),the current-especially in the PDB format-take an enormous number of bytes. In the case of structures deposited in the PDB

76

Macromolecular Structure Modeling from 3DEM Using VolRover 2.01  

PubMed Central

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

Zhang, Qin; Bettadapura, Radhakrishna

2012-01-01

77

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

PubMed Central

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

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

2014-01-01

78

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

PubMed

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

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

2014-05-01

79

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

SciTech Connect

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.

Ren, Zhong; Š rajer, Vukica; Knapp, James E.; Royer, Jr., William E. (Mercer); (UMASS, MED); (UC)

2013-04-08

80

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

PubMed Central

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. PMID:22171006

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

2012-01-01

81

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

PubMed

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. PMID:22171006

Ren, Zhong; Srajer, Vukica; Knapp, James E; Royer, William E

2012-01-01

82

MolProbity : all-atom structure validation for macromolecular crystallography  

Microsoft Academic Search

MolProbity is a structure-validation web service that provides broad-spectrum solidly based evaluation of model quality at both the global and local levels for both proteins and nucleic acids. It relies heavily on the power and sensitivity provided by optimized hydrogen placement and all-atom contact analysis, complemented by updated versions of covalent-geometry and torsion-angle criteria. Some of the local corrections can

Vincent B. Chen; W. Bryan Arendall; Jeffrey J. Headd; Daniel A. Keedy; Robert M. Immormino; Gary J. Kapral; Laura W. Murray; David C. Richardson

2010-01-01

83

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

Microsoft Academic Search

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

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

1998-01-01

84

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

NASA Technical Reports Server (NTRS)

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.

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

1991-01-01

85

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

NASA Astrophysics Data System (ADS)

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

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

2011-07-01

86

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

PubMed

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

Egelman, Edward H

2010-02-01

87

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

NASA Technical Reports Server (NTRS)

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.

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

1991-01-01

88

Structure and property relations of macromolecular self-assemblies at interfaces  

NASA Astrophysics Data System (ADS)

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.

Yang, Zhihao

89

Visualizing Macromolecular Complexes with In Situ Liquid Scanning Transmission Electron Microscopy  

SciTech Connect

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.

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

2012-11-01

90

What Macromolecular Crowding Can Do to a Protein  

PubMed Central

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

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

2014-01-01

91

The role of macromolecular stability in desiccation tolerance  

Microsoft Academic Search

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

W. Wolkers

1998-01-01

92

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

E-print Network

interactions of HSs can be explored directly with the high-resolution in situ x-ray spectromicroscopy methods Substances of Soils and General Theory of Humification (Balkema, Brookfield, VT, 1995). 3. R. Schwarzenbach., Methods of Soil Analysis: Part 3, Chemical Methods (Soil Science Society of America, Madison, WI, 1996). 9

Dunin-Borkowski, Rafal E.

93

Automated macromolecular crystallization screening  

DOEpatents

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.

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

2005-03-01

94

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

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

Terwilliger, Thomas C.; Bricogne, Gerard

2014-01-01

95

Macromolecular Crystallization in Microfluidics for the International Space Station  

NASA Technical Reports Server (NTRS)

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.

Monaco, Lisa A.; Spearing, Scott

2003-01-01

96

RECENT ADVANCES IN MACROMOLECULAR HYDRODYNAMIC MODELING  

PubMed Central

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

Aragon, Sergio R.

2010-01-01

97

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

SciTech Connect

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.

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

1995-07-01

98

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

Microsoft Academic Search

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

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

1994-01-01

99

?-Orthogonal Pericyclic Macromolecular Photoligation.  

PubMed

A photochemical strategy enabling ?-orthogonal reactions is introduced to construct macromolecular architectures and to encode variable functional groups with site-selective precision into a single molecule by the choice of wavelength. ?-Orthogonal pericyclic reactions proceed independently of one another by the selection of functional groups that absorb light of specific wavelengths. The power of the new concept is shown by a one-pot reaction of equimolar quantities of maleimide with two polymers carrying different maleimide-reactive endgroups, that is, a photoactive diene (photoenol) and a nitrile imine (tetrazole). Under selective irradiation at ?=310-350?nm, any maleimide (or activated ene) end-capped compound reacts exclusively with the photoenol functional polymer. After complete conversion of the photoenol, subsequent irradiation at ?=270-310?nm activates the reaction of the tetrazole group with functional enes. The versatility of the approach is shown by ?-orthogonal click reactions of complex maleimides, functional enes, and polymers to the central polymer scaffold. PMID:25620295

Hiltebrandt, Kai; Pauloehrl, Thomas; Blinco, James P; Linkert, Katharina; Börner, Hans G; Barner-Kowollik, Christopher

2015-02-23

100

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...

101

Structure, Vol. 13, 339341, March, 2005, 2005 Elsevier Ltd All rights reserved. DOI 10.1016/j.str.2005.02.010 EditorialMacromolecular Assemblies Highlighted  

E-print Network

," presents Joachim Frank (Wadsworth Center) also describesten research articles and five reviews on the deter in space and illustrated by its application to a number of viruses. time. Macromolecular complexes vary consumption. such as the rice dwarf virus and the acrosomal bundle, Technical advances on several frontiers

Sali, Andrej

102

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

Microsoft Academic Search

The distributions of sulphur-containing compounds generated by flash pyrolysis of macromolecular sedimentary organic matter (kerogen, coal, asphaltenes) were studied by gas chromatography in combination with Sselective flame photometric detection or mass spectrometry. The abundance of S-containing pyrolysis products in the pyrolysates relative to other products was highly variable depending on the sample but the types of products were generally similar,

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

1989-01-01

103

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

PubMed Central

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

Sweet, R. M.; Soares, A.

2010-01-01

104

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

Microsoft Academic Search

The distributions of sulphur-containing compounds generated by flash pyrolysis of macromolecular sedimentary\\u000aorganic matter (kerogen, coal, asphaltenes) were studied by gas chromatography in combination with S-selective\\u000aflame photometric detection or mass spectrometry. The abundance of S-containing pyrolysis products in the\\u000apyrolysates relative to other products was highly variable depending on the sample but the types of products were\\u000agenerally similar,

J. S. Sinninghe Damsté; T. I. Eglinton; J. W. de Leeuw; P. A. Schenk

1989-01-01

105

A database of macromolecular motions.  

PubMed

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

Gerstein, M; Krebs, W

1998-09-15

106

A database of macromolecular motions.  

PubMed Central

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

Gerstein, M; Krebs, W

1998-01-01

107

Vacuum structure around identity based solutions  

E-print Network

We explore vacuum structure in bosonic open string field theory expanded around an identity based solution parameterized by $a$ (>= -1/2). Analyzing the expanded theory by using level truncation approximation up to level 14, we find that the theory has a stable vacuum solution for $a$>-1/2. The vacuum energy and the gauge invariant overlap numerically approach those of the tachyon vacuum solution with increasing truncation level. Also we find that, at $a$=-1/2, there exists an unstable vacuum solution in the expanded theory and it rapidly becomes the trivial zero configuration just above $a$=-1/2. The numerical behavior of the two gauge invariants suggests that the unstable solution corresponds to the perturbative open string vacuum. These results reasonably support the expectation that the identity based solution is a trivial pure gauge configuration for $a$>-1/2, but it can be regarded as the tachyon vacuum solution at $a$=-1/2.

Isao Kishimoto; Tomohiko Takahashi

2009-10-16

108

Enhancement and simplification of macromolecular images.  

PubMed Central

Computer graphics programs have been devised to display selected atomic features and to simplify images of complex macromolecular structures. By using boundary outlines, adjustment of size and shape of the molecular components, color coding, shading, and selective omission of obscuring detail, attention can be focused on specific interactions which determine higher levels of organization. A balanced color table has been constructed in which different hues have equal steps in brightness; this table has facilitated distinction of atom types and sequence coding together with representation of an optimum range of depth cueing and surface shading. The graphics system has been used with the atomic coordinates of the tobacco mosaic virus structure to simplify images of the protein subunit, to illustrate intermolecular interactions, and to relate subunit packing arrangements in different assemblies to the underlying atomic structure. The system has also been used to construct a schematic representation of the polyomavirus capsid, based on low resolution data. Application of artistic methods contributes to the effective presentation and interpretation of detailed scientific information about complex macromolecular structures. Images FIGURE 1 FIGURE 2 FIGURE 3 FIGURE 4 FIGURE 5 FIGURE 6 FIGURE 7 FIGURE 8 FIGURE 9 FIGURE 10 FIGURE 11 FIGURE 12 FIGURE 13 FIGURE 14 FIGURE 15 FIGURE 16 FIGURE 17 FIGURE 18 PMID:3382707

Namba, K; Caspar, D L; Stubbs, G

1988-01-01

109

Atomic-resolution structural information from scattering experiments on macromolecules in solution  

NASA Astrophysics Data System (ADS)

The pair-distance distribution function (PDDF) contains all structural information probed in an elastic scattering experiment of macromolecular solutions. However, in small-angle x-ray scattering (SAXS) or small-angle neutron scattering (SANS) experiments only their Fourier transform is measured over a restricted range of scattering angles. We therefore developed a mathematically simple and computationally efficient method to calculate the PDDFs as well as accurate scattering intensities from molecular dynamics simulations. The calculated solution scattering intensities are in excellent agreement with SAXS and wide-angle x-ray scattering (WAXS) experiments for a series of proteins. The corresponding PDDFs are remarkably rich in features reporting on the detailed protein structure. Using an inverse Fourier transform method, most of these features can be recovered if scattering intensities are measured up to a momentum transfer of q?2-3Å-1. Our results establish that high-precision solution scattering experiments utilizing x-ray free-electron lasers and third generation synchrotron sources can resolve subnanometer structural detail, well beyond size, shape, and fold.

Köfinger, Jürgen; Hummer, Gerhard

2013-05-01

110

Fluid Physics and Macromolecular Crystal Growth in Microgravity  

NASA Technical Reports Server (NTRS)

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.

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

111

Sequence-Dependent Solution Structure and  

E-print Network

Sequence-Dependent Solution Structure and Motions of 13 TATA/TBP (TATA-Box Binding Protein is a well-known example of a DNA promoter sequence recognized by the TATA box binding protein (TBP) through differences in activating transcription. To investigate the subtle role of sequence-dependent motion within

Schlick, Tamar

112

Interfacial inhibitors: targeting macromolecular complexes.  

PubMed

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

Pommier, Yves; Marchand, Christophe

2012-01-01

113

Multiscale Macromolecular Simulation: Role of Evolving Ensembles  

PubMed Central

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 timestep 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

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

2013-01-01

114

Quaternary structure of hemoglobin in solution  

NASA Astrophysics Data System (ADS)

Many important proteins perform their physiological functions under allosteric control, whereby the binding of a ligand at a specific site influences the binding affinity at a different site. Allosteric regulation usually involves a switch in protein conformation upon ligand binding. The energies of the corresponding structures are comparable, and, therefore, the possibility that a structure determined by x-ray diffraction in the crystalline state is influenced by its intermolecular contacts, and thus differs from the solution structure, cannot be excluded. Here, we demonstrate that the quaternary structure of tetrameric human normal adult carbonmonoxy-hemoglobin can readily be determined in solution at near-physiological conditions of pH, ionic strength, and temperature by NMR measurement of 15N-1H residual dipolar couplings in weakly oriented samples. The structure is found to be a dynamic intermediate between two previously solved crystal structures, known as the R and R2 states. Exchange broadening at the subunit interface points to a rapid equilibrium between different structures that presumably include the crystallographically observed states.

Lukin, Jonathan A.; Kontaxis, Georg; Simplaceanu, Virgil; Yuan, Yue; Bax, Ad; Ho, Chien

2003-01-01

115

Viscoelastic surfactant solutions: model systems for rheological research  

Microsoft Academic Search

The molecular constitution of viscoelastic gels is customarily described in terms of networks, which may have a transient or permanent character. Such supermolecular structures are often observed in biological or macromolecular systems, but can even occur in dilute solutions of some detergents. Surfactant molecules in solution, under suitable conditions, assemble reversibly into large aggregates of rod-like geometry. Depending on the

H. Rehage; H. Hoffmann

1991-01-01

116

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...

117

Macromolecular Crowding Modulates Folding Mechanism of ?/? Protein Apoflavodoxin  

PubMed Central

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 ?/? 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 (?c) as well as of crowding agent geometry (sphere or spherocylinder) at high ?c. 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

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

2009-01-01

118

Generating Triangulated Macromolecular Surfaces by Euclidean Distance Transform  

PubMed Central

Macromolecular surfaces are fundamental representations of their three-dimensional geometric shape. Accurate calculation of protein surfaces is of critical importance in the protein structural and functional studies including ligand-protein docking and virtual screening. In contrast to analytical or parametric representation of macromolecular surfaces, triangulated mesh surfaces have been proved to be easy to describe, visualize and manipulate by computer programs. Here, we develop a new algorithm of EDTSurf for generating three major macromolecular surfaces of van der Waals surface, solvent-accessible surface and molecular surface, using the technique of fast Euclidean Distance Transform (EDT). The triangulated surfaces are constructed directly from volumetric solids by a Vertex-Connected Marching Cube algorithm that forms triangles from grid points. Compared to the analytical result, the relative error of the surface calculations by EDTSurf is <2–4% depending on the grid resolution, which is 1.5–4 times lower than the methods in the literature; and yet, the algorithm is faster and costs less computer memory than the comparative methods. The improvements in both accuracy and speed of the macromolecular surface determination should make EDTSurf a useful tool for the detailed study of protein docking and structure predictions. Both source code and the executable program of EDTSurf are freely available at http://zhang.bioinformatics.ku.edu/EDTSurf. PMID:19956577

Xu, Dong; Zhang, Yang

2009-01-01

119

'Hot' Macromolecular Crystals  

SciTech Connect

Transcriptional regulator protein TM1030 from the hyperthermophile Thermotoga maritima, as well as its complex with DNA, was crystallized at a wide range of temperatures. Crystallization plates were incubated at 4, 20, 37, and 50 C over 3 weeks. The best crystals of TM1030 in complex with DNA were obtained at 4, 20, and 37 C, while TM1030 alone crystallized almost equally well in all temperatures. The crystals grown at different temperatures were used for X-ray diffraction experiments and their structures were compared. Surprisingly, the models of TM1030 obtained from crystals grown at different temperatures are similar in quality. While there are some examples of structures of proteins grown at elevated temperatures in the PDB, these temperatures appear to be underrepresented. Our studies show that crystals of some proteins may be grown and are stable at broad range of temperatures. We suggest that crystallization experiments at elevated temperatures could be used as a standard part of the crystallization protocol.

Koclega, Katarzyna D.; Chruszcz, Maksymilian; Zimmerman, Matthew D.; Bujacz, Grzegorz; Minor, Wladek (UV); (ITB-Poland)

2010-09-07

120

Facile Preparation of a Macromolecular Benzophenone Photoinitiator  

NASA Astrophysics Data System (ADS)

Photoinitiators play important roles in the preparation of photo-cured resins. Macromolecular as well as reactive photoinitiators have attracted much attention both in industry and in academia due to the disadvantages of conventional small molecular photoinitiators such as volatility and mobility. A macromolecular benzophenone photoinitiator was designed and efficiently synthesized in this study. Hydroxyl-containing Michler's ketone was firstly synthesized in 82% yield, followed by reacting with toluene di-isocyanate (TDI) to prepare polyurethanetype macromolecular benzophenone photoinitiator.

Huang, Qinghua; Gu, Lingling; Bai, Xiongxiong; Cheng, Chuanjie

2014-08-01

121

Analytical model for macromolecular partitioning during yeast cell division  

PubMed Central

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

2014-01-01

122

Structures of TraI in Solution  

PubMed Central

Bacterial conjugation, a DNA transfer mechanism involving transport of one plasmid strand from donor to recipient, is driven by plasmid-encoded proteins. The F TraI protein nicks one F plasmid strand, separates cut and uncut strands, and pilots the cut strand through a secretion pore into the recipient. TraI is a modular protein with identifiable nickase, ssDNA-binding, helicase and protein-protein interaction domains. While domain structures corresponding to roughly 1/3 of TraI have been determined, there has been no comprehensive structural study of the entire TraI molecule, nor an examination of structural changes to TraI upon binding DNA. Here, we combine solution studies using small-angle scattering and circular dichroism spectroscopy with molecular Monte Carlo and molecular dynamics simulations to assess solution behavior of individual and groups of domains. Despite having several long (>100 residues) apparently disordered or highly dynamic regions, TraI folds into a compact molecule. Based on the biophysical characterization, we have generated models of intact TraI. These data and the resulting models have provided clues to the regulation of TraI function. PMID:24898939

Clark, Nicholas J.; Raththagala, Madushi; Wright, Nathan T.; Buenger, Elizabeth A.; Schildbach, Joel F.; Krueger, Susan; Curtis, Joseph E.

2014-01-01

123

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

PubMed Central

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. ?-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-? 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

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

2012-01-01

124

Structuring of polymer solutions upon solvent evaporation  

NASA Astrophysics Data System (ADS)

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.

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

2015-02-01

125

Structure and aggregation in model tetramethylurea solutions.  

PubMed

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

Gupta, Rini; Patey, G N

2014-08-14

126

Structure and aggregation in model tetramethylurea solutions  

NASA Astrophysics Data System (ADS)

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.

Gupta, Rini; Patey, G. N.

2014-08-01

127

Outrunning free radicals in room-temperature macromolecular crystallography.  

PubMed

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 ? Fc receptor IIIa), a virus (bovine enterovirus serotype 2) and a membrane protein (human A(2A) 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

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

2012-07-01

128

Structure and interactions in simple solutions.  

PubMed Central

Neutron scattering with hydrogen/deuterium isotopic substitution techniques has been used to investigate the full range of structural interactions in a dilute 0.02 mol fraction solution of tertiary butanol in water, both in the absence and in the presence of a small amount of sodium chloride. Emphasis is given to the detailed pictures of the intermolecular interactions that have been derived using the empirical potential structure refinement technique. Analysis has been performed to the level of the spatial density distribution functions that illustrate the orientational dependence of the intermolecular interactions between all combinations of molecular and ionic components. The results show the key structural motifs involved in the interactions between the various components in a complex aqueous system. They underline the structural versatility of the water molecule in accommodating a range of different kinds of interactions while retaining its characteristic first-neighbour interaction geometry. Within this framework, the results highlight the complex interplay between the polar, non-polar and charged molecular interactions that exist in the system. PMID:15306374

Bowron, D T

2004-01-01

129

Macromolecular Crystal Growth by Means of Microfluidics  

NASA Technical Reports Server (NTRS)

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.

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

2002-01-01

130

Quantum chemistry of macromolecular shape  

NASA Astrophysics Data System (ADS)

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

Mezey, Paul G.

131

International summer school on macromolecular crystallographic computing. Final report  

SciTech Connect

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.

NONE

1998-08-01

132

Organoactinide chemistry: synthesis, structure, and solution dynamics  

SciTech Connect

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.

Brennan, J.G.

1985-12-01

133

Toll-like receptor signalling through macromolecular protein complexes.  

PubMed

The molecular mechanisms by which pattern recognition receptors (PRRs) signal are increasingly well understood. Toll-like receptor 4 (TLR4) signals through two separate pairs of adaptor proteins Mal/MyD88 and Tram/Trif. Structural studies have revealed a common theme for PRR signalling in that their signalling proteins form large macromolecular complexes which are thought to form the active signalling complex. The first of these to be characterised was the MyD88 signalling complex Myddosome. Many questions remain unanswered however. In particular it is unclear whether these signalling complexes form within the living cell, how many of each signalling protein is within the intracellular Myddosome and whether the stoichiometry can vary in a ligand-dependent manner. In this review we will discuss what is known about the macromolecular complexes thought to be important for TLR4 signalling. PMID:25081091

Bryant, Clare E; Symmons, Martyn; Gay, Nicholas J

2015-02-01

134

A macromolecular model for the endothelial surface layer  

NASA Astrophysics Data System (ADS)

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.

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

2006-03-01

135

Macromolecular synthesis by yeasts under frozen conditions  

E-print Network

by the protein synthesis inhibitor cycloheximide. Experi- ments at -5°C under frozen and liquid conditionsMacromolecular synthesis by yeasts under frozen conditions Pierre Amato,* Shawn Doyle and Brent C

Christner, Brent C.

136

Atomic Structure Schrdinger equation has approximate solutions for multi-  

E-print Network

Atomic Structure Schrödinger equation has approximate solutions for multi- electron atoms, which indicate that all atoms are like hydrogen Atomic Structure Schrödinger equation has approximate solutions 3s 3p 3d Energy hydrogen multi-electron #12;Atomic Structure · orbitals are populated by electrons

Zakarian, Armen

137

An autonomous structural health monitoring solution  

NASA Astrophysics Data System (ADS)

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.

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

2013-05-01

138

Modeling the tripartite drug efflux pump archetype: structural and functional studies of the macromolecular constituents reveal more than their names imply.  

PubMed

It is a remarkable age in molecular biology when one can argue that our current understanding of a process is influenced as much by structural studies as it is by genetic and physiological manipulations. This statement is particularly poignant with membrane proteins for which structural knowledge has been long impeded by the inability to easily obtain crystal structures in a lipid matrix. Thus, several high-resolution structures of the components comprising tripartite multidrug efflux pumps from Escherichia coli and Pseudomonas aeruginosa are now available and were received with much acclaim over ever-evolving crystal structures of soluble, aqueous proteins. These structures, in conjunction with functional mutagenesis studies, have provided insight into substrate capture and binding domains and redefined the potential interactions between individual pump constituents. However, correct assembly of the components is still a matter of debate as is the functional contribution of each to the translocation of drug substrates over long distances spanning the Gram-negative cell envelope. PMID:16433187

Elkins, C A; Beenken, K E

2005-12-01

139

Analytical solution for the structure of ADAFs  

NASA Astrophysics Data System (ADS)

The standard advection-dominated accretion flow (ADAF) is studied using a set of self-similar analytical solutions in spherical coordinates. Our new solutions are useful for studying ADAFs without dealing with the usual mathematical complexity. We assume that the r? component of the stress tensor dominates and the latitudinal component of the velocity is negligible; moreover, the fluid is incompressible and the solutions are radially self-similar. We show that our analytical solutions display most of the important properties of ADAFs that have already been obtained through detailed numerical solutions. According to our solutions, the density and pressure of the flow decrease from the equator to the polar regions and this reduction depends on the amount of advected energy. We also show analytically that an ADAF tends to a quasi-spherical configuration as more energy is advected with the radial flow.

Shadmehri, Mohsen

2014-08-01

140

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

PubMed

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

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

2015-06-15

141

The promise of macromolecular crystallization in microfluidic chips  

NASA Technical Reports Server (NTRS)

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.

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

2003-01-01

142

Structural characterisation of macromolecular organic material in air particulate matter using Py-GC-MS and solid state 13C-NMR.  

PubMed

Organic air particulate matter was analysed by applying the techniques of Py-GC-MS (pyrolysis-gas chromatography-mass spectrometry) and solid state 13C-NMR (nuclear magnetic resonance). Particles dislodged from air particulate filters and humic acid extracted from these filters were studied for structural components. The structural components of the air particles and extracted humic acid consisted of compounds originating from biomacromolecules, namely, lignin, carbohydrates, protein and lipids. The main components identified for each class included: (1) methoxyphenols originating from lignin; (2) furans, aldehydes and ketones from carbohydrates; (3) pyrrole, indoles from protein; and (4) many hydrocarbons from lipid structures. Single ion monitoring (SIM) and tetramethyl ammonium hydroxide (TMAH) methylation were utilised for detection of aliphatic hydrocarbons and acidic components, respectively. Hydrocarbons ranging from C9 to C28 were detected by SIM analysis, while aliphatic acids ranged from C9 to C18. The majority of components analysed directly in the air particles were similar to those from the humic acid extracts. Many of the structural components of air particles were typical of humic substances of soil and aqueous systems and these were attributed to both biogenic and anthropogenic sources. PMID:11296741

Subbalakshmi, Y; Patti, A F; Lee, G S; Hooper, M A

2000-12-01

143

Constructing efficient solutions structure of multiobjective linear programming  

Microsoft Academic Search

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

Hong Yan; Quanling Wei; Jun Wang

2005-01-01

144

A Sco protein among the hypothetical proteins of Bacillus lehensis G1: Its 3D macromolecular structure and association with Cytochrome C Oxidase  

PubMed Central

Background At least a quarter of any complete genome encodes for hypothetical proteins (HPs) which are largely non-similar to other known, well-characterized proteins. Predicting and solving their structures and functions is imperative to aid understanding of any given organism as a complete biological system. The present study highlights the primary effort to classify and cluster 1202 HPs of Bacillus lehensis G1 alkaliphile to serve as a platform to mine and select specific HP(s) to be studied further in greater detail. Results All HPs of B. lehensis G1 were grouped according to their predicted functions based on the presence of functional domains in their sequences. From the metal-binding group of HPs of the cluster, an HP termed Bleg1_2507 was discovered to contain a thioredoxin (Trx) domain and highly-conserved metal-binding ligands represented by Cys69, Cys73 and His159, similar to all prokaryotic and eukaryotic Sco proteins. The built 3D structure of Bleg1_2507 showed that it shared the ?????? core structure of Trx-like proteins as well as three flanking ?-sheets, a 310 –helix at the N-terminus and a hairpin structure unique to Sco proteins. Docking simulations provided an interesting view of Bleg1_2507 in association with its putative cytochrome c oxidase subunit II (COXII) redox partner, Bleg1_2337, where the latter can be seen to hold its partner in an embrace, facilitated by hydrophobic and ionic interactions between the proteins. Although Bleg1_2507 shares relatively low sequence identity (47%) to BsSco, interestingly, the predicted metal-binding residues of Bleg1_2507 i.e. Cys-69, Cys-73 and His-159 were located at flexible active loops similar to other Sco proteins across biological taxa. This highlights structural conservation of Sco despite their various functions in prokaryotes and eukaryotes. Conclusions We propose that HP Bleg1_2507 is a Sco protein which is able to interact with COXII, its redox partner and therefore, may possess metallochaperone and redox functions similar to other documented bacterial Sco proteins. It is hoped that this scientific effort will help to spur the search for other physiologically relevant proteins among the so-called “orphan” proteins of any given organism. PMID:24641837

2014-01-01

145

Core-Shell Structure, Biodegradation, and Drug Release Behavior of Poly(lactic acid)/Poly(ethylene glycol) Block Copolymer Micelles Tuned by Macromolecular Stereostructure.  

PubMed

Poly(ethylene glycol)-b-poly(l-lactic acid)-b-poly(d-lactic acid) (PEG-b-PLLA-b-PDLA) stereoblock copolymers were synthesized by sequential ring-opening polymerization. Their micelle formation, precise micelle structure, biodegradation, and drug release behavior were systematically investigated and compared with the PEG-b-poly(lactic acid) (PEG-b-PLA) diblock copolymers with various PLA stereostructures and PEG-b-PLLA/PEG-b-PDLA enantiomeric mixture. Stereoblock copolymers having comparable PLLA and PDLA block lengths and enantiomerically-mixed copolymers assemble into the stereocomplexed core-shell micelles, while the isotactic and atactic PEG-b-PLA copolymers formed the homocrystalline and amorphous micelles, respectively. The PLA segments in stereoblock copolymer micelles show smaller crystallinity than those in the isotactic and enantiomerically-mixed ones, attributed to the short block length and presence of covalent junction between PLLA and PDLA blocks. As indicated by the synchrotron radiation small-angle X-ray scattering results, the stereoblock copolymer micelles have larger size, micellar aggregation number, core radius, smaller core density, and looser packing of core-forming segments than the isotactic and enantiomerically-mixed copolymer micelles. These unique structural characteristics cause the stereoblock copolymer micelles to possess higher drug loading content, slower degradation, and drug release rates. PMID:25555131

Ma, Chenlei; Pan, Pengju; Shan, Guorong; Bao, Yongzhong; Fujita, Masahiro; Maeda, Mizuo

2015-02-01

146

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)

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.

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

2001-11-01

147

WAXS studies of the structural diversity of hemoglobin in solution.  

SciTech Connect

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.

Makowski, L.; Bardhan, J.; Gore, D.; Lal, J.; Mandava, S.; Park, S.; Rodi, D. J.; Ho, N. T.; Ho, C.; Fischetti, R. F. (Biosciences Division); ( MCS); (Northeastern Univ.); (Illinois Inst. of Tech.); (Carnegie Mellon Univ.)

2011-01-01

148

Flexibility damps macromolecular crowding effects on protein folding dynamics: Application to the murine prion protein (121-231)  

NASA Astrophysics Data System (ADS)

A model of protein folding kinetics is applied to study the combined effects of protein flexibility and macromolecular crowding on protein folding rate and stability. It is found that the increase in stability and folding rate promoted by macromolecular crowding is damped for proteins with highly flexible native structures. The model is applied to the folding dynamics of the murine prion protein (121-231). It is found that the high flexibility of the native isoform of the murine prion protein (121-231) reduces the effects of macromolecular crowding on its folding dynamics. The relevance of these findings for the pathogenic mechanism are discussed.

Bergasa-Caceres, Fernando; Rabitz, Herschel A.

2014-01-01

149

HIGH PRESSURE CRYOCOOLING FOR MACROMOLECULAR CRYSTALLOGRAPHY  

E-print Network

Science High School and continued his education in Seoul National University (SNU) majoring in Physics for the Degree of Doctor of Philosophy by Chae Un Kim January 2008 #12;© 2008 Chae Un Kim #12;HIGH PRESSUREHIGH PRESSURE CRYOCOOLING FOR MACROMOLECULAR CRYSTALLOGRAPHY A Dissertation Presented

Gruner, Sol M.

150

Constructing efficient solutions structure of multiobjective linear programming  

NASA Astrophysics Data System (ADS)

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

Yan, Hong; Wei, Quanling; Wang, Jun

2005-07-01

151

Structural modification of supersaturated BCC-Nd(Al) solid solution  

Microsoft Academic Search

The metastable Nd(Al) supersaturated solid solution with the BCC structure was synthesized by the melt-spinning method. The thermal stability of the supersaturated solid solution was studied by differential scanning calorimetry (DSC) and electrical-resistance measurements. The structural modification was determined by X-ray diffraction (XRD) and transmission electron microscopy (TEM). A constrained BCC lattice was found due to the smaller Al atoms

W. S. Sun; E. D. Wu; H. F. Zhang; Z. Q. Hu

2005-01-01

152

A computational study of hydration, solution structure, and dynamics in dilute carbohydrate solutions  

E-print Network

A computational study of hydration, solution structure, and dynamics in dilute carbohydrate of the structure and dynamics of water near single carbohydrate molecules glucose, trehalose, and sucrose at 0 and 30 °C. The presence of a carbohydrate molecule has a number of significant effects on the microscopic

153

Solution Structures of Two Homologous Venom Peptides from Sicarius dolichocephalus  

E-print Network

Solution Structures of Two Homologous Venom Peptides from Sicarius dolichocephalus Nikolaus M putative venom peptides from Sicarius dolichocephalus. These peptides were identified from cDNA libraries created from venom gland mRNA and then recombinantly expressed. They are the first structures from any

Loening, Niko

154

Atomic scale structure of ionic and semiconducting solid solutions  

Microsoft Academic Search

Experimental studies of the atomic scale structure of ionic and semiconducting solid solutions have shown that the bond-length mismatch is partially accommodated by microscopic lattice distortions and that the values of the nearest-neighbour bond lengths are intermediate between those of the corresponding pure compounds and the average Vegard value. Here the authors investigate theoretically the atomic scale structure of alloys

A. Baldereschi; M. Peressi

1993-01-01

155

The Effect of Macromolecular Crowding, Ionic Strength and Calcium Binding on Calmodulin Dynamics  

PubMed Central

The flexibility in the structure of calmodulin (CaM) allows its binding to over 300 target proteins in the cell. To investigate the structure-function relationship of CaM, we combined methods of computer simulation and experiments based on circular dichroism (CD) to investigate the structural characteristics of CaM that influence its target recognition in crowded cell-like conditions. We developed a unique multiscale solution of charges computed from quantum chemistry, together with protein reconstruction, coarse-grained molecular simulations, and statistical physics, to represent the charge distribution in the transition from apoCaM to holoCaM upon calcium binding. Computationally, we found that increased levels of macromolecular crowding, in addition to calcium binding and ionic strength typical of that found inside cells, can impact the conformation, helicity and the EF hand orientation of CaM. Because EF hand orientation impacts the affinity of calcium binding and the specificity of CaM's target selection, our results may provide unique insight into understanding the promiscuous behavior of calmodulin in target selection inside cells. PMID:21829336

Wang, Qian; Liang, Kao-Chen; Czader, Arkadiusz; Waxham, M. Neal; Cheung, Margaret S.

2011-01-01

156

Structure Determination of Biological Macromolecules in Solution Using NMR spectroscopy  

Microsoft Academic Search

Abstract A detailed understanding of the function of a biological macromolecule,requires knowledge,of its three-dimensional structure. Most atomic-resolution structures of biological macromolecules have been solved either by x-ray diffraction in single crystals or by nuclear magnetic resonance (NMR) in solution. This review surveys the method,of NMR structure determination. First a brief introduction to NMR and its basic concepts is presented. The

Gerhard Wider

157

Structural properties of methanol-polyamidoamine dendrimer solutions  

NASA Astrophysics Data System (ADS)

We used small angle x-ray scattering to study interparticle structural properties of polyamidoamine starburst dendrimers (PAMAM, with an ethylenediamine central core) in methanol solutions. We have explored the intensity profiles for solutions of starbursts of different generations (g=2, 3.5, 4) at various concentrations. We find from the measured spectra that the half-integer generation, g=3.5, is characterized by pronounced interparticle correlations also in the very dilute regime. By means of a simple statistical-mechanical model, widely used in charged complex fluids (proteins and ionic micellar solutions), we calculate in this latter case the dendrimer-dendrimer structure factor S(q). The results obtained give clear indication of a partial ionization process which involves the carboxylate (COO-Na+) terminal groups of the dendrimer. The calculated macroion charge number, independent of the solution concentration, is Z0~=6.

Micali, Norberto; Scolaro, Luigi Monsu'; Romeo, Andrea; Lombardo, Domenico; Lesieur, Pierre; Mallamace, Francesco

1998-11-01

158

Influence of the extraction time on macromolecular parameters of galactomannans.  

PubMed

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

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

2015-02-13

159

Changes in electronic structure of copper films in aqueous solutions  

Microsoft Academic Search

The possibilities for using x-ray absorption spectroscopy (XAS) and resonant inelastic x-ray scattering (RIXS) to probe the Cu oxidation state and changes in the electronic structure during interaction between copper and ground-water solutions were examined. Surface modifications induced by chemical reactions of oxidized 100 Å Cu films with Cl-, SO42- and HCO3- ions in aqueous solutions with various concentrations were

K. O. Kvashnina; S. M. Butorin; A. Modin; I. Soroka; M. Marcellini; J.-H. Guo; L. Werme; J. Nordgren

2007-01-01

160

Use of Capillaries for Macromolecular Crystallization in a Cryogenic Dewar  

NASA Technical Reports Server (NTRS)

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.

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

2002-01-01

161

Macromolecular neutron crystallography at the Protein Crystallography Station (PCS)  

PubMed Central

The Protein Crystallography Station (PCS) at Los Alamos Neutron Science Center is a high-performance beamline that forms the core of a capability for neutron macromolecular structure and function determination. Neutron diffraction is a powerful technique for locating H atoms and can therefore provide unique information about how biological macro­molecules function and interact with each other and smaller molecules. Users of the PCS have access to neutron beam time, deuteration facilities, the expression of proteins and the synthesis of substrates with stable isotopes and also support for data reduction and structure analysis. The beamline exploits the pulsed nature of spallation neutrons and a large electronic detector in order to collect wavelength-resolved Laue patterns using all available neutrons in the white beam. The PCS user facility is described and highlights from the user program are presented. PMID:21041938

Kovalevsky, Andrey; Fisher, Zoe; Johnson, Hannah; Mustyakimov, Marat; Waltman, Mary Jo; Langan, Paul

2010-01-01

162

Macromolecular Crystallization with Microfluidic Free-Interface Diffusion  

SciTech Connect

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.

Segelke, B

2005-02-24

163

Cooperative Macromolecular Disassembly via the Heat Shock Chaperone Hsc70  

NASA Astrophysics Data System (ADS)

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.

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

2008-03-01

164

Structural cluster analysis of chemical reactions in solution  

NASA Astrophysics Data System (ADS)

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

Gallet, Grégoire A.; Pietrucci, Fabio

2013-08-01

165

Solution Structures of Two Homologous Venom Peptides from Sicarius dolichocephalus  

PubMed Central

We present solution-state NMR structures for two putative venom peptides from Sicarius dolichocephalus. These peptides were identified from cDNA libraries created from venom gland mRNA and then recombinantly expressed. They are the first structures from any species of Sicarius spiders, and the first peptide structures for any haplogyne spiders. These peptides are homologous to one another, and while they have at most only 20% sequence identity with known venom peptides their structures follow the inhibitor cystine knot motif that has been found in a broad range of venom peptides. PMID:23342149

Loening, Nikolaus M.; Wilson, Zachary N.; Zobel-Thropp, Pamela A.; Binford, Greta J.

2013-01-01

166

Structural modification of supersaturated BCC-Nd(Al) solid solution  

NASA Astrophysics Data System (ADS)

The metastable Nd(Al) supersaturated solid solution with the BCC structure was synthesized by the melt-spinning method. The thermal stability of the supersaturated solid solution was studied by differential scanning calorimetry (DSC) and electrical-resistance measurements. The structural modification was determined by X-ray diffraction (XRD) and transmission electron microscopy (TEM). A constrained BCC lattice was found due to the smaller Al atoms entering the BCC-Nd lattice. Two evident transformation stages were found during the heating process. The lower activation energy and negative temperature coefficient of the resistivity (TCR) suggest that a continuous structural transformation occur, which results from the softening mode of the highly metastable BCC structure. The strongly distorted and ultra-fine microstructure was observed directly by TEM.

Sun, W. S.; Wu, E. D.; Zhang, H. F.; Hu, Z. Q.

2005-01-01

167

Solution Structure of a Quinomycin Bisintercalator-DNA Complex  

Microsoft Academic Search

A quinomycin antibiotic UK-63052 (designated QN) exhibits a chemical structure related to the antibiotic echinomycin which is known to bisintercalate into DNA. Common features among these antibiotics include two heterocyclic aromatic ring systems propagating from a cross-bridged cyclic octadepsipeptide scaffold. We report on the solution structure of the QN-d(A1-C2-A3-C4-G5-T6-G7-T8) complex (one QN molecule per duplex) based on a combined NMR-molecular

Huifen Chen; Dinshaw J. Patel

1995-01-01

168

Conformational Variability of Solution Nucelar Magnetic Resonance Structures  

Microsoft Academic Search

In structure determination by X-ray crystallography and solution NMR spectroscopy, experimental data are collected as time and ensemble-averages. Thus, in principle, appropriate time and ensemble-averaged models should be used. Refinement of an ensemble of conformers rather than one single structure against the experimental NMR data could, however, result in overfitting the data because of the significantly increased number of parameters.

Alexandre M. J. J. Bonvin; Axel T. Brünger

1995-01-01

169

Use of Capillaries for Macromolecular Crystallization in a Cryogenic Dewar  

NASA Technical Reports Server (NTRS)

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

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

2001-01-01

170

Exact Coherent Structures in Pipe Flow: Travelling Wave Solutions  

E-print Network

continuation procedure based upon key physical mechanisms thought generic to wall-bounded shear flows of the observed transition. Pipe flow is then just one of a class of wall-bounded shear flows which suffer1 Exact Coherent Structures in Pipe Flow: Travelling Wave Solutions H. Wedin & R.R. Kerswell

Burton, Geoffrey R.

171

Solution of large eigenvalue problems in electronic structure calculations  

Microsoft Academic Search

Predicting the structural and electronic properties of complex systems is one of the outstanding problems in condensed matter physics. Central to most methods used in molecular dynamics is the repeated solution of large eigenvalue problems. This paper reviews the source of these eigenvalue problems, describes some techniques for solving them, and addresses the difficulties and challenges which are faced. Parallel

Y. Saad; A. Stathopoulos; J. Chelikowsky; K. Wu; S. Ö?üt

1996-01-01

172

Numerical Solution of Singular ODE Eigenvalue Problems in Electronic Structure  

E-print Network

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

Koch, Othmar

173

Advances in macromolecular data storage  

NASA Astrophysics Data System (ADS)

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.

Mansuripur, Masud

2014-09-01

174

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

PubMed

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

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

2013-04-01

175

Development of macromolecular prodrug for rheumatoid arthritis?  

PubMed Central

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

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

2012-01-01

176

Large-volume protein crystal growth for neutron macromolecular crystallography.  

PubMed

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

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

2015-04-01

177

Revealing the macromolecular targets of complex natural products  

NASA Astrophysics Data System (ADS)

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’.

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

178

Automated macromolecular crystal detection system and method  

DOEpatents

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.

Christian, Allen T. (Tracy, CA); Segelke, Brent (San Ramon, CA); Rupp, Bernard (Livermore, CA); Toppani, Dominique (Fontainebleau, FR)

2007-06-05

179

Structural and Spectroscopic Properties of Water Around Small Hydrophobic Solutes  

PubMed Central

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

Montagna, Maria; Sterpone, Fabio; Guidoni, Leonardo

2013-01-01

180

Heterotic domain wall solutions and SU(3) structure manifolds  

E-print Network

We examine compactifications of heterotic string theory on manifolds with SU(3) structure. In particular, we study N = 1/2 domain wall solutions which correspond to the perturbative vacua of the 4D, N =1 supersymmetric theories associated to these compactifications. We extend work which has appeared previously in the literature in two important regards. Firstly, we include two additional fluxes which have been, heretofore, omitted in the general analysis of this situation. This allows for solutions with more general torsion classes than have previously been found. Secondly, we provide explicit solutions for the fluxes as a function of the torsion classes. These solutions are particularly useful in deciding whether equations such as the Bianchi identities can be solved, in addition to the Killing spinor equations themselves. Our work can be used to straightforwardly decide whether any given SU(3) structure on a six-dimensional manifold is associated with a solution to heterotic string theory. To illustrate how to use these results, we discuss a number of examples taken from the literature.

James Gray; Magdalena Larfors; Dieter Lust

2013-01-28

181

Electronic structures of Ascaris trypsin inhibitor in solution  

NASA Astrophysics Data System (ADS)

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.

Zheng, Haoping

2003-11-01

182

Gorgon and Pathwalking: Macromolecular Modeling Tools for Subnanometer Resolution Density Maps  

PubMed Central

The complex interplay of proteins and other molecules, often in the form of large transitory assemblies, are critical to cellular function. Today, X-ray crystallography and electron cryo-microscopy (cryo-EM) are routinely used to image these macromolecular complexes, though often at limited resolutions. Despite the rapidly growing number of macromolecular structures, few tools exist for modeling and annotating structures in the range of 3-10Å resolution. To address this need, we have developed a number of utilities specifically targeting subnanometer resolution density maps. As part of the 2010 Cryo-EM Modeling Challenge, we demonstrated two of our latest de novo modeling tools, Pathwalking and Gorgon, as well as a tool for secondary structure identification (SSEHunter) and a new rigid-body/flexible fitting tool in Gorgon. In total, we submitted 30 structural models from ten different subnanometer resolution data sets in four of the six challenge categories. Each of our utlities produced accurate structural models and annotations across the various density maps. In the end, the utilities that we present here offer users a robust toolkit for analyzing and modeling protein structure in macromolecular assemblies at non-atomic resolutions. PMID:22696403

Baker, Matthew L.; Baker, Mariah R.; Hryc, Corey F.; Ju, Tao; Chiu, Wah

2013-01-01

183

Gorgon and pathwalking: macromolecular modeling tools for subnanometer resolution density maps.  

PubMed

The complex interplay of proteins and other molecules, often in the form of large transitory assemblies, are critical to cellular function. Today, X-ray crystallography and electron cryo-microscopy (cryo-EM) are routinely used to image these macromolecular complexes, though often at limited resolutions. Despite the rapidly growing number of macromolecular structures, few tools exist for modeling and annotating structures in the range of 3-10 Å resolution. To address this need, we have developed a number of utilities specifically targeting subnanometer resolution density maps. As part of the 2010 Cryo-EM Modeling Challenge, we demonstrated two of our latest de novo modeling tools, Pathwalking and Gorgon, as well as a tool for secondary structure identification (SSEHunter) and a new rigid-body/flexible fitting tool in Gorgon. In total, we submitted 30 structural models from ten different subnanometer resolution data sets in four of the six challenge categories. Each of our utlities produced accurate structural models and annotations across the various density maps. In the end, the utilities that we present here offer users a robust toolkit for analyzing and modeling protein structure in macromolecular assemblies at non-atomic resolutions. PMID:22696403

Baker, Matthew L; Baker, Mariah R; Hryc, Corey F; Ju, Tao; Chiu, Wah

2012-09-01

184

Development of solution techniques for nonlinear structural analysis  

NASA Technical Reports Server (NTRS)

Nonlinear structural solution methods in the current research literature are classified according to order of the solution scheme, and it is shown that the analytical tools for these methods are uniformly derivable by perturbation techniques. A new perturbation formulation is developed for treating an arbitrary nonlinear material, in terms of a finite-difference generated stress-strain expansion. Nonlinear geometric effects are included in an explicit manner by appropriate definition of an applicable strain tensor. A new finite-element pilot computer program PANES (Program for Analysis of Nonlinear Equilibrium and Stability) is presented for treatment of problems involving material and geometric nonlinearities, as well as certain forms on nonconservative loading.

Vos, R. G.; Andrews, J. S.

1974-01-01

185

The Yeast Exosome Functions as a Macromolecular Cage to Channel  

E-print Network

The Yeast Exosome Functions as a Macromolecular Cage to Channel RNA Substrates for Degradation.cell.2009.08.042 SUMMARY The exosome is a conserved macromolecular com- plex essential for RNA degradation. The nine-subunit core of the eukaryotic exosome shares a similar barrel-like architecture with prokaryotic

Bedwell, David M.

186

Kinetic analysis of macromolecular interactions using surface plasmon resonance biosensors  

Microsoft Academic Search

Surface plasmon resonance based biosensors are being used to define the kinetics of a wide variety of macromolecular interactions. As the popularity of this approach grows, experimental design and data analysis methods continue to evolve. These advances are making it possible to accurately define the assembly mechanisms and rate constants associated with macromolecular interactions.

David G Myszka

1997-01-01

187

Travelling Wave Solutions in Multigroup Age-Structured Epidemic Models  

NASA Astrophysics Data System (ADS)

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

Ducrot, Arnaut; Magal, Pierre; Ruan, Shigui

2010-01-01

188

Solution of axisymmetric fluid structure interaction problems with NASTRAN  

NASA Technical Reports Server (NTRS)

The solution of axisymmetric acoustic fluid structure interaction problems, employing the NASTRAN computer program is presented. A previously developed 3-D Cartesian Coordinates pressure element formulation is adapted especially for axisymmetric elements. Analogous to the 3-D Cartesian Coordinate predecessor, the fluid portion of the problem is modeled with finite elements wherein one of the displacement components serves as a dummy variable for the pressure unknowns. Two alternatives for implementation of the analogy are presented: (1) an approximate method by which dummy values of G, and nu are used to approximately invoke the analogy wherein the accuracy of the approximation is made as close as desired to the proper analogy within an arbitrary small parameter epsiton; (2) an exact method whereby the NASTRAN FORTRAN coding is slightly changed to invoke the analogy exactly. Comparison of the finite element solution to the exact solution to the same problem is given.

Kalinowski, A. J.; Nebelung, C. W.

1982-01-01

189

Three-Dimensional Structure of Fucosyllactoses in an Aqueous Solution  

Microsoft Academic Search

H and C NMR spectra of four fucosyllactoses were analyzed and interresidual NOEs were detected in solution. Several interresidual NOE cross peaks between non-direct-bonding pyranoses were obtained in common with trisaccharides including fucose. Three-dimensional (3D) structures of the four saccharides were simulated with DADAS90 software using distance constraints estimated by NOE intensity. Results suggest approximate C2 rotating symmetry in the

Yasuko Ishizuka; Tadashi Nemoto; Masako Fujiwara; Ken-ichi Fujita; Hiroshi Nakanishi

1999-01-01

190

Progress in rational methods of cryoprotection in macromolecular crystallography  

PubMed Central

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

Alcorn, Thomas; Juers, Douglas H.

2010-01-01

191

Reconstruction of SAXS Profiles from Protein Structures  

PubMed Central

Small angle X-ray scattering (SAXS) is used for low resolution structural characterization of proteins often in combination with other experimental techniques. After briefly reviewing the theory of SAXS we discuss computational methods based on 1) the Debye equation and 2) Spherical Harmonics to compute intensity profiles from a particular macromolecular structure. Further, we review how these formulas are parameterized for solvent density and hydration shell adjustment. Finally we introduce our solution to compute SAXS profiles utilizing GPU acceleration. PMID:24688746

Putnam, Daniel K.; Lowe, Edward W.

2013-01-01

192

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

PubMed

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

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

2014-10-21

193

Nitric Oxide Release Part I. Macromolecular Scaffolds  

PubMed Central

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

Riccio, Daniel A.; Schoenfisch, Mark H.

2012-01-01

194

Solution Structures of Two FHA1-Phosphothreonine Peptide Complexes Provide Insight into the Structural  

E-print Network

Solution Structures of Two FHA1-Phosphothreonine Peptide Complexes Provide Insight into the Structural Basis of the Ligand Specificity of FHA1 from Yeast Rad53 Chunhua Yuan1 , Suganya Yongkiettrakul3 of Biochemistry 3 Ohio State Biochemistry Program and 4 Campus Chemical Instrument Center, The Ohio State

Tsai, Ming-Daw

195

Brownian Dynamics Simulation of Protein Solutions: Structural and Dynamical Properties  

PubMed Central

The study of solutions of biomacromolecules provides an important basis for understanding the behavior of many fundamental cellular processes, such as protein folding, self-assembly, biochemical reactions, and signal transduction. Here, we describe a Brownian dynamics simulation procedure and its validation for the study of the dynamic and structural properties of protein solutions. In the model used, the proteins are treated as atomically detailed rigid bodies moving in a continuum solvent. The protein-protein interaction forces are described by the sum of electrostatic interaction, electrostatic desolvation, nonpolar desolvation, and soft-core repulsion terms. The linearized Poisson-Boltzmann equation is solved to compute electrostatic terms. Simulations of homogeneous solutions of three different proteins with varying concentrations, pH, and ionic strength were performed. The results were compared to experimental data and theoretical values in terms of long-time self-diffusion coefficients, second virial coefficients, and structure factors. The results agree with the experimental trends and, in many cases, experimental values are reproduced quantitatively. There are no parameters specific to certain protein types in the interaction model, and hence the model should be applicable to the simulation of the behavior of mixtures of macromolecules in cell-like crowded environments. PMID:21112303

Mereghetti, Paolo; Gabdoulline, Razif R.; Wade, Rebecca C.

2010-01-01

196

Lysozyme Protein Solution with an Intermediate Range Order Structure  

SciTech Connect

The formation of equilibrium clusters has been studied in both a prototypical colloidal system and protein solutions. The appearance of a low-Q correlation peak in small angle scattering patterns of lysozyme solution was attributed to the cluster-cluster correlation. Consequently, the presence of long-lived clusters has been established. By quantitatively analyzing both the SANS (small angle neutron scattering) and NSE (neutron spin echo) data of lysozyme solution using statistical mechanics models, we conclusively show in this paper that the appearance of a low-Q peak is not a signature of the formation of clusters. Rather, it is due to the formation of an intermediate range order structure governed by a short-range attraction and a long-range repulsion. We have further studied dynamic features of a sample with high enough concentration at which clusters are formed in solution. From the estimation of the mean square displacement by using short-time and long-time diffusion coefficient measured by NSE and NMR, we find that these clusters are not permanent but have a finite lifetime longer than the time required to diffuse over a distance of a monomer diameter.

Liu, Yun [National Institute of Standards and Technology (NIST); Porcar, L. [National Institute of Standards and Technology (NIST); Chen, Wei-Ren [ORNL; Chen, Jinhong [Memorial Sloan-Kettering Cancer Center; Falus, Peter [ORNL; Fratini, Emiliano [University of Florence; Faraone, Antonio [National Institute of Standards and Technology (NIST); Baglioni, P [University of Florence

2011-01-01

197

Hierarchical Order Parameters for Macromolecular Assembly Simulations I: Construction and Dynamical Properties of Order Parameters  

PubMed Central

Macromolecular assemblies often display a hierarchical organization of macromolecules or their sub-assemblies. To model this, we have formulated a space warping method that enables capturing overall macromolecular structure and dynamics via a set of coarse-grained order parameters (OPs). This article is the first of two describing the construction and computational implementation of an additional class of OPs that has built into them the hierarchical architecture of macromolecular assemblies. To accomplish this, first, the system is divided into subsystems, each of which is described via a representative set of OPs. Then, a global set of variables is constructed from these subsystem-centered OPs to capture overall system organization. Dynamical properties of the resulting OPs are compared to those of our previous nonhierarchical ones, and implied conceptual and computational advantages are discussed for a 100ns, 2 million atom solvated Human Papillomavirus-like particle simulation. In the second article, the hierarchical OPs are shown to enable a multiscale analysis that starts with the N-atom Liouville equation and yields rigorous Langevin equations of stochastic OP dynamics. The latter is demonstrated via a force-field based simulation algorithm that probes key structural transition pathways, simultaneously accounting for all-atom details and overall structure. PMID:22661911

Singharoy, Abhishek; Sereda, Yuriy

2012-01-01

198

Critical Reviews in Biochemistry and Molecular Biology, 30(5):351-385 ( 1995) Structures of Protein Complexes  

E-print Network

, solution strucutre. 1. INTRODUCTION The size of macromolecular structures that can be solved by nuclear for these advances comprise three- and four-dimensional heteronuclear NMR tech- niques to circumvent problems of all the complexes that have been solved by NMR but to provide the reader with a feel for the type

Clore, G. Marius

199

Solution structure of the luzopeptin-DNA complex  

SciTech Connect

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.

Zhang, Xiaolu; Patel, D.J. (Columbia Univ., New York, NY (USA))

1991-04-23

200

Solution structure of the human signaling protein RACK1  

PubMed Central

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

2010-01-01

201

Development of an online UV-visible microspectrophotometer for a macromolecular crystallography beamline.  

PubMed

Measurement of the UV-visible absorption spectrum is a convenient technique for detecting chemical changes of proteins, and it is therefore useful to combine spectroscopy and diffraction studies. An online microspectrophotometer for the UV-visible region was developed and installed on the macromolecular crystallography beamline, BL38B1, at SPring-8. This spectrophotometer is equipped with a difference dispersive double monochromator, a mercury-xenon lamp as the light source, and a photomultiplier as the detector. The optical path is mostly constructed using mirrors, in order to obtain high brightness in the UV region, and the confocal optics are assembled using a cross-slit diaphragm like an iris to eliminate stray light. This system can measure optical densities up to a maximum of 4.0. To study the effect of radiation damage, preliminary measurements of glucose isomerase and thaumatin crystals were conducted in the UV region. Spectral changes dependent on X-ray dose were observed at around 280 nm, suggesting that structural changes involving Trp or Tyr residues occurred in the protein crystal. In the case of the thaumatin crystal, a broad peak around 400 nm was also generated after X-ray irradiation, suggesting the cleavage of a disulfide bond. Dose-dependent spectral changes were also observed in cryo-solutions alone, and these changes differed with the composition of the cryo-solution. These responses in the UV region are informative regarding the state of the sample; consequently, this device might be useful for X-ray crystallography. PMID:24121346

Shimizu, Nobutaka; Shimizu, Tetsuya; Baba, Seiki; Hasegawa, Kazuya; Yamamoto, Masaki; Kumasaka, Takashi

2013-11-01

202

Solution to certain problems in the failure of composite structures  

NASA Astrophysics Data System (ADS)

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.)

Goodsell, Johnathan

203

Romp: The Method of Choice for Precise Macromolecular Engineering and Synthesis of Smart Materials  

NASA Astrophysics Data System (ADS)

The recent advances in olefin metathesis highlight the impact of Ring Opening Metathesis Polymerisation (ROMP) as a powerful technique for macromolecular engineering and synthesis of smart materials with well-defined structures. ROMP has attracted a considerable research attention recently particularly by industry largely due to the development of well-defined metal complexes as initiators and also because of the award of the Noble Prize for Chemistry in 2005 to three scientists (Chauvin, Grubbs, Schrock) for their contributions in this area. This chapter discusses several interesting examples in order to demonstrate that ROMP is a power tool in macromolecular engineering and that it allows the design and synthesis of polymers with novel topologies.

Khosravi, Ezat; Castle, Thomas C.; Kujawa, Margaret; Leejarkpai, Jan; Hutchings, Lian R.; Hine, Peter J.

204

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

PubMed Central

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. PMID:20382986

Garman, Elspeth F.

2010-01-01

205

Exploring conformational modes of macromolecular assemblies by multi-particle cryo-EM  

PubMed Central

Summary Single particle cryo-electron microscopy (cryo-EM) is a technique aimed at structure determination of large macromolecular complexes in their unconstrained, physiological conditions. The power of the method has been demonstrated in selected studies where for highly symmetric molecules the resolution attained permitted backbone tracing. However, most molecular complexes appear to exhibit intrinsic conformational variability necessary to perform their functions. Therefore, it is now increasingly recognized that sample heterogeneity constitutes a major methodological challenge for cryo-EM. To overcome it dedicated experimental and particularly computational multi-particle approaches have been developed. Their applications point to the future of cryo-EM as an experimental method uniquely suited to visualize the conformational modes of large macromolecular complexes and machines. PMID:19767196

Spahn, Christian M.T.; Penczek, Pawel A.

2009-01-01

206

Structure of solutions of the buoyancy -- drag equation  

NASA Astrophysics Data System (ADS)

In this paper, the well-known buoyancy-drag equation (BDE) is studied. This equation describes the non linear regime of Rayleigh -- Taylor instabilities and also the structure of the mixing zone where both fluids are present. Analytical solutions of the BDE are derived for time-dependent accelerations, ?(t), of the form ?(t) ˜ t^n where the exponent n can be positive, negative or zero. It is shown, first, that the width, h(t), of the mixing zone behaves like hn(t) ˜ t^n+2 and, second, provided the initial conditions satisfy some constraints, the special solution hn(t) is an attractor for t going to infinity. On the other hand, the behavior of the asymtotic solutions for ?(t) ˜ t^n is examined in terms of the drag coefficient, Cd, that is present in the drag force (proportional to the square of the derivative dh/dt) in the right hand side of the BDE. Critical values for this coefficient are derived analytically and it is shown that the asymptotic behaviors are strongly dependent on the value of Cd. These results are also evidenced from numerical simulations achieved with the CLAWPACK numerical package.

Bouquet, Serge; Falize, Emeric; Gandeboeuf, Pierre; Pailhoriès, Pierre

2008-04-01

207

Interfacial structures of acidic and basic aqueous solutions  

SciTech Connect

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.

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

2008-10-20

208

Generating Triangulated Macromolecular Surfaces by Euclidean Distance Transform  

E-print Network

of EDTSurf for generating three major macromolecular surfaces of van der Waals surface, solvent-accessible surface and molecular surface, using the technique of fast Euclidean Distance Transform (EDT). The triangulated surfaces are constructed directly from...

Xu, Dong; Zhang, Yang

2009-12-02

209

JBluIce-EPICS control system for macromolecular crystallography.  

SciTech Connect

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.

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

2011-01-01

210

Solution structure and dynamics of human S100A14.  

PubMed

Human S100A14 is a member of the EF-hand calcium-binding protein family that has only recently been described in terms of its functional and pathological properties. The protein is overexpressed in a variety of tumor cells and it has been shown to trigger receptor for advanced glycation end products (RAGE)-dependent signaling in cell cultures. The solution structure of homodimeric S100A14 in the apo state has been solved at physiological temperature. It is shown that the protein does not bind calcium(II) ions and exhibits a "semi-open" conformation that thus represents the physiological structure of the S100A14. The lack of two ligands in the canonical EF-hand calcium(II)-binding site explains the negligible affinity for calcium(II) in solution, and the exposed cysteines and histidine account for the observed precipitation in the presence of zinc(II) or copper(II) ions. PMID:23197251

Bertini, Ivano; Borsi, Valentina; Cerofolini, Linda; Das Gupta, Soumyasri; Fragai, Marco; Luchinat, Claudio

2013-02-01

211

Solution structure of the core SMN–Gemin2 complex  

PubMed Central

In humans, assembly of spliceosomal snRNPs (small nuclear ribonucleoproteins) begins in the cytoplasm where the multi-protein SMN (survival of motor neuron) complex mediates the formation of a seven-membered ring of Sm proteins on to a conserved site of the snRNA (small nuclear RNA). The SMN complex contains the SMN protein Gemin2 and several additional Gemins that participate in snRNP biosynthesis. SMN was first identified as the product of a gene found to be deleted or mutated in patients with the neurodegenerative disease SMA (spinal muscular atrophy), the leading genetic cause of infant mortality. In the present study, we report the solution structure of Gemin2 bound to the Gemin2-binding domain of SMN determined by NMR spectroscopy. This complex reveals the structure of Gemin2, how Gemin2 binds to SMN and the roles of conserved SMN residues near the binding interface. Surprisingly, several conserved SMN residues, including the sites of two SMA patient mutations, are not required for binding to Gemin2. Instead, they form a conserved SMN/Gemin2 surface that may be functionally important for snRNP assembly. The SMN–Gemin2 structure explains how Gemin2 is stabilized by SMN and establishes a framework for structure–function studies to investigate snRNP biogenesis as well as biological processes involving Gemin2 that do not involve snRNP assembly. PMID:22607171

Sarachan, Kathryn L.; Valentine, Kathleen G.; Gupta, Kushol; Moorman, Veronica R.; Gledhill, John M.; Bernens, Matthew; Tommos, Cecilia; Wand, A. Joshua; Van Duyne, Gregory D.

2012-01-01

212

Solution Structures of Rat Amylin Peptide: Simulation, Theory, and Experiment  

PubMed Central

Abstract Amyloid deposits of amylin in the pancreas are an important characteristic feature found in patients with Type-2 diabetes. The aggregate has been considered important in the disease pathology and has been studied extensively. However, the secondary structures of the individual peptide have not been clearly identified. In this work, we present detailed solution structures of rat amylin using a combination of Monte Carlo and molecular dynamics simulations. A new Monte Carlo method is presented to determine the free energy of distinct biomolecular conformations. Both folded and random-coil conformations of rat amylin are observed in water and their relative stability is examined in detail. The former contains an ?-helical segment comprised of residues 7–17. We find that at room temperature the folded structure is more stable, whereas at higher temperatures the random-coil structure predominates. From the configurations and weights we calculate the ?-carbon NMR chemical shifts, with results that are in reasonable agreement with experiments of others. We also calculate the infrared spectrum in the amide I stretch regime, and the results are in fair agreement with the experimental line shape presented herein. PMID:20141758

Reddy, Allam S.; Wang, Lu; Lin, Yu-Shan; Ling, Yun; Chopra, Manan; Zanni, Martin T.; Skinner, James L.; De Pablo, Juan J.

2010-01-01

213

Yeast Frataxin Solution Structure, Iron Binding, and Ferrochelatase Interaction†‡  

PubMed Central

The mitochondrial protein frataxin is essential for cellular regulation of iron homeostasis. Although the exact function of frataxin is not yet clear, recent reports indicate the protein binds iron and can act as a mitochondrial iron chaperone to transport Fe(II) to ferrochelatase and ISU proteins within the heme and iron–sulfur cluster biosynthetic pathways, respectively. We have determined the solution structure of apo yeast frataxin to provide a structural basis of how frataxin binds and donates iron to the ferrochelatase. While the protein's ?–?-sandwich structural motif is similar to that observed for human and bacterial frataxins, the yeast structure presented in this report includes the full N-terminus observed for the mature processed protein found within the mitochondrion. In addition, NMR spectroscopy was used to identify frataxin amino acids that are perturbed by the presence of iron. Conserved acidic residues in the helix 1–strand 1 protein region undergo amide chemical shift changes in the presence of Fe(II), indicating a possible iron-binding site on frataxin. NMR spectroscopy was further used to identify the intermolecular binding interface between ferrochelatase and frataxin. Ferrochelatase appears to bind to frataxin's helical plane in a manner that includes its iron-binding interface. PMID:15610019

He, Yanan; Alam, Steven L.; Proteasa, Simona V.; Zhang, Yan; Lesuisse, Emmanuel; Dancis, Andrew; Stemmler, Timothy L.

2010-01-01

214

Polydisulfide Based Biodegradable Macromolecular Magnetic Resonance Imaging Contrast Agents  

PubMed Central

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

Lu, Zheng-Rong; Wu, Xueming

2011-01-01

215

Automation of sample mounting for macromolecular crystallography.  

PubMed

A standard sample holder and vial for cryocooled macromolecular crystals has been defined for use with robotic sample changers. This SPINE standard sample holder is a modified version, with added features and specifications, of sample holders in common use. In particular, the SPINE standard meets the precision required for automatic sample exchange and includes a cap that is identified by a two-dimensional datamatrix code as well as an optional vial. At the ESRF, the sample holder standard is in use with the EMBL/ESRF/BM14 robotic sample changer (SC3) which is installed on eight beamlines. The SC3 can hold up to 50 crystals stored in five baskets. A datamatrix reader in the SC3 ensures safe management of the sample flow and facilitates fully automatic screening and characterization of samples. Tools for handling and transporting 50 samples in a dry shipping dewar have been developed. In addition to the SC3, the SPINE sample holder is currently compatible with a number of other robotic sample changers. PMID:17001102

Cipriani, F; Felisaz, F; Launer, L; Aksoy, J S; Caserotto, H; Cusack, S; Dallery, M; di-Chiaro, F; Guijarro, M; Huet, J; Larsen, S; Lentini, Mario; McCarthy, J; McSweeney, S; Ravelli, R; Renier, M; Taffut, C; Thompson, A; Leonard, G A; Walsh, M A

2006-10-01

216

Macromolecular transport in heart valves. I. Studies of rat valves with horseradish peroxidase.  

PubMed

The present study aims to experimentally elucidate subtle structural features of the rat valve leaflet and the related nature of macromolecular transport across its endothelium and in its subendothelial space, information necessary to construct a rational theoretical model that can explain observation. After intravenous injection of horseradish peroxidase (HRP), we perfusion-fixed the aortic valve of normal Sprague-Dawley rats and found under light microscopy that HRP leaked through the leaflet's endothelium at very few localized brown spots, rather than uniformly. These spots grew nearly as rapidly with HRP circulation time before euthanasia as aortic spots, particularly when the time axis only included the time the valve was closed. These results suggest that macromolecular transport in heart valves depends not only on the direction normal to, but also parallel to, the endothelial surface and that convection, as well as molecular diffusion, plays an important role in macromolecular transport in heart valves. Transmission electron microscopy of traverse leaflet sections after 4-min HRP circulation showed a very thin ( approximately 150 nm), sparse layer immediately beneath the endothelium where the HRP concentration was much higher than that in the matrix below it. Nievelstein-Post et al.'s (Nievelstein-Post P, Mottino G, Fogelman A, Frank J. Arterioscler Thromb 14: 1151-1161, 1994) ultrarapid freezing/rotary shadow etching of the normal rabbit valve's subendothelial space supports the existence of this very thin, very sparse "valvular subendothelial intima," in analogy to the vascular subendothelial intima. PMID:17277015

Zeng, Zhongqing; Yin, Yongyi; Huang, An-Li; Jan, Kung-Ming; Rumschitzki, David S

2007-06-01

217

Conformational Statistics of Semi-Flexible Macromolecular Chains with Internal Joints  

PubMed Central

Fluctuations in the bending angles at internal irregularities of DNA and RNA (such as symmetric loops, bulges, and nicks/gaps) have been observed from various experiments. However, little effort has been made to computationally predict and explain the statistical behavior of semi-flexible chains with internal defects. In this paper, we describe the general structure of these macromolecular chains as inextensible elastic chains with one or more internal joints which have limited ranges of rotation, and propose a method to compute the probability density functions of the end-to-end pose of these macromolecular chains. Our method takes advantage of the operational properties of the non-commutative Fourier transform for the group of rigid-body motions in three-dimensional space, SE(3). Two representative types of joints, the hinge for planar rotation and the ball joint for spatial rotation, are discussed in detail. The proposed method applies to various stiffness models of semi-flexible chain-like macromolecules. Examples are calculated using the Kratky-Porod model with specified stiffness, angular fluctuation, and joint locations. Entropic effects associated with internal angular fluctuations of semi-flexible macromolecular chains with internal joints can be computed using this formulation. Our method also provides a potential tool to detect the existence of internal irregularities. PMID:21243113

Zhou, Yu

2010-01-01

218

Structure and dynamics of aqueous solution of uranyl ions  

SciTech Connect

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.

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

2014-04-24

219

Solution structure, aggregation behavior, and flexibility of human relaxin-2.  

PubMed

Relaxin is a member of the relaxin/insulin peptide hormone superfamily and is characterized by a two-chain structure constrained by three disulfide bonds. Relaxin is a pleiotropic hormone and involved in a number of physiological and pathogenic processes, including collagen and cardiovascular regulation and tissue remodelling during pregnancy and cancer. Crystallographic and ultracentrifugation experiments have revealed that the human form of relaxin, H2 relaxin, self-associates into dimers, but the significance of this is poorly understood. Here, we present the NMR structure of a monomeric, amidated form of H2 relaxin and compare its features and behavior in solution to those of native H2 relaxin. The overall structure of H2 relaxin is retained in the monomeric form. H2 relaxin amide is fully active at the relaxin receptor RXFP1 and thus dimerization is not required for biological activity. Analysis of NMR chemical shifts and relaxation parameters identified internal motion in H2 relaxin at the pico-nanosecond and milli-microsecond time scales, which is commonly seen in other relaxin and insulin peptides and might be related to function. PMID:25547165

Haugaard-Kedström, Linda M; Hossain, Mohammed Akhter; Daly, Norelle L; Bathgate, Ross A D; Rinderknecht, Ernst; Wade, John D; Craik, David J; Rosengren, K Johan

2015-03-20

220

Structure and dynamics of aqueous solution of uranyl ions  

NASA Astrophysics Data System (ADS)

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.

Chopra, Manish; Choudhury, Niharendu

2014-04-01

221

Hydration structure of salt solutions from ab initio molecular dynamics  

SciTech Connect

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.

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

2013-01-07

222

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

PubMed Central

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

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

2012-01-01

223

Solution-processable graphene nanomeshes with controlled pore structures  

NASA Astrophysics Data System (ADS)

Graphene nanomeshes (GNMs) which can be cheaply produced on a large scale and processed through wet approaches are important materials for various applications, including catalysis, composites, sensors and energy related systems. Here, we report a method for large scale preparation of GNMs by refluxing reduced graphene oxide sheets in concentrated nitric acid solution (e.g., 8 moles per liter). The diameters of nanopores in GNM sheets can be readily modulated from several to hundreds nanometers by varying the time of acid treatment. The porous structure increased the specific surface areas of GNMs and the transmittances of GNM-based thin films. Furthermore, GNMs have large number of carboxyl groups at the edges of their nanopores, leading to good dispersibility in aqueous media and strong peroxidase-like catalytic activity.

Wang, Xiluan; Jiao, Liying; Sheng, Kaixuan; Li, Chun; Dai, Liming; Shi, Gaoquan

2013-06-01

224

Three-dimensional solution structure of Acanthamoeba profilin-I  

PubMed Central

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

1993-01-01

225

Solution of Large Eigenvalue Problems in Electronic Structure Calculations  

E-print Network

. Predicting the structural and electronic properties of complex systems is one of the outstanding problems in condensed matter physics. Central to most methods used in molecular dynamics is the repeated solution of large eigenvalue problems. This paper reviews the source of these eigenvalue problems, describes some techniques for solving them, and addresses the difficulties and challenges which are faced. Parallel implementations are also discussed. 1 Introduction One of the fundamental problems encountered today in chemistry and physics is to understand the dynamics of microscopic particles. It is possible to explain or predict certain material properties at a microscopic scale from knowledge of their initial state and given external perturbations. For example, it may be desirable in certain cases to follow the dynamics of atoms/electrons until a `steady state' corresponding to minimum total energy is reached. The numerical problems to be solved in these calculations are among th...

Y. Saad; A. Stathopoulos; J. Chelikowsky; K. Wu; S. Ogut

1995-01-01

226

Characterization of Chitin and Chitosan Molecular Structure in Aqueous Solution  

SciTech Connect

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 ?-chitin nanoparticle, adopt the so-called 2-fold helix with ? and ? 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.

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

2008-12-01

227

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

NASA Astrophysics Data System (ADS)

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.

Lonie, David C.; Zurek, Eva

2012-03-01

228

Synchrotron radiation macromolecular crystallography: science and spin-offs  

PubMed Central

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.

Helliwell, John R.; Mitchell, Edward P.

2015-01-01

229

Canadian Macromolecular Crystallography Facility (CMCF) 08ID-1 status update  

NASA Astrophysics Data System (ADS)

The Canadian Macromolecular Crystallography Facility (CMCF) 08ID-1 beamline at the Canadian Light Source (CLS) is in the later stages of commissioning. The photon source is a small-gap in-vacuum undulator (SGU), which was designed in-house with a support structure and vacuum chamber from RMP of Italy. The undulator magnets were shimmed at the CLS and the SGU was installed in the 2.9 GeV storage ring. The storage ring has had currents up to 300 mA safely injected and stored since its first light in the diagnostic beamline in December of 2003. At these storage ring currents, the 7th harmonic of the SGU will yield a photon flux on the sample at the endstation on the order of ˜5×1012 at 12 keV. The overall design of the beamline includes white beam slits, indirectly cryo-cooled first crystal of the DCM and sagittally focusing second crystal, and vertically focussing ULE mirror. The endstation of the beamline is innovative and robust, and was manufactured by ACCEL according to CLS specifications. The beamline controls, are being developed based on EPICS, and complemented with a user-friendly interface. The scientific goal of the 08ID-1 beamline is to operate a protein crystallography MAD beamline suitable for studying small crystals and crystals with large unit cells.

Duffy, Alan; Fodje, Michel; Berg, Russ; Grochulski, Pawel

2007-11-01

230

Synchrotron radiation macromolecular crystallography: science and spin-offs.  

PubMed

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

Helliwell, John R; Mitchell, Edward P

2015-03-01

231

Rheological Properties and Structure of Aqueous Solutions of Polysaccharides. Solutions of Sodium Carboxymethylcellulose Fractions of Different Molar Mass  

Microsoft Academic Search

Rheological and spectrophotometric data are obtained that confirm the difference in the conformational state of Na-CMC macromolecules with a degree of polymerization of 120, 916, and 1740 in aqueous solution. It was found that the nonlinearity of the concentration curves of both the structural characteristics and the flow activation parameters is a distinctive feature of the solutions of the fraction

S. M. Prusova; I. V. Ryabinina; A. N. Prusov

2002-01-01

232

Macromolecular networks and intelligence in microorganisms  

PubMed Central

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

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

233

Macromolecular Topography Leaps into the Digital Age  

NASA Technical Reports Server (NTRS)

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.

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

2003-01-01

234

Solution structure of the strawberry allergen Fra a 1  

PubMed Central

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 ?-sheet, two short V-shaped ?-helices and a long C-terminal ?-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

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

2012-01-01

235

Analytical solution of thermal magnetization on memory stabilizer structures  

E-print Network

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 [arXiv:0907.0394v1] for finite size systems. Analytical solutions show that there is no finite critical temperature, Tc=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.

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

2010-06-24

236

Analytical solution of thermal magnetization on memory stabilizer structures  

SciTech Connect

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.

Tomita, Yu; Viteri, C. Ricardo; Brown, Kenneth R. [Schools of Chemistry and Biochemistry, Computational Science and Engineering, and Physics, Georgia Institute of Technology, Atlanta, Georgia 30332 (United States)

2010-10-15

237

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

NASA Astrophysics Data System (ADS)

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.

Richmond, Geraldine

2013-03-01

238

a Procedural Solution to Model Roman Masonry Structures  

NASA Astrophysics Data System (ADS)

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.

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

2013-07-01

239

Macromolecular Crowding Directs Extracellular Matrix Organization and Mesenchymal Stem Cell Behavior  

E-print Network

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

Zeiger, Adam Scott

240

Macromolecular crystallography beamline X25 at the NSLS  

PubMed Central

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

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

241

A macromolecular prodrug strategy for combinatorial drug delivery.  

PubMed

A novel macromolecular prodrug strategy was developed for the combinatorial delivery of two poorly water-soluble drugs, dexamethasone and doxorubicin. In this work, dexamethasone was firstly conjugated onto a water-soluble modified polysaccharide by an acid-labile hydrazone linkage. The resultant macromolecular prodrug had an amphiphilic character and could self-assemble into spherical polymeric micelles in aqueous system. With these micelles, doxorubicin was then encapsulated into their hydrophobic cores. For the conjugated dexamethasone and encapsulated doxorubicin, they could exhibit independent and acid-sensitive release characteristics. For the doxorubicin-loaded prodrug micelles, they were easily be internalized by living cells and showed obvious antitumor activity. PMID:24407691

Li, Nan-Nan; Lin, Jiantao; Gao, Di; Zhang, Li-Ming

2014-03-01

242

Solution state structures of human pancreatic amylin and pramlintide  

PubMed Central

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 ? 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

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

2009-01-01

243

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

NASA Astrophysics Data System (ADS)

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.

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

2015-02-01

244

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

NASA Technical Reports Server (NTRS)

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.

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

2001-01-01

245

Bis(imidazolylidene)s as modular building blocks for monomeric and macromolecular organometallic materials.  

PubMed

The synthetic and structural progression surrounding N-heterocyclic carbenes has given rise to great functional and architectural diversity in organometallic chemistry, catalysis, and materials science. The development of new, modular scaffolds for bridging transition metals is essential in order to expand the boundaries of these scientific areas. This Frontier article summarizes recent advances in the synthesis and study of ditopic ligands displaying two linearly opposed carbene moieties and emphasizes their versatility in the preparation of new organometallic and macromolecular materials. The conclusion previews their utility in conjugated organic/inorganic hybrid materials with potential applications in the emerging fields of molecular- and nanoelectronics. PMID:16924285

Boydston, Andrew J; Bielawski, Christopher W

2006-09-14

246

Facilities for macromolecular crystallography at the Helmholtz-Zentrum Berlin  

PubMed Central

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

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

2012-01-01

247

Facilities for macromolecular crystallography at the Helmholtz-Zentrum Berlin.  

PubMed

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

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

2012-05-01

248

Dimensionality Reduction Techniques to Improve the Reliability of Model-Based Structural Health Monitoring Solutions  

Microsoft Academic Search

Model-updating solutions are rarely unique: A limited number of measured values may be represented by different optimal numerical models. In Structural Health Monitoring (SHM) a fundamental goal is the determination of the realistic structural condition rather than an \\

B Karczewski; P Lubasch; M Schnellenbach-Held

249

Structure of supersaturated solution and crystal nucleation induced by diffusion  

NASA Astrophysics Data System (ADS)

The effect of a seed crystal on nucleation of L-alanine from a quiescent supersaturated solution was investigated. When a seed crystal was not used, nucleation did not occur at least for 5 h. When a seed crystal was introduced into the supersaturated solution with careful attention to avoid convection of the solution, fine crystals appeared at the place far from the seed crystal. At that time, there was no convection at the place that fine crystals appeared. Namely, there was no possibility that those fine crystals came from the surface of seed crystal. We supposed that nucleation was induced by directional diffusion of solute molecules caused by growth of the seed crystal. In order to prove this hypothesis, we designed an experiment using an apparatus composed of two compartments divided by a dialysis membrane that L-alanine molecules could freely permeate. Two supersaturated solutions having a supersaturation ratio of 1.2 and a smaller ratio were placed in the two compartments in the absence of seed crystals. This apparatus allowed the directional diffusion of solute molecules between two solutions. Nucleation occurred within 30 min. The frequency of nucleation among 7-times repeated experiments was in proportion to the difference of supersaturation ratio between the two solutions. This result poses a new mechanism of the secondary nucleation that the directional diffusion caused by growth of existing crystals induces nucleation.

Ooshima, Hiroshi; Igarashi, Koichi; Iwasa, Hideo; Yamamoto, Ren

2013-06-01

250

Local structure analysis of BaTiO3-KNbO3 solid solution  

NASA Astrophysics Data System (ADS)

The atomic-scale structure of a solid solution of BaTiO3 (BT) and KNbO3 (KN) has been studied using high-energy X-ray diffraction, X-ray absorption fine structure, and atomic pair-distribution function analysis techniques. We prepared BT-KN solid solution using KNbTiO5, in which Ti and Nb atoms are arranged randomly. The average structure of the BT-KN solid solution was cubic and the local structure is also reproduced by the cubic structure. It is rare that a solid solution synthesized from ferroelectric materials has the local structure of a paraelectric material. Since the original correlation of BT or KN was lost, ferroelectricity disappeared in the BT-KN solid solution.

Yoneda, Yasuhiro; Kohara, Shinji; Kumada, Nobuhiro; Wada, Satoshi

2014-09-01

251

The Lunar Internal Structure Model: Problems and Solutions  

NASA Astrophysics Data System (ADS)

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

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

252

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

E-print Network

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

Barthelat, Francois

253

Neutron Macromolecular Crystallography (NMC) can provide accurate hydrogen atom  

E-print Network

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

Pennycook, Steve

254

Roles of partly unfolded conformations in macromolecular self-assembly  

Microsoft Academic Search

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

Keiichi Namba

2001-01-01

255

Relationship between structure of hydrocolloid gels and solutions and flavour release  

Microsoft Academic Search

To provide further insight into the relationship between the structure of hydrocolloid solutions and gels and perception of taste and flavour, solutions of gelatin and locust bean gum (LBG), and gels prepared from mixtures of (a) high acetyl and low acetyl and gellan (b) carrageenan and LBG were studied. Both the solutions contained sodium chloride and the gels were flavoured

Andreas Koliandris; Angelie Lee; Anne-Laure Ferry; Sandra Hill; John Mitchell

2008-01-01

256

Structural Arrest in Dense Star-Polymer Solutions F. Sciortino,1  

E-print Network

Structural Arrest in Dense Star-Polymer Solutions G. Foffi,1 F. Sciortino,1 P. Tartaglia,1 E of disordered arrested states in star-polymer solutions. DOI: 10.1103/PhysRevLett.90.238301 PACS numbers: 83. Especially at high functionalities, the solutions display a gelation transition, i.e., a dynamical arrest

Sciortino, Francesco

257

The structure of ionic aqueous solutions at interfaces: an intrinsic structure analysis.  

PubMed

We investigate the interfacial structure of ionic solutions consisting of alkali halide ions in water at concentrations in the range 0.2-1.0 molal and at 300 K. Combining molecular dynamics simulations of point charge ion models and a recently introduced computational approach that removes the averaging effect of interfacial capillary waves, we compute the intrinsic structure of the aqueous interface. The interfacial structure is more complex than previously inferred from the analysis of mean profiles. We find a strong alternating double layer structure near the interface, which depends on the cation and anion size. Relatively small changes in the ion diameter disrupt the double layer structure, promoting the adsorption of anions or inducing the density enhancement of small cations with diameters used in simulation studies of lithium solutions. The density enhancement of the small cations is mediated by their strong water solvation shell, with one or more water molecules "anchoring" the ion to the outermost water layer. We find that the intrinsic interfacial electrostatic potential features very strong oscillations with a minimum at the liquid surface that is ?4 times stronger than the electrostatic potential in the bulk. For the water model employed in this work, SPC/E, the electrostatic potential at the water surface is ?-2 V, equivalent to ?80 k(B)T (for T = 300 K), much stronger than previously considered. Furthermore, we show that the utilization of the intrinsic surface technique provides a route to extract ionic potentials of mean force that are not affected by the thermal fluctuations, which limits the accuracy of most past approaches including the popular umbrella sampling technique. PMID:22998280

Bresme, Fernando; Chacón, Enrique; Tarazona, Pedro; Wynveen, Aaron

2012-09-21

258

The structure of ionic aqueous solutions at interfaces: An intrinsic structure analysis  

NASA Astrophysics Data System (ADS)

We investigate the interfacial structure of ionic solutions consisting of alkali halide ions in water at concentrations in the range 0.2-1.0 molal and at 300 K. Combining molecular dynamics simulations of point charge ion models and a recently introduced computational approach that removes the averaging effect of interfacial capillary waves, we compute the intrinsic structure of the aqueous interface. The interfacial structure is more complex than previously inferred from the analysis of mean profiles. We find a strong alternating double layer structure near the interface, which depends on the cation and anion size. Relatively small changes in the ion diameter disrupt the double layer structure, promoting the adsorption of anions or inducing the density enhancement of small cations with diameters used in simulation studies of lithium solutions. The density enhancement of the small cations is mediated by their strong water solvation shell, with one or more water molecules "anchoring" the ion to the outermost water layer. We find that the intrinsic interfacial electrostatic potential features very strong oscillations with a minimum at the liquid surface that is ˜4 times stronger than the electrostatic potential in the bulk. For the water model employed in this work, SPC/E, the electrostatic potential at the water surface is ˜-2 V, equivalent to ˜80 kBT (for T = 300 K), much stronger than previously considered. Furthermore, we show that the utilization of the intrinsic surface technique provides a route to extract ionic potentials of mean force that are not affected by the thermal fluctuations, which limits the accuracy of most past approaches including the popular umbrella sampling technique.

Bresme, Fernando; Chacón, Enrique; Tarazona, Pedro; Wynveen, Aaron

2012-09-01

259

Thermodynamic anomalies and structural fluctuations in aqueous solutions of tertiary butyl alcohol  

E-print Network

In this work, we discuss the connection between the anomalies of the thermodynamic properties, experimentally observed in tertiary butyl alcohol (TBA) and water solutions, and the molecular clustering in these solutions, as revealed by molecular dynamics (MD) simulations. These anomalies are observed in relatively dilute solutions of about 0.03 to 0.08 mole fraction of TBA and become more pronounced at low temperatures. MD simulations show that these solutions exhibit shortranged (order of 1 nm), shortlived (tens of picoseconds) "micelle-like" structural fluctuations in the same concentration range. We attribute the anomalies in the thermodynamic properties of aqueous TBA solutions to these structural fluctuations on the molecular scale.

Deepa Subramanian; Jeffery B. Klauda; Jan Leys; Mikhail A. Anisimov

2013-08-16

260

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

NASA Technical Reports Server (NTRS)

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.

Arya, V. K.

1990-01-01

261

Solution structure of the granular starch binding domain of Aspergillus niger glucoamylase bound to -cyclodextrin  

E-print Network

Solution structure of the granular starch binding domain of Aspergillus niger glucoamylase bound the catalytic domains of hydrolytic enzymes. Glucoamylase 1 (G1) from Aspergillus niger, an enzyme used widely of insoluble polysaccharides. Results: The solution structure of the SBD of A. niger G1 bound to -cyclodextrin

Williamson, Mike P.

262

In Vitro Structural Changes of Nano-Bacterial Cellulose immersed in Phosphate Buffer Solution  

E-print Network

In Vitro Structural Changes of Nano-Bacterial Cellulose immersed in Phosphate Buffer Solution-bacterial cellulose, Structural changes, Degradation, Phosphate buffer solution Abstract. Nano-bacterial cellulose (nBC), secreted by Acetobacter xylinum, is expected to have potential applications in tissue engineering

Zheng, Yufeng

263

Localization of bound water in the solution structure of a complex of the erythroid  

E-print Network

words: bound water, GATA-1-DNA complex, NMR solution structure, protein hydration Introduction A numberLocalization of bound water in the solution structure of a complex of the erythroid transcription as a monomer to the asymmetric consensus target sequence (T/A)GATA- (A/G) found in the cis-regulatory elements

Clore, G. Marius

264

New Insights into Histidine Triad Proteins: Solution Structure of a Streptococcus pneumoniae PhtD Domain  

E-print Network

New Insights into Histidine Triad Proteins: Solution Structure of a Streptococcus pneumoniae Pht membranes of Streptococcus pneumoniae (S. pneumoniae) demonstrate that native PhtD and AdcAII interact into Histidine Triad Proteins: Solution Structure of a Streptococcus pneumoniae PhtD Domain and Zinc Transfer

Paris-Sud XI, Université de

265

Assessing the Quality of Solution Nuclear Magnetic Resonance Structures by Complete Cross-Validation  

Microsoft Academic Search

Structure determination of macromolecules in solution by nuclear magnetic resonance (NMR) spectroscopy involves the fitting of atomic models to the observed nuclear Overhauser effect (NOE) data. Complete cross-validation has been used to define reliable and unbiased criteria for the quality of solution NMR structures. The method is based on the partitioning of NOE data into test sets and the cross-validation

Axel T. Brunger; G. Marius Clore; Angela M. Gronenborn; Rainer Saffrich; Michael Nilges

1993-01-01

266

NON-STRUCTURAL FLOOD MANAGEMENT SOLUTIONS FOR THE LOWER FRASER VALLEY,  

E-print Network

NON-STRUCTURAL FLOOD MANAGEMENT SOLUTIONS FOR THE LOWER FRASER VALLEY, BRITISH COLUMBIA by Tamsin OF THE REQUIREMENTS FOR THE DEGREE OF MASTER OF RESOURCE MANAGEMENT in the School of Resource and Environmental of Project: Non-Structural Flood Management Solutions for the Lower Fraser Valley, British Columbia Examining

267

Structural rearrangements in hairy-rod polymer solutions undergoing shear  

Microsoft Academic Search

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

Loic Hilliou; Dimitris Vlassopoulos; Matthias Rehahn

1999-01-01

268

Novel macrocyclic uracil derivatives: Structure in solid and solution  

Microsoft Academic Search

Isomeric pyrimidinophanes containing uracil moieties and nitrogen atoms in bridges have been synthesized and characterized by a variety of methods both in solid and in solution. Unambiguous assignment of mutual arrangement of C(4)pyrO groups at different pyrimidine rings in isomers is made by X-ray diffraction. In solutions the arrangement of C(4)pyrO groups of the isomeric pyrimidinophanes results in different dipole

Vyacheslav Semenov; Aidar Gubaidullin; Olga Kataeva; Olga Lodochnikova; Alina Timosheva; Vladimir Kataev; Rashit Giniyatullin; Anton Nikolaev; Alla Chernova; Roald Shagidullin; Adilya Nafikova; Vladimir Reznik

2006-01-01

269

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

NASA Astrophysics Data System (ADS)

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.

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

2012-02-01

270

A Solid-State NMR Method for Solution of Zeolite Crystal Structures  

Microsoft Academic Search

Since zeolites are notoriously difficult to prepare as large single crystals, structure determination usually relies on powder X-ray diffraction (XRD). However, structure solution (i.e., deriving an initial structural model) directly from powder XRD data is often very difficult due to the diffraction phase problem and the high degree of overlap between the individual reflections, particularly for materials with the structural

Darren H. Brouwer; Richard J. Darton; Russell E. Morris; Malcolm H. Levitt

2005-01-01

271

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

PubMed Central

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

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

2013-01-01

272

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

PubMed

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

Jaskolski, Mariusz; Dauter, Zbigniew; Wlodawer, Alexander

2014-09-01

273

Developing Force Fields from the Microscopic Structure of Solutions.  

PubMed

We have been developing force fields designed for the eventual simulation of peptides and proteins using the Kirkwood-Buff (KB) theory of solutions as a guide. KB theory provides exact information on the relative distributions for each species present in solution. This information can also be obtained from computer simulations. Hence, one can use KB theory to help test and modify the parameters commonly used in biomolecular studies. A series of small molecule force fields representative of the fragments found in peptides and proteins have been developed. Since this approach is guided by the KB theory, our results provide a reasonable balance in the interactions between self-association of solutes and solute solvation. Here, we present our progress to date. In addition, our investigations have provided a wealth of data concerning the properties of solution mixtures, which is also summarized. Specific examples of the properties of aromatic (benzene, phenol, p-cresol) and sulfur compounds (methanethiol, dimethylsulfide, dimethyldisulfide) and their mixtures with methanol or toluene are provided as an illustration of this kind of approach. PMID:20161692

Ploetz, Elizabeth A; Bentenitis, Nikolaos; Smith, Paul E

2010-03-25

274

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

NASA Astrophysics Data System (ADS)

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.

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

2015-03-01

275

Structural monitoring system with fiber Bragg grating sensors: Implementation and software solution  

E-print Network

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.

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

2014-01-01

276

Imaging Macromolecular Interactions at an Interface  

PubMed Central

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

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

2010-01-01

277

Effect of Base Sequence on G-Wire Formation in Solution  

PubMed Central

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

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

2010-01-01

278

Evidence for water structuring forces between surfaces  

SciTech Connect

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.

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

2011-01-01

279

Structural health monitoring - better solutions using fiber optic sensors?  

Microsoft Academic Search

This work focuses on results from recent research carried out to create and then investigate the performance of a number of different fiber optic sensor systems developed to monitor the changes occurring to civil engineering structures over time, both physical and chemical and which underpin their structural integrity.

S. K. T. Grattan; S. E. Taylor; P. A. M. Basheer; T. Sun; K. T. V. Grattan

2009-01-01

280

Use of Plastic Capillaries for Macromolecular Crystallization  

NASA Technical Reports Server (NTRS)

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.

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

2003-01-01

281

DOT2: Macromolecular Docking With Improved Biophysical Models  

PubMed Central

Computational docking is a useful tool for predicting macromolecular complexes, which are often difficult to determine experimentally. Here we present the DOT2 software suite, an updated version of the DOT intermolecular docking program. DOT2 provides straightforward, automated construction of improved biophysical models based on molecular coordinates, offering checkpoints that guide the user to include critical features. DOT has been updated to run more quickly, allow flexibility in grid size and spacing, and generate a complete list of favorable candidate configu-rations. Output can be filtered by experimental data and rescored by the sum of electrostatic and atomic desolvation energies. We show that this rescoring method improves the ranking of correct complexes for a wide range of macromolecular interactions, and demonstrate that biologically relevant models are essential for biologically relevant results. The flexibility and versatility of DOT2 accommodate realistic models of complex biological systems, improving the likelihood of a successful docking outcome. PMID:23695987

Roberts, Victoria A.; Thompson, Elaine E.; Pique, Michael E.; Perez, Martin S.; Eyck, Lynn Ten

2015-01-01

282

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

PubMed Central

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

Zeng, Zhongqing; Jan, Kung-Ming

2012-01-01

283

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

E-print Network

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

Woodall, Jerry M.

284

Solution Structure of the Tumor Necrosis Factor Receptor-1 Death Domain  

E-print Network

Solution Structure of the Tumor Necrosis Factor Receptor-1 Death Domain Steven F. Sukits1 , Lih 02140, USA Tumor necrosis factor receptor-1 death domain (TNFR-1 DD) is the intra- cellular functional members of the death domain superfamily. The secondary structure and three- dimensional structure of R347K

Powers, Robert

285

Solution-Phase Structural Characterization of Supramolecular Assemblies by Molecular Diffraction  

E-print Network

association and exclusion. Introduction The preparation of molecular squares, rectangles, triangles, and other: Structures of four molecular squares based on rhenium coordination chemistry have been characterized of structures for pyrazine- and bipyridine-edged squares measured in solution with structures determined

286

The solution structure of bovine pancreatic trypsin inhibitor at high pressure  

E-print Network

The solution structure of bovine pancreatic trypsin inhibitor at high pressure MICHAEL P difficult to obtain protein structures at high pres- sure. Crystallography of proteins at high pressure tend to dissolve or crack at high pressure. Consequently, there are only two crystal structures

Williamson, Mike P.

287

Aqueous solutions. 1. Structural thermodynamic internal pressure of water  

SciTech Connect

The 3-D hydrogen bonding gives water its unique structural properties (e.g., the configuration can vary on a molecular level even at constant volume) and gives rise to an internal structural pressure, p/sub s/. This pressure provides a link between macroscopic and microscopic properties, p/sub s/ has been analyzed in terms of dielectric correlations and relaxations and compared with related quantities from an infrared orientation-defect (OD) model. In the limit, as p/sub s/ approaches zero, the water structure appears to approach that of glassy water. 3 tables.

Leyendekkers, J.V.

1983-08-18

288

Characterization of Water-Soluble Macromolecular Substances in Cloud Water  

Microsoft Academic Search

In this contribution we present to our knowledge the first investigations of macromolecular, often called humic-like substances (HULIS) in cloud water samples and compare them with water-soluble extracts from atmospheric PM2.5, soils and waters to study its possible origin. Chemical analysis was done using high performance liquid chromatography (HPLC) coupled with UV and diode array detector, and HPLC coupled with

Jinsheng Feng; Detlev Möller

2004-01-01

289

Mechanisms of Human Arrhythmia Syndromes: Abnormal Cardiac Macromolecular Interactions  

NSDL National Science Digital Library

Many cardiac ion channels exist within macromolecular signaling complexes, comprised of pore-forming subunits that associate with auxiliary subunits, regulatory enzymes, and targeting proteins. This complex protein assembly ensures proper modulation of channel activity and ion homeostasis. The association of genetic defects in regulatory and targeting proteins to inherited arrhythmia syndromes has led to a better understanding of the critical role these proteins play in ion channel modulation.

2007-10-01

290

A 3D cellular context for the macromolecular world  

PubMed Central

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

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

291

Impact of synchrotron radiation on macromolecular crystallography: a personal view  

PubMed Central

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

Dauter, Zbigniew; Jaskolski, Mariusz; Wlodawer, Alexander

2010-01-01

292

Thermodynamics and Statistical Mechanics of Macromolecular Systems  

NASA Astrophysics Data System (ADS)

Preface and outline; 1. Introduction; 2. Statistical mechanics: a modern review; 3. The complexity of minimalistic lattice models for protein folding; 4. Monte Carlo and chain growth methods for molecular simulations; 5. First insights to freezing and collapse of flexible polymers; 6. Crystallization of elastic polymers; 7. Structural phases of semiflexible polymers; 8. Generic tertiary folding properties of proteins in mesoscopic scales; 9. Protein folding channels and kinetics of two-state folding; 10. Inducing generic secondary structures by constraints; 11. Statistical analyses of aggregation processes; 12. Hierarchical nature of phase transitions; 13. Adsorption of polymers at solid substrates; 14. Hybrid protein-substrate interfaces; 15. Concluding remarks and outlook; Notes; References; Index.

Bachmann, Michael

2014-04-01

293

Solution Structure of the HU Protein from Bacillus stearothermophilus  

Microsoft Academic Search

The histone-like protein HU fromBacillus stearothermophilusis a dimer with a molecular mass of 19.5 kDa that is capable of bending DNA. An X-ray structure has been determined, but no structure could be established for a large part of the supposed DNA-binding ?-arms. Using distance and dihedral constraints derived from triple-resonance NMR data of a13C\\/15N doubly-labelled HU protein 49 distance geometry

Hans Vis; Matteo Mariani; Constantin E. Vorgias; Keith S. Wilson; Robert Kaptein; Rolf Boelens

1995-01-01

294

Dynamic coupling of asymmetric shear wall structures: an analytical solution  

Microsoft Academic Search

In this paper, a dynamic analysis is presented for coupled flexural-warping torsional vibration of asymmetric shear wall structures in tall buildings. Due to the asymmetry of the structure, the free vibration is a coupled one, where laterally flexural vibrations in two orthogonal directions are coupled by a warping torsional vibration. Based on the continuum approach and D’Alembert’s principle, the governing

J. S. Kuang; S. C. Ng

2001-01-01

295

Macromolecular Assemblage in the Design of a Synthetic AIDS Vaccine  

NASA Astrophysics Data System (ADS)

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.

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

1992-05-01

296

MUFOLD: A new solution for protein 3D structure prediction  

PubMed Central

There have been steady improvements in protein structure prediction during the past 2 decades. However, current methods are still far from consistently predicting structural models accurately with computing power accessible to common users. Toward achieving more accurate and efficient structure prediction, we developed a number of novel methods and integrated them into a software package, MUFOLD. First, a systematic protocol was developed to identify useful templates and fragments from Protein Data Bank for a given target protein. Then, an efficient process was applied for iterative coarse-grain model generation and evaluation at the C? or backbone level. In this process, we construct models using interresidue spatial restraints derived from alignments by multidimensional scaling, evaluate and select models through clustering and static scoring functions, and iteratively improve the selected models by integrating spatial restraints and previous models. Finally, the full-atom models were evaluated using molecular dynamics simulations based on structural changes under simulated heating. We have continuously improved the performance of MUFOLD by using a benchmark of 200 proteins from the Astral database, where no template with >25% sequence identity to any target protein is included. The average root-mean-square deviation of the best models from the native structures is 4.28 Å, which shows significant and systematic improvement over our previous methods. The computing time of MUFOLD is much shorter than many other tools, such as Rosetta. MUFOLD demonstrated some success in the 2008 community-wide experiment for protein structure prediction CASP8. PMID:19927325

Zhang, Jingfen; Wang, Qingguo; Barz, Bogdan; He, Zhiquan; Kosztin, Ioan; Shang, Yi; Xu, Dong

2010-01-01

297

INTERNATIONAL Macromolecular crystal growth and optimisation methods  

E-print Network

& Pharmaceutical Chemistry, 11635 Athens, Greece The purification of proteins: Objectives and strategy, choice Professor John R. Helliwell, Professor of Structural Chemistry and Chair, School of Chemistry, University, Senior Researcher, N.C.S.R. "Demokritos", Institute of Physical Chemistry, Athens, Greece. Member

298

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

SciTech Connect

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.

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

2006-08-01

299

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

PubMed

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

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

2011-05-01

300

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

SciTech Connect

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.

Mereghetti, Paolo; Wade, Rebecca C.

2012-07-26

301

Developing A Bitwise Macromolecular Assembly Simulator  

E-print Network

a c t i o n A s s e m b l e d BMAS ODE Trimer 10 -3 10 0 10 3 10 6 Time[s] 0 0.2 0.4 0.6 0.8 1 F r a c t i o n A s s e m b l e d BMAS ODE Four Layer Trimer 10 -3 10 0 10 3 10 6 Time[s] 0 0.2 0.4 0.6 0.8 1 F r a c t i o n A s s e m b l e d BMAS...); Saiz and Vilar (2006); Bray and Lay (1997); Sweeny et al. (2008)). The final class of reaction that might occur is one in which the final structure that is formed would have more subunits than the full structure (Fig. 1d). As mentioned above, our...

Xu, Zaikun

2014-08-31

302

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

E-print Network

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

Wider, Gerhard

303

Finite element solution of transient fluid-structure interaction problems  

NASA Technical Reports Server (NTRS)

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.

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

1991-01-01

304

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

PubMed Central

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

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

305

ANOVA-HDMR structure of the higher order nodal diffusion solution  

SciTech Connect

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)

Bokov, P. M.; Prinsloo, R. H.; Tomasevic, D. I. [South African Nuclear Energy Corporation - Necsa, Building 1900, P.O. Box 582, 0001 Pretoria (South Africa)

2013-07-01

306

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

Microsoft Academic Search

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

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

2008-01-01

307

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

E-print Network

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

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

2009-10-22

308

Element-by-element Solution Procedures for Nonlinear Structural Analysis  

NASA Technical Reports Server (NTRS)

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.

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

1984-01-01

309

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

PubMed

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 ?* orbital through solvent-to-solute charge transfer. PMID:25760386

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

2015-04-14

310

nature | methods A nano-positioning system for macromolecular structural  

E-print Network

Supplementary Figure 4 DNA1 in presence of TFIIB Supplementary Figure 5 Pol II pull down experiments Supplementary Figure 6 Radial profiles of fuzzy spheres of RNA 1 Supplementary Figure 7 Radial profiles of fuzzy), Rpb7 (red), template DNA strand (blue), non-template DNA strand (cyan) and RNA product (red

Ulm, Universität

311

Molecular Structure of Hydrochloric acid (if in aqueous solution)  

NSDL National Science Digital Library

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

2002-09-10

312

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

PubMed Central

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

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

2008-01-01

313

EDM-DEDM and protein crystal structure solution.  

PubMed

Electron-density modification (EDM) procedures are the classical tool for driving model phases closer to those of the target structure. They are often combined with automated model-building programs to provide a correct protein model. The task is not always performed, mostly because of the large initial phase error. A recently proposed procedure combined EDM with DEDM (difference electron-density modification); the method was applied to the refinement of phases obtained by molecular replacement, ab initio or SAD phasing [Caliandro, Carrozzini, Cascarano, Giacovazzo, Mazzone & Siliqi (2009), Acta Cryst. D65, 249-256] and was more effective in improving phases than EDM alone. In this paper, a novel fully automated protocol for protein structure refinement based on the iterative application of automated model-building programs combined with the additional power derived from the EDM-DEDM algorithm is presented. The cyclic procedure was successfully tested on challenging cases for which all other approaches had failed. PMID:19390153

Caliandro, Rocco; Carrozzini, Benedetta; Cascarano, Giovanni Luca; Giacovazzo, Carmelo; Mazzone, Anna Maria; Siliqi, Dritan

2009-05-01

314

Molecular solutes in ionic liquids: a structural perspective.  

PubMed

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

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

2007-11-01

315

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

PubMed Central

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

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

316

Investigations on the structure of DMSO and acetone in aqueous solution  

SciTech Connect

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.

McLain, Sylvia E [ORNL; Soper, Alan K [ORNL

2007-01-01

317

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

NASA Astrophysics Data System (ADS)

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.

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

2012-05-01

318

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

NASA Technical Reports Server (NTRS)

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.

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

1995-01-01

319

Investigations on the structure of dimethyl sulfoxide and acetone in aqueous solution.  

PubMed

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. PMID:17994835

McLain, Sylvia E; Soper, Alan K; Luzar, Alenka

2007-11-01

320

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

SciTech Connect

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.

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

321

Comparison of Burnett, super-Burnett and Monte Carlo solutions for hypersonic shock structure  

NASA Technical Reports Server (NTRS)

The continuum Navier-Stokes, Burnett, and super-Burnett equations are solved for one-dimensional shock structures in various monoatomic gases. Solutions for a hard sphere gas, argon, and a Maxwellian gas from Mach 1.3 to Mach 50 are obtained. A numerical method utilizing the complete time-dependent continuum equations and obtaining the steady-state shock structure by allowing the system to relax from arbitrary initial conditions is employed. Shock density, velocity, temperature, and entropy profiles are also obtained using the direct simulation Monte Carlo method, and these results are used as bases for comparison for continuum solution profiles. It is shown that the Burnett equations yield shock structure solutions in much closer agreement to both Monte Carlo and experimental results than do the Navier-Stokes equations. Solutions to the super-Burnett equations with coefficients as presently derived, however, are considered to be inferior to those of the Burnett equations.

Fiscko, Kurt A.; Chapman, Dean R.

1989-01-01

322

Analytical solutions for transient and steady state beam loading in arbitrary traveling wave accelerating structures  

Microsoft Academic Search

Analytical solutions are derived for both transient and steady state gradient distributions in the traveling wave (TW) accelerating structures with arbitrary variation of parameters over the structure length. The results of the unloaded and beam loaded cases are presented. Finally, the exact analytical shape of the rf pulse waveform was found in order to apply the transient beam loading compensation

A. Lunin; V. Yakovlev; A. Grudiev

2011-01-01

323

J. Mol. Biol. (1996) 264, 585602 The NMR Solution Structure of Intestinal Fatty  

E-print Network

J. Mol. Biol. (1996) 264, 585­602 The NMR Solution Structure of Intestinal Fatty Acid structure of rat intestinal fatty acid-binding protein (I-FABP) complexed with palmitate has been determined and the location and conformation of the bound fatty acid. 7 1996 Academic Press Limited Keywords: intestinal fatty

Ponder, Jay

324

Solvent structural contributions to the dissolution process of an apolar solute in water  

NASA Astrophysics Data System (ADS)

We have examined structural features of aqueous microenvironments in the neighborhood of an apolar solute (Xe atom) using molecular dynamics techniques and the simple point charge model to represent the solvent. A detailed comparative study of equilibrium spatial correlations of the solvent structures in bulk and in the neighborhood of the Xe atom was performed. We have also obtained structural information for water surrounding a cavity spontaneously generated in liquid water. Our results indicate the absence of any significant solvent reorientation following the introduction of an apolar solute in a cavity existing in the bulk liquid; this agrees with results from recent neutron scattering experiments.

Re, Mario; Laria, Daniel; Fernández-Prini, Roberto

1996-02-01

325

Hydration structures of 2-butoxyethanol monomer and micelle in solution  

NASA Astrophysics Data System (ADS)

We determined the hydration numbers of 2-butoxyethanol (2BE) molecules in the monomeric and the micellar form using terahertz time-domain attenuated total reflection spectroscopy. The hydration number of the 2BE monomer is somewhat larger than that of the 2BE molecule in micelles due to the presence of immobilized water molecules around the hydrophobic surface of the 2BE monomer. The hydration number of the 2BE monomer decreases with increasing the temperature, whereas the hydration number of the 2BE micelle is almost unchanged up to 47 °C. This indicates that strongly bound hydration water molecules should exist and make a self-organized structure on the micelle surface.

Arikawa, Takashi; Nagai, Masaya; Tanaka, Koichiro

2009-07-01

326

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

PubMed

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

Tsuru, T; Chrzan, D C

2015-01-01

327

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

PubMed Central

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

Tsuru, T.; Chrzan, D. C.

2015-01-01

328

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

NASA Astrophysics Data System (ADS)

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.

Tsuru, T.; Chrzan, D. C.

2015-03-01

329

Methods to determine the pressure dependence of the molecular order parameter in (bio)macromolecular fibres.  

PubMed

The experimental realization and an algorithm for analysing the pressure dependence of the molecular order parameter of specific structural moieties in (bio)macromolecular fibres are described. By employing a diamond anvil cell (DAC) the polarization-dependent IR-transmission and in parallel, using an integrated microscope, the macroscopic orientation of the fibres is determined. This enables one to separate between order and disorder at macroscopic and microscopic scales. Using the example of spider silk the pressure dependence of the molecular order parameter of alanine groups being located within nano-crystalline building blocks is deduced and found to decrease reversibly by 0.01 GPa(-1) when varying the external hydrostatic pressure between 0 and 3 GPa. PMID:25557527

Anton, Arthur Markus; Gutsche, Christof; Kossack, Wilhelm; Kremer, Friedrich

2015-01-28

330

Phase transitions of macromolecular microsphere composite hydrogels based on the stochastic Cahn-Hilliard equation  

NASA Astrophysics Data System (ADS)

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.

Li, Xiao; Ji, Guanghua; Zhang, Hui

2015-02-01

331

Macromolecular crowding and confinement: biochemical, biophysical, and potential physiological consequences*  

PubMed Central

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

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

2009-01-01

332

Effects of Macromolecular Crowding on the Collapse of Biopolymers  

NASA Astrophysics Data System (ADS)

Experiments show that macromolecular crowding modestly reduces the size of intrinsically disordered proteins even at a volume fraction (? ) similar to that in the cytosol, whereas DNA undergoes a coil-to-globule transition at very small ? . We show using a combination of scaling arguments and simulations that the polymer size R¯ g(? ) depends on x =R¯ g(0 )/D , where D is the ? -dependent distance between the crowders. If x ?O (1 ) , there is only a small decrease in R¯ g(? ) as ? increases. When x ?O (1 ) , a cooperative coil-to-globule transition is induced. Our theory quantitatively explains a number of experiments.

Kang, Hongsuk; Pincus, Philip A.; Hyeon, Changbong; Thirumalai, D.

2015-02-01

333

Macromolecular Crowding as a Suppressor of Human IAPP Fibril Formation and Cytotoxicity  

PubMed Central

The biological cell is known to exhibit a highly crowded milieu, which significantly influences protein aggregation and association processes. As several cell degenerative diseases are related to the self-association and fibrillation of amyloidogenic peptides, understanding of the impact of macromolecular crowding on these processes is of high biomedical importance. It is further of particular relevance as most in vitro studies on amyloid aggregation have been performed in diluted solution which does not reflect the complexity of their cellular surrounding. The study presented here focuses on the self-association of the type-2 diabetes mellitus related human islet amyloid polypeptide (hIAPP) in various crowded environments including network-forming macromolecular crowding reagents and protein crowders. It was possible to identify two competing processes: a crowder concentration and type dependent stabilization of globular off-pathway species and a – consequently - retarded or even inhibited hIAPP fibrillation reaction. The cause of these crowding effects was revealed to be mainly excluded volume in the polymeric crowders, whereas non-specific interactions seem to be most dominant in protein crowded environments. Specific hIAPP cytotoxicity assays on pancreatic ?-cells reveal non-toxicity for the stabilized globular species, in contrast to the high cytotoxicity imposed by the normal fibrillation pathway. From these findings it can be concluded that cellular crowding is able to effectively stabilize the monomeric conformation of hIAPP, hence enabling the conduction of its normal physiological function and prevent this highly amyloidogenic peptide from cytotoxic aggregation and fibrillation. PMID:23922768

Seeliger, Janine; Werkmüller, Alexander; Winter, Roland

2013-01-01

334

NMR studies on the solution structure of a deletion mutant of the transcarboxylase biotin carrier subunit.  

PubMed

A deletion mutant of the transcarboxylase biotin carrier protein was completely labeled with 13C and 15N. A multitude of 2D and 3D NMR spectra were recorded and assigned. An NMR solution structure was derived from the data and compared in detail with the recently published structure of the wild-type. It is shown that deletion of 30% of the amino acids does not alter the structure of the rigid protein core. PMID:12297230

Jank, Matthias M; Sadowsky, Jack D; Peikert, Claudia; Berger, Stefan

2002-10-01

335

Solution structure of the cAMP-dependent protein kinase  

SciTech Connect

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.

Trewhella, J.; Olah, G.A. [Los Alamos National Lab., NM (United States); Walsh, D.A.; Mitchell, R.D. [Univ. of California, Davis, CA (United States)

1998-12-31

336

Analytical solutions for transient and steady state beam loading in arbitrary traveling wave accelerating structures  

SciTech Connect

Analytical solutions are derived for both transient and steady state gradient distributions in the traveling wave (TW) accelerating structures with arbitrary variation of parameters over the structure length. The results of the unloaded and beam loaded cases are presented. Finally, the exact analytical shape of the rf pulse waveform was found in order to apply the transient beam loading compensation scheme during the structure filling time. The obtained theoretical formulas were cross-checked by direct numerical simulations on the CLIC main linac accelerating structure and demonstrated a good agreement. The proposed methods provide a fast and reliable tool for the initial stage of the TW structure analysis.

Lunin, A.; Yakovlev, V.; /Fermilab; Grudiev, A.; /CERN

2011-05-02

337

Structure and Interactions in Concentrated Diblock Copolymer Solutions  

NASA Astrophysics Data System (ADS)

We report on investigations of polystyrene/polyisoprene (PS/PI) diblock copolymers suspended in decane using small angle scattering techniques. The primary objective of this research is the understanding of the bulk properties and structure in concentrated diblock copolymers in a solvent selective for one block. In this case, decane is a good solvent for polyisoprene. Suspending PS/PI diblocks in decane at low concentrations produces monodisperse, spherical micelles comprising a dense core of polystyrene and a diffuse corona of polyisoprene. These micelles are well idealized as spherical cores with a fixed number of polyisoprene chains tethered to the surface. Since the local curvature plays an important role in determining the coronal density profile, the core radius and aggregation number are experimentally calculated. This experimental characterization lends each polymeric micelle to a description of the micellar architecture and pair-interaction potential through use of self-consistent mean field equations for tethered-chain systems. We use these pair-potentials to describe the liquid-like interference and disorder-order transition observed experimentally. Gillan's method, subject to a Rogers-Young closure, provides a description of the liquid-state. Density functional theory, specifically the modified weighted density approximation of Denton and Ashcroft, is used to estimate the solid-state. We supplement these calculations with a semi-quantitative phase diagram demonstrating the diversity in phase behavior resulting from tuning the range of the repulsions by varying block asymmetry; the phase diagram includes regions of face-centered cubic (FCC) and body-centered cubic (BCC) crystals depending on the range of the coronal layer thickness relative to the core dimension. In addition to these studies, we conclude with a discussion of the phase behavior of diblock copolymers at concentrations intermediate to those witnessing cubic micellar crystals and the ordered melt morphology; a region where shape transitions are anticipated. We find a curious mechanism for these transitions that first includes the melting of the micellar crystal. We present a qualitative argument for this order-disorder transition upon increasing the polymer concentration that focuses on a loss of the osmotic pressure gradient.

McConnell, Glen A.

338

Local structure of the halite-sylvine solid solution according to the computer simulation data  

SciTech Connect

The structural, elastic, and thermodynamic properties of halite NaCl and sylvine KCl and the miscibility properties of the NaCl-KCl solid solution found by computer simulation are in good agreement with the experimental data. Analysis of the relaxation of the solid solution structure suggests that both anion and cation sublattices are distorted; however, the anion sublattice is distorted much more strongly. Calculations of the local bond valence at all types of ions in the solid solution show opposite deviations from the balance at cations, whereas the general balance is retained. The values of the electrostatic potential in the ion positions reflect weakening of bonding in the solid solution with respect to its pure components. In addition, with an increase in the average interatomic distance in the first coordination sphere around cations, the modulus of the electrostatic potential at cations decreases.

Urusov, V. S., E-mail: urusov@geol.msu.ru; Leonenko, E. V. [Moscow State University (Russian Federation)

2008-09-15

339

Dependence of lubrication regime on structure of aquaeous solutions of polymeric surfactants  

SciTech Connect

This article investigates the influence of the structurization processes in 1% aqueous solutions of homologues of comb-shaped polyampholytes on the lubrication regime. The viscosities of the aqueous solutions of the polyampholytes were measured in a thermostated cell, by means of constant-pressure capillary viscometry, in the temperature range 300-350/sup 0/K. The fluids were checked in a friction tester with a contact system consisting of a flat disk and three pin specimens with a diameter of 6 mm. The results indicate that the increase in viscosity with increasing temperature in aqueous solutions of strongly hydrophobic polyampholytes is related to an increase in the intermolecular interaction and the formation of a three-dimensional network connecting the macromolecules of the polyampholytes in the solution. It is concluded that structurization in lubricating media can have a substantial effect on the lubrication regime and on the wear and deformation characteristics of the interacting materials under conditions of external friction.

Maifet, Y.P.; Krivenko, I.I.; Pilyavskii, V.S.; Tanchuk, Y.V.

1984-03-01

340

Microscopic structure of travelling wave solutions in a class of stochastic interacting particle systems  

Microsoft Academic Search

We obtain exact travelling wave solutions for three families of stochastic one-dimensional non-equilibrium lattice models with open boundaries. These solutions describe the diffusive motion and microscopic structure of (i) shocks in the partially asymmetric exclusion process with open boundaries, (ii) a lattice Fisher wave in a reaction–diffusion system, and (iii) a domain wall in non-equilibrium Glauber–Kawasaki dynamics with magnetization current.

K. Krebs; F. H. Jafarpour; G. M. Schutz

2003-01-01

341

Finite element solution for the structural behavior of a scientific balloon  

NASA Astrophysics Data System (ADS)

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.

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

1993-02-01

342

Structural and nanomechanical comparison of epitaxially and solution-grown amyloid ?25-35 fibrils.  

PubMed

A?25-35, the fibril-forming, biologically active toxic fragment of the full-length amyloid ?-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 1640cm(-1), indicating that ?-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 A?25-35 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

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

2015-05-01

343

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

NASA Astrophysics Data System (ADS)

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.

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

2013-11-01

344

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

PubMed Central

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

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

2013-01-01

345

Structural hierarchy of several proteins observed by wide-angle solution scattering.  

PubMed

In the present study using a high-intensity X-ray beam from a third-generation synchrotron radiation source, it is demonstrated that a wide-angle X-ray scattering (WAXS) profile from several globular proteins in solution can reflect not only the overall structures (approximately 300 A distance resolution) but also intramolecular structures ranging to secondary structures (approximately 2.5 A distance resolution). The proteins treated in the present experiments are classified as different types of structure categories, namely, as all-alpha, all-beta and alpha + beta proteins. Here the full-range experimental scattering curves are compared with the theoretical curves, suggesting a further availability of the SR-WAXS method for studies of structure hierarchy and the function of proteins in solutions. PMID:12091726

Hirai, Mitsuhiro; Iwase, Hiroki; Hayakawa, Tomohiro; Miura, Keiko; Inoue, Katsuaki

2002-07-01

346

Electronic structure and solution behavior of a tris(N,N'-diphenylhydrazido)manganese(IV) propeller complex.  

PubMed

The electronic structure and magnetic properties of the manganese(IV) trihydrazide propeller complex, Li(2)Mn(?(2)-PhN-NPh)(3)L(2) (1, L = tetrahydrofuran, diethyl ether), are explored. EPR and solid-state magnetometry studies are indicative of a high spin Mn(IV) with a S = 3/2 spin state. Solution-phase magnetic measurements result in a measured ?(eff) less than that expected for a S = 3/2, indicating a solution-phase equilibrium with a lower-spin species. Concentration-dependent magnetic susceptibility measurements identify clustering of 1 to an antiferromagnetically coupled multinuclear complex as the most likely explanation for the solution behavior. Comparative infrared spectroscopy in solution and solid phase are described which support speciation in solution. PMID:22610376

Kondaveeti, Sandeep K; Vaddypally, Shivaiah; McCall, Jeffrey D; Zdilla, Michael J

2012-07-14

347

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

E-print Network

Atomistic Modeling of Macromolecular Crowding Predicts Modest Increases in Protein Folding that macromolecular crowding can increase protein folding stability, but depending on details of the models (e.g., how on the effects of macro- molecular crowding on protein folding and binding stability has been reached. Crowders

Weston, Ken

348

Effect of Macromolecular Crowding on Protein Binding Stability: Modest Stabilization and Significant Biological Consequences  

E-print Network

of macromolecular crowding on protein oligomerization have been documented in a number of studies. Among the first that when fetal hemoglobin is used as a therapy for sickle cell anemia, which is caused by poly- merization of sickle hemoglobin, macromolecular crowding, arising from the high hemoglobin concentrations in red cells

Weston, Ken

349

Effects of macromolecular transport and stochastic fluctuations on dynamics of genetic regulatory systems  

E-print Network

of macromolecular transport: passive diffusion and active transport along cytoskeletal ele- ments mediated by motorEffects of macromolecular transport and stochastic fluctuations on dynamics of genetic regulatory transport and stochastic fluctua- tions on dynamics of genetic regulatory systems. Am. J. Physiol. 277 (Cell

Byrne, John H.

350

Perturbation-based Markovian Transmission Model for Macromolecular Machinery in Cell  

E-print Network

Perturbation-based Markovian Transmission Model for Macromolecular Machinery in Cell Hsiao-Mei Lu-based Markovian Transmission Model for studying the dynamics of signal trans- mission in macromolecular machinery The functional activities of cellular machinery often in- volves the dynamics of large macromolecules

Dai, Yang

351

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

PubMed

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

Hudait, Arpa; Molinero, Valeria

2014-06-01

352

Patchy worm-like micelles: solution structure studied by small-angle neutron scattering  

E-print Network

Triblock terpolymers exhibit a rich self-organization behavior including the formation of fascinating cylindrical core-shell structures with a phase separated corona. After crystallization-induced self-assembly of polystryrene-(block)-polyethylene-(block)-poly(methyl methacrylate) triblock terpolymers (abbreviated as SEMs = Styrene-Ethylene-Methacrylates) from solution, worm-like core-shell micelles with a patchy corona of polystryrene and poly(methyl methacrylate) were observed by transmission electron microscopy. However, the solution structure is still a matter of debate. Here, we present a method to distinguish in-situ between a Janus-type (two faced) and a patchy (multiple compartments) configuration of the corona. To discriminate between both models the scattering intensity must be determined mainly by one corona compartment. Contrast variation in small-angle neutron scattering enables us to focus on one compartment of the SEMs. The results validate the existence of the patchy structure also in solution.

S. Rosenfeldt; F. Luedel; C. Schulreich; T. Hellweg; A. Radulescu; J. Schmelz; H. Schmalz; L. Harnau

2012-09-20

353

Self-organization of amphiphilic macromolecules with local helix structure in concentrated solutions.  

PubMed

Concentrated solutions of amphiphilic macromolecules with local helical structure were studied by means of molecular dynamic simulations. It is shown that in poor solvent the macromolecules are assembled into wire-like aggregates having complex core-shell structure. The core consists of a hydrophobic backbone of the chains which intertwine around each other. It is protected by the shell of hydrophilic side groups. In racemic mixture of right-hand and left-hand helix macromolecules the wire-like complex is a chain of braid bundles of macromolecules with the same chirality stacking at their ends. The average number of macromolecules in the wire cross-section is close to that of separate bundles observed in dilute solutions of such macromolecules. The effects described here could serve as a simple model of self-organization in solutions of macromolecules with local helical structure. PMID:22938259

Glagolev, M K; Vasilevskaya, V V; Khokhlov, A R

2012-08-28

354

Sequence-specific sup 1 H NMR assignments and solution structure of bovine pancreatic polypeptide  

SciTech Connect

Sequence-specific {sup 1}H NMR assignments for the 36 residue bovine pancreatic polypeptide (bPP) have been completed. The secondary and tertiary structure of bPP in solution has been determined from experimental NMR data. It is shown that bPP has a very well-defined C-terminal {alpha}-helix involving residues 15-32. Although regular secondary structure cannot be clearly defined in the N-terminal region, residues 15-32. Although regular secondary structure cannot be clearly defined in the N-terminal region, residues 4-8 maintain a rather ordered conformation in solution. This is attributed primarily to the hydrophobic interaction between this region and the C-terminal helix. The two segments of the structure are joined by a turn which is poorly defined. The four end residues both at the N-terminus and the C-terminus are highly disordered in solution. The overall fold of the bPP molecule is very closely similar to that found in the crystal structure of avian pancreatic polypeptide (aPP). The RMS deviation for backbone atoms of residues 4-8 and 15-32 between the bPP mean structure and the aPP crystal structure is 0.65 {angstrom}, although there is only 39% identity of the residues. Furthermore, the average conformations of some (mostly from the {alpha}-helix) side chains of bPP in solution are closely similar to those of aPP in the crystal structure. A large number of side chains of bPP, however, show significant conformational averaging in solution.

Xiang Li; Dobson, C.M. (Univ. of Oxford (United Kingdom)); Sutcliffe, M.J. (Leicester Univ. (United Kingdom)); Schwartz, T.W. (Lab. for Molecular Endocrinology, Copenhagen (Denmark))

1992-02-04

355

Crowding and hydrodynamic interactions likely dominate in vivo macromolecular motion  

NASA Astrophysics Data System (ADS)

To begin to elucidate the principles of intermolecular dynamics in the crowded environment of cells, employing brownian dynamics (BD) simulations, we examined possible mechanism(s) responsible for the great reduction in diffusion constants of macromolecules in vivo from that at infinite dilution. In an Escherichia coli cytoplasm model comprised of 15 different macromolecule types at physiological concentrations, BD simulations of molecular-shaped and equivalent sphere representations were performed with a soft repulsive potential. At cellular concentrations, the calculated diffusion constant of GFP is much larger than experiment, with no significant shape dependence. Next, using the equivalent sphere system, hydrodynamic interactions (HI) were considered. Without adjustable parameters, the in vivo experimental GFP diffusion constant was reproduced. Finally, the effects of nonspecific attractive interactions were examined. The reduction in diffusivity is very sensitive to macromolecular radius with the motion of the largest macromolecules dramatically slowed down; this is not seen if HI dominate. In addition, long-lived clusters involving the largest macromolecules form if attractions dominate, whereas HI give rise to significant, size independent intermolecular dynamic correlations. These qualitative differences provide a testable means of differentiating the importance of HI vs. nonspecific attractive interactions on macromolecular motion in cells.

Skolnick, Jeffrey

2011-03-01

356

Bioelectrochemical activity of an electroactive macromolecular weight coenzyme derivative  

NASA Astrophysics Data System (ADS)

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.

Liu, Pu; Zheng, Haitao; Nie, Pingping; Wei, Yaotian; Feng, Zhenchao; Sun, Tao

2009-07-01

357

An efficient closed-form solution for acoustic emission source location in three-dimensional structures  

SciTech Connect

This paper presents an efficient closed-form solution (ECS) for acoustic emission(AE) source location in three-dimensional structures using time difference of arrival (TDOA) measurements from N receivers, N ? 6. The nonlinear location equations of TDOA are simplified to linear equations. The unique analytical solution of AE sources for unknown velocity system is obtained by solving the linear equations. The proposed ECS method successfully solved the problems of location errors resulting from measured deviations of velocity as well as the existence and multiplicity of solutions induced by calculations of square roots in existed close-form methods.

Li, Xibing [School of Resources and Safety Engineering, Central South University, Changsha, 410083 (China)] [School of Resources and Safety Engineering, Central South University, Changsha, 410083 (China); Dong, Longjun, E-mail: csudlj@163.com [School of Resources and Safety Engineering, Central South University, Changsha, 410083 (China) [School of Resources and Safety Engineering, Central South University, Changsha, 410083 (China); Australian Centre for Geomechanics, The University of Western Australia, Crawley, 6009 (Australia)

2014-02-15

358

The Effect of Cholesterol on the Solution Structure of Proteins of Photosystem II. Protein Secondary Structure and  

E-print Network

The Effect of Cholesterol on the Solution Structure of Proteins of Photosystem II. Protein, 1998 Cholesterol induces large perturbations in the physical proper- ties of membranes, especially at physiological temperatures. This study was designed to examine the interaction of cholesterol with lipid

Carpentier, Robert

359

Solution Structure of the DFF-C Domain of DFF45/ ICAD. A Structural Basis for the Regulation of  

E-print Network

* and Shigeyuki Yokoyama Protein Research Group Genomic Sciences Center RIKEN Yokohama Institute 1-7-22, Suehiro, by acting as both a folding chaperone and a DNase inhibitor of DFF40/CAD. Here, we present the solution structure of the C-terminal domain of DFF45, which is essential for its chaperone-like activity

Karplus, Kevin

360

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

PubMed

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

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

2008-07-24

361

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

NASA Astrophysics Data System (ADS)

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.

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

2014-05-01

362

A Solution Adaptive Structured/Unstructured Overset Grid Flow Solver with Applications to Helicopter Rotor Flows  

NASA Technical Reports Server (NTRS)

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.

Duque, Earl P. N.; Biswas, Rupak; Strawn, Roger C.

1995-01-01

363

Recent Major Improvements to the ALS Sector 5 MacromolecularCrystallography Beamlines  

SciTech Connect

Although the Advanced Light Source (ALS) was initially conceived primarily as a low energy (1.9GeV) 3rd generation source of VUV and soft x-ray radiation it was realized very early in the development of the facility that a multipole wiggler source coupled with high quality, (brightness preserving), optics would result in a beamline whose performance across the optimal energy range (5-15keV) for macromolecular crystallography (MX) would be comparable to, or even exceed, that of many existing crystallography beamlines at higher energy facilities. Hence, starting in 1996, a suite of three beamlines, branching off a single wiggler source, was constructed, which together formed the ALS Macromolecular Crystallography Facility. From the outset this facility was designed to cater equally to the needs of both academic and industrial users with a heavy emphasis placed on the development and introduction of high throughput crystallographic tools, techniques, and facilities--such as large area CCD detectors, robotic sample handling and automounting facilities, a service crystallography program, and a tightly integrated, centralized, and highly automated beamline control environment for users. This facility was immediately successful, with the primary Multiwavelength Anomalous Diffraction beamline (5.0.2) in particular rapidly becoming one of the foremost crystallographic facilities in the US--responsible for structures such as the 70S ribosome. This success in-turn triggered enormous growth of the ALS macromolecular crystallography community and spurred the development of five additional ALS MX beamlines all utilizing the newly developed superconducting bending magnets ('superbends') as sources. However in the years since the original Sector 5.0 beamlines were built the performance demands of macromolecular crystallography users have become ever more exacting; with growing emphasis placed on studying larger complexes, more difficult structures, weakly diffracting or smaller crystals, and on more rapidly screening larger numbers of candidate crystals; all of these requirements translate directly into a pressing need for increased flux, a tighter beam focus and faster detectors. With these growing demands in mind a major program of beamline and detector upgrades was initiated in 2004 with the goal of dramatically enhancing all aspects of beamline performance. Approximately $3 million in funding from diverse sources including NIH, LBL, the ALS, and the industrial and academic members of the beamline Participating Research Team (PRT), has been employed to develop and install new high performance beamline optics and to purchase the latest generation of CCD detectors. This project, which reached fruition in early 2007, has now fulfilled all of its original goals--boosting the flux on all three beamlines by up to 20-fold--with a commensurate reduction in exposure and data acquisition times for users. The performance of the Sector 5.0 beamlines is now comparable to that of the latest generation ALS superbend beamlines and, in the case of beamline 5.0.2, even surpasses it by a considerable margin. Indeed, the present performance of this beamline is now, once again, comparable to that envisioned for many MX beamlines planned or under construction on newer or higher energy machines.

Morton, Simon A.; Glossinger, James; Smith-Baumann, Alexis; McKean, John P.; Trame, Christine; Dickert, Jeff; Rozales, Anthony; Dauz,Azer; Taylor, John; Zwart, Petrus; Duarte, Robert; Padmore, Howard; McDermott, Gerry; Adams, Paul

2007-07-01

364

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

PubMed Central

Protein–DNA interactions play a major role in all aspects of genetic activity within an organism, such as transcription, packaging, rearrangement, replication and repair. The molecular detail of protein–DNA interactions can be best visualized through crystallography, and structures emphasizing insight into the principles of binding and base-sequence recognition are essential to understanding the subtleties of the underlying mechanisms. An increasing number of high-quality DNA-binding protein structure determinations have been witnessed despite the fact that the crystallographic particularities of nucleic acids tend to pose specific challenges to methods primarily developed for proteins. Crystallographic structure solution of protein–DNA complexes therefore remains a challenging area that is in need of optimized experimental and computational methods. The potential of the structure-solution program ARCIMBOLDO for the solution of protein–DNA complexes has therefore been assessed. The method is based on the combination of locating small, very accurate fragments using the program Phaser and density modification with the program SHELXE. Whereas for typical proteins main-chain ?-helices provide the ideal, almost ubiquitous, small fragments to start searches, in the case of DNA complexes the binding motifs and DNA double helix constitute suitable search fragments. The aim of this work is to provide an effective library of search fragments as well as to determine the optimal ARCIMBOLDO strategy for the solution of this class of structures. PMID:24914984

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

2014-01-01

365

FitEM2EM--tools for low resolution study of macromolecular assembly and dynamics.  

PubMed

Studies of the structure and dynamics of macromolecular assemblies often involve comparison of low resolution models obtained using different techniques such as electron microscopy or atomic force microscopy. We present new computational tools for comparing (matching) and docking of low resolution structures, based on shape complementarity. The matched or docked objects are represented by three dimensional grids where the value of each grid point depends on its position with regard to the interior, surface or exterior of the object. The grids are correlated using fast Fourier transformations producing either matches of related objects or docking models depending on the details of the grid representations. The procedures incorporate thickening and smoothing of the surfaces of the objects which effectively compensates for differences in the resolution of the matched/docked objects, circumventing the need for resolution modification. The presented matching tool FitEM2EMin successfully fitted electron microscopy structures obtained at different resolutions, different conformers of the same structure and partial structures, ranking correct matches at the top in every case. The differences between the grid representations of the matched objects can be used to study conformation differences or to characterize the size and shape of substructures. The presented low-to-low docking tool FitEM2EMout ranked the expected models at the top. PMID:18974836

Frankenstein, Ziv; Sperling, Joseph; Sperling, Ruth; Eisenstein, Miriam

2008-01-01

366

Solution structure of an informationally complex high-affinity RNA aptamer to GTP  

Microsoft Academic Search

Higher-affinity RNA aptamers to GTP are more informationally complex than lower-affinity aptamers. Analog binding studies have shown thatthe additional informationneeded toimproveaffinity doesnot specify moreinteractions withthe ligand. Inlightof those observations, we would like to understand the structural characteristics that enable complex aptamers to bind their ligands with higher affinity. Here we present the solution structure of the 41-nt Class I GTP

JAMES M. CAROTHERS; JONATHAN H. DAVIS; JAMES J. CHOU; JACK W. SZOSTAK

2006-01-01

367

Three-dimensional structures of proteins in solution by nuclear magnetic resonance spectroscopy.  

PubMed

Nuclear magnetic resonance (NMR) spectroscopy has emerged in recent years as a powerful method for the determination of three dimensional structures of small proteins in solution. Major cornerstones towards these advances were the introduction of two dimensional NMR experiments in combination with high field superconducting magnets, as well as the development of computational procedures to convert NMR derived distances into a 3D structure. This article outlines the methodology employed and illustrates its applicability based on a variety of examples. PMID:2911557

Gronenborn, A M; Clore, G M

1989-01-01

368

Crystal structure, conformation and morphology of solution-spun poly(L-lactide) fibers  

Microsoft Academic Search

Depending on the spinning and drawing conditions, two crystal structures for solution-spun poly(L-lactide) are obtained. The pseudoorthorhombic a structure (a = 10.6, b = 6.1, and c = 28.8 A) con- tains two chains in the unit cell and is found at relatively low drawing temperatures and\\/or low hot-draw ratios. At higher drawing temperatures and\\/or higher hot-draw ratios a second

W. Hoogsteen; A. R. Postema; A. J. Pennings; Gerrit Ten Brinke; P. Zugenmaier

1990-01-01

369

Estimation of conductivity losses in a helix slow-wave structure using eigen-mode solutions  

Microsoft Academic Search

This paper presents a simple method of estimating the attenuation constant due to conductivity losses and surface finish in a helix slow-wave structure, using the quality factor and dispersion characteristics obtainable from the eigen-mode solutions through 3D HFSS modeling. The method has been benchmarked against two practical structures published in the literature, and effect of surface finish on the attenuation

P. Raja Ramana Rao; Subrata Kumar Datta

2008-01-01

370

Solvation of nitrophenol isomers: consequences for solute electronic structure and alkane/water partitioning.  

PubMed

Solute partitioning across a variety of alkane/aqueous interfaces was examined as a function of solute and alkane solvent structure. Solutes include p-nitrophenol (PNP), 3,5-dimethyl-p-nitrophenol (3,5-DMPNP), and 2,6-dimethyl-p-nitrophenol (2,6-DMPNP), the latter two being isomers distinguished solely by the location of methyl substituents on the aromatic ring. The alkane solvents included cylohexane, methylcyclohexane, octane, and iso-octane (2,2,4-trimethylpentane). PNP partitioned preferentially into the water by factors as high as 160:1. The dimethyl isomers partitioned more equally between water and the different alkanes. 2,6-DMPNP showed a 3-fold greater affinity for the alkane phase than 3,5-DMPNP. Ab initio calculations were used to characterize the molecular and electronic structure of the three solutes and to quantify individual contributions to each solute's solvation energy in model aqueous and alkane phases. Differences between 2,6-DMPNP and 3,5-DMPNP partitioning are interpreted based on the ability of the methyl groups in 2,6-DMPNP to weaken hydrogen bonding between the phenol group and adjacent water molecules. This diminished solvation interaction reduces the barrier to solute migration into the nonpolar organic phase despite the fact that 2,6-DMPNP has a larger (calculated) permanent, ground-state dipole than 3,5-DMPNP. PMID:19143574

Steel, William H; Foresman, James B; Burden, Daniel K; Lau, Yuen Y; Walker, Robert A

2009-01-22

371

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

NASA Technical Reports Server (NTRS)

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.

Fiscko, Kurt A.; Chapman, Dean R.

1988-01-01

372

Structural Properties of High and Low Density Water in a Supercooled Aqueous Solution of Salt  

E-print Network

We consider and compare the structural properties of bulk TIP4P water and of a sodium chloride aqueous solution in TIP4P water with concentration c = 0.67 mol/kg, in the metastable supercooled region. In a previous paper [D. Corradini, M. Rovere and P. Gallo, J. Chem. Phys. 132, 134508 (2010)] we found in both systems the presence of a liquid-liquid critical point (LLCP). The LLCP is believed to be the end point of the coexistence line between a high density liquid (HDL) and a low density liquid (LDL) phase of water. In the present paper we study the different features of water-water structure in HDL and LDL both in bulk water and in the solution. We find that the ions are able to modify the bulk LDL structure, rendering water-water structure more similar to the bulk HDL case. By the study of the hydration structure in HDL and LDL, a possible mechanism for the modification of the bulk LDL structure in the solution is identified in the substitution of the oxygen by the chloride ion in oxygen coordination shells.

D. Corradini; M. Rovere; P. Gallo

2011-01-27

373

2:1 Complex of 4-methylphenol with piperazine, structure in the solid and solution state  

NASA Astrophysics Data System (ADS)

The title complex has been obtained from the solution of 4-methylphenol and piperazine, and the crystal structure has been determined by X-ray diffraction analysis. The complex crystallizes in space group P-1, each piperazine molecule linking two 4-methylphenol molecules via H-bonding between the amine N atoms and the phenol hydroxyl group. 1H NMR spectra indicate that the complex formed with the aid of H-bonding exists also in the solution. The proton peaks assigned to the hydroxyl and amine groups in pure 4-methylphenol and piperazine merge into one in the title complex, which implies that the H-bond between the hydroxyl O and the amine N atoms is involved in a fast proton exchange process. The ESI-MS spectrum of the solution of the title complex also provides evidence for the existence of the 2:1 complex in the solution.

Jin, Zhimin; Xu, Duanjun; Pan, Yuanjiang; Xu, Yuanzhi; Chiang, Michael Yen-Nan

2001-01-01

374

Aqueous Solutions of Amino Acid Based Ionic Liquids. Dispersion and Structure  

E-print Network

New ionic liquids (ILs) are continuously introduced involving an increasing number of organic and inorganic ions. Amino acid based ILs (AAILs) represent a specific interest due to their natural origin and, allegedly, low cost. We apply our recently developed force field for imidazolium-based AAILs to investigate structure properties in their aqueous solutions via molecular dynamics (MD) simulations. By reporting cluster analysis, radial distribution functions and spatial distribution functions, we argue that AAIL ions are well dispersed in the aqueous media, irrespective of the AAIL content. Aqueous solutions of AAILs exhibit desirable properties as solvents for chemical engineering. The AAILs in relatively dilute aqueous solutions (10 mol% AAIL) exist as ion pairs, while more concentrated solutions feature certain amount of larger ionic aggregates.

Chaban, Vitaly V

2014-01-01

375

About Small Streams and Shiny Rocks: Macromolecular Crystal Growth in Microfluidics  

NASA Technical Reports Server (NTRS)

We are developing a novel technique with which we have grown diffraction quality protein crystals in very small volumes, utilizing chip-based, microfluidic ("LabChip") technology. With this technology volumes smaller than achievable with any laboratory pipette can be dispensed with high accuracy. We have performed a feasibility study in which we crystallized several proteins with the aid of a LabChip device. The protein crystals are of excellent quality as shown by X-ray diffraction. The advantages of this new technology include improved accuracy of dispensing for small volumes, complete mixing of solution constituents without bubble formation, highly repeatable recipe and growth condition replication, and easy automation of the method. We have designed a first LabChip device specifically for protein crystallization in batch mode and can reliably dispense and mix from a range of solution constituents. We are currently testing this design. 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 aboard the International Space Station.

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

2002-01-01

376

Improved reproducibility of unit-cell parameters in macromolecular cryocrystallography by limiting dehydration during crystal mounting  

PubMed Central

In macromolecular cryocrystallography unit-cell parameters can have low reproducibility, limiting the effectiveness of combining data sets from multiple crystals and inhibiting the development of defined repeatable cooling protocols. Here, potential sources of unit-cell variation are investigated and crystal dehydration during loop-mounting is found to be an important factor. The amount of water lost by the unit cell depends on the crystal size, the loop size, the ambient relative humidity and the transfer distance to the cooling medium. To limit water loss during crystal mounting, a threefold strategy has been implemented. Firstly, crystal manipulations are performed in a humid environment similar to the humidity of the crystal-growth or soaking solution. Secondly, the looped crystal is transferred to a vial containing a small amount of the crystal soaking solution. Upon loop transfer, the vial is sealed, which allows transport of the crystal at its equilibrated humidity. Thirdly, the crystal loop is directly mounted from the vial into the cold gas stream. This strategy minimizes the exposure of the crystal to relatively low humidity ambient air, improves the reproducibility of low-temperature unit-cell parameters and offers some new approaches to crystal handling and cryoprotection. PMID:25084331

Farley, Christopher; Burks, Geoffry; Siegert, Thomas; Juers, Douglas H.

2014-01-01

377

Solution Structure of Human and Bovine b2-Glycoprotein I Revealed by Small-angle  

E-print Network

Solution Structure of Human and Bovine b2-Glycoprotein I Revealed by Small-angle X-ray Scattering-Glycoprotein I (b2GPI) is a highly glycosylated phospholipid-binding plasma protein comprised of four for binding of autoantibodies. q 2002 Elsevier Science Ltd. All rights reserved Keywords: b2-glycoprotein I

Hammel, Michal - School of Biological Sciences, University of Missouri

378

Solution Structure of the CBM10 Cellulose Binding Module from Pseudomonas Xylanase A,  

E-print Network

Solution Structure of the CBM10 Cellulose Binding Module from Pseudomonas Xylanase A, S. Raghothama), whose common function is to attach the enzyme to the polymeric substrate. Xylanase A from Pseudomonas fluorescens subsp. cellulosa (Pf Xyn10A) consists of a family 10 catalytic domain, an N-terminal family IIa

Williamson, Mike P.

379

Protein folding, protein structure and the origin of life: Theoretical methods and solutions of dynamical problems  

NASA Technical Reports Server (NTRS)

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.

Weaver, D. L.

1982-01-01

380

Phase behavior and structure formation in linear multiblock copolymer solutions by Monte Carlo simulation  

E-print Network

Phase behavior and structure formation in linear multiblock copolymer solutions by Monte Carlo, strictly alternating multiblock copolymers of type AnBn m was studied using lattice Monte Carlo simulations properties. © 2008 American Institute of Physics. DOI: 10.1063/1.2905231 I. INTRODUCTION Linear multiblock

381

Structure and Interactions of Fish Type III Antifreeze Protein in Solution  

PubMed Central

Abstract It has been suggested that above a critical protein concentration, fish Type III antifreeze protein (AFP III) self-assembles to form micelle-like structures that may play a key role in antifreeze activity. To understand the complex activity of AFP III, a comprehensive description of its association state and structural organization in solution is necessary. We used analytical ultracentrifugation, analytical size-exclusion chromatography, and dynamic light scattering to characterize the interactions and homogeneity of AFP III in solution. Small-angle neutron scattering was used to determine the low-resolution structure in solution. Our results clearly show that at concentrations up to 20 mg mL?1 and at temperatures of 20°C, 6°C, and 4°C, AFP III is monomeric in solution and adopts a structure compatible with that determined by crystallography. Surface tension measurements show a propensity of AFP III to localize at the air/water interface, but this surface activity is not correlated with any aggregation in the bulk. These results support the hypothesis that each AFP III molecule acts independently of the others, and that specific intermolecular interactions between monomers are not required for binding to ice. The lack of attractive interactions between monomers may be functionally important, allowing for more efficient binding and covering of the ice surface. PMID:20643081

Salvay, Andrés G.; Gabel, Frank; Pucci, Bernard; Santos, Javier; Howard, Eduardo I.; Ebel, Christine

2010-01-01

382

Structure, Problems and Possibilities for Their Solution in External Evaluation of Colleges  

ERIC Educational Resources Information Center

The article grounds the structure of the external evaluation of colleges at the level of the non-university higher education sector, and it reveals the problems met in this process as well as possibilities for their solution: the phenomenon of the external evaluation of colleges is discussed and its concept is presented; the external evaluation…

Rostlund, Ausra; Savickiene, Izabela

2010-01-01

383

Lithium Diisopropylamide Solvated by Monodentate and Bidentate Ligands: Solution Structures and Ligand Binding  

E-print Network

Lithium Diisopropylamide Solvated by Monodentate and Bidentate Ligands: Solution Structures, 1997X Abstract: 6Li and 15N NMR spectroscopic studies of lithium diisopropylamide ([6Li]LDA and [6Li,15 are correlated with those obtained previously for lithium hexamethyldisilazide. Introduction Despite

Collum, David B.

384

Parallel-vector solution of large-scale structural analysis problems on supercomputers  

NASA Technical Reports Server (NTRS)

A direct linear equation solution method based on the Choleski factorization procedure is presented which exploits both parallel and vector features of supercomputers. The new equation solver is described, and its performance is evaluated by solving structural analysis problems on three high-performance computers. The method has been implemented using Force, a generic parallel FORTRAN language.

Storaasli, Olaf O.; Nguyen, Duc T.; Agarwal, Tarun K.

1989-01-01

385

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

SciTech Connect

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.

Terwilliger, Thomas C [Los Alamos National Laboratory; Adams, Paul D [LBNL; Read, Randy J [UNIV OF CAMBRIDGE; Mccoy, Airlie J [UNIV OF CAMBRIDGE

2008-01-01

386

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

E-print Network

Supramolecular porphyrinic prisms: coordinative assembly and solution phase X-ray structural 2006 DOI: 10.1039/b610025b Supramolecular porphyrin prisms have been obtained via coordinative self on the formation of well defined prism-shaped assemblies featuring three, six, or nine porphyrins and comprising

387

Solution Nuclear Magnetic Resonance Structure of Membrane-Integral Diacylglycerol Kinase  

Microsoft Academic Search

Escherichia coli diacylglycerol kinase (DAGK) represents a family of integral membrane enzymes that is unrelated to all other phosphotransferases. We have determined the three-dimensional structure of the DAGK homotrimer with the use of solution nuclear magnetic resonance. The third transmembrane helix from each subunit is domain-swapped with the first and second transmembrane segments from an adjacent subunit. Each of DAGK's

Wade D. Van Horn; Hak-Jun Kim; Charles D. Ellis; Arina Hadziselimovic; Endah S. Sulistijo; Murthy D. Karra; Changlin Tian; Frank D. Sönnichsen; Charles R. Sanders

2009-01-01

388

Effects of surfactants on emulsification and secondary structure of lysozyme in aqueous solutions  

Microsoft Academic Search

This paper reports our investigations on the secondary structure of lysozyme in aqueous solution with D2O and comparing systems emulsified with ionic and non-ionic amphiphiles, respectively. The opposite effect of concentration of surfactants on the lysozyme aqueous system was studied and the activity of lysozyme by the turbidimetric assay with different kinds of surfactant was compared. The effect of different

Liu Huizhou; Yang Weijing; Chen Jiayong

1998-01-01

389

Pressure-dependent Changes in the Solution Structure of Hen Egg-white Lysozyme  

E-print Network

Pressure-dependent Changes in the Solution Structure of Hen Egg-white Lysozyme Mohamed Refaee1 conditions, because these clarify the physical constraints on pro- teins. One obvious extreme is pressure, but so far little is known of the behavior of proteins under pressure, largely for technical reasons. We

Williamson, Mike P.

390

On macromolecular refinement at subatomic resolution withinteratomic scatterers  

SciTech Connect

A study of the accurate electron density distribution in molecular crystals at subatomic resolution, better than {approx} 1.0 {angstrom}, requires more detailed models than those based on independent spherical atoms. A tool conventionally used in small-molecule crystallography is the multipolar model. Even at upper resolution limits of 0.8-1.0 {angstrom}, the number of experimental data is insufficient for the full multipolar model refinement. As an alternative, a simpler model composed of conventional independent spherical atoms augmented by additional scatterers to model bonding effects has been proposed. Refinement of these mixed models for several benchmark datasets gave results comparable in quality with results of multipolar refinement and superior of those for conventional models. Applications to several datasets of both small- and macro-molecules are shown. These refinements were performed using the general-purpose macromolecular refinement module phenix.refine of the PHENIX package.

Afonine, Pavel V.; Grosse-Kunstleve, Ralf W.; Adams, Paul D.; Lunin, Vladimir Y.; Urzhumtsev, Alexandre

2007-11-09

391

Size-exclusion chromatography system for macromolecular interaction analysis  

DOEpatents

A low pressure, microcomputer controlled system employing high performance liquid chromatography (HPLC) allows for precise analysis of the interaction of two reversibly associating macromolecules such as proteins. Since a macromolecular complex migrates faster than its components during size-exclusion chromatography, the difference between the elution profile of a mixture of two macromolecules and the summation of the elution profiles of the two components provides a quantifiable indication of the degree of molecular interaction. This delta profile is used to qualitatively reveal the presence or absence of significant interaction or to rank the relative degree of interaction in comparing samples and, in combination with a computer simulation, is further used to quantify the magnitude of the interaction in an arrangement wherein a microcomputer is coupled to analytical instrumentation in a novel manner.

Stevens, Fred J. (Downers Grove, IL)

1988-01-01

392

The analysis of macromolecular interactions by sedimentation equilibrium  

PubMed Central

The study of macromolecular interactions by sedimentation equilibrium is a highly technical method that requires great care in both the experimental design and data analysis. The complexity of the interacting system that can be analyzed is only limited by the ability to deconvolute the exponential contributions of each of the species to the overall concentration gradient. This is achieved in part through the use of multi-signal data collection and the implementation of soft mass conservation. We illustrate the use of these constraints in SEDPHAT through the study of an A + B + B ? AB + B ? ABB system and highlight some of the technical challenges that arise. We show that both the multi-signal analysis and mass conservation result in a precise and robust data analysis and discuss improvements that can be obtained through the inclusion of data from other methods such as sedimentation velocity and isothermal titration calorimetry. PMID:21167941

Ghirlando, Rodolfo

2010-01-01

393

Macromolecular contrast agents for MR mammography: current status.  

PubMed

Macromolecular contrast media (MMCM) encompass a new class of diagnostic drugs that can be applied with dynamic MRI to extract both physiologic and morphologic information in breast lesions. Kinetic analysis of dynamic MMCM-enhanced MR data in breast tumor patients provides useful estimates of tumor blood volume and microvascular permeability, typically increased in cancer. These tumor characteristics can be applied to differentiate benign from malignant lesions, to define the angiogenesis status of cancers, and to monitor tumor response to therapy. The most immediate challenge to the development of MMCM-enhanced mammography is the identification of those candidate compounds that demonstrate the requisite long intravascular distribution and have the high tolerance necessary for clinical use. Potential mammographic applications and limitations of various MMCM, defined by either experimental animal testing or clinical testing in patients, are reviewed in this article. PMID:12599002

Daldrup-Link, Heike E; Brasch, Robert C

2003-02-01

394

Macromolecular crystal growth experiments on International Microgravity Laboratory--1.  

PubMed Central

Macromolecular crystal growth experiments, using satellite tobacco mosaic virus (STMV) and canavalin from jack beans as samples, were conducted on a US Space Shuttle mission designated International Microgravity Laboratory--1 (IML-1), flown January 22-29, 1992. Parallel experiments using identical samples were carried out in both a vapor diffusion-based device (PCG) and a liquid-liquid diffusion-based instrument (CRYOSTAT). The experiments in each device were run at 20-22 degrees C and at colder temperatures. Crystals were grown in virtually every trial, but the characteristics of the crystals were highly dependent on the crystallization technique employed and the temperature experience of the sample. In general, very good results, based on visual inspection of the crystals, were obtained in both PCG and CRYOSTAT. Unusually impressive results were, however, achieved for STMV in the CRYOSTAT instrument. STMV crystals grown in microgravity by liquid-liquid diffusion were more than 10-fold greater in total volume than any STMV crystals previously grown in the laboratory. X-ray diffraction data collected from eight STMV crystals grown in CRYOSTAT demonstrated a substantial improvement in diffraction quality over the entire resolution range when compared to data from crystals grown on Earth. In addition, the extent of the diffraction pattern for the STMV crystals grown in space extended to 1.8 A resolution, whereas the best crystals that were ever grown under conditions of Earth's gravity produced data limited to 2.3 A resolution. Other observations indicate that the growth of macromolecular crystals is indeed influenced by the presence or absence of gravity. These observations further suggest, consistent with earlier results, that the elimination of gravity provides a more favorable environment for such processes. PMID:1303744

Day, J.; McPherson, A.

1992-01-01

395

Radiation damage to nucleoprotein complexes in macromolecular crystallography  

PubMed Central

Significant progress has been made in macromolecular crystallography over recent years in both the understanding and mitigation of X-ray induced radiation damage when collecting diffraction data from crystalline proteins. In contrast, despite the large field that is productively engaged in the study of radiation chemistry of nucleic acids, particularly of DNA, there are currently very few X-ray crystallographic studies on radiation damage mechanisms in nucleic acids. Quantitative comparison of damage to protein and DNA crystals separately is challenging, but many of the issues are circumvented by studying pre-formed biological nucleoprotein complexes where direct comparison of each component can be made under the same controlled conditions. Here a model protein–DNA complex C.Esp1396I is employed to investigate specific damage mechanisms for protein and DNA in a biologically relevant complex over a large dose range (2.07–44.63?MGy). In order to allow a quantitative analysis of radiation damage sites from a complex series of macromolecular diffraction data, a computational method has been developed that is generally applicable to the field. Typical specific damage was observed for both the protein on particular amino acids and for the DNA on, for example, the cleavage of base-sugar N1—C and sugar-phosphate C—O bonds. Strikingly the DNA component was determined to be far more resistant to specific damage than the protein for the investigated dose range. At low doses the protein was observed to be susceptible to radiation damage while the DNA was far more resistant, damage only being observed at significantly higher doses. PMID:25723923

Bury, Charles; Garman, Elspeth F.; Ginn, Helen Mary; Ravelli, Raimond B. G.; Carmichael, Ian; Kneale, Geoff; McGeehan, John E.

2015-01-01

396

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

NASA Astrophysics Data System (ADS)

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.

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

1998-06-01

397

Solution of quadratic matrix equations for free vibration analysis of structures.  

NASA Technical Reports Server (NTRS)

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.

Gupta, K. K.

1973-01-01

398

Automating crystallographic structure solution and refinement of protein–ligand complexes  

PubMed Central

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

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

399

X-ray absorption spectroscopic investigation of the electronic structure differences in solution and crystalline oxyhemoglobin  

PubMed Central

Hemoglobin (Hb) is the heme-containing O2 transport protein essential for life in all vertebrates. The resting high-spin (S = 2) ferrous form, deoxy-Hb, combines with triplet O2, forming diamagnetic (S = 0) oxy-Hb. Understanding this electronic structure is the key first step in understanding transition metal–O2 interaction. However, despite intense spectroscopic and theoretical studies, the electronic structure description of oxy-Hb remains elusive, with at least three different descriptions proposed by Pauling, Weiss, and McClure-Goddard, based on theory, spectroscopy, and crystallography. Here, a combination of X-ray absorption spectroscopy and extended X-ray absorption fine structure, supported by density functional theory calculations, help resolve this debate. X-ray absorption spectroscopy data on solution and crystalline oxy-Hb indicate both geometric and electronic structure differences suggesting that two of the previous descriptions are correct for the Fe–O2 center in oxy-Hb. These results support the multiconfigurational nature of the ground state developed by theoretical results. Additionally, it is shown here that small differences in hydrogen bonding and solvation effects can tune the ground state, tipping it into one of the two probable configurations. These data underscore the importance of solution spectroscopy and show that the electronic structure in the crystalline form may not always reflect the true ground-state description in solution. PMID:24062465

Wilson, Samuel A.; Green, Evan; Mathews, Irimpan I.; Benfatto, Maurizio; Hodgson, Keith O.; Hedman, Britt; Sarangi, Ritimukta

2013-01-01

400

Solution-adaptive structured-unstructured grid method for unsteady turbomachinery analysis. Part I: Methodology  

NASA Astrophysics Data System (ADS)

A solution-adaptive method for the time-accurate analysis of two-dimensional flows in multistage turbomachinery is presented. The method employs a hybrid structured-unstructured zonal grid topology in conjunction with appropriate modeling equations and solution techniques in each zone, thus combining the advantages of both structured and unstructured grid methods. The viscous flow region in the immediate vicinity of the airfoils is resolved on structured O-type grids, while the rest of the domain is discretized using an unstructured mesh of triangular cells. In the inner regions, the Navier-Stokes equations are solved using an implicit, third-order accurate, upwind-biased scheme. The use of both central difference and upwind schemes is explored for the solution of the Euler equations in the outer regions. An efficient and robust grid adaptation strategy, including both grid refinement and coarsening capabilities, is developed for the unstructured grid regions. Methodologies for the accurate, conservative transfer of information at the interface between the structured and unstructured domains, as well as that between two unstructured grids in relative motion, are also developed. For generality, three-dimensional effects of stream-tube contraction are modeled. The numerical methodology is presented in detail in the present article (Part I). Results obtained using this method and comparisons of these results with experimental data and earlier structured-grid based methods are presented in a companion article (Part II).

Mathur, Sanjay R.; Madavan, Nateri K.; Rajagopalan, R. Ganesh

1994-07-01

401

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

SciTech Connect

Highlights: •We have determined solution structures of CEH-37 homedomain. •CEH-37 HD has a compact ?-helical structure with HTH DNA binding motif. •Solution structure of CEH-37 HD shares its molecular topology with that of the homeodomain proteins. •Residues in the N-terminal region and HTH motif are important in binding to Caenorhabditis elegans telomeric DNA. •CEH-37 could play an important role in telomere function via DNA binding. -- Abstract: The nematode Caenorhabditis elegans protein CEH-37 belongs to the paired OTD/OTX family of homeobox-containing homeodomain proteins. CEH-37 shares sequence similarity with homeodomain proteins, although it specifically binds to double-stranded C. elegans telomeric DNA, which is unusual to homeodomain proteins. Here, we report the solution structure of CEH-37 homeodomain and molecular interaction with double-stranded C. elegans telomeric DNA using nuclear magnetic resonance (NMR) spectroscopy. NMR structure shows that CEH-37 homeodomain is composed of a flexible N-terminal region and three ?-helices with a helix-turn-helix (HTH) DNA binding motif. Data from size-exclusion chromatography and fluorescence spectroscopy reveal that CEH-37 homeodomain interacts strongly with double-stranded C. elegans telomeric DNA. NMR titration experiments identified residues responsible for specific binding to nematode double-stranded telomeric DNA. These results suggest that C. elegans homeodomain protein, CEH-37 could play an important role in telomere function via DNA binding.

Moon, Sunjin [Structural Biochemistry and Molecular Biophysics Lab, Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749 (Korea, Republic of)] [Structural Biochemistry and Molecular Biophysics Lab, Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749 (Korea, Republic of); Lee, Yong Woo; Kim, Woo Taek [Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749 (Korea, Republic of)] [Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749 (Korea, Republic of); Lee, Weontae, E-mail: wlee@spin.yonsei.ac.kr [Structural Biochemistry and Molecular Biophysics Lab, Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749 (Korea, Republic of)] [Structural Biochemistry and Molecular Biophysics Lab, Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749 (Korea, Republic of)

2014-01-10

402

Structure and dynamics of a polysaccharide matrix: aqueous solutions of bacterial levan.  

PubMed

The polysaccharide levan is a homopolymer of fructose and appears in nature as an important structural component of some bacterial biofilms. This paper reports the structural and dynamic properties of aqueous solutions of levan of various origin obtained from dynamic rheological, small-angle X-ray scattering, static and dynamic light scattering, as well as density and sound velocity measurements, determination of polymer branching after per-O-methylation, and microscopy. Besides samples of commercially available levan from Zymomonas mobilis and Erwinia herbicola, we also isolated, purified, and studied a levan sample from the biofilm of Bacillus subtilis. The results of dynamic rheological and light scattering measurements revealed very interesting viscoelastic properties of levan solutions even at very low polymer concentrations. The findings were complemented by small-angle X-ray scattering data that revealed some important differences in the structure of the aqueous levan solutions at the molecular level. Besides presenting detailed dynamic and structural results on the polysaccharide systems of various levans, one of the essential goals of this work was to point out the level of structural information that may be obtained for such polymer systems by combining basic physicochemical, rheological, and various light scattering techniques. PMID:24654746

Benigar, Elizabeta; Dogsa, Iztok; Stopar, David; Jamnik, Andrej; Kralj Cigi?, Irena; Tomši?, Matija

2014-04-15

403

An integrated method for the transient solution of reduced order models of geometrically nonlinear structures  

NASA Astrophysics Data System (ADS)

For repeated transient solutions of geometrically nonlinear structures, the numerical effort often poses a major obstacle. Thus it may become necessary to introduce a reduced order model which accelerates the calculations considerably while taking into account the nonlinear effects of the full order model in order to maintain accuracy. This work yields an integrated method that allows for rapid, accurate and parameterisable transient solutions. It is applicable if the structure is discretised in time and in space and its dynamic equilibrium described by a matrix equation. The projection on a reduced basis is introduced to obtain the reduced order model. Three approaches, each responding to one of the requirements of rapidity, accuracy and parameterisation, are united to form the integrated method. The polynomial formulation of the nonlinear terms renders the solution of the reduced order model autonomous from the finite element formulation and ensures a rapid solution. The update and augmentation of the reduced basis ensures the accuracy, because the simple introduction of a constant basis seems to be insufficient to account for the nonlinear behaviour. The interpolation of the reduced basis allows adapting the reduced order model to different external parameters. A Newmark-type algorithm provides the backbone of the integrated method. The application of the integrated method on test-cases with geometrically nonlinear finite elements confirms that this method enables a rapid, accurate and parameterisable transient solution.

Lülf, Fritz Adrian; Tran, Duc-Minh; Matthies, Hermann G.; Ohayon, Roger

2015-02-01

404

Grain boundary structure and solute segregation in titanium-doped sapphire bicrystals  

SciTech Connect

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.

Taylor, Seth T.

2002-05-17

405

Engineering polyelectrolyte multilayer structure at the nanometer length scale by tuning polymer solution conformation.  

NASA Astrophysics Data System (ADS)

Chitosan (a weak polycation) and heparin (a strong polyanion) are used to make polyelectrolyte multilayers (PEM). PEM thickness and composition are determined as a function of solution pH (4.6 to 5.8) and ionic strength (0.1 to 0.5 M). Over this range, increasing pH increases the PEM thickness; however, the sensitivity to changes in pH is a strong function of ionic strength. The PEM thickness data are correlated to the polymer conformation in solution. Polyelectrolyte conformation in solution is characterized by gel permeation chromatography (GPC). The highest sensitivity of PEM structure to pH is obtained at intermediate ionic strength. Different interactions govern the conformation and adsorption phenomena at low and high ionic strength, leading to reduced sensitivity to solution pH at extreme ionic strengths. The correspondence between PEM thickness and polymer solution conformation offers opportunities to tune polymer thin film structure at the nanometer length scale by controlling simple, reproducible processing conditions.

Boddohi, Soheil; Killingsworth, Christopher; Kipper, Matt

2008-03-01

406

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

NASA Astrophysics Data System (ADS)

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).

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

2011-05-01

407

Structural properties and adsorption capacity of holocellulose aerogels synthesized from an alkali hydroxide-urea solution  

NASA Astrophysics Data System (ADS)

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.

Kwon, Gu-Joong; Kim, Dae-Young; Hwang, Jae-Hyun; Kang, Joo-Hyon

2014-05-01

408

Effect of different alkaline solutions on crystalline structure of cellulose at different temperatures.  

PubMed

Effect of alkaline solutions such as 10% NaOH, NaOH/urea and NaOH/ethylene glycol solutions on crystalline structure of different cellulosic fibers (cotton linter and filter paper) was investigated at room temperature and -4°C. The highest dissolution of cotton linter and filter paper was observed in NaOH/ethylene glycol at both temperatures. X-ray patterns of treated cotton linter with different alkaline solutions at low temperature showed only two diffractions at 2?=12.5° and 21.0°, which belonged to the crystalline structure of cellulose II. CP/MAS (13)C NMR spectra showed the doublet peaks at 89.2 ppm and 88.3 ppm representing C4 resonance for cellulose I at room temperature, Whereas, at low temperature the doublet peaks were observed at 89.2 ppm and 87.8 ppm representing C4 resonance for cellulose II. Degree of polymerization of cellulose plays an important role in cellulose dissolution in different alkaline solutions and temperatures, where, a low temperature gives high dissolutions percentage with change in crystalline structure from cellulose I to cellulose II forms. PMID:25439945

Keshk, Sherif M A S

2015-01-22

409

Theory of Polymer Chains in Poor Solvent: Single-Chain Structure, Solution Thermodynamics and Theta Point  

E-print Network

Using the language of the Flory chi parameter, we develop a theory that unifies the treatment of the single-chain structure and the solution thermodynamics of polymers in poor solvents. The structure of a globule and its melting thermodynamics is examined using the self-consistent filed theory. Our results show that the chain conformation involves three states prior to the globule-to-coil transition: the fully-collapsed globule, the swollen globule and the molten globule, which are distinguished by the core density and the interfacial thickness. By examining the chain-length dependence of the melting of the swollen globule, we find universal scaling behavior in the chain properties near the Theta point. The information of density profile and free energy of the globule is used in the dilute solution thermodynamics to study the phase equilibrium of polymer solution. Our results show different scaling behavior of the solubility of polymers in the dilute solution compared to the F-H theory, both in the chi dependence and the chain-length dependence. From the perspectives of single chain structure and solution thermodynamics, our results verifies the consistency of the Theta point defined by different criteria in the limit of infinite chain length: the disappearance of the second viral coefficient, the abrupt change in chain size and the critical point in the phase diagram of the polymer solution. Our results show the value of chi at the Theta point is 0.5 (for the case of equal monomer and solvent volume), which coincides with the value predicted from the F-H theory.

Rui Wang; Zhen-Gang Wang

2014-06-05

410

Morphology control, defect engineering and photoactivity tuning of ZnO crystals by graphene oxide--a unique 2D macromolecular surfactant.  

PubMed

Zinc oxide (ZnO) nanostructured materials have received significant attention because of their unique physicochemical and electronic properties. In particular, the functional properties of ZnO are strongly dependent on its morphology and defect structure, particularly for a semiconductor ZnO-based photocatalyst. Here, we demonstrate a simple strategy for simultaneous morphology control, defect engineering and photoactivity tuning of semiconductor ZnO by utilizing the unique surfactant properties of graphene oxide (GO) in a liquid phase. By varying the amount of GO added during the synthesis process, the morphology of ZnO gradually evolves from a one dimensional prismatic rod to a hexagonal tube-like architecture while GO is converted into reduced GO (RGO). In addition, the introduction of GO can create oxygen vacancies in the lattice of ZnO crystals. As a result, the absorption edge of the wide band gap semiconductor ZnO is effectively extended to the visible light region, which thus endows the RGO-ZnO nanocomposites with visible light photoactivity; in contrast, the bare ZnO nanorod is only UV light photoactive. The synergistic integration of the unique morphology and the presence of oxygen vacancies imparts the RGO-ZnO nanocomposite with remarkably enhanced visible light photoactivity as compared to bare ZnO and its counterpart featuring different structural morphologies and the absence of oxygen vacancies. Our promising results highlight the versatility of the 2D GO as a solution-processable macromolecular surfactant to fabricate RGO-semiconductor nanocomposites with tunable morphology, defect structure and photocatalytic performance in a system-materials-engineering way. PMID:24513962

Pan, Xiaoyang; Yang, Min-Quan; Xu, Yi-Jun

2014-03-28

411

Structure of 2 molar NaOH in aqueous solution from neutron diffraction and empirical potential structure refinement  

SciTech Connect

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.

McLain, Sylvia E.; Imberti, Silvia; Soper, Alan K.; Botti, Alberto; Bruni, Fabio; Ricci, Maria Antonietta [ISIS Facility, Rutherford Appleton Laboratory, Chilton, Didcot, OXON OX11 0QX (United Kingdom); ISIS Facility, Rutherford Appleton Laboratory, Chilton, Didcot, OXON OX11 0QX, United Kingdom and CNR-ISC, Sezione di Firenze, via Madonna del Piano 10, 50019 Sesto Fiorentino (Finland) (Italy); ISIS Facility, Rutherford Appleton Laboratory, Chilton, Didcot, OXON OX11 0QX (United Kingdom); Dipartimento di Fisica E. Amaldi, Universita degli Studi Roma Tre, Via della Vasca Navale 84, 00146 Rome (Italy)

2006-09-01

412

Solution structure of peptide AG4 used to form silver nanoparticles  

SciTech Connect

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.

Lee, Eunjung [Division of Bioscience and Biotechnology, RCD, Konkuk University, Hwayang-Dong 1, Kwangjin-Ku, Seoul 143-701 (Korea, Republic of); Kim, Dae-Hee [Department of Environmental Science and Engineering, Gwangju Institute of Science and Technology, Gwangju 500-712 (Korea, Republic of); Woo, Yoonkyung [Division of Bioscience and Biotechnology, RCD, Konkuk University, Hwayang-Dong 1, Kwangjin-Ku, Seoul 143-701 (Korea, Republic of); Hur, Ho-Gil [Department of Environmental Science and Engineering, Gwangju Institute of Science and Technology, Gwangju 500-712 (Korea, Republic of); Lim, Yoongho [Division of Bioscience and Biotechnology, RCD, Konkuk University, Hwayang-Dong 1, Kwangjin-Ku, Seoul 143-701 (Korea, Republic of)], E-mail: yoongho@konkuk.ac.kr

2008-11-21

413

Families of solutions to the generalized Ginzburg-Landau equation and structural transitions between them  

SciTech Connect

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.

Ovchinnikov, Yu. N., E-mail: ovc@itp.ac.ru [Max-Planck Institute for Physics of Complex Systems (Germany)

2013-09-15

414

Macromolecular docking of a three-body system: the recognition of human growth hormone by its receptor.  

PubMed Central

Human growth hormone (hGH) binds to its receptor (hGHr) in a three-body interaction: one molecule of the hormone and two identical monomers of the receptor form a trimer. Curiously, the hormone-receptor interactions in the trimer are not equivalent and the formation of the complex occurs in a specific kinetic order (Cunningham BC, Ultsch M, De Vos AM, Mulkerrin MG, Clauser KR, Wells JA, 1991, Science 254:821-825). In this paper, we model the recognition of hGH to the hGHr using shape complementarity of the three-dimensional structures and macromolecular docking to explore possible binding modes between the receptor and hormone. The method, reported previously (Hendrix DK, Kuntz ID, 1998, Pacific symposium on biocomputing 1998, pp 1234-1244), is based upon matching complementary-shaped strategic sites on the molecular surface. We modify the procedure to examine three-body systems. We find that the order of binding seen experimentally is also essential to our model. We explore the use of mutational data available for hGH to guide our model. In addition to docking hGH to the hGHr, we further test our methodology by successfully reproducing 16 macromolecular complexes from X-ray crystal structures, including enzyme-inhibitor, antibody-antigen, protein dimer, and protein-DNA complexes. PMID:10338012

Hendrix, D. K.; Klein, T. E.; Kuntz, I. D.; Klien, T. E.

1999-01-01

415

Problem Description:Problem Description: Biotic and Abiotic Regulators of Soil RespirationBiotic and Abiotic Regulators of Soil Respiration Proposed Solution:Proposed Solution: Structural Equation Modeling: an Integrated ApproachStructural Equation Modeli  

E-print Network

Problem Description:Problem Description: Biotic and Abiotic Regulators of Soil RespirationBiotic and Abiotic Regulators of Soil Respiration Proposed Solution:Proposed Solution: Structural Equation Modeling: an Integrated ApproachStructural Equation Modeling: an Integrated Approach Understanding Soil Respiration: an

Hamilton, Michael P.

416

Solution structure of apamin determined by nuclear magnetic resonance and distance geometry  

SciTech Connect

The solution structure of the bee venom neurotoxin apamin has been determined with a distance geometry program using distance constraints derived from NMR. Twenty embedded structures were generated and refined by using the program DSPACE. After error minimization using both conjugate gradient and dynamics algorithms, six structures had very low residual error. Comparisons of these show that the backbone of the peptide is quite well-defined with the largest rms difference between backbone atoms in these structures of 1.34 /Angstrom/. The side chains have far fewer constraints and show greater variability in their positions. The structure derived here is generally consistent with the qualitative model previously described, with most differences occurring in the loop between the ..beta..-turn (residues 2-5) and the C-terminal ..cap alpha..-helix (residues 9-17). Comparisons are made with previously derived models from NMR data and other methods.

Pease, J.H.B.; Wemmer, D.E.

1988-11-01

417

Heterogeneity of large macromolecular complexes revealed by 3-D cryo-EM variance analysis  

PubMed Central

Macromolecular structure determination by cryo-electron microscopy (EM) and single particle analysis are based on the assumption that imaged molecules have identical structure. With the increased size of processed datasets it becomes apparent that many complexes coexist in a mixture of conformational states or contain flexible regions. As the cryo-EM data is collected in form of projections of imaged molecules, the information about variability of reconstructed density maps is not directly available. To address this problem, we describe a new implementation of the bootstrap resampling technique that yields estimates of voxel-by-voxel variance of a structure reconstructed from the set of its projections. We introduced a novel highly efficient reconstruction algorithm that is based on direct Fourier inversion and which incorporates correction for the transfer function of the microscope, thus extending the resolution limits of variance estimation. We also describe a validation method to determine the number of resampled volumes required to achieve stable estimate of the variance. The proposed bootstrap method was applied to a dataset of 70S ribosome complexed with tRNA and the elongation factor G. The variance map revealed regions of high variability: the L1 protein, the EF-G and the 30S head and the ratchet-like subunit rearrangement. The proposed method of variance estimation opens new possibilities for single particle analysis, by extending applicability of the technique to heterogeneous datasets of macromolecules, and to complexes with significant conformational variability. PMID:19081053

Zhang, Wei; Kimmel, Marek; Spahn, Christian M.T.; Penczek, Pawel A.

2008-01-01

418

Solution Structures of Spinach Acyl Carrier Protein with Decanoate and Stearate†  

PubMed Central

Acyl carrier protein (ACP) is a cofactor in a variety of biosynthetic pathways, including fatty acid metabolism. Thus it is of interest to determine structures of physiologically relevant ACP-fatty acid complexes. We report here the NMR solution structures of spinach ACP with decanoate (10:0-ACP) and stearate (18:0-ACP) attached to the 4? phosphopantetheine prosthetic group. The protein in the fatty acid complexes adopts a single conformer, unlike apo- and holo-ACP, which interconvert in solution between two major conformers. The protein component of both 10:0- and 18:0-ACP adopts the four-helix bundle topology characteristic of ACP, and a fatty acid binding cavity was identified in both structures. Portions of the protein close in space to the fatty acid and the 4? phosphopantetheine were identified using filtered/edited NOESY experiments. A docking protocol was used to generate protein structures containing bound fatty acid for 10:0- and 18:0-ACP. In both cases, the predominant structure contained fatty acid bound down the center of the helical bundle, in agreement with the location of the fatty acid binding pockets. These structures demonstrate the conformational flexibility of spinach-ACP and suggest how the protein changes to accommodate its myriad binding partners. PMID:16618110

Zornetzer, Gregory A.; Fox, Brian G.; Markley, John L.

2008-01-01

419

Influence of the organized structure of 1-alkyl-3-methylimidazolium tetrafluoroborates on the rotational diffusion of structurally similar nondipolar solutes.  

PubMed

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

Gangamallaiah, V; Dutt, G B

2014-11-26

420

A structural study of the intermolecular interactions of tyramine in the solid state and in solution  

NASA Astrophysics Data System (ADS)

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.

Quevedo, Rodolfo; Nuñez-Dallos, Nelson; Wurst, Klaus; Duarte-Ruiz, Álvaro

2012-12-01

421

Molecular mobility and microscopic structure changes in ?-carrageenan solutions studied by gradient NMR.  

PubMed

Changes in the molecular mobility of ?-carrageenan were observed by the pulsed field gradient stimulated echo (PGSTE) and Carr-Purcell-Meiboom-Gill (CPMG) methods for elucidating the molecular aspect of the sol-to-gel transition. The echo signal intensity of ?-carrageenan without a gradient, Ikap(0), decreased steeply near the sol-to-gel temperature (Tsg), suggesting that ?-carrageenan chains formed aggregates and a network structure. Below Tsg, the spin-spin relaxation time T2 and the diffusion coefficient of ?-carrageenan (Dkap) increased with decreasing temperature, indicating that the solute ?-carrageenan chains have a lower molecular weight Mw than chains involved in the aggregation. The diffusion coefficient of pullulan (Dpul) added as a probe molecule in ?-carrageenan solutions was measured, and the characteristic hydrodynamic screening length, ?, was then estimated from the degree of diffusion restriction. Below a certain temperature, Dkap reached a higher value than that of Dpul, suggesting that the Mw of solute ?-carrageenan became lower than that of pullulan. GPC measurements confirmed the presence of ?-carrageenan chains with a lower Mw than that of pullulan. A simple physical model of the structural change in ?-carrageenan solution was proposed with a bimodal distribution of ?-carrageenan with higher and lower Mw than the pullulan probe. The higher Mw chains form the gel network restricting the probe's diffusion, and the lower Mw chains increase the effective viscosity. The concentration of the high Mw solute ?-carrageenan chains in 1%, 2% and 4% ?-carrageenan solutions was estimated from Ikap(0) and the total ?-carrageenan concentration, and the relation with pullulan diffusion was studied. PMID:23618293

Zhao, Qiuhua; Brenner, Tom; Matsukawa, Shingo

2013-06-01

422

Permeability of lipid-coated polymer capsule membranes to solutes: effects of temperature and chemical structure of solutes.  

PubMed

The permeability of di-stearyldimethylammonium-coated polyamide capsule membranes to KCl, and tetra-methylammonium (4C1N), tetra-propylammonium (4C3N), and tetra-butylammonium (4C4N) bromides was investigated at temperatures below and above the phase transition temperature of the amphiphile coat and compared with that of non-coated polyamide capsule membranes. The rate of solute permeation through the non-coated capsule membranes for all permeants increased gradually with rise in temperature. When the capsule was coated with the amphiphile, the rate was reduced by a factor of 2-200 relative to that through the non-coated semipermeable capsule membranes and changed drastically or slightly at the phase transition temperature of the amphiphile coat, depending on the chemical structure of permeants. The permeation of hydrophilic KCl and slightly hydrophobic 4C1N was greatly supressed by the amphiphile coat below the phase transition temperature while it was enhanced above that temperature. On the contrary, the permeation rate of the moderately hydrophobic and bulky 4C3N increased monotonically with rising temperature. No change in the permeation rate was observed with the highly hydrophobic and bulky 4C4N at all temperatures. PMID:7650591

Totomi, N; Makino, K; Inoue, S; Kondo, T

1995-01-01

423

Investigations of peptide structural stability in vacuo   

E-print Network

Gas-phase analytical techniques provide very valuable tools for tackling the structural complexity of macromolecular structures such as those encountered in biological systems. Conformational dynamics of polypeptides and ...

Kalapothakis, Jason Michael Drosos

2010-06-28

424

Numerical solution of quadratic matrix equations for free vibration analysis of structures  

NASA Technical Reports Server (NTRS)

This paper is concerned with the efficient and accurate solution of the eigenvalue problem represented by quadratic matrix equations. Such matrix forms are obtained in connection with the free vibration analysis of structures, discretized by finite 'dynamic' elements, resulting in frequency-dependent stiffness and inertia matrices. The paper presents a new numerical solution procedure of the quadratic matrix equations, based on a combined Sturm sequence and inverse iteration technique enabling economical and accurate determination of a few required eigenvalues and associated vectors. An alternative procedure based on a simultaneous iteration procedure is also described when only the first few modes are the usual requirement. The employment of finite dynamic elements in conjunction with the presently developed eigenvalue routines results in a most significant economy in the dynamic analysis of structures.

Gupta, K. K.