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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.; Bunkoczi, Gabor; 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

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

E-print Network

and thus inhibit the oxidation of organic matter and facilitate the stabilization of organic C by soils (3 the soil and sediment solution chemistry and their biogeochemical processes. These chemical and structural., Methods of Soil Analysis: Part 3, Chemical Methods (Soil Science Society of America, Madison, WI, 1996). 9

Dunin-Borkowski, Rafal E.

5

Analysis of macromolecular structures by pulsed NMR  

NASA Astrophysics Data System (ADS)

The T2 spin-spin relaxation curves obtained by pulsed NMR techniques can readily be used to study important features of macromolecular systems quite distinct from their chemical structure. Such features refer to more physical properties such as molecular size, flexibility and mobility, the influence of solvent and temperature on this motion (which is related to viscosity), crystalline fraction and the rate of crystallization, polymerisation and other chemical reactions where there is a considerable change in dimensions etc. It can also serve to determine the degree of crosslinking, where this forms a partial or complete network. However it appears to indicate the presence of a network even when no permanent network is revealed by alternative and well-established techniques such as solubility and swelling which require much longer times. This difference is ascribed to the presence of some intermolecular binding somewhat akin to permanent crosslinks, but of a very shortlived dynamic nature, and this is referred to as due to entanglements between adjacent macromolecules. The T2 measurements reveal their presence if the life-time of these entanglements is comparable or longer than the period ofmeasurement by pulsed NMR. The usual formulae used to determine network formation by permanent crosslinks can be applied to such systems with entanglements or with entanglements plus crosslinks, so that the elastic properties can be determined by NMR T2 measurements. Over a long time only the permanent crosslinks will provide elastic recovery but for sufficiently short times the entanglements provide an additional restoring force and this may be taken to be the cause of the rheological property referred to as creep and viscosity. Since the entanglements but not the permanent crosslinks depend on temperature, many of these physical properties and their variation with temperature can be related directly to the effect of these entanglements as determined by these T2 measurements and derived from pulsed NMR. Another feature which emerges from these investigations is their dependence on solvent where present. The total variation can be ascribed to molecular dimensions and the free volume available for their motion (and hence their freedom to become disentangled). This free volume is influenced by temperature and concentration of solvent where present. The meaning of these T2 responses have been deduced from the changes in pulsed NMR responses to a series of macromolecular systems whose properties have been modified to known extents by known radiation doses. The interpretation of the T2 relaxation patterns obtained from other macromolecular structures now becomes possible. We can therefore hope to see this technique used not only for polymers but especially for biological systems where considerable changes of molecular behaviour such as conformation and motion can result from very minute chemical modifications. Such sensitive features might be for example molecular entanglements and concentration, radiation or chemically-induced crosslinking or degradation (scission), disruption of a regular refolding sequence etc. This T2 technique is particularly suitable for following such changes.

Charlesby, A.

6

The Phenix Software for Automated Determination of Macromolecular Structures  

PubMed Central

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

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

2011-01-01

7

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

8

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

9

The structural dynamics of macromolecular processes  

PubMed Central

Summary Dynamic processes involving macromolecular complexes are essential to cell function. These processes take place over a wide variety of length scales from nanometers to micrometers, and over time scales from nanoseconds to many minutes. As a result, information from a variety of different experimental and computational approaches is required. We review the relevant sources of information and introduce a framework for integrating the data to produce representations of dynamic processes. PMID:19223165

Russel, Daniel; Lasker, Keren; Phillips, Jeremy; Schneidman-Duhovny, Dina; Velazquez-Muriel, Javier A.; Sali, Andrej

2009-01-01

10

A new principle for macromolecular structure determination  

NASA Astrophysics Data System (ADS)

Protein NMR spectroscopy is a modern experimental technique for elucidating the three-dimensional structure of biological macromolecules in solution. From the data-analytical point of view, structure determination has always been considered an optimisation problem: much effort has been spent on the development of minimisation strategies; the underlying rationale, however, has not been revised. Conceptual difficulties with this approach arise since experiments only provide incomplete structural information: structure determination is an inference problem and demands for a probabilistic treatment. In order to generate realistic conformations, strong prior assumptions about physical interactions are indispensable. These interactions impose a complex structure on the posterior distribution making simulation of such models particularly difficult. We demonstrate, that posterior sampling is feasible using a combination of multiple Markov Chain Monte Carlo techniques. We apply the methodology to a sparse data set obtained from a perdeuterated sample of the Fyn SH3 domain.

Habeck, Michael; Rieping, Wolfgang; Nilges, Michael

2004-04-01

11

Macromolecular electron microscopy in the era of structural genomics  

Microsoft Academic Search

Macromolecular machines carry out many cellular functions. Cryo-electron microscopy (cryo-EM) is emerging as a powerful method for studying the structure, assembly and dynamics of such macromolecules, and their interactions with substrates. With resolutions still improving, ‘single-particle’ analyses are already depicting secondary structure. Moreover, cryo-EM can be combined in several ways with X-ray diffraction to enhance the resolution of cryo-EM and

Wolfgang Baumeister; Alasdair C. Steven

2000-01-01

12

Refinement of macromolecular structures against neutron data with SHELXL2013  

PubMed Central

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

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

2014-01-01

13

Cryo-Electron Tomography for Structural Characterization of Macromolecular Complexes  

PubMed Central

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

Cope, Julia; Heumann, John; Hoenger, Andreas

2011-01-01

14

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; Andre, Ingemar

2011-01-01

15

A specification for defining and annotating regions of macromolecular structures  

SciTech Connect

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

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

1995-12-31

16

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

17

Conformational States of Macromolecular Assemblies Explored by Integrative Structure Calculation  

PubMed Central

Summary A detailed description of macromolecular assemblies in multiple conformational states can be very valuable for understanding cellular processes. At present, structural determination of most assemblies in different biologically relevant conformations cannot be achieved by a single technique and thus requires an integrative approach that combines information from multiple sources. Different techniques require different computational methods to allow efficient and accurate data processing and analysis. Here, we summarize the latest advances and future challenges in computational methods that help the interpretation of data from two techniques—mass spectrometry and three-dimensional cryo-electron microscopy (with focus on alignment and classification of heterogeneous subtomograms from cryo-electron tomography). We evaluate how new developments in these two broad fields will lead to further integration with atomic structures to broaden our picture of the dynamic behavior of assemblies in their native environment. PMID:24010709

Thalassinos, Konstantinos; Pandurangan, Arun Prasad; Xu, Min; Alber, Frank; Topf, Maya

2013-01-01

18

Automated identification of elemental ions in macromolecular crystal structures  

PubMed Central

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

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

2014-01-01

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

Timely deposition of macromolecular structures is necessary for peer review  

PubMed Central

Most of the macromolecular structures in the Protein Data Bank (PDB), which are used daily by thousands of educators and scientists alike, are determined by X-ray crystallography. It was examined whether the crystallographic models and data were deposited to the PDB at the same time as the publications that describe them were submitted for peer review. This condition is necessary to ensure pre-publication validation and the quality of the PDB public archive. It was found that a significant proportion of PDB entries were submitted to the PDB after peer review of the corresponding publication started, and many were only submitted after peer review had ended. It is argued that clear description of journal policies and effective policing is important for pre-publication validation, which is key in ensuring the quality of the PDB and of peer-reviewed literature. PMID:24311569

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

2013-01-01

21

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

22

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

23

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

24

Protonate3D: Assignment of ionization states and hydrogen coordinates to macromolecular structures  

PubMed Central

A new method, called Protonate3D, is presented for the automated prediction of hydrogen coordinates given the 3D coordinates of the heavy atoms of a macromolecular structure. Protonate3D considers side-chain “flip,” rotamer, tautomer, and ionization states of all chemical groups, ligands, and solvent, provided suitable templates are available in a parameter file. The energy model includes van der Waals, Coulomb, solvation, rotamer, tautomer, and titration effects. The results of computational validation experiments suggest that Protonate3D can accurately predict the location of hydrogen atoms in macromolecular structures. Proteins 2009. © 2008 Wiley-Liss, Inc. PMID:18814299

Labute, Paul

2009-01-01

25

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

26

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

27

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

28

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

29

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

30

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

31

Multi-resolution Contour-based Fitting of Macromolecular Structures  

E-print Network

structures from electron micrographs have evolved into a powerful method for studying the structure, assembly. The proposed Laplacian ®lter is combined with a six-dimensional search using fast Fourier transforms to rapidly-30 A� ) is critical for image reconstructions from electron microscopy (EM). The new algorithm enables

Wriggers, Willy

32

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

33

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

PubMed Central

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

2013-01-01

34

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

35

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

36

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

37

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

38

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

39

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

40

Hydropyrolysis of insoluble carbonaceous matter in the Murchison meteorite: new insights into its macromolecular structure1  

Microsoft Academic Search

The major organic component of carbonaceous chondrites is a solvent-insoluble, high molecular weight macromolecular material that constitutes at least 70% of the total organic content in these meteorites. Analytical pyrolysis is often used to thermally decompose macromolecular organic matter in an inert atmosphere into lower molecular weight fragments that are more amenable to conventional organic analytical techniques. Hydropyrolysis refers to

M. A. SEPHTON; G. D Love; J. S. WATSON; A. B. VERCHOVSKY; I. P. WRIGHT; C. E. SNAPE; I. GILMOUR

2004-01-01

41

MetalPDB: a database of metal sites in biological macromolecular structures.  

PubMed

We present here MetalPDB (freely accessible at http://metalweb.cerm.unifi.it), a novel resource aimed at conveying the information available on the three-dimensional (3D) structures of metal-binding biological macromolecules in a consistent and effective manner. This is achieved through the systematic and automated representation of metal-binding sites in proteins and nucleic acids by way of Minimal Functional Sites (MFSs). MFSs are 3D templates that describe the local environment around the metal(s) independently of the larger context of the macromolecular structure embedding the site(s), and are the central objects of MetalPDB design. MFSs are grouped into equistructural (broadly defined as sites found in corresponding positions in similar structures) and equivalent sites (equistructural sites that contain the same metals), allowing users to easily analyse similarities and variations in metal-macromolecule interactions, and to link them to functional information. The web interface of MetalPDB allows access to a comprehensive overview of metal-containing biological structures, providing a basis to investigate the basic principles governing the properties of these systems. MetalPDB is updated monthly in an automated manner. PMID:23155064

Andreini, Claudia; Cavallaro, Gabriele; Lorenzini, Serena; Rosato, Antonio

2013-01-01

42

MetalPDB: a database of metal sites in biological macromolecular structures  

PubMed Central

We present here MetalPDB (freely accessible at http://metalweb.cerm.unifi.it), a novel resource aimed at conveying the information available on the three-dimensional (3D) structures of metal-binding biological macromolecules in a consistent and effective manner. This is achieved through the systematic and automated representation of metal-binding sites in proteins and nucleic acids by way of Minimal Functional Sites (MFSs). MFSs are 3D templates that describe the local environment around the metal(s) independently of the larger context of the macromolecular structure embedding the site(s), and are the central objects of MetalPDB design. MFSs are grouped into equistructural (broadly defined as sites found in corresponding positions in similar structures) and equivalent sites (equistructural sites that contain the same metals), allowing users to easily analyse similarities and variations in metal–macromolecule interactions, and to link them to functional information. The web interface of MetalPDB allows access to a comprehensive overview of metal-containing biological structures, providing a basis to investigate the basic principles governing the properties of these systems. MetalPDB is updated monthly in an automated manner. PMID:23155064

Andreini, Claudia; Cavallaro, Gabriele; Lorenzini, Serena; Rosato, Antonio

2013-01-01

43

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

PubMed Central

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

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

2011-01-01

44

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

SciTech Connect

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

Munshi, Parthapratim [ORNL] [ORNL; Myles, Dean A A [ORNL] [ORNL; Robertson, Lee [ORNL] [ORNL; Stoica, Alexandru Dan [ORNL] [ORNL; Crow, Lowell [ORNL] [ORNL; Kovalevskyi, Andrii Y [ORNL] [ORNL; Koritsanszky, Tibor S [ORNL] [ORNL; Chakoumakos, Bryan C [ORNL] [ORNL; Blessing, Robert [Hauptman-Woodward Medical Research Institute] [Hauptman-Woodward Medical Research Institute; Meilleur, Flora [ORNL] [ORNL

2013-01-01

45

Apparatus for the Study of the Dielectric Properties of Macromolecular Solutions under Flow  

Microsoft Academic Search

Some solutions show a change in value of their dielectric constant and specific conductance when subjected to shearing stresses produced by a velocity gradient established within them. A detailed account is given of an apparatus which has been used for studying this effect. The solution to be investigated is placed in the annular space between two concentric cylinders. The gap

H. G. Jerrard; T. A. Fisher; B. A. W. Simmons

1960-01-01

46

SedNMR: a web tool for optimizing sedimentation of macromolecular solutes for SSNMR.  

PubMed

We have proposed solid state NMR (SSNMR) of sedimented solutes as a novel approach to sample preparation for biomolecular SSNMR without crystallization or other sample manipulations. The biomolecules are confined by high gravity--obtained by centrifugal forces either directly in a SSNMR rotor or in a ultracentrifugal device--into a hydrated non-crystalline solid suitable for SSNMR investigations. When gravity is removed, the sample reverts to solution and can be treated as any solution NMR sample. We here describe a simple web tool to calculate the relevant parameters for the success of the experiment. PMID:24243317

Ferella, Lucio; Luchinat, Claudio; Ravera, Enrico; Rosato, Antonio

2013-12-01

47

Macromolecular Crystallization in Microgravity  

NASA Technical Reports Server (NTRS)

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

Snell, Edward H.; Helliwell, John R.

2004-01-01

48

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

PubMed Central

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

Fernandez, Cristina; Minton, Allen P.

2008-01-01

49

Complexation of Statins with ?-Cyclodextrin in Solutions of Small Molecular Additives and Macromolecular Colloids  

NASA Astrophysics Data System (ADS)

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

Süle, András; Csempesz, Ferenc

50

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

Microsoft Academic Search

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

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

2005-01-01

51

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

52

Asphalts and asphaltenes: Macromolecular structure, precipitation properties, and flow in porous media  

NASA Astrophysics Data System (ADS)

Depending on rock and fluid properties, more than 50% of reservoir oil in place is normally produced by enhanced oil recovery (EOR) methods. Among the EOR techniques, miscible flooding is one of the most efficient and widely-used methods. However, this method can suffer from the formation and precipitation of asphalt aggregates. In addition, asphalt deposition is also a major hindrance to heavy oil production, and even primary recovery operations. Asphalt deposition can alter the reservoir rock properties, fluid saturation distribution, fluid flow properties, and eventually the ultimate oil recovery. The shortage of studies on the macromolecular structure and growth mechanisms of asphalt particles is the main reason for the unsuccessful modeling of their precipitation properties. The equivocal behavior of asphalt under some specific conditions could be the other reason. In this research we look at the problem of asphalt formation, flow, and precipitation from three different angles. We analyze extensive small-angle X-ray and neutron scattering data, precipitation data, and molecular weight distribution measurements, and show that they all suggest conclusively that asphalts and asphaltenes are fractal aggregates, and their growth mechanisms are diffusion-limited particle (DLP) and diffusion-limited cluster-cluster (DLCC) aggregation processes. These results lead us to development of a scaling equation of state for predicting asphalt precipitation properties, such as its onset and amount of precipitation. Another result of our study is an analytical equation for modeling the molecular weight distribution of asphalt and asphaltene aggregates. In addition, asphalt phase behavior in miscible and immiscible injections is studied. The effect of the governing thermodynamic factors, such as the pressure, temperature, and composition of the oil and precipitation agents, on the asphalt aggregation and disaggregation processes are investigated. Finally, a model is developed to study the flow of an asphalt-containing oil through a reservoir. A large volume of the field data are analyzed for delineating the asphalt precipitation and release mechanisms in the reservoir and the resulting patterns of the permeability alteration.

Rassamdana, Hossein

53

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

54

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

NASA Astrophysics Data System (ADS)

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.

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

2014-05-01

55

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

E-print Network

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

Sherrill, David

56

Modelling macromolecular networks: two meetings  

E-print Network

for identifying the dynamics of macromolecular interactions, the morphodynamics of biologi- cal structures invaders and inducing actin contraction to target the movement of the cell towards bacteria. This example illustrated well a new level of complexity not previously seen in model chemotactic systems in bacteria

Carbone, Alessandra

57

Teaching macromolecular modeling.  

PubMed Central

Training newcomers to the field of macromolecular modeling is as difficult as is training beginners in x-ray crystallography, nuclear magnetic resonance, or other methods in structural biology. In one or two lectures, the most that can be conveyed is a general sense of the relationship between modeling and other structural methods. If a full semester is available, then students can be taught how molecular structures are built, manipulated, refined, and analyzed on a computer. Here we describe a one-semester modeling course that combines lectures, discussions, and a laboratory using a commercial modeling package. In the laboratory, students carry out prescribed exercises that are coordinated to the lectures, and they complete a term project on a modeling problem of their choice. The goal is to give students an understanding of what kinds of problems can be attacked by molecular modeling methods and which problems are beyond the current capabilities of those methods. PMID:1489919

Harvey, S C; Tan, R K

1992-01-01

58

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

59

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

60

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

61

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

62

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

63

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

64

Harvesting and Cryo-cooling Crystals of Membrane Proteins Grown in Lipidic Mesophases for Structure Determination by Macromolecular Crystallography  

PubMed Central

An important route to understanding how proteins function at a mechanistic level is to have the structure of the target protein available, ideally at atomic resolution. Presently, there is only one way to capture such information as applied to integral membrane proteins (Figure 1), and the complexes they form, and that method is macromolecular X-ray crystallography (MX). To do MX diffraction quality crystals are needed which, in the case of membrane proteins, do not form readily. A method for crystallizing membrane proteins that involves the use of lipidic mesophases, specifically the cubic and sponge phases1-5, has gained considerable attention of late due to the successes it has had in the G protein-coupled receptor field6-21 (www.mpdb.tcd.ie). However, the method, henceforth referred to as the in meso or lipidic cubic phase method, comes with its own technical challenges. These arise, in part, due to the generally viscous and sticky nature of the lipidic mesophase in which the crystals, which are often micro-crystals, grow. Manipulating crystals becomes difficult as a result and particularly so during harvesting22,23. Problems arise too at the step that precedes harvesting which requires that the glass sandwich plates in which the crystals grow (Figure 2)24,25 are opened to expose the mesophase bolus, and the crystals therein, for harvesting, cryo-cooling and eventual X-ray diffraction data collection. The cubic and sponge mesophase variants (Figure 3) from which crystals must be harvested have profoundly different rheologies4,26. The cubic phase is viscous and sticky akin to a thick toothpaste. By contrast, the sponge phase is more fluid with a distinct tendency to flow. Accordingly, different approaches for opening crystallization wells containing crystals growing in the cubic and the sponge phase are called for as indeed different methods are required for harvesting crystals from the two mesophase types. Protocols for doing just that have been refined and implemented in the Membrane Structural and Functional Biology (MS&FB) Group, and are described in detail in this JoVE article (Figure 4). Examples are given of situations where crystals are successfully harvested and cryo-cooled. We also provide examples of cases where problems arise that lead to the irretrievable loss of crystals and describe how these problems can be avoided. In this article the Viewer is provided with step-by-step instructions for opening glass sandwich crystallization wells, for harvesting and for cryo-cooling crystals of membrane proteins growing in cubic and in sponge phases. PMID:22971942

Li, Dianfan; Boland, Coilin; Aragao, David; Walsh, Kilian; Caffrey, Martin

2012-01-01

65

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

PubMed

This review presents an overview of the highlights of major concepts involving the anatomical routes for the transport of macromolecules and the transmigration of cellular elements across the blood-brain barrier (BBB) during inflammation. The particular focus will include inflammatory leukocytes, neoplastic cells and pathogenic microorganisms including specific types of viruses, bacteria and yeasts. The experimental animal models presented here have been employed successfully by the authors in several independent experiments during the past twenty-five years for investigations of pathologic alterations of the BBB after a variety of experimentally induced injuries and inflammatory conditions in mammalian and non-mammalian animal species. The initial descriptions of endothelial cell (EC) vesicles or caveolae serving as mini-transporters of fluid substances essentially served as a springboard for many subsequent discoveries during the past half century related to mechanisms of uptake of materials into ECs and whether or not pinocytosis is related to the transport of these materials across EC barriers under normal physiologic conditions and after tissue injury. In the mid-1970's, the authors of this review independently applied morphologic techniques (transmission electron microscopy-TEM), in conjunction with the plant protein tracer horseradish peroxidase (HRP) to investigate macromolecular transport structures that increased after the brain and spinal cord had been subjected to a variety of injuries. Based on morphologic evidence from these studies of BBB injury, the authors elaborated a unique EC system of modified caveolae that purportedly fused together forming transendothelial cell channels, and later similar EC profiles defined as vesiculo-canalicular or vesiculo-tubular structures (VTS, Lossinsky, et al., 1999). These EC structures were observed in association with increased BBB permeability of tracers including exogenously injected HRP, normally excluded from the intercellular milieu of the CNS. Subsequent studies of non-BBB-type tumor ECs determined that the EC VTS and other vesicular structures were defined by others as vesiculo-vacuolar organelles (VVOs, Kohn et al., 1992; Dvorak et al., 1996). Collectively, these structures appear to represent a type of anatomical gateway to the CNS likely serving as conduits. However, these CNS conduits become patent only in damaged ECs for the passage of macromolecules, and purportedly for inflammatory and neoplastic cells as well (Lossinsky et al., 1999). In this review, we focus attention on the similarities and differences between caveolae, fused racemic vesicular bundles, endothelial tubules and channels (VTS and the VVOs) that are manifest in normal, non-BBB-type blood vessels, and in the BBB after injury. This review will present evidence that the previous studies by the authors and other researchers established a framework for subsequent transmission (TEM), scanning (SEM) and high-voltage electron microscopic (HVEM) investigations concerning ultrastructural, ultracytochemical and immunoultra-structural alterations of the cerebral ECs and the mechanisms of the BBB transport that occurs after CNS injury. This review is not intended to include all of the many observations that might be included in a general historical overview of the development of the EC channel hypothesis, but it will discuss several of the major contributions. We have attempted to present some of the structural evidence that supports our early contributions and those made by other investigators by highlighting major features of these EC structures that are manifest in the injured BBB. We have focused on currently established concepts and principles related to mechanisms for the transendothelial transport of macromolecules after CNS injury and also offer a critical appraisal of some of this literature. Finally, we describe more recent concepts of transBBB avenues for viruses, including HIV-1, bacterial and mycotic organisms, as well as inflammatory and neoplastic cell adhesion and migration across the in

Lossinsky, A S; Shivers, R R

2004-04-01

66

A Model for Macromolecular Crystallization  

NASA Technical Reports Server (NTRS)

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

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

2001-01-01

67

Pharmaceutical Powder Diffraction: Structure Solution from PXRD  

E-print Network

Pharmaceutical Powder Diffraction: Structure Solution from PXRD How reliable are our structures? Pharmaceutical Powder Diffraction: Structure Solution from PXRD How reliable are our structures? Maryjane

68

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

69

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

PubMed Central

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

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

2013-01-01

70

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

PubMed

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

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

2013-01-01

71

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

PubMed Central

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

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

2008-01-01

72

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

PubMed

The structural effect of biodegradable macromolecular magnetic resonance imaging (MRI) contrast agents, polydisulfide gadolinium (Gd)(III) chelates, on their in vitro degradability, and cardiovascular and tumor imaging were evaluated in mice. Polydisulfide Gd(III) chelates, Gd-DTPA cystamine copolymers (GDCC), Gd-DTPA l-cystine copolymers (GDCP), Gd-DTPA d-cystine copolymers (dGDCP) and Gd-DTPA glutathione (oxidized) copolymers (GDGP), with different sizes and narrow molecular weight distribution were prepared and evaluated both in vitro and in vivo in mice bearing MDA-MB-231 tumor xenografts. GDGP with large steric hindrance around the disulfide bonds had greater T(1) and T(2) relaxivities than GDCC, GDCP and dGDCP. The degradability of the polydisulfide by the endogenous thiols decreased with increasing steric effects around the disulfide bonds in the order of GDCC>GDCP, dGDCP>GDGP. The size and degradability of the contrast agents had a significant impact on vascular contrast enhancement kinetics. The agents with a large size and low degradability resulted in more prolonged vascular enhancement than the agents with a small size and high degradability. It seems that the size and degradability of the agents did not significantly affect tumor enhancement. All agents resulted in significant contrast enhancement in tumor tissue. This study has demonstrated that the vascular enhancement kinetics of the polydisulfide MRI contrast agents can be controlled by their sizes and structures. The polydisulfide Gd(III) chelates are promising biodegradable macromolecular MRI contrast agents for magnetic resonance angiography and cancer imaging. PMID:18814987

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

2009-05-01

73

Macromolecular bases of antischistosomal therapy.  

PubMed

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

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

2011-01-01

74

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

75

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

PubMed

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

2014-10-01

76

Generating Triangulated Macromolecular Surfaces by Euclidean Distance Transform  

E-print Network

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...

Xu, Dong; Zhang, Yang

2009-12-02

77

The ELLIPS suite of macromolecular conformation algorithms  

Microsoft Academic Search

This paper describes a series of four programmes for the PC based on ellipsoidal representations of macromolecular shape\\u000a in solution using Universal shape functions. ELLIPS1 is based on simple ellipsoid of revolution models (where two of the three axes of the ellipsoid are fixed equal to each other).\\u000a If the user types in a value for a shape function from

S. E. Harding; John C. Horton; H. Cölfen

1997-01-01

78

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

PubMed

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

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

1995-09-01

79

Macromolecular character of amber  

SciTech Connect

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

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

1989-03-15

80

Structure of supersaturated zincate solutions  

SciTech Connect

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

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

1985-09-01

81

Working at higher magnifications in scanning electron microscopy with secondary and backscattered electrons on metal coated biological specimens and imaging macromolecular cell membrane structures.  

PubMed

Membrane structures of macromolecular dimensions were imaged with high resolution secondary electron type I (SE-I) signal contrasts on metal coated biological specimens. The quality of the surface information was strongly dependent on the signal used for microscopy and on the properties of metal films, i.e., thickness, continuity, structure and decoration effects. Films of 10 nm thickness produced so much type II electrons that identical images were obtained with the conventional SE-II and BSE-II signals. In such images, the type I SE signal was so low that only very weak contrasts were recognizable. If the films--continuous or discontinuous--were composed of large metal aggregates (gold and platinum) a strong micro-roughness contrast was produced by the type II signal. At high magnifications (100,000 x) this background signal greatly reduced the S/N ratio of the SE-I signal. A similar effect was previously shown to be produced by the type III background signal. The type II background signal minimized when continuous films of small aggregates (tantalum and chromium) were applied. SE-I contrast dominated in the image if the film thickness was limited to 1 nm. Additionally, it was found that gold and platinum decorated membrane surface structures, less than 20 nm in size, and did not reveal all the topographic information available (size, shape, orientation spacing of small surface features) but merely displayed center-to-center distances. These decoration effects were avoided and extensive topographic information was obtained through surface coating with Ta or Cr. PMID:4095499

Peters, K R

1985-01-01

82

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

83

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

84

Practical structure solution with ARCIMBOLDO  

PubMed Central

Since its release in September 2009, the structure-solution program ARCIMBOLDO, based on the combination of locating small model fragments such as polyalanine ?-helices with density modification with the program SHELXE in a multisolution frame, has evolved to incorporate other sources of stereochemical or experimental information. Fragments that are more sophisticated than the ubiquitous main-chain ?-­helix can be proposed by modelling side chains onto the main chain or extracted from low-homology models, as locally their structure may be similar enough to the unknown one even if the conventional molecular-replacement approach has been unsuccessful. In such cases, the program may test a set of alternative models in parallel against a specified figure of merit and proceed with the selected one(s). Experimental information can be incorporated in three ways: searching within ARCIMBOLDO for an anomalous fragment against anomalous differences or MAD data or finding model fragments when an anomalous substructure has been determined with another program such as SHELXD or is subsequently located in the anomalous Fourier map calculated from the partial fragment phases. Both sources of information may be combined in the expansion process. In all these cases the key is to control the workflow to maximize the chances of success whilst avoiding the creation of an intractable number of parallel processes. A GUI has been implemented to aid the setup of suitable strategies within the various typical scenarios. In the present work, the practical application of ARCIMBOLDO within each of these scenarios is described through the distributed test cases. PMID:22505254

Rodríguez, Dayté; Sammito, Massimo; Meindl, Kathrin; de Ilarduya, Iñaki M.; Potratz, Marianus; Sheldrick, George M.; Usón, Isabel

2012-01-01

85

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

86

RapiData: a Practical Course in Macromolecular X-ray Diffraction Data Measurement and Structure Solving at the NSLS  

SciTech Connect

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.

Sweet, R.; Soares, A

2010-01-01

87

Translational diffusion of macromolecular assemblies measured using transverse relaxation-optimized PFG-NMR  

PubMed Central

In structural biology, pulsed field gradient (PFG) NMR for characterization of size and hydrodynamic parameters of macromolecular solutes has the advantage over other techniques that the measurements can be recorded with identical solution conditions as used for NMR structure determination or for crystallization trials. This paper describes two transverse relaxation-optimized (TRO) 15N-filtered PFG stimulated-echo (STE) experiments for studies of macromolecular translational diffusion in solution, 1H-TRO-STE and 15N-TRO-STE, which include CRINEPT and TROSY elements. Measurements with mixed micelles of the Escherichia coli outer membrane protein X (OmpX) and the detergent Fos-10 were used for a systematic comparison of 1H-TRO-STE and 15N-TRO-STE with conventional 15N-filtered STE experimental schemes. The results provide an extended platform for evaluating the NMR experiments available for diffusion measurements in structural biology projects with molecular particles of different size ranges. An initial application of the 15N-TRO-STE experiment with very long diffusion delays showed that the tedradecamer structure of the 800 kDa Thermus thermophilus chaperonin GroEL is preserved in aqueous solution over the temperature range 25–60°C. PMID:21919531

Horst, Reto; Horwich, Arthur L.

2012-01-01

88

Stochastic dynamics of macromolecular-assembly networks.  

NASA Astrophysics Data System (ADS)

The formation and regulation of macromolecular complexes provides the backbone of most cellular processes, including gene regulation and signal transduction. The inherent complexity of assembling macromolecular structures makes current computational methods strongly limited for understanding how the physical interactions between cellular components give rise to systemic properties of cells. Here we present a stochastic approach to study the dynamics of networks formed by macromolecular complexes in terms of the molecular interactions of their components [1]. Exploiting key thermodynamic concepts, this approach makes it possible to both estimate reaction rates and incorporate the resulting assembly dynamics into the stochastic kinetics of cellular networks. As prototype systems, we consider the lac operon and phage ? induction switches, which rely on the formation of DNA loops by proteins [2] and on the integration of these protein-DNA complexes into intracellular networks. This cross-scale approach offers an effective starting point to move forward from network diagrams, such as those of protein-protein and DNA-protein interaction networks, to the actual dynamics of cellular processes. [1] L. Saiz and J.M.G. Vilar, submitted (2005). [2] J.M.G. Vilar and L. Saiz, Current Opinion in Genetics & Development, 15, 136-144 (2005).

Saiz, Leonor; Vilar, Jose

2006-03-01

89

Assembly of allosteric macromolecular switches: lessons from PKA  

PubMed Central

Protein kinases are dynamic molecular switches that have evolved to be only transiently activated. Kinase activity is embedded within a conserved kinase core, which is typically regulated by associated domains, linkers and interacting proteins. Moreover, protein kinases are often tethered to large macromolecular complexes to provide tighter spatiotemporal control. Thus, structural characterization of kinase domains alone is insufficient to explain protein kinase function and regulation in vivo. Recent progress in structural characterization of cyclic AMP-dependent protein kinase (PKA) exemplifies how our knowledge of kinase signalling has evolved by shifting the focus of structural studies from single kinase subunits to macromolecular complexes. PMID:22992589

Taylor, Susan S.; Ilouz, Ronit; Zhang, Ping; Kornev, Alexandr P.

2014-01-01

90

Probing the hydration water diffusion of macromolecular surfaces and interfaces  

Microsoft Academic Search

We probe the translational dynamics of the hydration water surrounding the macromolecular surfaces of selected polyelectrolytes, lipid vesicles and intrinsically disordered proteins with site specificity in aqueous solutions. These measurements are made possible by the recent development of a new instrumental and methodological approach based on Overhauser dynamic nuclear polarization (DNP)-enhanced nuclear magnetic resonance (NMR) spectroscopy. This technique selectively amplifies

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

2011-01-01

91

Macromolecular interactions Biologically important macromolecular interactions are highly specific  

E-print Network

macromolecular interaction often results in diseases--many signaling molecules are oncogenes (i.e. will cause modified ("phosphorylated") by addition of a phosphate group by enzymes called receptor tyrosine kinases is performed by enzymes called phosphatases inside the cell outside the cell RTK #12;pTyr is essential for SH2

Park, Sheldon

92

Molecular Control of Macromolecular Properties  

NASA Astrophysics Data System (ADS)

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

Holcombe, Thomas Wesley, III

93

Small-scale hydrous pyrolysis of macromolecular material in meteorites  

NASA Astrophysics Data System (ADS)

The hydrous pyrolysis method, usually performed on several hundred grams of terrestrial rock sample, has been scaled down to accommodate less than two grams of meteorite sample. This technique makes full use of the high yields associated with hydrous pyrolysis experiments and permits the investigation of the meteorite macromolecular material, the major organic component in carbonaceous meteorites. The hydrous pyrolysis procedure transforms the high molecular weight macromolecular material into low molecular weight fragments. The released entities can then be extracted with supercritical fluid extraction. In contrast to the parent structure, the pyrolysis products are amenable for analysis by gas chromatography-based techniques. When subjected to hydrous pyrolysis, two carbonaceous chondrites (Orgueil and Cold Bokkeveld) released generally similar products, which consisted of abundant volatile aromatic and alkyl-substituted aromatic compounds. These results revealed the ability of small-scale hydrous pyrolysis to dissect extraterrestrial macromolecular material and thereby reveal its organic constitution.

Sephton, M. A.; Pillinger, C. T.; Gilmour, I.

1998-12-01

94

Model of the structure of sucrose solutions  

Microsoft Academic Search

1.The observed properties of the sucrose-water system over the entire range of concentrations investigated can be explained with the aid of the continual model of an aqueous solution of sucrose without calling upon the concept of a microscopic separation of phases.2.The model developed predicts a continual transition from the structure of a solution with a low concentration of sucrose to

I. S. Gulyi; V. M. Klimovich

1991-01-01

95

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

PubMed

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. PMID:23767571

Köfinger, Jürgen; Hummer, Gerhard

2013-05-01

96

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

97

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

98

Nanoscale structure in crystalline solid solution alloys  

Microsoft Academic Search

The importance of local structure to the physical properties of alloys is receiving increasing attention. Recent measurements of the short-range nanoscale structure in metallic solid solution alloys reveal both the local chemical order and the chemically sensitive nearneighbor distances. These measurements are made possible by intense and tunable synchrotron X radiation; X-ray energy is adjusted to vary the x-ray scattering

X. Jiang

1996-01-01

99

Adaptation to high temperatures through macromolecular dynamics by neutron scattering.  

PubMed

Work on the relationship between hyperthermophile protein dynamics, stability and activity is reviewed. Neutron spectroscopy has been applied to measure and compare the macromolecular dynamics of various hyperthermophilic and mesophilic proteins, under different conditions. First, molecular dynamics have been analyzed for the hyperthermophile malate dehydrogenase from Methanococcus jannaschii and a mesophilic homologue, the lactate dehydrogenase from Oryctolagus cunniculus (rabbit) muscle. The neutron scattering approach has provided independent measurements of the global flexibility and structural resilience of each protein, and it has been demonstrated that macromolecular dynamics represents one of the molecular mechanisms of thermoadaptation. The resilience was found to be higher for the hyperthermophilic protein, thus ensuring similar flexibilities in both enzymes at their optimal activity temperature. Second, the neutron method has been developed to quantify the average macromolecular flexibility and resilience within the natural crowded environment of the cell, and mean macromolecular motions have been measured in vivo in psychrophile, mesophile, thermophile and hyperthermophile bacteria. The macromolecular resilience in bacteria was found to increase with adaptation to high temperatures, whereas flexibility was maintained within narrow limits, independent of physiological temperature for all cells in their active state. Third, macromolecular motions have been measured in free and immobilized dihydrofolate reductase from Escherichia coli. The immobilized mesophilic enzyme has increased stability and decreased activity, so that its properties are changed to resemble those of a thermophilic enzyme. Quasi-elastic neutron scattering measurements have also been performed to probe the protein motions. Compared to the free enzyme, the average height of the activation free energy barrier to local motions was found to be increased by 0.54 kcal.mol(-1) in the immobilized dihydrofolate reductase, a value that is of the same order as expected from the theoretical rate equation. PMID:17683333

Tehei, Moeava; Zaccai, Giuseppe

2007-08-01

100

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

PubMed

The availability of intense microbeam macromolecular crystallography beamlines at third-generation synchrotron sources has enabled data collection and structure solution from microcrystals of <10?µm in size. The increased likelihood of severe radiation damage where microcrystals or particularly sensitive crystals are used forces crystallographers to acquire large numbers of data sets from many crystals of the same protein structure. The associated analysis and merging of multi-crystal data is currently a manual and time-consuming step. Here, a computer program, BLEND, that has been written to assist with and automate many of the steps in this process is described. It is demonstrated how BLEND has successfully been used in the solution of a novel membrane protein. PMID:23897484

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

2013-08-01

101

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

PubMed Central

The availability of intense microbeam macromolecular crystallography beamlines at third-generation synchrotron sources has enabled data collection and structure solution from microcrystals of <10?µm in size. The increased likelihood of severe radiation damage where microcrystals or particularly sensitive crystals are used forces crystallographers to acquire large numbers of data sets from many crystals of the same protein structure. The associated analysis and merging of multi-crystal data is currently a manual and time-consuming step. Here, a computer program, BLEND, that has been written to assist with and automate many of the steps in this process is described. It is demonstrated how BLEND has successfully been used in the solution of a novel membrane protein. PMID:23897484

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

2013-01-01

102

MACROMOLECULAR PHYSIOLOGY OF PLASTIDS  

PubMed Central

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

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

1970-01-01

103

Searching for likeness in a database of macromolecular complexes.  

PubMed

A software tool and workflow based on distance geometry is presented that can be used to search for local similarity in substructures in a comprehensive database of experimentally derived macromolecular structure. The method does not rely on fold annotation, specific secondary structure assignments, or sequence homology and may be used to locate compound substructures of multiple segments spanning different macromolecules that share a queried backbone geometry. This generalized substructure searching capability is intended to allow users to play an active part in exploring the role specific substructures play in larger protein domains, quaternary assemblies of proteins, and macromolecular complexes of proteins and polynucleotides. The user may select any portion or portions of an existing structure or complex to serve as a template for searching, and other structures that share the same structural features are identified, retrieved and overlaid to emphasize substructural likeness. Matching structures may be compared using a variety of integrated tools including molecular graphics for structure visualization and matching substructure sequence logos. A number of examples are provided that illustrate how generalized substructure searching may be used to understand both the similarity, and individuality of specific macromolecular structures. Web-based access to our substructure searching services is freely available at https://drugsite.msi.umn.edu. PMID:24047445

Van Voorst, Jeffrey R; Finzel, Barry C

2013-10-28

104

Combined effects of agitation, macromolecular crowding, and interfaces on amyloidogenesis.  

PubMed

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

2012-11-01

105

Nonpolar solutes enhance water structure within hydration shells while reducing  

E-print Network

Nonpolar solutes enhance water structure within hydration shells while reducing interactions surrounding a nonpolar solute. The spatial distribution functions of the water molecules surrounding benzene shell surrounding both solutes. In addition, benzene showed a strong preference for hydrogen bonding

Raschke, Tanya M.

106

Translational diffusion and solution structure of microemulsions  

SciTech Connect

For isotopic solution phases in surfactant systems which contain large amounts of water and hydrocarbon, the self-diffusion coefficients were determined for several components to obtain information on solution structure. Phases studied were one surfactant phase in a nonionic surfactant system and one microemulsion phase in an ionic surfactant + cosurfacant system. The systems chosen were tetraethyleneglycol dodecyl ether-exadecane-water and sodium octylbenzenesulfonate-pentanol decane-sodium chloride-water. The experimental techniques used were the open-ended capillary tube method using radioactive labeling and the NMR (H/sub 1/ and H/sub 2/ NMR) spin-echo pulsed-field gradient method. Over wide composition ranges in both systems both hydrocarbon and water (+ counterion) diffusion is rapid over macroscopic distances demonstrating that the solutions are both hydrocarbon and water continuous. The results do not show areas with oil-in-water and water-in-oil microemulsions with a sharp transition between the 2 types of aggregates.

Lindman, B.; Nilsson, P.G.; Kamenka, N.; Kathopoulis, T.M.; Brun, B.

1980-09-18

107

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

108

Multiscale methods for macromolecular simulations.  

PubMed

In this article we review the key modeling tools available for simulating biomolecular systems. We consider recent developments and representative applications of mixed quantum mechanics/molecular mechanics (QM/MM), elastic network models (ENMs), coarse-grained molecular dynamics, and grid-based tools for calculating interactions between essentially rigid protein assemblies. We consider how the different length scales can be coupled, both in a sequential fashion (e.g. a coarse-grained or grid model using parameterization from MD simulations), and via concurrent approaches, where the calculations are performed together and together control the progression of the simulation. We suggest how the concurrent coupling approach familiar in the context of QM/MM calculations can be generalized, and describe how this has been done in the CHARMM macromolecular simulation package. PMID:18721882

Sherwood, Paul; Brooks, Bernard R; Sansom, Mark S P

2008-10-01

109

The MX2 macromolecular crystallography beamline: a wiggler X-ray source at the LNLS.  

PubMed

The Brazilian Synchrotron Light Laboratory [Laboratório Nacional de Luz Síncrotron (LNLS), Campinas, SP, Brazil] is the first commissioned synchrotron light source in the southern hemisphere. The first wiggler macromolecular crystallography beamline (MX2) at the LNLS has been recently constructed and brought into operation. Here the technical design, experimental set-up, parameters of the beamline and the first experimental results obtained at MX2 are described. The beamline operates on a 2.0 T hybrid 30-pole wiggler, and its optical layout includes collimating mirror, Si(111) double-crystal monochromator and toroidal bendable mirror. The measured flux density at the sample position at 8.7 eV reaches 4.8 x 10(11) photons s(-1) mm(-2) (100 mA)(-1). The beamline is equipped with a MarResearch Desktop Beamline Goniostat (MarDTB) and 3 x 3 MarMosaic225 CCD detector, and is controlled by a customized version of the Blu-Ice software. A description of the first X-ray diffraction data sets collected at the MX2 LNLS beamline and used for macromolecular crystal structure solution is also provided. PMID:19096177

Guimarães, Beatriz G; Sanfelici, Lucas; Neuenschwander, Regis T; Rodrigues, Flávio; Grizolli, Walan C; Raulik, Marco A; Piton, James R; Meyer, Bernd C; Nascimento, Alessandro S; Polikarpov, Igor

2009-01-01

110

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

111

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

PubMed Central

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

Rambo, Robert P.; Tainer, John A.

2010-01-01

112

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

E-print Network

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

Liu, Yun, 1973-

2005-01-01

113

Nucleotide's bilinear indices: Novel bio-macromolecular descriptors for bioinformatics studies of nucleic acids. I. Prediction of paromomycin's affinity constant with HIV1 ?-RNA packaging region  

Microsoft Academic Search

A new set of nucleotide-based bio-macromolecular descriptors are presented. This novel approach to bio-macromolecular design from a linear algebra point of view is relevant to nucleic acids quantitative structure-activity relationship (QSAR) studies. These bio-macromolecular indices are based on the calculus of bilinear maps on ?n[bmk(x¯m,y¯m):?n×?n??] in canonical basis. Nucleic acid's bilinear indices are calculated from kth power of non-stochastic and

Yovani Marrero-Ponce; Sadiel E. Ortega-Broche; Yunaimy Echeverría Díaz; Ysaias J. Alvarado; Nestor Cubillan; Gladys Casas Cardoso; Francisco Torrens; Facundo Pérez-Giménez

2009-01-01

114

Ionically gelled alginate foams: physical properties controlled by operational and macromolecular parameters.  

PubMed

Alginates in the format of scaffolds provide important functions as materials for cell encapsulation, drug delivery, tissue engineering and wound healing among others. The method for preparation of alginate-based foams presented here is based on homogeneous, ionotropic gelation of aerated alginate solutions, followed by air drying. The method allows higher flexibility and better control of the pore structure, hydration properties and mechanical integrity compared to foams prepared by other techniques. The main variables for tailoring hydrogel properties include operational parameters such as degree of aeration and mixing times and concentration of alginate, as well as macromolecular properties such as the type of alginate (chemical composition and molecular weight distribution). Exposure of foams to ?-irradiation resulted in a dose-dependent (0-30 kGy) reduction in molecular weight of the alginate and a corresponding reduction in tensile strength of the foams. PMID:22991894

Andersen, Therese; Melvik, Jan Egil; Gåserød, Olav; Alsberg, Eben; Christensen, Bjørn E

2012-11-12

115

Solution NMR of Large Molecules and Assemblies †  

Microsoft Academic Search

Solution NMR spectroscopy represents a powerful tool for examining the structure and function of biological macromolecules. The advent of multidimensional (2D-4D) NMR, together with the widespread use of uniform isotopic labeling of proteins and RNA with the NMR-active isotopes, 15N and 13C, opened the door to detailed analyses of macromolecular structure, dynamics, and interactions of smaller macromolecules (<25 kDa). Over

Mark P. Foster; Craig A. McElroy; Carlos D. Amero

2007-01-01

116

Dielectric and structural properties of aqueous nonpolar solute mixtures  

NASA Astrophysics Data System (ADS)

The dielectric properties and molecular structure of water mixtures with different nonpolar solutes (methane and noble gases) are studied using molecular dynamics. The water-water, water-solute, and solute-solute interactions are calculated using the combination of a polarizable potential [J. Li, Z. Zhou, and R. J. Sadus, J. Chem. Phys. 127, 154509 (2007), 10.1063/1.2786449] for water plus the Lennard-Jones potential. The effect of solute size and concentration on the solubility of the system, hydrogen bonding, dielectric constant, and dipole moment are investigated over a temperature range of 278-750 K and solute percentage mole fractions up to 30%. Solute particles affect the structure of water, resulting in the compression of oxygen-oxygen and oxygen-hydrogen radial distribution functions. The influence of the solute extends both to relatively low concentrations and high temperatures. The coordination numbers of aqueous solutions of the nonpolar solutes appear to be proportional to the size of the solute particles. Our study shows the destructive influence of the nonpolar solute on both the tetrahedral water structure and hydrogen bond formation at solute concentrations greater than 30%. The presence of nonpolar particles typically decreases both the dielectric constant and dipole moment. The decrease of dielectric constant and water dipole moment is directly proportional to the solute concentration and temperature.

Shvab, I.; Sadus, Richard J.

2012-09-01

117

The prestressability problem of tensegrity structures: some analytical solutions  

E-print Network

The prestressability problem of tensegrity structures: some analytical solutions Cornel Sultan a formulate the general prestressability conditions for tensegrity structures. These conditions are expressed as a set of nonlinear equations and inequalities on the tendon tensions. Several examples of tensegrity

Sultan, Cornel

118

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

119

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

120

Modeling the macromolecular background in Nuclear Magnetic Resonance spectroscopic signals  

E-print Network

1 Modeling the macromolecular background in Nuclear Magnetic Resonance spectroscopic signals D- noising, nonparametric modeling, macromolecular back- ground. I. INTRODUCTION Nuclear Magnetic Resonance Engineering (ESAT-SCD), Leuven, Belgium Abstract--Metabolite quantitation of Nuclear Magnetic Resonance

121

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

122

Accounting for Large Amplitude Protein Deformation during in Silico Macromolecular Docking  

PubMed Central

Rapid progress of theoretical methods and computer calculation resources has turned in silico methods into a conceivable tool to predict the 3D structure of macromolecular assemblages, starting from the structure of their separate elements. Still, some classes of complexes represent a real challenge for macromolecular docking methods. In these complexes, protein parts like loops or domains undergo large amplitude deformations upon association, thus remodeling the surface accessible to the partner protein or DNA. We discuss the problems linked with managing such rearrangements in docking methods and we review strategies that are presently being explored, as well as their limitations and success. PMID:21541061

Bastard, Karine; Saladin, Adrien; Prevost, Chantal

2011-01-01

123

Accounting for large amplitude protein deformation during in silico macromolecular docking.  

PubMed

Rapid progress of theoretical methods and computer calculation resources has turned in silico methods into a conceivable tool to predict the 3D structure of macromolecular assemblages, starting from the structure of their separate elements. Still, some classes of complexes represent a real challenge for macromolecular docking methods. In these complexes, protein parts like loops or domains undergo large amplitude deformations upon association, thus remodeling the surface accessible to the partner protein or DNA. We discuss the problems linked with managing such rearrangements in docking methods and we review strategies that are presently being explored, as well as their limitations and success. PMID:21541061

Bastard, Karine; Saladin, Adrien; Prévost, Chantal

2011-01-01

124

Master's programme in Macromolecular Materials Programme outline  

E-print Network

. Guidelines and recommendations for course combinations will be given. Courses corresponding to 15 ECTS can be available for application earlier.The application deadline is 15 January 2012. LAnguAge of instruction and development trends. To receive a Degree of Master of Science in Macromolecular materials, the students should

Lagergren, Jens

125

Numerical solution techniques for structural instability problems  

Microsoft Academic Search

ABSTRACT Purpose: The purpose is to overcome,numerical,problems,arising in structural instability numerical computations for equilibrium configurations corresponding to increasing loads on structures having points of instability or more generally large non linearity. Design\\/methodology\\/approach: The used numerical methodology,was the finite element method,with the particular technique of non linear transient dynamic analysis. In such way dynamic equilibrium paths, which are able to lead

E. Armentani; C. Calí; G. Cricrí; F. Caputo; R. Esposito

2006-01-01

126

Two-dimensional macromolecular distributions reveal detailed architectural features in high-amylose starches.  

PubMed

Two-dimensional (2D) structural distributions based on macromolecular size and branch chain-length are obtained for three maize starches with different amylose contents (one normal and two high-amylose varieties). Data were obtained using an analytical methodology combining chemical fractionation, enzymatic debranching, and offline 2D size-exclusion chromatography with multiple detection. The 2D distributions reveal novel features in the branching structure of high-amylose maize starches. Normal maize starch shows well-resolved structural topologies, corresponding to the amylopectin and amylose macromolecular populations. However, high-amylose maize starches exhibit very complex topologies with significant features between those of amylose and amylopectin, showing the presence of distinct intermediate components. These have the macromolecular size of amylose but similar branching structure to amylopectin, except for a higher proportion of longer branches. These structural features of the intermediate components can be related to a less tightly controlled biosynthesis of the branching structures in high-amylose maize starch mutants, which may prevent these molecules from maturing into full-size amylopectin. This altered macromolecular branched architecture of high-amylose starches probably contribute to their better nutritional properties. PMID:25256517

Vilaplana, Francisco; Meng, Di; Hasjim, Jovin; Gilbert, Robert G

2014-11-26

127

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

PubMed

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

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

2013-07-01

128

Curvilinear All-Atom Multiscale (CAM) Theory of Macromolecular Dynamics  

Microsoft Academic Search

A method is introduced for simulating long timescale macromolecular structural fluctuations and transitions with atomic-scale\\u000a detail. The N-atom Liouville equation for the macromolecule\\/host medium system provides the starting point for the analysis. Order parameters\\u000a characterizing overall macromolecular architecture are demonstrated to be slowly evolving.\\u000a \\u000a \\u000a \\u000a For single-stranded macromolecules, a curvilinear coordinate provides a way to introduce the order parameters. Using a

Z. Shreif; P. Ortoleva

2008-01-01

129

Complexation of Actinides in Solution: Thermodynamic Measurementsand Structural Characterization  

SciTech Connect

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

Rao, L.

2007-02-01

130

Large Structures: which Solutions for Health Monitoring?  

NASA Astrophysics Data System (ADS)

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

Camp, G.; Carreaud, P.; Lançon, H.

2013-07-01

131

Data Management System at the Photon Factory Macromolecular Crystallography Beamline  

NASA Astrophysics Data System (ADS)

Macromolecular crystallography is a very powerful tool to investigate three-dimensional structures of macromolecules at the atomic level, and is widely spread among structural biology researchers. Due to recent upgrades of the macromolecular crystallography beamlines at the Photon Factory, beamline throughput has improved, allowing more experiments to be conducted during a user's beam time. Although the number of beamlines has increased, so has the number of beam time applications. Consequently, both the experimental data from users' experiments and data derived from beamline operations have dramatically increased, causing difficulties in organizing these diverse and large amounts of data for the beamline operation staff and users. To overcome this problem, we have developed a data management system by introducing commercial middleware, which consists of a controller, database, and web servers. We have prepared several database projects using this system. Each project is dedicated to a certain aspect such as experimental results, beam time applications, beam time schedule, or beamline operation reports. Then we designed a scheme to link all the database projects.

Yamada, Y.; Matsugaki, N.; Chavas, L. M. G.; Hiraki, M.; Igarashi, N.; Wakatsuki, S.

2013-03-01

132

An investigation into methods of solution for nonlinear structural problems  

E-print Network

AN INVESTIGATION INTO METHODS OF SOLUTION FOR NONLINEAR STRUCTURAL PROBLEMS A Thesis bY EDWIN E. EENKEL Submitted to the Graduate College of Texas ASM University in partial fulfillment of the requirements for the degree of MASTER OF SCIENCE... December 1973 Major Subject: Interdisplinary Engineering AN INVESTIGATION INTO METHODS OF SOLUTION FOR NONLINEAR STRUCTURAL PROBLEMS A Thesis EDNIN E. HENKEL Approved as to style and content by: (Chairman of Committee) (Head of Department) (Member...

Henkel, Edwin Eugene

2012-06-07

133

Structure and Thermophysical Properties of Fullerene C60 Aqueous Solutions  

Microsoft Academic Search

The structure and thermophysical properties of fullerene C60aqueous solutions were investigated both experimentally and theoretically. The aggregation kinetics results indicated that the structure of fullerene C60aggregates in water could be described as a fractal system. The IR and electronic absorption spectra obtained confirm the presence of the crystalline phase in aqueous solution. The numerical values of thermodynamic coefficientsaP,ßT,ßS,cP, andcV, and

Yu. I. Prylutskyy; S. S. Durov; L. A. Bulavin; I. I. Adamenko; K. O. Moroz; I. I. Geru; I. N. Dihor; P. Scharff; P. C. Eklund; L. Grigorian

2001-01-01

134

CCMR: On the Microscopic Structure of Dilute Solutions  

NSDL National Science Digital Library

The changes in the molecular structure of the solvent due to the introduction of solute molecules in the infinitely dilute limit are studied in a one dimensional model in which molecules interact only with their nearest neighbors via square well potentials. The pair distribution function for two solute molecules in an otherwise pure solvent structure is calculated in terms of the thermodynamic variables, and the potentials of interaction between molecules in the model.

Toledo, J.

2007-08-29

135

Internal organisation of the nucleus: assembly of compartments by macromolecular crowding and the nuclear matrix model  

Microsoft Academic Search

Many and possibly all macromolecules in the nucleus are segregated into discrete compartments, but the current model that this is achieved by a fibrillar nuclear matrix which structures the nuclear interior and compartments is not consistent with all experimental observations, as reviewed here. New results are presented which suggest that macromolecular crowding forces play a crucial role in the assembly

Ronald Hancock

2004-01-01

136

Novel structure of static multisoliton solutions in the Skyrme model  

NASA Astrophysics Data System (ADS)

An economical discretization of the Skyrme model on a cubic lattice is used to calculate static multisoliton solutions. Previously known solutions corresponding to baryon numbers B=1 and 2 are reproduced and new solutions corresponding to B=3, 4, 5 and 6 are found. Surfaces of constant baryon number density are presented and reveal the rich internal structure of the new solutions. In particular, the pion fields describing the solitons with B=3 and 4 are found to possess tetrahedral (43>m) and octahedral (m3m) symmetry, respectively.

Braaten, Eric; Townsend, Steve; Carson, Larry

1990-01-01

137

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...

Gray, James; Lust, Dieter

2012-01-01

138

Solution-space structure of (some) optimization problems  

NASA Astrophysics Data System (ADS)

We study numerically the cluster structure of random ensembles of two NP-hard optimization problems originating in computational complexity, the vertex-cover problem and the number partitioning problem. We use branch-and-bound type algorithms to obtain exact solutions of these problems for moderate system sizes. Using two methods, direct neighborhood-based clustering and hierarchical clustering, we investigate the structure of the solution space. The main result is that the correspondence between solution structure and the phase diagrams of the problems is not unique. Namely, for vertex cover we observe a drastic change of the solution space from large single clusters to multiple nested levels of clusters. In contrast, for the number-partitioning problem, the phase space looks always very simple, similar to a random distribution of the lowest-energy configurations. This holds in the ''easy''/solvable phase as well as in the ''hard''/unsolvable phase.

Hartmann, A. K.; Mann, A.; Radenbach, W.

2008-01-01

139

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

140

Energy characteristics of structures in aqueous solutions of sucrose  

Microsoft Academic Search

Structures arising in sucrose solutions of various concentrations are modeled. A computer simulation by the molecular mechanics\\u000a method proves the existence of three aqueous sucrose structures, which depends on the ratio between water and sucrose molecules.\\u000a The calculated data are in good agreement with the experimental results obtained by different methods.

L. D. Bobrovnik; A. M. Grekhov; I. S. Gulyi

1998-01-01

141

Structure of outer membrane protein G by solution NMR spectroscopy  

PubMed Central

The bacterial outer membrane protein G (OmpG), a monomeric pH-gated porin, was overexpressed in Escherichia coli and refolded in ?-octyl glucoside micelles. After transfer into dodecylphosphocholine micelles, the solution structure of OmpG was determined by solution NMR spectroscopy at pH 6.3. Complete backbone assignments were obtained for 234 of 280 residues based on CA, CB, and CO connection pathways determined from a series of TROSY-based 3D experiments at 800 MHz. The global fold of the 14-stranded ?-barrel was determined based on 133 long-range NOEs observed between neighboring strands and local chemical shift and NOE information. The structure of the barrel is very similar to previous crystal structures, but the loops of the solution structure are quite flexible. PMID:17911261

Liang, Binyong; Tamm, Lukas K.

2007-01-01

142

Macromolecular nanotheranostics for multimodal anticancer therapy.  

PubMed

Macromolecular carrier materials based on N-(2-hydroxypropyl)methacrylamide (HPMA) are prototypic and well-characterized drug delivery systems that have been extensively evaluated in the past two decades, both at the preclinical and at the clinical level. Using several different imaging agents and techniques, HPMA copolymers have been shown to circulate for prolonged periods of time, and to accumulate in tumors both effectively and selectively by means of the Enhanced Permeability and Retention (EPR) effect. Because of this, HPMA-based macromolecular nanotheranostics, i.e. formulations containing both drug and imaging agents within a single formulation, have been shown to be highly effective in inducing tumor growth inhibition in animal models. In patients, however, as essentially all other tumor-targeted nanomedicines, they are generally only able to improve the therapeutic index of the attached active agent by lowering its toxicity, and they fail to improve the efficacy of the intervention. Bearing this in mind, we have recently reasoned that because of their biocompatibility and their beneficial biodistribution, nanomedicine formulations might be highly suitable systems for combination therapies. In the present manuscript, we briefly summarize several exemplary efforts undertaken in this regard in our labs in the past couple of years, and we show that long-circulating and passively tumor-targeted macromolecular nanotheranostics can be used to improve the efficacy of radiochemotherapy and of chemotherapy combinations. PMID:21901211

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

2011-10-01

143

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

E-print Network

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.

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

2011-05-26

144

Structure factor and thermodynamics of rigid dendrimers in solution  

E-print Network

The ''polymer reference interaction site model'' (PRISM) integral equation theory is used to determine the structure factor of rigid dendrimers in solution. The theory is quite successful in reproducing experimental structure factors for various dendrimer concentrations. In addition, the structure factor at vanishing scattering vector is calculated via the compressibility equation using scaled particle theory and fundamental measure theory. The results as predicted by both theories are systematically smaller than the experimental and PRISM data for platelike dendrimers.

L. Harnau; S. Rosenfeldt; M. Ballauff

2007-05-23

145

Solution structure of ?-conotoxin MVIIA using 2D NMR spectroscopy  

Microsoft Academic Search

The solution structure of ?-conotoxin MVIIA (SNX-111), a peptide toxin from the fish hunting cone snail Conus magus and a high-affinity blocker of N-type calcium channels, was determined by 2D NMR spectroscopy. The backbones of the best 44 structures match with an average pairwise RMSD of 0.59 angstroms. The structures contain a short segment of triple-stranded ?-sheet involving residues 6–8,

Vladimir J. Basus; Laszlo Nadasdi; J. Ramachandran; George P. Miljanich

1995-01-01

146

Exact coherent structures in pipe flow: travelling wave solutions  

Microsoft Academic Search

Three-dimensional travelling wave solutions are found for pressure-driven fluid flow through a circular pipe. They consist of three well-defined flow features streamwise rolls and streaks which dominate and streamwise-dependent wavy structures. The travelling waves can be classified by the m-fold rotational symmetry they possess about the pipe axis with m {=} 1,2,3,4,5 and 6 solutions identified. All are born out

H. Wedin; R. R. Kerswell

2004-01-01

147

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

148

Macromolecular neutron crystallography at the Protein Crystallography Station (PCS).  

PubMed

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

2010-11-01

149

A primer in macromolecular linguistics.  

PubMed

Polymeric macromolecules, when viewed abstractly as strings of symbols, can be treated in terms of formal language theory, providing a mathematical foundation for characterizing such strings both as collections and in terms of their individual structures. In addition this approach offers a framework for analysis of macromolecules by tools and conventions widely used in computational linguistics. This article introduces the ways that linguistics can be and has been applied to molecular biology, covering the relevant formal language theory at a relatively nontechnical level. Analogies between macromolecules and human natural language are used to provide intuitive insights into the relevance of grammars, parsing, and analysis of language complexity to biology. © 2012 Wiley Periodicals, Inc. Biopolymers 99: 203-217, 2013. PMID:23034580

Searls, David B

2013-03-01

150

Processes of ordered structure formation in polypeptide thin film solutions.  

SciTech Connect

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

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

2010-06-17

151

The Promise of Macromolecular Crystallization in Micro-fluidic Chips  

NASA Technical Reports Server (NTRS)

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

vanderWoerd, Mark; Ferree, Darren; Pusey, Marc

2003-01-01

152

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

153

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

154

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

155

The Dynamic Structure of Thrombin in Solution Brian Fuglestad,  

E-print Network

The Dynamic Structure of Thrombin in Solution Brian Fuglestad, Paul M. Gasper, Marco Tonelli, J Facility at Madison, University of Wisconsin, Madison, Wisconsin ABSTRACT The backbone dynamics of human a-thrombin, and activating it for catalysis (1,2). The resulting a-thrombin cleaves 12 known substrates, including fibrin

Komives, Elizabeth A.

156

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

157

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

158

Revealing the macromolecular targets of complex natural products.  

PubMed

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'. PMID:25411885

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

159

Effects of Daflon 500mg on postischemic macromolecular leak syndrome in striated skin muscle of the hamster.  

PubMed

We have recently shown that the purified micronized flavonoid fraction (90% diosmin and 10% hesperidin) Daflon 500 mg attenuates reperfusion injury in the striated skin muscle of the hamster. Herein, we report on the action of Daflon 500 mg on postischemic macromolecular leakage of FITC-dextran 150 kD provoked by tourniquet ischemia. Intravital fluorescence microscopy was used for analysis of macromolecular leakage in the microcirculation model of the hamster. A tourniquet ischemia of 4 h duration was induced followed by reperfusion. Animals were treated by gavage of Daflon 500 mg (n = 6) for 8 days at a daily dose of 30 mg kg(-1) body weight. Control animals received equivalent volumes of the vehicle (5% Arabic gum solution, n = 6). Measurements of the microcirculatory parameters were made before induction of ischemia and at 0.5, 2 and 24 h of reperfusion. After induction of ischemia, macromolecular leakage from postcapillary venules was significantly enhanced in vehicle-treated animals. Treatment with Daflon 500 mg significantly attenuated macromolecular leakage of FITC-dextran 150 kD. Preliminary data from a histomorphometric analysis (n = 3/experimental group) indicated that the number of emigrated (extravascular) leukocytes after ischemia reperfusion was markedly reduced in Daflon 500 mg-treated animals as compared to controls. These data indicate that Daflon 500 mg prevents leakage of the macromolecular tracer FITC-dextran 150 kD from postcapillary venules after postischemic reperfusion, presumably through an inhibitory action on the emigration of activated leukocytes. PMID:9477038

Nolte, D; Pickelman, S; Schütze, E; Möllmann, M; Messmer, K

1997-01-01

160

Empirical Magnetic Structure Solution of Frustrated Spin Systems  

NASA Astrophysics Data System (ADS)

Frustrated magnetism plays a central role in the phenomenology of exotic quantum states. However, since the magnetic structures of frustrated systems are often aperiodic, there has been the problem that they cannot be determined by using traditional crystallographic techniques. Here we show that the magnetic component of powder neutron scattering data is actually sufficiently information-rich to drive magnetic structure solution for frustrated systems, including spin ices, spin liquids, and molecular magnets. Our methodology employs ab initio reverse Monte Carlo refinement, making informed use of an additional constraint that minimizes variance in local spin environments. The atomistic spin configurations obtained in this way not only reflect a magnetic structuresolution” but also reproduce the full three-dimensional magnetic scattering pattern.

Paddison, Joseph A. M.; Goodwin, Andrew L.

2012-01-01

161

Solution Structures of Nanoassemblies Based on Pyrogallol[4]arenes.  

PubMed

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

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

2014-10-21

162

Heterotic domain wall solutions and SU(3) structure manifolds  

NASA Astrophysics Data System (ADS)

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 4 D, {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.

Gray, James; Larfors, Magdalena; Lüst, Dieter

2012-08-01

163

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

164

Macromolecular conformational dynamics in torsional angle space  

NASA Astrophysics Data System (ADS)

A Brownian dynamics treatment in torsional angle space is presented for the simulation of conformational dynamics of macromolecules with fixed bond lengths and bond angles and with an arbitrary intramolecular potential energy function. The advantages of the torsional angle space treatment over similar treatments (Brownian dynamics or molecular dynamics) in atomic coordinate space are that, first, the number of variables is reduced by roughly a factor of 10 and, second, the integration time step size is increased by 3 to 4 orders of magnitude (because, by confining the treatment to the torsional angle space, the time step size is not limited by the fast oscillation modes of covalent bonds but rather by the slow motion of macromolecular segments whose time scale is roughly 3 to 4 orders of magnitude larger than that of bond oscillations). Consequently, the exploration of global conformational relaxation processes becomes computationally possible. The treatment is tested by studying the folding kinetics of off-lattice chains with fixed bond lengths and bond angles and with prescribed sequences. The present treatment is a general purpose one applicable to all macromolecular conformational relaxation processes (e.g., protein folding kinetics, drug/ligand docking on to target proteins, conformational multiple-minima problems, etc.). It serves as a complement to the molecular dynamics or Brownian dynamics treatments in atomic coordinate space.

He, Siqian; Scheraga, Harold A.

1998-01-01

165

Advanced design solutions for underground structures at nurek hydroelectric station  

Microsoft Academic Search

Conclusions  \\u000a \\u000a \\u000a \\u000a 1. \\u000a \\u000a The large series of investigation carried out and the intensive search for rational design solutions, enabled a number of\\u000a advanced solutions to be developed relating to the arrangement and design of the underground structures of the Nurek hydroelectric\\u000a station, resulting in a substantial economy of resources and a reduction in construction time.\\u000a \\u000a \\u000a \\u000a \\u000a 2. \\u000a \\u000a It is necessary to continue

V. F. Ilyushin

1977-01-01

166

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

167

Solution structure of the loops of bacteriorhodopsin closely resembles the crystal structure.  

PubMed

Bacteriorhodopsin is one of very few transmembrane proteins for which high resolution structures have been solved. The structure shows a bundle of seven helices connected by six turns. Some turns in proteins are stabilized by short range interactions and can behave as small domains. These observations suggest that peptides containing the sequence of the turns in a membrane protein such as bacteriorhodopsin may form stable turn structures in solution. To test this hypothesis, we determined the solution structure of three peptides each containing the sequence of one of the turns in bacteriorhodopsin. The solution structures of the peptides closely resemble the structures of the corresponding turns in the high resolution structures of the intact protein. PMID:10825424

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

2000-06-01

168

nephrocystin SH3 structure Solution NMR structure of the SH3 domain of human nephrocystin  

E-print Network

nephrocystin SH3 structure - 1 - Solution NMR structure of the SH3 domain of human nephrocystin, Henkel, VTB-Enzymtechnologie, Dusseldorf, D-40191,Germany Short title : nephrocystin SH3 structure Keywords : NMR; protein folding; cytoskeleton; kidney disease; cell adhesion. #12;nephrocystin SH3

Paris-Sud XI, Université de

169

Superficial Macromolecular Arrays on the Cell Wall of Spirillum putridiconchylium  

PubMed Central

Electron microscopy of the cell envelope of Spirillum putridiconchylium, using negatively stained, thin-sectioned, and replicated freeze-etched preparations, showed two superficial wall layers forming a complex macromolecular pattern on the external surface. The outer structured layer was a linear array of particles overlying an inner tetragonal array of larger subunits. They were associated in a very regular fashion, and the complex was bonded to the outer, pitted surface of the lipopolysaccharide tripartite layer of the cell wall. The relationship of the components of the two structured layers was resolved with the aid of optical diffraction, combined with image filtering and reconstruction and linear and rotary integration techniques. The outer structural layer consisted of spherical 1.5-nm units set in double lines determined by the size and arrangement of 6- by 3-nm inner structural layer subunits, which bore one outer structural layer unit on each outer corner. The total effect of this arrangement was a double-ridged linear structure that was evident in surface replicas and negatively stained fragments of the whole wall. The packing of these units was not square but skewed by 2° off the perpendicular so that the “unit array” described by optical diffraction and linear integration appeared to be a deformed tetragon. The verity of the model was checked by using a photographically reduced image to produce an optical diffraction pattern for comparison with that of the actual layers. The correspondence was nearly perfect. Images PMID:4137219

Beveridge, T. J.; Murray, R. G. E.

1974-01-01

170

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

171

Oriented Structure of Pentablock Copolymers Induced by Solution Extrusion  

Microsoft Academic Search

Highly oriented structure of a poly(styrene-co-butadiene) pentablock copolymer (Mw; 104,700 g\\/mol, weight percentage of polybutadiene blocks; 29 wt of concentrated solutions. The pentablock copolymer was dissolved into mixtures of toluene and heptane, and the polymer concentration ranged from 40 wt extrusion, the pentablock copolymer was solidified either by coagulation in methanol or by evaporation of the solvent. Interestingly, a highly

Tamotsu Harada; Frank S. Bates; Timothy P. Lodge

2002-01-01

172

Parabolic geometries and normal Weyl structures First BGG operators and special solutions  

E-print Network

Parabolic geometries and normal Weyl structures First BGG operators and special solutions The comparison map Examples for projective structures Normal Weyl structures and special solutions of first BGG structures & BGG solutions #12;Parabolic geometries and normal Weyl structures First BGG operators

Drmota, Michael

173

Simulation and display of macromolecular complexes  

NASA Technical Reports Server (NTRS)

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

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

1977-01-01

174

Macromolecular recognition and macroscopic interactions by cyclodextrins.  

PubMed

Herein macromolecular recognition by cyclodextrins (CDs) is summarized. Recognition of macromolecules by CDs is classified as main-chain recognition or side-chain recognition. We found that CDs form inclusion complexes with various polymers with high selectivity. Polyrotaxanes in which many CDs are entrapped in a polymer chain were prepared. Tubular polymers were prepared from the polyrotaxanes. CDs were found to recognize side-chains of polymers selectively. CD host polymers were found to form gels with guest polymers in water. These gels showed self-healing properties. When azobenzene was used as a guest, the gel showed sol-gel transition by photoirradiation. When ferrocene was used, redox-responsive gels were obtained. Macroscopic self-assembly through molecular recognition has been discovered. Photoswitchable gel association and dissociation have been observed. PMID:23868461

Harada, Akira; Takashima, Yoshinori

2013-10-01

175

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

176

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

177

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

178

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

PubMed Central

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

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

2008-01-01

179

Solution structure of murine macrophage inflammatory protein-2.  

PubMed

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

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

1998-06-01

180

Nanoscale structure and dynamics of colloid-semiflexible polymer solutions  

NASA Astrophysics Data System (ADS)

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

Huh, Ji Yeon; Furst, Eric M.

2006-03-01

181

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

182

Fast macromolecular proton fraction mapping from a single off-resonance magnetization transfer measurement.  

PubMed

A new method was developed for fast quantitative mapping of the macromolecular proton fraction defined within the two-pool model of magnetization transfer. The method utilizes a single image with off-resonance saturation, a reference image for data normalization, and T(1), B(0), and B(1) maps with the total acquisition time ~10 min for whole-brain imaging. Macromolecular proton fraction maps are reconstructed by iterative solution of the matrix pulsed magnetization transfer equation with constrained values of other model parameters. Theoretical error model describing the variance due to noise and the bias due to deviations of constrained parameters from their actual values was formulated based on error propagation rules. The method was validated by comparison with the conventional multiparameter multipoint fit of the pulsed magnetization transfer model based on data from two healthy subjects and two multiple sclerosis patients. It was demonstrated theoretically and experimentally that accuracy of the method depends on the offset frequency and flip angle of the saturation pulse, and optimal ranges of these parameters are 4-7 kHz and 600°-900°, respectively. At optimal sampling conditions, the single-point method enables <10% relative macromolecular proton fraction errors. Comparison with the multiparameter fitting method revealed very good agreement with no significant bias and limits of agreement around ± 0.7%. PMID:22190042

Yarnykh, Vasily L

2012-07-01

183

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.

184

Solution structure of an isolated antibody VL domain.  

PubMed

The solution structure of the isolated VL domain of the anti-digoxin antibody 26-10 has been determined using data derived from heteronuclear multi-dimensional nuclear magnetic resonance (n.m.r.) experiments. Analytical ultracentrifugation and n.m.r. data demonstrate that the VL domain is only weakly associating (Kd = 2.5 (+/- 0.7) mM) and that it experiences a rapid monomer/dimer equilibrium under the n.m.r. experimental conditions. Therefore, the results reported here represent the first structure determination of an antibody VL domain in the absence of fixed quaternary interactions. The structure determination is based on 930 proton-proton distance constraints, 113 dihedral angle constraints, and 46 hydrogen bond constraints. Eighty initial structures were calculated with the variable target function program DIANA; of these, 31 were accepted on the basis of satisfaction of constraints (no distance constraint violations > 0.5 A; target function < 3.0 A2). Accepted DIANA structures were refined by restrained energy minimization using the X-PLOR program. The 15 best energy-minimized DIANA structures were chosen as a representative ensemble of solution conformations. The average root-mean-square differences (r.m.s.d.) between the individual structures of this ensemble and the mean coordinates is 0.85 (+/- 0.10) A for all backbone atoms and 1.29 (+/- 0.10) A for all heavy atoms. For beta-strands A, B, C, D, E and F, the average backbone atom r.m.s.d. to the mean structure is 0.46 (+/- 0.06) A. A higher-resolution ensemble, with all backbone atom and all heavy atom r.m.s.d.s. to the mean coordinates of 0.54 (+/- 0.08) A and 0.98 (+/- 0.12) A, respectively, was obtained by X-PLOR simulated annealing refinement of the 15 energy-minimized DIANA structures. A detailed analysis of the original ensemble of 15 energy-minimized DIANA structures is presented, as this ensemble retains a broader, and possibly more realistic, sampling of conformation space. The backbone atom and all heavy atom r.m.s.d.s between the mean energy-minimized DIANA structure and the X-ray derived coordinates of the VL domain within the Fab/digoxin complex are 1.05 A and 1.56 A, respectively. Subtle differences between the solution and X-ray structures occur primarily in CDR2, CDR3, beta-strands A, F and G, and localized regions of hydrophobic packing. Overall, these results demonstrate that the 26-10 VL domain conformation is determined primarily by intradomain interactions, and that quaternary VL-VH association induces relatively minor conformational adjustments. PMID:8107112

Constantine, K L; Friedrichs, M S; Metzler, W J; Wittekind, M; Hensley, P; Mueller, L

1994-02-11

185

New solution method for steady-state canopy structural loads  

SciTech Connect

A new computer code has been written to perform structural analysis canopies. Although an existing code, CANO, has been available, the new code has better convergence reliability, is more understandably written, and is easier to use. The equations have been reformulated for the new solution method. The new code assumes a symmetric canopy, a steady-state condition, and no strength in the vertical direction. It computes the inflated shape, loads in the horizontal members, radial members, vent lines, and suspension lines, and total drag. Constructed geometry, material properties, dynamic pressure, and pressure distribution are required as input.

Sundberg, W.D.

1986-08-01

186

Solution structure of Ca2+-free rat ?-parvalbumin  

PubMed Central

Mammals express two parvalbumins—an ? isoform and a ? isoform. In rat, the ?-parvalbumin (?-PV) exhibits superior divalent ion affinity. For example, the standard free energies for Ca2+ binding differ by 5.5 kcal/mol in 0.15 M KCl (pH 7.4). High-resolution structures of the Ca2+-bound proteins provide little insight into this disparity, prompting a structural analysis of the apo-proteins. A recent analysis of rat ?-PV suggested that Ca2+ removal provokes substantial conformational changes—reorientation of the C, D, and E helices; reorganization of the hydrophobic core; reduced interdomain contact; and remodeling of the AB domain. The energetic penalty attendant to reversing these changes, it was suggested, could contribute to the attenuated divalent ion-binding signature of that protein. That hypothesis is supported by data presented herein, describing the solution structure and peptide backbone dynamics of Ca2+-free rat ?-PV. In marked contrast to rat ?-PV, the apo- and Ca2+-loaded forms of the rat ? isoform are quite similar. Significant structural differences appear to be confined to the loop regions of the molecule. This finding implies that the ?-PV isoform enjoys elevated divalent ion affinity because the metal ion-binding events do not require major structural rearrangement and the concomitant sacrifice of binding energy. PMID:18218708

Henzl, Michael T.; Tanner, John J.

2008-01-01

187

Structure and dynamics of of solution polymerized polyureas  

NASA Astrophysics Data System (ADS)

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

Choi, Taeyi; Jeong, Youmi; Runt, James

2011-03-01

188

Solution structure of a baculoviral inhibitor of apoptosis (IAP) repeat.  

PubMed

Members of the inhibitor of apoptosis (IAP) family of proteins are able to inhibit cell death following viral infection, during development or in cell lines in vitro. All IAP proteins bear one or more baculoviral IAP repeats (BIRs). Here we describe the solution structure of the third BIR domain from the mammalian IAP homolog B (MIHB/c-IAP-1). The BIR domain has a novel fold that is stabilized by zinc tetrahedrally coordinated by one histidine and three cysteine residues. The structure consists of a series of short alpha-helices and turns with the zinc packed in an unusually hydrophobic environment created by residues that are highly conserved among all BIRs. PMID:10404221

Hinds, M G; Norton, R S; Vaux, D L; Day, C L

1999-07-01

189

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

190

Aqueous Solutions on Silica Surfaces: Structure and Dynamics from Simulations  

NASA Astrophysics Data System (ADS)

Our group is interested in understanding the properties of aqueous electrolyte solutions at interfaces. The fundamental questions we seek to answer include: (A) how does a solid structure perturb interfacial water? (B) How far from the solid does this perturbation persist? (C) What is the rate of water reorientation and exchange in the perturbed layer? (D) What happens in the presence of simple electrolytes? To address such topics we implemented atomistic molecular dynamics simulations. Recent results for water and simple electrolytes near silicon dioxide surfaces of various degrees of hydroxylation will be presented. The data suggest the formation of a layered aqueous structure near the interface. The density profile of interfacial water seems to dictate the density profiles of aqueous solutions containing NaCl, CaCl2, CsCl, and SrCl2 near the solid surfaces. These results suggest that ion-ion and ion-water correlations are extremely important factors that should be considered when it is desired to predict the distribution of electrolytes near a charged surface. Our results will benefit a number of practical applications including water desalination, exploitation of the oil shale in the Green River Basin, nuclear waste sites remediation, and design of nanofluidic devices.

Striolo, Alberto; Argyris, Dimitrios; Tummala, Naga Rajesh

2009-03-01

191

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

192

Macromolecular Diffusion in Self-Assembling Biodegradable Thermosensitive Hydrogels  

PubMed Central

Hydrogel formation triggered by a change in temperature is an attractive mechanism for in situ gelling biomaterials for pharmaceutical applications such as the delivery of therapeutic proteins. In this study, hydrogels were prepared from ABA triblock polymers having thermosensitive poly(N-(2-hydroxypropyl) methacrylamide lactate) flanking A-blocks and hydrophilic poly(ethylene glycol) B-blocks. Polymers with fixed length A blocks (~22 kDA) but differing PEG-midblock lengths (2, 4 and 10 kDa) were synthesized and dissolved in water with dilute fluorescein isothiocyanate (FITC)-labeled dextrans (70 and 500 kDA). Hydrogels encapsulating the dextrans were formed by raising the temperature. Fluorescence recovery after photobleaching (FRAP) studies showed that diffusion coefficients and mobile fractions of the dextran dyes decreased upon elevating temperatures above 25 °C. Confocal laser scanning microscopy and cryo-SEM demonstrated that hydrogel structure depended on PEG block length. Phase separation into polymer-rich and water-rich domains occurred to a larger extent for polymers with small PEG blocks compared to polymers with a larger PEG block. By changing the PEG block length and thereby the hydrogel structure, mobility of FITC-dextran could be tailored. At physiological pH the hydrogels degraded over time by ester hydrolysis, resulting in increased mobility of the encapsulated dye. Since diffusion can be controlled according to polymer design and concentration, plus temperature, these biocompatible hydrogels are attractive as potential in situ gelling biodegradable materials for macromolecular drug delivery. PMID:20885989

Vermonden, Tina; Jena, Sidhartha S.; Barriet, David; Censi, Roberta; van der Gucht, Jasper; Hennink, Wim E.; Siegel, Ronald A.

2009-01-01

193

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

194

Supramolecular structure of aqueous solutions of glucose according to dynamic light scattering data  

NASA Astrophysics Data System (ADS)

The nature and structure of large-scale fluctuations in aqueous glucose solutions were studied by dynamic light scattering. The two-component model of solution was used. The supramolecular structure of the solutions was determined and their phase diagram at low concentrations was schematically constructed. The volume of clusters in solution was calculated.

Vlasenko, T. S.; Zabashta, Yu. F.; Sysoev, V. M.

2014-08-01

195

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

NASA Astrophysics Data System (ADS)

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

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

2013-03-01

196

Solution structure of an A-tract DNA bend.  

PubMed

The solution structure of a DNA dodecamer d(GGCAAAAAACGG)/d(CCGTTTTTTGCC) containing an A-tract has been determined by NMR spectroscopy with residual dipolar couplings. The structure shows an overall helix axis bend of 19 degrees in a geometry consistent with solution and gel electrophoresis experiments. Fourteen degrees of the bending occurs in the GC regions flanking the A-tract. The remaining 5 degrees is spread evenly over its six AT base-pairs. The A-tract is characterized by decreasing minor groove width from the 5' to the 3' direction along the A strand. This is a result of propeller twist in the AT pairs and the increasing negative inclination of the adenine bases at the 3' side of the run of adenine bases. The four central thymine bases all have negative inclination throughout the A-tract with an average value of -6.1 degrees. Although this negative inclination makes the geometry of the A-tract different from all X-ray structures, the proton on N6 of adenine and the O4 of thymine one step down the helix are within distance to form bifurcated hydrogen bonds. The 5' bend of 4 degrees occurs at the junction between the GC flank and the A-tract through a combination of tilt and roll. The larger 3' bend, 10 degrees, occurs in two base steps: the first composed of tilt, -4.1 degrees, and the second a combination of tilt, -4.2 degrees, and roll, 6.0 degrees. This second step is a direct consequence of the change in inclination between an adjacent cytosine base, which has an inclination of -12 degrees, and the next base, a guanine, which has 3 degrees inclination. This bend is a combination of tilt and roll. The large change in inclination allows the formation of a hydrogen bond between the protons of N4 of the 3' cytosine and the O6 of the next 3' base, a guanine, stabilizing the roll component in the bend. These structural features differ from existing models for A-tract bends.For comparison, we also determined the structure of the control sequence, d(GGCAAGAAACGG)/d(CCGTTTCTTGCC), with an AT to GC transition in the center of the A-tract. This structure has no negative inclination in most of the bases within the A-tract, resulting in a bend of only 9 degrees. When ligated in phase, the control sequence has nearly normal mobility in gel electrophoresis experiments. PMID:11237619

MacDonald, D; Herbert, K; Zhang, X; Pologruto, T; Lu, P; Polgruto, T

2001-03-01

197

Neutron Laue diffraction in macromolecular crystallography  

NASA Astrophysics Data System (ADS)

The time scales required for conventional neutron diffraction analysis of biological single crystals at, or near, atomic resolution are prohibitive -: such studies are rarely performed. Laue (white beam) diffraction can provide a more rapid and efficient survey of reciprocal space, maximising the flux at the sample and stimulating large numbers of reflections simultaneously. A LAue DIffractometer (LADI), designed specifically for macromolecular crystallography, has been installed on a cold neutron guide at ILL. The detector comprises a large Gd2O3-doped neutron-sensitive image plate (400x800 mm) mounted on a cylindrical camera (318 mm diameter) that is read in phonographic mode after exposure. Detector response has been evaluated and performance indicators are given. Narrow (Quasi-Laue) band-passes (d?/?=8-20%) are often required for large unit-cell biological crystals in order to reduce reflection overlap and incoherent background. Laue and Quasi-Laue data have now been collected for a number of proteins and other biological crystals. Recent results are presented and future prospects reviewed.

Myles, D. A. A.; Bon, C.; Langan, P.; Cipriani, F.; Castagna, J. C.; Lehmann, M. S.; Wilkinson, C.

1998-04-01

198

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

PubMed Central

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

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

2012-01-01

199

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

200

Effect of salt solutions on radiosensitivity of mammalian cells. I. Specific ion effects.  

PubMed

The radiation isodose survival curve of cells subjected to a wide concentration range of sucrose solutions has two maxima separated by a minimum. Both cations and anions can alter the cellular radiosensitivity above and beyond the osmotic effect observed for cells treated with sucrose solutions. The basic shape of the isodose curve can also be modulated by changes in temperature and solution exposure times. Some of these alterations in radiosensitivity may be related to changes in the amount and structure of cellular water or macromolecular conformation or to the direct effect of the ions, expecially at high solute concentrations. PMID:301871

Raaphorst, G P; Kruuv, J

1977-07-01

201

A Combined Charged Residue-Field Emission Model of Macromolecular Electrospray Ionization  

PubMed Central

The mechanism of the multiple charging of macromolecules in electrospray ionization (ESI) continues to inspire debate and controversy. Recently, we proposed that the number of charges on a macromolecule is determined by the emission of small charge carriers from macromolecule-containing nanodroplets and that, after solvent evaporation, the remaining charge is transferred to the macromolecule. In this study, we tested the applicability of this new theory for macromolecular, positive-ion ESI mass spectrometry by measuring the mean charge states and charge distributions of globular proteins under non-denaturing and denaturing conditions. Predictions of protein mean charge states for native state proteins are in excellent agreement with mass spectrometric measurements, giving strong credence to the proposed theory. Theoretical predictions are also in good agreement with mean charge states measured for proteins in basic solutions (pH = 11.5). For some proteins in acidic solutions (pH = 2.1), the measured mean charge states are anomalously higher than the Rayleigh limit of a water droplet with a volume equivalent to that of the protein. We propose that some macromolecules that are highly charged in solution may desorb from charged droplets of the same polarity in a similar manner to that whereby charge carriers emit from nanodroplets, leading to “supercharged” macromolecular ions. Examination of rate expressions for solvent evaporation and charge-carrier emission demonstrates that the newly proposed model for ESI is consistent with previously reported ion-emission kinetics. Overall, we obtained additional experimental evidence for the charge carrier emission model for macromolecular charging, suggesting opportunities for understanding and applying ESI-MS. PMID:19117463

Carroll, James A.; Rohrs, Henry W.; Biswas, Pratim; Gross, Michael L.

2008-01-01

202

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

203

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

204

Aromatic moieties in meteoritic macromolecular materials: analyses by hydrous pyrolysis and ? 13C of individual compounds  

NASA Astrophysics Data System (ADS)

Hydrous pyrolysis, supercritical fluid extraction (SFE), gas chromatography-mass-spectrometry (GC-MS) and isotope ratio monitoring-gas chromatography-mass spectrometry (irm-GC-MS) were used to investigate the constitution of macromolecular materials in meteorites. Results from the carbonaceous chondrites Orgueil (CI1) and Cold Bokkeveld (CM2) were compared with those obtained previously from Murchison (CM2). Fragments of meteoritic macromolecular materials were produced by hydrous pyrolysis, extracted by SFE, and identified by GC-MS. The CI1 and CM2 hydrous pyrolysates all contain volatile aromatic compounds, some of which have aliphatic side chains, hydroxyl groups, and thiophene rings attached. The results indicate that the macromolecular materials in these meteorites are qualitatively similar. However, the pyrolysates show significant quantitative differences, with the products of ether linkages and condensed aromatic networks being less abundant in the more aqueously altered meteorites. In addition, the methylnaphthalene maturity parameter negatively correlates with aqueous alteration. These features are interpreted as the result of chemical reactions favored under hydrous conditions. Hence, the extent of aqueous alteration on the meteorite parent body appears to be the most important evolutionary stage in determining the final structure of macromolecular materials in the CI1 and CM2 meteorites. The carbon isotopic compositions of the fragments of macromolecular materials were determined by irm-GC-MS. ? 13C values for the hydrous pyrolysis products range from -25.5 to -10.2‰ for Orgueil and -22.9 to +4.0‰ for Cold Bokkeveld. These values can be compared to the -24.6 to -5.6‰ range obtained previously for Murchison. The low molecular weight components in each hydrous pyrolysate display shifts to increased 13C contents with carbon number. This indicates the production of simple organic entities by the preferential cracking of 12C- 12C bonds in more complex starting materials. The shifts extend from C 7 to C 8 for Orgueil and Cold Bokkeveld but from C 7 to C 10 for Murchison. Higher molecular weight components for all of the hydrous pyrolysates show a general trend of decreasing 13C content with carbon number. The higher molecular weight features can be explained by the preferential addition of 12C during the primary synthesis of the macromolecular materials. In addition, ? 13C values for the methylnaphthalenes are consistent with the addition of 12C to the most reactive site on the naphthalene parent molecule providing supporting evidence for synthesis. Hence, the macromolecular materials are composed of organic units created by both synthesis and cracking. Therefore, secondary processing by liquid water on the meteorite parent body exerts a strong control on the final molecular architecture of meteoritic macromolecular materials. Yet, the carbon isotopic compositions of some individual moieties may retain a record of primary synthesis.

Sephton, M. A.; Pillinger, C. T.; Gilmour, I.

2000-01-01

205

The solution structure of the copper clioquinol complex.  

PubMed

Clioquinol (5-chloro-7-iodo-8-hydroxyquinoline) recently has shown promising results in the treatment of Alzheimer's disease and in cancer therapy, both of which also are thought to be due to clioquinol's ability as a lipophilic copper chelator. Previously, clioquinol was used as an anti-fungal and anti-protozoal drug that was responsible for an epidemic of subacute myelo-optic neuropathy (SMON) in Japan during the 1960s, probably a myeloneuropathy arising from a clioquinol-induced copper deficiency. Previous X-ray absorption spectroscopy of solutions of copper chelates of clioquinol suggested unusual coordination chemistry. Here we use a combination of electron paramagnetic, UV-visible and X-ray absorption spectroscopies to provide clarification of the chelation chemistry between clioquinol and copper. We find that the solution structures for the copper complexes formed with stoichiometric and excess clioquinol are conventional 8-hydroxyquinolate chelates. Thus, the promise of clioquinol in new treatments for Alzheimer's disease and in cancer therapy is not likely to be due to any novel chelation chemistry, but rather due to other factors including the high lipophilicity of the free ligand and chelate complexes. PMID:24503514

Pushie, M Jake; Nienaber, Kurt H; Summers, Kelly L; Cotelesage, Julien J H; Ponomarenko, Olena; Nichol, Helen K; Pickering, Ingrid J; George, Graham N

2014-04-01

206

Solution-processable graphene nanomeshes with controlled pore structures  

PubMed Central

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. PMID:23770582

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

2013-01-01

207

Macromolecular crowding effects on coupled folding and binding.  

PubMed

Replica exchange molecular dynamics simulations are performed on the protein complex pKID-KIX to understand the effects of macromolecular crowding on coupled folding and binding events. A structure-based protein model at the residue level is adopted for the two proteins to include intramolecular conformational flexibility, while crowding macromolecules are represented as spherical particles. The interactions between crowders and protein residues can be either purely repulsive or a combination of short-range repulsion and intermediate-range attraction. Consistent with previous studies on rigid-body protein binding in the presence of spherical crowders, we find that the complex formation is stabilized by repulsive protein-crowder interactions and destabilized by sufficiently strong attractive protein-crowder interactions. Competition between stabilizing repulsive and destabilizing attractive interactions is quantitatively captured by a previous theoretical model developed for describing the change in the binding free energy of rigid proteins in a crowded environment. We find that protein flexibility has little effect on the thermodynamics of the pKID-KIX binding (with respect to bulk) for repulsive and weakly attractive protein-crowder interactions. For strong protein-crowder attractive interactions, the destabilizing effect due to crowding is attenuated by protein flexibility. Interestingly, the mechanism of coupled folding and binding observed in bulk remains unchanged under highly crowded conditions over a broad range of protein-crowder interaction strengths. Also, strong protein-crowder attractive interactions can significantly stabilize intermediate states involving partial contact between pKID and KIX domains. PMID:25302571

Kim, Young C; Bhattacharya, Apratim; Mittal, Jeetain

2014-11-01

208

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

209

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; Rosch, Paul; Hartl-Spiegelhauer, Olivia

2012-01-01

210

The NMR solution structure of recombinant RGD-hirudin  

SciTech Connect

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

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

2007-08-17

211

JBluIce–EPICS control system for macromolecular crystallography  

PubMed Central

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

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

2011-01-01

212

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

213

Effect of Escherichia coli enterotoxins on macromolecular absorption.  

PubMed Central

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

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

1994-01-01

214

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

Heroux, 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

215

Structure Formation in Semi-Dilute Polymer Solution during Electrospinning  

NASA Astrophysics Data System (ADS)

In our recent work it was shown that longitudinal stretching of electrospun highly entangled semi-dilute polymer solution caused by jet hydrodynamic forces, transforms the topological network to an almost fully-stretched state within less than 1 mm from the jet start (PRE, 2011). Further evolution of the polymer network is related to a disentanglement of polymer chains and transformation of the topological network structure. As was sown by Malkin et al., (Rheol. Acta, 2011) high deformation rate of a topological polymer network, results in reptations of macromolecules caused by uncompensated local forces, whereas Brownian motion effect is negligible. Based on this conclusion, we examine the disentanglement process, using a mechanical pulley-block system assembled from multiple pulleys suspended by elastic springs, and taut string connecting two blocks. Each pulley corresponds to a topological knot; the taut string corresponds to a reptated chain; the springs correspond to surrounded polymer chains; and the blocks correspond to local deformation force. It turned out that the system is sensitive to system parameters. The pulleys can approach each other and the string stops to move. Such a behavior corresponds to formation of bundle of knots of entangled chains. In other conditions, the string continuously moves while the pulleys did not approach each other which corresponds to disentanglement of polymer chains. These experiments clarify the disentanglement kinetics in rapid-deformed polymer system.

Zussman, Eyal; Paley, Yakov; Arinstein, Arkadii; Shuster, Kim

2012-02-01

216

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

217

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

218

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

219

Protein diffusion and macromolecular crowding in thylakoid membranes.  

PubMed

The photosynthetic light reactions of green plants are mediated by chlorophyll-binding protein complexes located in the thylakoid membranes within the chloroplasts. Thylakoid membranes have a complex structure, with lateral segregation of protein complexes into distinct membrane regions known as the grana and the stroma lamellae. It has long been clear that some protein complexes can diffuse between the grana and the stroma lamellae, and that this movement is important for processes including membrane biogenesis, regulation of light harvesting, and turnover and repair of the photosynthetic complexes. In the grana membranes, diffusion may be problematic because the protein complexes are very densely packed (approximately 75% area occupation) and semicrystalline protein arrays are often observed. To date, direct measurements of protein diffusion in green plant thylakoids have been lacking. We have developed a form of fluorescence recovery after photobleaching that allows direct measurement of the diffusion of chlorophyll-protein complexes in isolated grana membranes from Spinacia oleracea. We show that about 75% of fluorophores are immobile within our measuring period of a few minutes. We suggest that this immobility is due to a protein network covering a whole grana disc. However, the remaining fraction is surprisingly mobile (diffusion coefficient 4.6 +/- 0.4 x 10(-11) cm(2) s(-1)), which suggests that it is associated with mobile proteins that exchange between the grana and stroma lamellae within a few seconds. Manipulation of the protein-lipid ratio and the ionic strength of the buffer reveals the roles of macromolecular crowding and protein-protein interactions in restricting the mobility of grana proteins. PMID:18287489

Kirchhoff, Helmut; Haferkamp, Silvia; Allen, John F; Epstein, David B A; Mullineaux, Conrad W

2008-04-01

220

A Compact X-Ray System for Macromolecular Crystallography  

NASA Technical Reports Server (NTRS)

We describe the design and performance of a high flux x-ray system for a macromolecular crystallography that combines a microfocus x-ray generator (40 micrometer full width at half maximum spot size at a power level of 46.5 W) and a collimating polycapillary optic. The Cu Ka lpha x-ray flux produced by this optimized system through a 500,um diam orifice is 7.0 times greater than the x-ray flux previously reported by Gubarev et al. [M. Gubarev et al., J. Appl. Crystallogr. 33, 882 (2000)]. The x-ray flux from the microfocus system is also 2.6 times higher than that produced by a rotating anode generator equipped with a graded multilayer monochromator (green optic, Osmic Inc. CMF24-48-Cu6) and 40% less than that produced by a rotating anode generator with the newest design of graded multilayer monochromator (blue optic, Osmic, Inc. CMF12-38-Cu6). Both rotating anode generators operate at a power level of 5000 W, dissipating more than 100 times the power of our microfocus x-ray system. Diffraction data collected from small test crystals are of high quality. For example, 42 540 reflections collected at ambient temperature from a lysozyme crystal yielded R(sub sym)=5.0% for data extending to 1.70 A, and 4.8% for the complete set of data to 1.85 A. The amplitudes of the observed reflections were used to calculate difference electron density maps that revealed positions of structurally important ions and water molecules in the crystal of lysozyme using the phases calculated from the protein model.

Gubarev, Mikhail; Ciszak, Ewa; Ponomarev, Igor; Gibson, Walter; Joy, Marshall

2000-01-01

221

A Compact X-Ray System for Macromolecular Crystallography. 5  

NASA Technical Reports Server (NTRS)

We describe the design and performance of a high flux x-ray system for macromolecular crystallography that combines a microfocus x-ray generator (40 gm FWHM spot size at a power level of 46.5Watts) and a 5.5 mm focal distance polycapillary optic. The Cu K(sub alpha) X-ray flux produced by this optimized system is 7.0 times above the X-ray flux previously reported. The X-ray flux from the microfocus system is also 3.2 times higher than that produced by the rotating anode generator equipped with a long focal distance graded multilayer monochromator (Green optic; CMF24-48-Cu6) and 30% less than that produced by the rotating anode generator with the newest design of graded multilayer monochromator (Blue optic; CMF12-38-Cu6). Both rotating anode generators operate at a power level of 5000 Watts, dissipating more than 100 times the power of our microfocus x-ray system. Diffraction data collected from small test crystals are of high quality. For example, 42,540 reflections collected at ambient temperature from a lysozyme crystal yielded R(sub sym) 5.0% for the data extending to 1.7A, and 4.8% for the complete set of data to 1.85A. The amplitudes of the reflections were used to calculate difference electron density maps that revealed positions of structurally important ions and water molecules in the crystal of lysozyme using the phases calculated from the protein model.

Gubarev, Mikhail; Ciszak, Ewa; Ponomarev, Igor; Joy, Marshall

2000-01-01

222

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

223

Protein Diffusion and Macromolecular Crowding in Thylakoid Membranes1[W  

E-print Network

Protein Diffusion and Macromolecular Crowding in Thylakoid Membranes1[W] Helmut Kirchhoff*, Silvia by chlorophyll-binding protein complexes located in the thylakoid membranes within the chloroplasts. Thylakoid. To date, direct measurements of protein diffusion in green plant thylakoids have been lacking. We have

Allen, John F.

224

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

225

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

226

Ground Based Program for the Physical Analysis of Macromolecular Crystal Growth  

NASA Technical Reports Server (NTRS)

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

Malkin, Alexander J.

1998-01-01

227

Water and Solute Flow in a Highly-Structured Soil  

E-print Network

. An improved understanding of why water and solute follow particular flow paths is needed to identify soils that allow agricultural chemicals to move rapidly to groundwater. The rate that water and contaminants are transferred from the soil surface...

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

228

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

229

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

230

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

231

Structural qualia: a solution to the hard problem of consciousness  

PubMed Central

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

Loorits, Kristjan

2014-01-01

232

Structural and dynamic heterogeneity in a telechelic polymer solution Dmitry Bedrova,*, Grant Smitha  

E-print Network

indicating the existence of `dynamic heterogeneity' in polymeric and other glass-forming liquids [1]. RecentStructural and dynamic heterogeneity in a telechelic polymer solution Dmitry Bedrova,*, Grant dynamics in a model telechelic polymer solution. The transient structural heterogeneity associated

Utah, University of

233

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

E-print Network

and Provincial governments, and the creation of a government aided flood insurance program, are suggestedNON-STRUCTURAL FLOOD MANAGEMENT SOLUTIONS FOR THE LOWER FRASER VALLEY, BRITISH COLUMBIA by Tamsin of Project: Non-Structural Flood Management Solutions for the Lower Fraser Valley, British Columbia Examining

234

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

235

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

236

Stoichiogenomics: the evolutionary ecology of macromolecular elemental  

E-print Network

concerned with the requirements of biochemical function, structure, and/or the cellular milieu of DNA at functionally important DNA positions experience negative selective pressures either directly or via the product structure of the genome (i.e. its linear DNA sequence) have been previously documented in prokaryotes

Elser, Jim

237

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

NASA Astrophysics Data System (ADS)

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

Yumaguzhin, Valeriy

2014-11-01

238

The concentration-dependence of macromolecular parameters.  

PubMed Central

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

Harding, S E; Johnson, P

1985-01-01

239

NMR solution structure of the human prion protein  

Microsoft Academic Search

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

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

2000-01-01

240

The prestressability problem of tensegrity structures: some analytical solutions  

Microsoft Academic Search

In this paper we formulate the general prestressability conditions for tensegrity structures. These conditions are expressed as a set of nonlinear equations and inequalities on the tendon tensions. Several examples of tensegrity structures for which the prestressability conditions can be analytically solved are then presented.

Cornel Sultan; Martin Corless; Robert E. Skelton

2001-01-01

241

NMR solution structure of the neurotrypsin Kringle domain.  

PubMed

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

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

2008-11-25

242

Integrated Force Method Solution to Indeterminate Structural Mechanics Problems  

NASA Technical Reports Server (NTRS)

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

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

2004-01-01

243

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

244

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

245

ATTEMPTS system: a macromolecular prodrug strategy for cancer drug delivery.  

PubMed

In order to reduce systemic toxicity and effectively deliver macromolecular drug into tumor cells, a system termed "ATTEMPTS" (antibody targeted, [protamine] triggered, electrically modified prodrug-type strategy) was developed in our laboratory. This approach was adapted from our previously reported heparin/protamine-based system for controlled delivery of protease drugs such as tissue- specific plasminogen activator (tPA). In this "ATTEMPTS" system, the cell-permeable protein drugs are synthesized by conjugating proteins to cell-penetrating peptides (CPPs). Cell penetration ability of such CPP-protein conjugates would initially be disabled, acting as a "prodrug", by forming polyelectrolyte complexes with a functionalized heparin-antibody moiety. The complexes would accumulate in tumor sites by the antibody targeting function, and then the local release of CPP-protein conjugates would be triggered by protamine. We applied this system to the macromolecular anticancer agents, such as the protein drugs (gelonin and asparaginase) as well as the polymerdrugs (polyrotaxane-doxorubicin and polyrotaxane-camptothecin). Both in vitro and preliminary in vivo studies demonstrated the regulable cell penetration behavior based on the competitive ionic interactions between CPP/heparin and heparin/protamine. Thus, this ATTEMPTS approach provides a multi-functionalized system incorporating the features of targeting, prodrug-like, triggerable release, and cell penetration ability for the delivery of macromolecular anticancer agents. A summary of our work on "ATTEMPTS" is presented in this review. PMID:20618157

Huang, Yongzhuo; Park, Yoon Shin; Wang, Jianxin; Moon, Cheol; Kwon, Young Min; Chung, Hee Sun; Park, Yoon Jeong; Yang, Victor C

2010-07-01

246

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

247

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

248

Effect of water structure on adsorption of thermosensitive polymer hydrogel in salt solutions  

SciTech Connect

Effects of temperature and additive salt on an adsorption property of thermosensitive polymer hydrogel were studied in terms of (1) phase transition temperature of the gel, (2) hydration structure of network of the gel in the various salt solutions, and (3) structure of water in the solutions. The adsorption properties of the gel were correlated fairly well with the phase transition temperature of the gel and the structure of water both on the network of the gel and in the bulk solution. 2 refs., 5 figs.

Nakano, Yoshio; Seida, Yoshimi [Tokyo Inst. of Technology, Tokohama (Japan)

1996-12-31

249

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

250

Mutvei's solution: An ideal agent for resolving microgrowth structures of biogenic carbonates  

E-print Network

illumination) and scanning electron microscopy can be used to analyze the microgrowth structures. WeMutvei's solution: An ideal agent for resolving microgrowth structures of biogenic carbonates Bernd as environmental and physiological proxies, and growth increments as calendars. Recognition of growth structures

Schöne, Bernd R.

251

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.

252

Effect of snow structure on water flow and solute transport  

Microsoft Academic Search

Water flow through a melting snow pack modifies its structure and stability and affects the release of water and nutrients into soils and surface waters. Field and laboratory observations indicate a large spatial variability on various scales of the liquid water content and flow, a dominant system feature currently not included in numerical models. We investigated experimentally water and dye

Peter A. Waldner; Martin Schneebeli; Ute Schultze-Zimmermann; Hannes Flühler

2004-01-01

253

Macromolecular lignin replication: A mechanistic working hypothesis  

Microsoft Academic Search

At the time of the first realization that the last step in lignin biosynthesis involves lignol radical coupling, it was difficult\\u000a to envisage how such a process could be regiospecifically controlled. It was thus natural to expect that lignin macromolecules\\u000a should have random primary structures. This has now been the prevailing assumption for almost fifty years, but of its correctness

Yi-ru Chen; Simo Sarkanen

2003-01-01

254

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

255

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

NASA Technical Reports Server (NTRS)

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

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

1992-01-01

256

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

257

nature | methods A nano-positioning system for macromolecular structural  

E-print Network

of the `satellite dye molecule' positions. Top view of the elongation complex with Pol II core (grey), Rpb4 (blue), Rpb7 (red), template DNA strand (blue), non-template DNA strand (cyan) and RNA product (red efficiency obtained in the absence (a,c,e,g,i) and presence (b,d,f,h) of TFIIB for the labelling sites DNA1

Ulm, Universität

258

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

259

STRUCTURAL HEALTH MONITORING SOLUTIONS FOR POWER PLANTS Benoit Jouan, Jurgen Rudolph, Steffen Bergholz  

E-print Network

STRUCTURAL HEALTH MONITORING SOLUTIONS FOR POWER PLANTS Benoit Jouan, J�urgen Rudolph, Steffen solutions gain in importance not only as part of the ageing management of nuclear power plant components but also in the context of conventional power plants and renewables such as wind power plants. Consequently

Paris-Sud XI, Université de

260

On the Structure of Numerical Solutions of Flow Simulation by Implicit Scheme  

Microsoft Academic Search

In the present paper, the structure of the asymptotic numerical solutions which were calculated by using implicit schemes were studied. Analytical discussions and numerical tests for fully implicit schemes of the Burgers' equation and several types of their linearized schemes were done. Furthermore, we tried to investigate the characteristics of ghost numerical solutions of incompressible fluid equations from viewpoints of

Itaru Hataue

2001-01-01

261

H. Ihee et al., "Ultrafast X-ray diffraction of transient molecular structures in solution."  

E-print Network

H. Ihee et al., "Ultrafast X-ray diffraction of transient molecular structures in solutionV. The scattered X-ray signal was recorded on a 133 mm diameter fiber-coupled MarCCD at well-defined delay times (t of the parent molecule, the transient intermediates and the products in the gas phase and in solution, were

Ihee, Hyotcherl

262

Superweakly interacting massive particle solutions to small scale structure problems.  

PubMed

Collisionless, cold dark matter in the form of weakly interacting massive particles (WIMPs) is well motivated in particle physics, naturally yields the observed relic density, and successfully explains structure formation on large scales. On small scales, however, it predicts too much power, leading to cuspy halos, dense cores, and large numbers of subhalos, in apparent conflict with observations. We consider super-WIMP dark matter, produced with large velocity in late decays at times 10(5) - 10(8) s. As analyzed by Kaplinghat in a more general setting, we find that super-WIMPs have sufficiently large free-streaming lengths and low phase space densities to help resolve small scale structure problems while preserving all of the above-mentioned WIMP virtues. PMID:16383891

Cembranos, Jose A R; Feng, Jonathan L; Rajaraman, Arvind; Takayama, Fumihiro

2005-10-28

263

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

NASA Astrophysics Data System (ADS)

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

Sephton, Mark A.

2013-04-01

264

Solution structure of an A-tract DNA bend 1 1 Edited by I. Tinoco  

Microsoft Academic Search

The solution structure of a DNA dodecamer d(GGCAAAAAACGG)\\/d(CCGTTTTTTGCC) containing an A-tract has been determined by NMR spectroscopy with residual dipolar couplings. The structure shows an overall helix axis bend of 19° in a geometry consistent with solution and gel electrophoresis experiments. Fourteen degrees of the bending occurs in the GC regions flanking the A-tract. The remaining 5° is spread evenly

Douglas MacDonald; Kristina Herbert; Xiaolin Zhang; Thomas Polgruto; Ponzy Lu

2001-01-01

265

Structures of bromoalkanes' photodissociation in solution by means of ultrafast extended x-ray absorption fine-structure spectroscopy  

PubMed Central

The structures of initial and final products of bromoalkanes' photodisociation reaction in cyclohexane solution have been measured with a bond length accuracy of 0.02 ? by means of ultrafast time-resolved extended x-ray absorption fine structure spectroscopy. The photoredaction mechanism is also discussed. PMID:12239341

Oulianov, D. A.; Tomov, I. V.; Dvornikov, A. S.; Rentzepis, P. M.

2002-01-01

266

Structure and dynamics of water in mixed solutions including laponite and PEO  

NASA Astrophysics Data System (ADS)

To investigate the structure and dynamics of water in mixed solutions including laponite clay particles and poly(ethylene oxide) (PEO), we measured the Raman spectra of the mixed solutions in the temperature range 283-313 K. The results show that the vibrational energies of the O-H stretching modes in the mixed solutions depend on the water content and temperature. The energy shifts of the O-H stretching modes are attributed to changes in the water structure. By applying a structural model of bulk water to the spectra in the O-H stretching region, the local structures of water in the solutions were analyzed. The result shows that the formation probability of hydrogen bonds in the solutions decreases as the water content decreases. Laponite and PEO have effects to disrupt the network structure of hydrogen bonds between water molecules. Further, it was found that laponite and PEO cause increase in the strength of hydrogen bonds of surrounding water,although the strength of the hydrogen bonds increases with the order water-laponite < water-water < water-PEO. It is concluded that water in laponite-PEO mixed solutions has a less-networked structure with strong hydrogen bonds compared with bulk water.

Morikubo, Satoshi; Sekine, Yurina; Ikeda-Fukazawa, Tomoko

2011-01-01

267

Structure and dynamics of water in mixed solutions including laponite and PEO.  

PubMed

To investigate the structure and dynamics of water in mixed solutions including laponite clay particles and poly(ethylene oxide) (PEO), we measured the Raman spectra of the mixed solutions in the temperature range 283-313 K. The results show that the vibrational energies of the O-H stretching modes in the mixed solutions depend on the water content and temperature. The energy shifts of the O-H stretching modes are attributed to changes in the water structure. By applying a structural model of bulk water to the spectra in the O-H stretching region, the local structures of water in the solutions were analyzed. The result shows that the formation probability of hydrogen bonds in the solutions decreases as the water content decreases. Laponite and PEO have effects to disrupt the network structure of hydrogen bonds between water molecules. Further, it was found that laponite and PEO cause increase in the strength of hydrogen bonds of surrounding water,although the strength of the hydrogen bonds increases with the order water-laponite < water-water < water-PEO. It is concluded that water in laponite-PEO mixed solutions has a less-networked structure with strong hydrogen bonds compared with bulk water. PMID:21280796

Morikubo, Satoshi; Sekine, Yurina; Ikeda-Fukazawa, Tomoko

2011-01-28

268

Macromolecular assemblies in reduced gravity environments  

NASA Technical Reports Server (NTRS)

The assembly of protein macro molecules into structures commonly produced within biological systems was achieved using in vitro techniques carried out in nominal as well as reduced gravity environments. Appropriate hardware was designed and fabricated to support such studies. Experimental protocols were matched to the available reduced gravity test opportunities. In evaluations of tubulin, fibrin and collagen assembly products the influence of differing gravity test conditions are apparent. Product homogeneity and organization were characteristic enhancements documented in reduced gravity samples. These differences can be related to the fluid flow conditions that exist during in vitro product formation. Reduced gravity environments may provide a robust opportunity for directing the products formed in a variety of bioprocessing applications.

Moos, Philip J.; Hayes, James W.; Stodieck, Louis S.; Luttges, Marvin W.

1990-01-01

269

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

PubMed

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

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

2013-02-01

270

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

PubMed

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

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

1995-09-01

271

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

PubMed

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

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

2014-01-01

272

Minimizing distortion in truss structures - A Hopfield network solution  

NASA Technical Reports Server (NTRS)

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

Fu, B.; Hajela, P.

1992-01-01

273

Minimizing distortion in truss structures -- a Hopfield network solution  

NASA Technical Reports Server (NTRS)

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

Fu, B.; Hajela, P.

1993-01-01

274

Solution structure of a dynein motor domain associated light chain.  

PubMed

Dyneins are molecular motors that translocate towards the minus ends of microtubules. In Chlamydomonas flagellar outer arm dynein, light chain 1 (LC1) associates with the nucleotide binding region within the gamma heavy chain motor domain and consists of a central leucine-rich repeat section that folds as a cylindrical right handed spiral formed from six beta-beta-alpha motifs. This central cylinder is flanked by terminal helical subdomains. The C-terminal helical domain juts out from the cylinder and is adjacent to a hydrophobic surface within the repeat region that is proposed to interact with the dynein heavy chain. The position of the C-terminal domain on LC1 and the unexpected structural similarity between LC1 and U2A' from the human spliceosome suggest that this domain interacts with the dynein motor domain. PMID:10876244

Wu, H; Maciejewski, M W; Marintchev, A; Benashski, S E; Mullen, G P; King, S M

2000-07-01

275

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

276

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

PubMed

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

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

2001-08-01

277

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

PubMed Central

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

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

2001-01-01

278

Macromolecular salen catalyst with largely enhanced catalytic activity.  

PubMed

A dinuclear copper(II) Schiff-base complex was immobilized in a poly(acrylate) matrix by emulsion polymerization. The spheric microbeads were used for aerobic catalytic oxidation of 3,5-di-tert-butylcatechol into 3,5-di-tert-butylquinone in methanol at ambient temperature to study the contribution of the macromolecular matrix to the overall rate acceleration of the reaction. The polymeric catalyst catalyzes the oxidation about 1 order of magnitude faster (kcat/knon = 470,000) than its low molecular weight analogue (kcat/knon = 60,000). PMID:18081306

Striegler, Susanne; Gichinga, Moses G; Dittel, Michael

2008-01-17

279

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, German; Minton, Allen P.

2009-01-01

280

Design of artificial selenoenzymes based on macromolecular scaffolds.  

PubMed

The selenoenzyme glutathione peroxidase has received increased attention as one of the antioxidative enzymes exerting important biological roles in living bodies. Over the past decades, much effort has been invested to mimic its catalytic behavior for understanding enzymatic catalytic mechanisms and also for developing potential medicines. A great number of artificial GPxs, ranging from small molecular compounds to macromolecular ones, have been designed and prepared by combining the concept of recognition and catalysis using chemical, biological and supramolecular strategies. In this article, we specify the development of artificial GPxs based on macromolecules as scaffolds, and discuss the power of reduced models in studying the bio-catalytic nature of selenoenzymes. PMID:20632366

Huang, Xin; Yin, Yanzhen; Liu, Junqiu

2010-12-01

281

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; Werkmuller, Alexander; Winter, Roland

2013-01-01

282

Improvements toward highly accurate diffraction experiments at the macromolecular micro-crystallography beamline BL-17A  

PubMed Central

BL-17A is a macromolecular crystallography beamline dedicated to diffraction experiments conducted using micro-crystals and structure determination studies using a lower energy X-ray beam. In these experiments, highly accurate diffraction intensity measurements are definitively important. Since this beamline was constructed, the beamline apparatus has been improved in several ways to enable the collection of accurate diffraction data. The stability of the beam intensities at the sample position was recently improved by modifying the monochromator. The diffractometer has also been improved. A new detector table was installed to prevent distortions in the diffractometer’s base during the repositioning of the diffractometer detector. A new pinhole system and an on-axis viewing system were installed to improve the X-ray beam profile at the sample position and the centering of tiny crystal samples. PMID:24121344

Yamada, Yusuke; Chavas, Leonard M. G.; Igarashi, Noriyuki; Hiraki, Masahiko; Wakatsuki, Soichi; Matsugaki, Naohiro

2013-01-01

283

Site-selective electroless nickel plating on patterned thin films of macromolecular metal complexes.  

PubMed

We demonstrate a simple route to depositing nickel layer patterns using photocross-linked polymer thin films containing palladium catalysts, which can be used as adhesive interlayers for fabrication of nickel patterns on glass and plastic substrates. Electroless nickel patterns can be obtained in three steps: (i) the pattern formation of partially quaterized poly(vinyl pyridine) by UV irradiation, (ii) the formation of macromolecular metal complex with palladium, and (iii) the nickel metallization using electroless plating bath. Metallization is site-selective and allows for a high resolution. And the resulting nickel layered structure shows good adhesion with glass and plastic substrates. The direct patterning of metallic layers onto insulating substrates indicates a great potential for fabricating micro/nano devices. PMID:21069972

Kimura, Mutsumi; Yamagiwa, Hiroki; Asakawa, Daisuke; Noguchi, Makoto; Kurashina, Tadashi; Fukawa, Tadashi; Shirai, Hirofusa

2010-12-01

284

J. Mol. Biol. (1986) 191,553-561 Solution Structure of Human Growth Hormone  

E-print Network

in hGHRF, nothing is known about its structure in solution. In this paper we present a combined c. Wetekam, personal communication). We show that, although neither peptide has an ordered structure in water), respectively. Both peptides were >99% pure as judged by high-pressure liquid chromatography. Samples for c

Clore, G. Marius

285

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

E-print Network

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

286

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

PubMed

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

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

2012-11-01

287

An Analytical Solution for Transient Thermal Response of an Insulated Structure  

NASA Technical Reports Server (NTRS)

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

Blosser, Max L.

2012-01-01

288

The NMR structure of cyclosporin A bound to cyclophilin in aqueous solution  

SciTech Connect

Cyclosporin A bound to the presumed receptor protein cyclophilin was studied in aqueous solution at pH 6.0 by nuclear magnetic resonance spectroscopy using uniform {sup 15}N- or {sup 13}C-labeling of cyclosporin A and heteronuclear spectral editing techniques. With an input of 108 intramolecular NOEs and four vicinal {sup 3}J{sub HN{alpha}} coupling constants, the three-dimensional structure of cyclosporin A bound to cyclophilin was calculated with the distance geometry program DISMAN, and the structures resulting from 181 converged calculations were energy refined with the program FANTOM. A group of 120 conformers was selected on the basis of the residual constraint violations and energy criteria to represent the solution structure. The average of the pairwise root-mean-square distances calculated for the backbone atoms of the 120 structures was 0.58 {angstrom}. The structure represents a novel conformation of cyclosporin A, for which the backbone conformation is significantly different from the previously reported structures in single crystals and in chloroform solution. The structure has all peptide bonds in the trans form, contains no elements of regular secondary structure and no intramolecular hydrogen bonds, and exposes nearly all polar groups to its environment. The root-mean-square distance between the backbone atoms of the crystal structure of cyclosporin A and the mean of the 120 conformers representing the NMR structure of cyclosporin A bound to cyclophilin is 2.5 {angstrom}.

Weber, C.; Wilder, G.; von Freyberg, B.; Braun, W.; Wuethrich, K. (Eidgenoessische Technische Hochschule-Hoenggerberg, Zuerich (Switzerland)); Traber, R.; Widmer, H. (Sandoz Pharma AG, Basel (Switzerland))

1991-07-02

289

Variable effects of soman on macromolecular secretion by ferret trachea  

SciTech Connect

The purpose of this study was to examine the effect of the anticholinesterase agent, soman, on macromolecular secretion by ferret trachea, in vitro. We mounted pieces of ferret trachea in Ussing-type chambers. Secreted sulfated macromolecules were radiolabeled by adding 500 microCi of {sup 35}SO{sub 4} to the submucosal medium and incubating for 17 hr. Soman added to the submucosal side produced a concentration-dependent increase in radiolabeled macromolecular release with a maximal secretory response (mean +/- SD) of 202 +/- 125% (n = 8) relative to the basal secretion rate at a concentration of 10{sup {minus} 7} M. The addition of either 10{sup {minus}6} M pralidoxime (acetylcholinesterase reactivator) or 10{sup {minus}6} M atropine blocked the response to 10{sup {minus}7} M soman. At soman concentrations greater than 10{sup {minus}7} M, secretion rate decreased and was not significantly different from basal secretion. Additional experiments utilizing acetylcholine and the acetylcholinesterase inhibitor, physostigmine, suggest that inhibition of secretion by high concentrations of soman may be due to a secondary antagonistic effect of soman on muscarinic receptors.

McBride, R.K.; Zwierzynski, D.J.; Stone, K.K.; Culp, D.J.; Marin, M.G. (Univ. of Rochester School of Medicine and Dentistry, NY (USA))

1991-01-01

290

On the calculation of absolute macromolecular binding free energies  

PubMed Central

The standard framework for calculating the absolute binding free energy of a macromolecular association reaction A + B ? AB with an association constant KAB is to equate chemical potentials of the species on the left- and right-hand sides of this reaction and evaluate the chemical potentials from theory. This theory involves (usually hidden) assumptions about what constitutes the bound species, AB, and where the contribution of the solvent appears. We present here an alternative derivation that can be traced back to Bjerrum, in which the expectation value of KAB is obtained directly through the statistical mechanical method of evaluating its ensemble (Boltzmann-weighted) average. The generalized Bjerrum approach more clearly delineates: (i) the different contributions to binding; (ii) the origin of the much-discussed and somewhat controversial association entropy term; and (iii) where the solvent contribution appears. This approach also allows approximations required for practical evaluation of the binding constant in complex macromolecular systems, to be introduced in a well defined way. We provide an example, with application to test cases that illustrate a range of binding behavior. PMID:12149474

Luo, Hengbin; Sharp, Kim

2002-01-01

291

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

292

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

NASA Astrophysics Data System (ADS)

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

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

2000-06-01

293

Cation distribution, structure and magnetic properties of lithium manganese iron oxide spinel solid solutions  

Microsoft Academic Search

Single phase cubic spinel compounds LixMn1+xFe2?2xO4 (x=0, …, 1) were obtained by thermal decomposition of freeze-dried formate solutions of appropriate composition. The samples were characterized by X-ray powder diffraction and Rietveld refinement, XANES, 57Fe Mössbauer spectroscopy and magnetization measurements. The combination of these methods provides useful conclusions concerning the structure, cation distribution and properties of the spinel solid solutions. The

C. Wende; Kh. Olimov; H. Modrow; F. E. Wagner; H.. Langbein

2006-01-01

294

Structure of fluid mixtures near a solute: A density functional approach  

NASA Astrophysics Data System (ADS)

The structure of fluid mixtures near a spherical solute is studied using a density functional approach and computer simulation. The input direct correlation function is obtained from integral equation theory with an accurate closure relation. The density and concentration profiles of binary as well as ternary hard-sphere mixtures near a large hard-spherical solute compare quite well with the computer simulation results over a wide range of parametric conditions.

Patra, Chandra N.

2014-09-01

295

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

SciTech Connect

The stability of the grain structure in 2219-O aluminum alloy friction stir welds during solution treatment has been investigated. Experimental results show that the solution treatment causes drastic grain growth, Grain growth initiates at the surface and the bottom of the weld and then extends to the weld centre within several minutes. The solution treatment temperature and the welding heat input have a significant effect on grain growth. The higher the solution temperature, or the higher the welding heat input, the greater the grain growth. The instability of the grains is attributed to an imbalance between thermodynamic driving forces for grain growth and the pinning forces impeding grain boundary migration during solution treatment.

Chen, Y.C. [National Key Laboratory of Precision Hot Processing of Metals, Harbin Institute of Technology, Harbin 150001 (China) and National Key Laboratory of Advanced Welding Production Technology, Harbin Institute of Technology, Harbin 150001 (China)]. E-mail: armstrong@hit.edu.cn; Feng, J.C. [National Key Laboratory of Advanced Welding Production Technology, Harbin Institute of Technology, Harbin 150001 (China); Liu, H.J. [National Key Laboratory of Advanced Welding Production Technology, Harbin Institute of Technology, Harbin 150001 (China)

2007-02-15

296

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

297

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

NASA Astrophysics Data System (ADS)

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.

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

2012-08-01

298

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

299

Mathieu function solutions for photoacoustic waves in sinusoidal one-dimensional structures  

NASA Astrophysics Data System (ADS)

The photoacoustic effect for a one-dimensional structure, the sound speed of which varies sinusoidally in space, is shown to be governed by an inhomogeneous Mathieu equation with the forcing term dependent on the spatial and temporal properties of the exciting optical radiation. New orthogonality relations, traveling wave Mathieu functions, and solutions to the inhomogeneous Mathieu equation are found, which are used to determine the character of photoacoustic waves in infinite and finite length phononic structures. Floquet solutions to the Mathieu equation give the positions of the band gaps, the damping of the acoustic waves within the band gaps, and the dispersion relation for photoacoustic waves. The solutions to the Mathieu equation give the photoacoustic response of the structure, show the space equivalent of subharmonic generation and acoustic confinement when waves are excited within band gaps.

Wu, Binbin; Diebold, Gerald J.

2012-07-01

300

Mathieu function solutions for photoacoustic waves in sinusoidal one-dimensional structures.  

PubMed

The photoacoustic effect for a one-dimensional structure, the sound speed of which varies sinusoidally in space, is shown to be governed by an inhomogeneous Mathieu equation with the forcing term dependent on the spatial and temporal properties of the exciting optical radiation. New orthogonality relations, traveling wave Mathieu functions, and solutions to the inhomogeneous Mathieu equation are found, which are used to determine the character of photoacoustic waves in infinite and finite length phononic structures. Floquet solutions to the Mathieu equation give the positions of the band gaps, the damping of the acoustic waves within the band gaps, and the dispersion relation for photoacoustic waves. The solutions to the Mathieu equation give the photoacoustic response of the structure, show the space equivalent of subharmonic generation and acoustic confinement when waves are excited within band gaps. PMID:23005556

Wu, Binbin; Diebold, Gerald J

2012-07-01

301

Inactivation of recombinant human brain-type creatine kinase during denaturation by guanidine hydrochloride in a macromolecular crowding system.  

PubMed

In this study, we quantitatively examined the effects of the macromolecular crowding agents, polyethylene glycol 2000 (PEG 2000) and dextran 70, on guanidine hydrochloride (GdnHCl)-induced denaturation of recombinant human brain-type creatine kinase (rHBCK). Our results showed that both PEG 2000 and dextran 70 had a protective effect on the inactivation of rHBCK induced by 0.5 M GdnHCl at 25 °C. The presence of 200 g/L PEG 2000 resulted in the retention of 35.33 % of rHBCK activity after 4 h of inactivation, while no rHBCK activity was observed after denaturation in the absence of macromolecular crowding agents. The presence of PEG 2000 and dextran 70 at a concentration of 100 g/L could decelerate the k (2) value of the slow track to 21 and 33 %, respectively, in comparison to values obtained in the absence of crowding agents. Interestingly, inactivation of rHBCK in the presence of 200 g/L PEG 2000 followed first-order monophasic kinetics, with an apparent rate constant of 8?×?10(-5)?s(-1). The intrinsic fluorescence results showed that PEG 2000 was better than dextran 70 at stabilizing rHBCK conformation. In addition, the results of the phase diagram indicate that more intermediates may be captured when rHBCK is denatured in a macromolecular crowding system. Mixed crowding agents did not produce better results than single crowding agents, but the protective effects of PEG 2000 on the inactivation and unfolding of rHBCK tended to increase as the ratio of PEG 2000 increased in the mixed crowding agent solution. Though it is not clear which crowding agents more accurately simulated the intracellular environment, this study could lead to a better understanding of protein unfolding in the intracellular environment. PMID:23179281

Fan, Yong-Qiang; Liu, Hong-Jian; Li, Chang; Luan, Yu-Shi; Yang, Jun-Mo; Wang, Yu-Long

2013-01-01

302

Solution structure of a parallel-stranded G-quadruplex DNA.  

PubMed

This paper reports on the solution structure of a parallel-stranded G-quadruplex formed by the Tetrahymena telomeric sequence d(T-T-G-G-G-G-T) whose NMR parameters in potassium cation containing solution were previously published from our laboratory. The structure was determined by combining a quantitative analysis of the NMR data with molecular dynamics calculations including relaxation matrix refinement. The combined NMR-computational approach yielded a set of seven distance-refined structures with pairwise RMSDs ranging from 0.66 to 1.30 A for the central G-G-G-G tetranucleotide segment. Four of the seven structures were refined further using complete relaxation-matrix calculations to yield solution structures with pairwise RMSDs ranging from 0.64 to 1.04 A for the same tetranucleotide segment. The R-factors also decreased on proceeding from the distance-refined to relaxation matrix-refined structures. The four strands of the G-quadruplex are aligned in parallel and are related by a 4-fold symmetry axis coincident with the helix axis. Individual guanines from each strand form planar G.G.G.G tetrad arrangements with each tetrad stabilized by eight hydrogen bonds involving the Watson-Crick and Hoogsteen edges of the guanine bases. All guanines adopt anti glycosidic torsion angles and S type sugar puckers in this right-handed parallel-stranded G-quadruplex structure. The four G.G.G.G tetrad planes stack on each other with minimal overlap of adjacent guanine base planes within individual strands. The thymine residues are under-defined in the solution structure of the d(T-T-G-G-G-G-T) G-quadruplex and sample amongst multiple conformations in solution. PMID:8263919

Wang, Y; Patel, D J

1993-12-20

303

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

304

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

305

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

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

2014-01-01

306

942 nature structural biology volume 8 number 11 november 2001 Solution structure of a viral  

E-print Network

. The minimized mean structure is used. The side chains of the catalytic Asp triad are shown in purple, and the disulfide bond is in dark blue. c, Ribbon diagram of Pol with secondary structural elements and with the 8 of the catalytic Asp triad are shown in purple. d, Structure-based sequence alignment of Pol X with the palm

Tsai, Ming-Daw

307

Backbone solution structures of proteins using residual dipolar couplings: Application to a novel structural genomics target  

Microsoft Academic Search

Structural genomics (or proteomics) activities are critically dependent on the availability of high-throughput structure determination methodology. Development of such methodology has been a particular challenge for NMR based structure determination because of the demands for isotopic labeling of proteins and the requirements for very long data acquisition times. We present here a methodology that gains efficiency from a focus on

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

2005-01-01

308

Backbone solution structures of proteins using residual dipolar couplings: application to a novel structural genomics target  

Microsoft Academic Search

Structural genomics (or proteomics) activities are critically dependent on the availability of high-throughput structure determination methodology. Development of such methodology has been a particular challenge for NMR based structure determination because of the demands for isotopic labeling of proteins and the requirements for very long data acquisition times. We present here a methodology that gains efficiency from a focus on

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

2005-01-01

309

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

NASA Astrophysics Data System (ADS)

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

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

2011-12-01

310

Creating Effective Insulation Solutions, Taking into Account the Law of Affinity Structures in Construction Materials  

E-print Network

Abstract: Theoretical approach to the creation of thermal insulation solutions with high thermo-physical and physical-mechanical properties. When you create a material with the desired characteristics used previously suggested by the authors, the law of affinity structures in construction materials, allowing to predict and obtain building composites with desired properties. The results of research on the production of composite binders using waste perlite manufacture for thermal barrier solutions. The microstructure insulation solutions. The method of electron microprobe analysis revealed that between cement and perlite chemical interactions occur. The compositions composite binders for insulating solutions based on local raw materials and plasticizers. The composite binders optimal composition have a compressive strength of 95.2 MPa. It is proved that when using the suggested approaches for creating material may get effective insulating solutions with high heat-shielding properties. Key words: Law of affinity structures in construction materials Composite binders Expanded perlite insulation solutions on the basis of dry construction mixtures Microstructure Microprobe analysis of spectral Thermal and performance characteristics Physical and mechanical properties

Lesovik Valeriy Stanislavovich; Zagorodnuk Liliya Hasanovna; Andrey Vasilevich Shkarin; Denis Alekseevich Belikov; Anna Aleks; Rovna Kuprina

311

Accurate structure factor determination and electron charge distributions of binary cubic solid solutions  

Microsoft Academic Search

By combining the accurate low-angle X-ray structure factors of binary cubic solid solutions determined by high-energy electron diffraction (HEED) with higher-angle values obtained by interpolation between best pure-element form factors, a complete set of accurate X-ray structure factors for these alloys can be produced. This approach is an improvement over previous analyses of this sort, where the pure-element form factors

Alan G. Fox; Robert M. Fisher

1986-01-01

312

Macromolecular therapeutics in cancer treatment: the EPR effect and beyond.  

PubMed

In this review, I have discussed various issues of the cancer drug targeting primarily related to the EPR (enhanced permeability and retention) effect, which utilized nanomedicine or macromolecular drugs. The content goes back to the development of the first polymer-protein conjugate anticancer agent SMANCS and development of the arterial infusion in Lipiodol formulation into the tumor feeding artery (hepatic artery for hepatoma). The brief account on the EPR effect and its definition, factors involved, heterogeneity, and various methods of augmentation of the EPR effect, which showed remarkably improved clinical outcomes are also discussed. Various obstacles involved in drug developments and commercialization are also discussed through my personal experience and recollections. PMID:22595146

Maeda, Hiroshi

2012-12-10

313

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

314

On macromolecular refinement at subatomic resolution with interatomic scatterers.  

PubMed

A study of the accurate electron-density distribution in molecular crystals at subatomic resolution (better than approximately 1.0 A) requires more detailed models than those based on independent spherical atoms. A tool that is conventionally used in small-molecule crystallography is the multipolar model. Even at upper resolution limits of 0.8-1.0 A, the number of experimental data is insufficient for 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 data sets gave results that were comparable in quality with the results of multipolar refinement and superior to those for conventional models. Applications to several data sets of both small molecules and macromolecules are shown. These refinements were performed using the general-purpose macromolecular refinement module phenix.refine of the PHENIX package. PMID:18007035

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

2007-11-01

315

Structural transitions of monoolein bicontinuous cubic phase induced by inclusion of protein lysozyme solutions  

E-print Network

Inclusion of protein lysozyme molecules in lipidic monoolein cubic phase induces a transition from a $\\rm Pn\\bar{3}m$ structure to $\\rm Im\\bar{3}m$ one. Small-angle X-ray scattering (SAXS) method with high intensity synchrotron radiation enabled us to follow closely the transition depending on the conditions of lysozyme solutions. We showed that concentrated lysozyme solutions induced the appearance of the $\\rm Im\\bar{3}m$ structure coexisting with the $\\rm Pn\\bar{3}m$ structure. From the relation between the lattice parameters of these two structures it was shown that they were related by the Bonnet transformation of underlying triply periodic minimal surfaces. We found that the transition also occurred at lower lysozyme concentration when NaCl induced attraction between lysozyme molecules. The origin of the transition was considered as a frustration in the cubic phase where lysozyme molecules were highly confined. A simple estimation of the frustration was given, which took into account of the translational entropy of lysozyme molecules. At the highest concentration of lysozyme and NaCl the $\\rm Im\\bar{3}m$ structure was found to disappear and left only the $\\rm Pn\\bar{3}m$ structure. This was probably either due to the crystallization or phase separation of lysozyme solutions ongoing microscopically, which absorbed lysozyme molecules from channels of the cubic phase and thus removed the frustration.

S. Tanaka; S. Maki; M. Ataka

2006-05-25

316

Ultrafast dynamics and hydrogen-bond structure in aqueous solutions of model peptides.  

PubMed

The dynamics of water molecules in the hydration layers of proteins are critical for biological function. Here the molecular dynamics in aqueous solutions of model hydrophilic and amphiphilic dipeptides are studied as a function of concentration using the ultrafast optical Kerr effect (OKE). The OKE is a direct time-domain method which yields both picosecond time scale molecular dynamics and low-frequency (Terahertz) Raman spectra, which contain information on the hydrogen-bonded structure of aqueous solutions. Two distinct concentration regimes are identified, above and below 0.4 M peptide concentration. In the low-concentration regime the tetrahedral water structure is largely preserved but the structural dynamics in water are slowed significantly by interaction with the peptide. The slow down is more marked for the hydrophilic than the amphiphilic peptide. Suppression of water structural dynamics observed is greater than that reported for retardation of the water reorientation in NMR, reflecting the different dynamics probed by these different methods. Above 0.4 M the tetrahedral water structure is more strongly perturbed, a contribution to the THz Raman spectrum from the solvated peptide is observed, and structural dynamics in the solution are markedly slowed. This is assigned to slow relaxation within an H-bonded network of peptide molecules. The strong concentration dependence observed goes some way toward explaining disagreements between different measurements of the dynamics of peptide solvation which have appeared in the literature. PMID:20666567

Mazur, Kamila; Heisler, Ismael A; Meech, Stephen R

2010-08-19

317

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

318

Structure of a dilute aqueous solution of argon. A Monte Carlo simulation  

NASA Astrophysics Data System (ADS)

A Monte Carlo simulation of a dilute aqueous solution of argon has been performed in the canonical (T,V,N) ensemble. The argon-water pair potential energy function has been obtained, with a best fitting procedure, from a set of 85 ab initio SCF energy values calculated with an extended basis set. Both energetic and structural evidences supporting the hypothesis of water structure promotion by nonpolar solutes are provided. Water molecules close to argon are oriented in a way similar to that of a crystalline clathrate cage. This analogy however is restricted to a local environment, which suggests that only parts of a real clathrate cage are present at a given time in this solution.

Alagona, Giuliano; Tani, Alessandro

1980-01-01

319

Structure of Concentrated HCl Solutions Department of Physical Chemistry and the Fritz Haber Research Center, The Hebrew UniVersity,  

E-print Network

Structure of Concentrated HCl Solutions Noam Agmon Department of Physical Chemistry and the Fritz Form: October 14, 1997X A pentagonal ring is suggested as the basic structural unit of HCl(H2O)6 and (HCl)2(H2O)6 in solution. Modeled after the X-ray structure of a caged H13O6 + compound, it contains

Agmon, Noam

320

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.

321

HOUSEHOLD AND STRUCTURAL INSECTS Laboratory Evaluation of Boric Acid-Sugar Solutions as Baits  

E-print Network

HOUSEHOLD AND STRUCTURAL INSECTS Laboratory Evaluation of Boric Acid-Sugar Solutions as Baits of boric acid and tend to be less efÃ?cacious than other insecticide baits. The purpose of this study and expressed as lethal time90, the time taken to kill 90% of the cockroaches. Results showed that boric acid

322

Coagulation-diffusion systems: Derivation and existence of solutions for the diffuse interface structure equations  

NASA Astrophysics Data System (ADS)

This paper considers an infinite system of partial differential equations, the coagulation-diffusion equations, which add spatial diffusion to the classical coagulation equations. The main emphasis is placed on deriving an infinite system of ordinary differential equations which described the structured interface between reacting coagulation and dilute concentration. Existence of solutions to interfacial equaitons is proven under spatial boundary conditions.

Slemrod, M.

1990-12-01

323

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

2010-01-01

324

Tertiary structure of human complement component C5a in solution from nuclear magnetic resonance data  

Microsoft Academic Search

The tertiary structure for the region 1-63 of the 74 amino acid human complement protein C5a in solution was calculated from a large number of distance constraints derived from nuclear Overhauser effects with an angular distance geometry algorithm. The protein consists of four helices juxtaposed in an approximately antiparallel topology connected by peptide loops located at the surface of the

Erik R. P. Zuiderweg; David G. Nettesheim; Karl W. Mollison; George W. Carter

1989-01-01

325

Solution structure of the DNA binding domain of AraC protein  

Microsoft Academic Search

We report the solution struc- ture of the DNA binding do- main of the Escherichia coli regulatory protein AraC determined in the absence of DNA. The 20 lowest energy structures, determined on the basis of 1507 unambiguous nuclear Overhauser restraints and 180 angle restraints, are well resolved with a pair wise backbone root mean square deviation of 0.7 A ?

Michael E. Rodgers; Robert Schleif

2009-01-01

326

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

327

Solution structure of the loops of bacteriorhodopsin closely resembles the crystal structure  

Microsoft Academic Search

Bacteriorhodopsin is one of very few transmembrane proteins for which high resolution structures have been solved. The structure shows a bundle of seven helices connected by six turns. Some turns in proteins are stabilized by short range interactions and can behave as small domains. These observations suggest that peptides containing the sequence of the turns in a membrane protein such

Madan Katragadda; James L. Alderfer; Philip L. Yeagle

2000-01-01

328

Solution-cast high-aspect-ratio polymer structures from direct-write templates.  

PubMed

This letter presents a novel strategy for template synthesis of polymer structures with laser machined substrates. User-designed patterns of submicrometer holes with aspect ratios >10:1 and depths >10 ?m were produced by focusing 160 fs, 5.2 ?J laser pulses on the surface of fused silica with a high numerical aperture microscope objective. Some holes were enlarged by chemical etching. Polymer solutions were cast into the templates to create high-aspect-ratio polymer structures using replication. Engineered polymer structures prepared by this unique method are useful for a number of applications such as high surface area electrodes and biological substrates. PMID:23244771

Rajput, D; Costa, L; Lansford, K; Terekhov, A; Hofmeister, W

2013-01-01

329

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.; Bunkoczi, Gabor; Headd, Jeffrey J.; McCoy, Airlie J.; Oeffner, Robert D.; Read, Randy J.; Terwilliger, Thomas C.; Adams, Paul D.

2014-01-01

330

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

331

High-throughput screening of optimal solution conditions for structural biological studies by fluorescence correlation spectroscopy  

PubMed Central

Protein aggregation is an essential molecular event in a wide variety of biological situations, and is a causal factor in several degenerative diseases. The aggregation of proteins also frequently hampers structural biological analyses, such as solution NMR studies. Therefore, precise detection and characterization of protein aggregation are of crucial importance for various research fields. In this study, we demonstrate that fluorescence correlation spectroscopy (FCS) using a single-molecule fluorescence detection system enables the detection of otherwise invisible aggregation of proteins at higher protein concentrations, which are suitable for structural biological experiments, and consumes relatively small amounts of protein over a short measurement time. Furthermore, utilizing FCS, we established a method for high-throughput screening of protein aggregation and optimal solution conditions for structural biological experiments. PMID:19388076

Sugiki, Toshihiko; Yoshiura, Chie; Kofuku, Yutaka; Ueda, Takumi; Shimada, Ichio; Takahashi, Hideo

2009-01-01

332

Thermodynamic behaviour and structural properties of an aqueous sodium chloride solution upon supercooling  

E-print Network

We present the results of a molecular dynamics simulation study of thermodynamic and structural properties upon supercooling of a low concentration sodium chloride solution in TIP4P water and the comparison with the corresponding bulk quantities. We study the isotherms and the isochores for both the aqueous solution and bulk water. The comparison of the phase diagrams shows that thermodynamic properties of the solution are not merely shifted with respect to the bulk. Moreover, from the analysis of the thermodynamic curves, both the spinodal line and the temperatures of maximum density curve can be calculated. The spinodal line appears not to be influenced by the presence of ions at the chosen concentration, while the temperatures of maximum density curve displays both a mild shift in temperature and a shape modification with respect to bulk. Signatures of the presence of a liquid-liquid critical point are found in the aqueous solution. By analysing the water-ion radial distribution functions of the aqueous solution we observe that upon changing density, structural modifications appear close to the spinodal. For low temperatures additional modifications appear also for densities close to that corresponding to a low density configurational energy minimum.

D. Corradini; P. Gallo; M. Rovere

2008-05-16

333

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

334

A hybrid computational-experimental approach for automated crystal structure solution  

NASA Astrophysics Data System (ADS)

Crystal structure solution from diffraction experiments is one of the most fundamental tasks in materials science, chemistry, physics and geology. Unfortunately, numerous factors render this process labour intensive and error prone. Experimental conditions, such as high pressure or structural metastability, often complicate characterization. Furthermore, many materials of great modern interest, such as batteries and hydrogen storage media, contain light elements such as Li and H that only weakly scatter X-rays. Finally, structural refinements generally require significant human input and intuition, as they rely on good initial guesses for the target structure. To address these many challenges, we demonstrate a new hybrid approach, first-principles-assisted structure solution (FPASS), which combines experimental diffraction data, statistical symmetry information and first-principles-based algorithmic optimization to automatically solve crystal structures. We demonstrate the broad utility of FPASS to clarify four important crystal structure debates: the hydrogen storage candidates MgNH and NH3BH3; Li2O2, relevant to Li-air batteries; and high-pressure silane, SiH4.

Meredig, Bryce; Wolverton, C.

2013-02-01

335

Solution structural characterization of coiled-coil peptide-polymer side-conjugates.  

PubMed

Detailed structural characterization of protein-polymer conjugates and understanding of the interactions between covalently attached polymers and biomolecules will build a foundation to design and synthesize hybrid biomaterials. Conjugates based on simple protein structures are ideal model system to achieve these ends. Here we present a systematic structural study of coiled-coil peptide-poly(ethylene glycol) (PEG) side-conjugates in solution, using circular dichroism, dynamic light scattering, and small-angle X-ray scattering, to determine the conformation of conjugated PEG chains. The overall size and shape of side-conjugates were determined using a cylindrical form factor model. Detailed structural information of the covalently attached PEG chains was extracted using a newly developed model where each peptide-PEG conjugate was modeled as a Gaussian chain attached to a cylinder, which was further arranged in a bundle-like configuration of three or four cylinders. The peptide-polymer side-conjugates were found to retain helix bundle structure, with the polymers slightly compressed in comparison with the conformation of free polymers in solution. Such detailed structural characterization of the peptide-polymer conjugates, which elucidates the conformation of conjugated PEG around the peptide and assesses the effect of PEG on peptide structure, will contribute to the rational design of this new family of soft materials. PMID:22575010

Shu, Jessica Y; Lund, Reidar; Xu, Ting

2012-06-11

336

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

337

Structure and intermolecular interactions in selected binary solutions studied by X-ray methods  

NASA Astrophysics Data System (ADS)

The results of X-ray structural studies of liquid chloroanisole C6H4OCH3Cl and 10% solutions of chloroanisole in 1,4-dimethylbenzene C8H10 are presented. It is the first paper on an X-ray diffraction study of the liquid solutions of chloroanisole. The X-ray measurements were made at 293 K for the scattering angle range 2? varying from 6° to 120°. Averaged scattered X-ray angular distributions I¯(S) were determined. The angular distributions of the intensity of X-ray scattered by 10% solutions of chloroanisole in 1,4-dimethylbenzene were compared to the angular distributions obtained for liquid ortho-, meta- and para-chloroanisole. The differential radial distribution functions of electron density 4?r?j,knK[?k(r)-?0] were numerically found using the Fourier analysis from a modified Warren, Krutter and Morningstar equation. To the maxima of DRDFs, interatomic and intermolecular distances were assigned. The use of short-wave radiation from an X-ray tube with a molybdenum anode permitted determination of the spheres of intermolecular ordering in the studied liquids and their solutions. The experimental results were used to plot models of the most highly probable mutual disposition of the molecules in liquid chloroanisole and their solutions. The benzene rings of two molecules are situated in parallel plane what results in antiparallel setting of the dipole moments of the chloroanisole molecules. X-ray structural analysis was applied to determine the packing coefficients of chloroanisole molecules. The results obtained in this paper confirm the specific structural properties of the solutions studied.

Drozdowski, Henryk; Romaniuk, Anna; B?aszczak, Zdzis?aw

2013-12-01

338

Structure and dimerization of translation initiation factor aIF5B in solution  

SciTech Connect

Highlights: Black-Right-Pointing-Pointer aIF5B forms maximum 5.0-6.8% irreversible dimers in solution. Black-Right-Pointing-Pointer Sedimentation coefficients for monomer and dimer are 3.64 and 5.51 {+-} 0.29 S. Black-Right-Pointing-Pointer Adding only 2% glycerol prevents dimerization. Black-Right-Pointing-Pointer SAXS on aIF5B monomer gave an R{sub g} of 37.5 {+-} 0.2 A and a D{sub max} of {approx}130 A. Black-Right-Pointing-Pointer There are universal structural differences between aIF5B and Escherichia coli IF2. -- Abstract: Translation initiation factor 5B (IF5B) is required for initiation of protein synthesis. The solution structure of archaeal IF5B (aIF5B) was analysed by small-angle X-ray scattering (SAXS) and dynamic light scattering (DLS) and was indicated to be in both monomeric and dimeric form. Sedimentation equilibrium (SE) analytical ultracentrifugation (AUC) of aIF5B indicated that aIF5B forms irreversible dimers in solution but only to a maximum of 5.0-6.8% dimer. Sedimentation velocity (SV) AUC at higher speed also indicated the presence of two species, and the sedimentation coefficients s{sub 20,w}{sup 0} were determined to be 3.64 and 5.51 {+-} 0.29 S for monomer and dimer, respectively. The atomic resolution (crystallographic) structure of aIF5B (Roll-Mecak et al. ) was used to model monomer and dimer, and theoretical sedimentation coefficients for these models were computed (3.89 and 5.63 S, respectively) in good agreement with the sedimentation coefficients obtained from SV analysis. Thus, the structure of aIF5B in solution must be very similar to the atomic resolution structure of aIF5B. SAXS data were acquired in the same buffer with the addition of 2% glycerol to inhibit dimerization, and the resultant monomeric aIF5B in solution did indeed adopt a structure very similar to the one reported earlier for the protein in crystalline form. The p(r) function indicated an elongated conformation supported by a radius of gyration of 37.5 {+-} 0.2 A and a maximum dimension of {approx}130 A. The effects of glycerol on the formation of dimers are discussed. This new model of aIF5B in solution shows that there are universal structural differences between aIF5B and the homologous protein IF2 from Escherichia coli.

Rasmussen, Louise Caroe Vohlander [Department of Molecular Biology, Aarhus University, Gustav Wieds Vej 10, DK-8000 Aarhus C (Denmark)] [Department of Molecular Biology, Aarhus University, Gustav Wieds Vej 10, DK-8000 Aarhus C (Denmark); Oliveira, Cristiano Luis Pinto [Department of Chemistry, Centre for mRNP Biogenesis and Metabolism, and iNANO Interdisciplinary Nanoscience Center, Aarhus University, Langelandsgade 140, DK-8000 Aarhus C (Denmark)] [Department of Chemistry, Centre for mRNP Biogenesis and Metabolism, and iNANO Interdisciplinary Nanoscience Center, Aarhus University, Langelandsgade 140, DK-8000 Aarhus C (Denmark); Byron, Olwyn [Glasgow Biomedical Research Center, University of Glasgow, Glasgow G12 8QQ, Scotland (United Kingdom)] [Glasgow Biomedical Research Center, University of Glasgow, Glasgow G12 8QQ, Scotland (United Kingdom); Jensen, Janni Mosgaard [Department of Molecular Biology, Aarhus University, Gustav Wieds Vej 10, DK-8000 Aarhus C (Denmark)] [Department of Molecular Biology, Aarhus University, Gustav Wieds Vej 10, DK-8000 Aarhus C (Denmark); Pedersen, Jan Skov [Department of Chemistry, Centre for mRNP Biogenesis and Metabolism, and iNANO Interdisciplinary Nanoscience Center, Aarhus University, Langelandsgade 140, DK-8000 Aarhus C (Denmark)] [Department of Chemistry, Centre for mRNP Biogenesis and Metabolism, and iNANO Interdisciplinary Nanoscience Center, Aarhus University, Langelandsgade 140, DK-8000 Aarhus C (Denmark); Sperling-Petersen, Hans Uffe [Department of Molecular Biology, Aarhus University, Gustav Wieds Vej 10, DK-8000 Aarhus C (Denmark)] [Department of Molecular Biology, Aarhus University, Gustav Wieds Vej 10, DK-8000 Aarhus C (Denmark); Mortensen, Kim Kusk, E-mail: kkm@science.au.dk [Department of Molecular Biology, Aarhus University, Gustav Wieds Vej 10, DK-8000 Aarhus C (Denmark)

2011-12-09

339

Structural and vibrational study of the tautomerism of histamine free-base in solution.  

PubMed

Infrared and Raman spectroscopy in H(2)O and D(2)O and quantum Density Functional calculations were used to determine the structure of histamine free-base in aqueous solution. A quantum mechanical study of the tautomeric equilibrium of histamine free-base in solution was performed at the 6-311G level. Electronic correlation energies were included by using the hybrid functional B3LYP. The solvent was simulated as a continuum characterized by a dielectric constant, and the quantum system (solute) was placed in an ellipsoidal cavity. Solute-solvent electrostatic interaction was calculated by means a multipolar moment expansion introduced in the Hamiltonian. Four relevant histamine conformations were optimized by allowing all the geometrical parameters to vary independently, which involved both the gauche-trans and the N3H-N1H tautomerisms. The calculated free energies predicted N3H-gauche as the most stable one of histamine free-base in solution. The order of stability is here completely altered with respect to previous results in gas phase, which presented the N1H-gauche conformer as the most stable structure. Our results also differ from previous Monte Carlo simulations, which obtained the N3H-trans conformer as the most stable in solution, although in this case, the histamine structures were kept frozen to the gas-phase geometry. Vibrational spectroscopy results support theoretical ones. Quadratic force fields for the four histamine conformers were achieved under the same calculation methodology. Previously, a general assignment of the infrared and Raman spectra of histamine free-base was proposed for solutions in both natural and heavy water. This allowed us to compare the experimental set of both wavenumbers and infrared intensities with the calculated ones. The lowest quadratic mean wavenumber deviation was obtained for the N3H-gauche conformer, in agreement with the free-energy calculations. Calculated infrared intensities were also compared to the experimental intensities, supporting this conformer as the relevant structure of histamine free-base in solution. It was then selected for a complete vibrational dynamics calculation, starting with a low-level scaling procedure to fit the set of calculated wavenumbers to the experimental values. The results were presented in terms of quadratic force constants, potential energy distribution, and normal modes. PMID:12590563

Ramírez, F Javier; Tuñón, Iñaki; Collado, Juan A; Silla, Estanislao

2003-02-26

340

On the influence of molecular structure on the conductivity of electrolyte solutions - sodium nitrate in water  

E-print Network

Theoretical calculations of the conductivity of sodium nitrate in water are presented and compared with experimental measurements. The method of direct correlation force in the framework of the interionic theory is used for the calculation of transport properties in connection with the associative mean spherical approximation (AMSA). The effective interactions between ions in solutions are derived with the help of Monte Carlo and Molecular Dynamics calculations on the Born-Oppenheimer level. This work is based on earlier theoretical and experimental studies of the structure of concentrated aqueous sodium nitrate solutions.

H. Krienke

2013-12-16

341

Hilbert Space Structures on the Solution Space of Klein-Gordon Type Evolution Equations  

E-print Network

We use the theory of pseudo-Hermitian operators to address the problem of the construction and classification of positive-definite invariant inner-products on the space of solutions of a Klein-Gordon type evolution equation. This involves dealing with the peculiarities of formulating a unitary quantum dynamics in a Hilbert space with a time-dependent inner product. We apply our general results to obtain possible Hilbert space structures on the solution space of the equation of motion for a classical simple harmonic oscillator, a free Klein-Gordon equation, and the Wheeler-DeWitt equation for the FRW-massive-real-scalar-field models.

Ali Mostafazadeh

2002-09-06

342

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

343

Visualizing Proteins and Macromolecular Complexes by Negative Stain EM: from Grid Preparation to Image Acquisition  

PubMed Central

Single particle electron microscopy (EM), of both negative stained or frozen hydrated biological samples, has become a versatile tool in structural biology 1. In recent years, this method has achieved great success in studying structures of proteins and macromolecular complexes 2, 3. Compared with electron cryomicroscopy (cryoEM), in which frozen hydrated protein samples are embedded in a thin layer of vitreous ice 4, negative staining is a simpler sample preparation method in which protein samples are embedded in a thin layer of dried heavy metal salt to increase specimen contrast 5. The enhanced contrast of negative stain EM allows examination of relatively small biological samples. In addition to determining three-dimensional (3D) structure of purified proteins or protein complexes 6, this method can be used for much broader purposes. For example, negative stain EM can be easily used to visualize purified protein samples, obtaining information such as homogeneity/heterogeneity of the sample, formation of protein complexes or large assemblies, or simply to evaluate the quality of a protein preparation. In this video article, we present a complete protocol for using an EM to observe negatively stained protein sample, from preparing carbon coated grids for negative stain EM to acquiring images of negatively stained sample in an electron microscope operated at 120kV accelerating voltage. These protocols have been used in our laboratory routinely and can be easily followed by novice users. PMID:22215030

Booth, David S.; Avila-Sakar, Agustin; Cheng, Yifan

2011-01-01

344

Structure determination of the seven-helical transmembrane receptor sensory rhodopsin II by solution NMR spectroscopy  

PubMed Central

Seven-helical membrane proteins represent a challenge for structural biology. Here, we report the first NMR structure determination of a detergent-solubilized seven-helical transmembrane (7TM) protein, the phototaxis receptor sensory rhodopsin II (pSRII) from Natronomonas pharaonis, as a proof of principle. The overall quality of the structure ensemble is extremely good (backbone root mean squared deviation of 0.48 Å) and agrees well with previously determined X-ray structures. Furthermore, measurements in more native-like small phospholipid bicelles indicate that the protein structure is the same as in detergent micelles, suggesting that environment specific effects are minimal when using mild detergents. We use our case study as a platform to discuss the feasibility of similar solution NMR studies for other 7TM proteins including members of the family of G protein-coupled receptors (GPCRs). PMID:20512150

Gautier, Antoine; Mott, Helen R.; Bostock, Mark J.; Kirkpatrick, John P.; Nietlispach, Daniel

2010-01-01

345

Solution structure and dynamics of human ubiquitin conjugating enzyme Ube2g2.  

PubMed

Ube2g2 is an E2 enzyme which functions as part of the endoplasmic reticulum-associated degradation (ERAD) pathway responsible for identification and degradation of misfolded proteins in the endoplasmic reticulum. In tandem with a cognate E3 ligase, Ube2g2 assembles K48-linked polyubiquitin chains and then transfers them to substrate, leading ultimately to proteasomal degradation of the polyubiquitin-tagged substrate. We report here the solution structure and backbone dynamics of Ube2g2 solved by nuclear magnetic resonance spectroscopy. Although the solution structure agrees well with crystallographic structures for the E2 core, catalytically important loops (encompassing residues 95-107 and 130-135) flanking the active site cysteine are poorly defined. (15)N spin relaxation and residual dipolar coupling analysis directly demonstrates that these two loops are highly dynamic in solution. These results suggest that Ube2g2 requires one or more of its protein partners, such as cognate E3, acceptor ubiquitin substrate or thiolester-linked donor ubiquitin, to assume its catalytically relevant conformation. Within the NMR structural ensemble, interactions were observed between His94 and the highly mobile loop residues Asp98 and Asp99, supporting a possible role for His94 as a general base activated by the carboxylate side-chains of Asp98 or Asp99. PMID:20014027

Ju, Tingting; Bocik, William; Majumdar, Ananya; Tolman, Joel R

2010-04-01

346

Solution structure and dynamics of human ubiquitin conjugating enzyme Ube2g2  

PubMed Central

Ube2g2 is an E2 enzyme which functions as part of the endoplasmic reticulum-associated degradation (ERAD) pathway responsible for identification and degradation of misfolded proteins in the endoplasmic reticulum. In tandem with a cognate E3 ligase, Ube2g2 assembles K48-linked polyubiquitin chains and then transfers them to substrate, leading ultimately to proteasomal degradation of the polyubiquitin-tagged substrate. We report here the solution structure and backbone dynamics of Ube2g2 solved by nuclear magnetic resonance spectroscopy. Although the solution structure agrees well with crystallographic structures for the E2 core, catalytically important loops (encompassing residues 95-107 and 130-135) flanking the active site cysteine are poorly defined. 15N spin relaxation and residual dipolar coupling analysis directly demonstrates that these two loops are highly dynamic in solution. These results suggest that Ube2g2 requires one or more of its protein partners, such as cognate E3, acceptor ubiquitin substrate or thiolester-linked donor ubiquitin, in order to assume its catalytically relevant conformation. Within the NMR structural ensemble, interactions were observed between His94 and the highly mobile loop residues Asp98 and Asp99, supporting a possible role for His94 as a general base activated by the carboxylate side-chains of Asp98 or Asp99. PMID:20014027

Ju, Tingting; Bocik, William; Majumdar, Ananya; Tolman, Joel R.

2009-01-01

347

The structures of native phosphorylated chicken cystatin and of a recombinant unphosphorylated variant in solution.  

PubMed

The solution structures of the phosphorylated form of native chicken cystatin and the recombinant variant AEF-S1M-M29I-M89L were determined by 2D, 3D and 4D-NMR. The structures turn out to be very similar, despite the substitutions and the phosphorylation of the wild-type. Their dominant feature is a five-stranded beta-sheet, which is wrapped around a five-turn alpha-helix, as shown by X-ray crystallographic studies of wild-type chicken cystatin. However, the NMR analysis shows that the second helix observed in the crystal is not present in solution. The phosphorylation occurs at S80, which is located in a flexible region. For this reason, very few effects on the structure are observed. Comparison of structures of the unphosphorylated variant and the wild-type shows small effects on H84 which is located in the supposed recognition site of the serine kinase. This recognition site appears to be well structured as a large loop-containing bulge of the beta-sheet. The N termini of both mutants, which contribute to a large extent to the binding to the proteinase, are very flexible. A loop structure involving the residues L7 to A10 as found in related inhibitors, such as in the kininogen domains 2 and 3, is not sufficiently populated to be observed. PMID:8263912

Dieckmann, T; Mitschang, L; Hofmann, M; Kos, J; Turk, V; Auerswald, E A; Jaenicke, R; Oschkinat, H

1993-12-20

348

Aromatic moieties in meteoritic macromolecular materials: analyses by hydrous pyrolysis and 13 C of individual compounds  

Microsoft Academic Search

Hydrous pyrolysis, supercritical fluid extraction (SFE), gas chromatography-mass-spectrometry (GC-MS) and isotope ratio monitoring-gas chromatography-mass spectrometry (irm-GC-MS) were used to investigate the constitution of macromolecular materials in meteorites. Results from the carbonaceous chondrites Orgueil (CI1) and Cold Bokkeveld (CM2) were compared with those obtained previously from Murchison (CM2). Fragments of meteoritic macromolecular materials were produced by hydrous pyrolysis, extracted by SFE,

M. A. Sephton; C. T. Pillinger; I. Gilmour

2000-01-01

349

Oligonuclear copper complexes of a bioinspired pyrazolate-bridging ligand: synthesis, structures, and equilibria in solution.  

PubMed

The synthesis of a new bioinspired dinucleating ligand scaffold based on a bridging pyrazolate with appended bis[2-(1-methylimidazolyl)methyl]aminomethyl chelate arms is reported. This ligand forms very stable copper complexes, and a series of different species is present in solution depending on the pH. Interconversions between these solution species are tracked and characterized spectroscopically, and X-ray crystallographic structures of three distinct complexes that correspond to the species present in solution from acidic to basic pH have been determined. Overall, this provides a comprehensive picture of the copper coordination chemistry of the new ligand system. Alterations in the protonation state are accompanied by changes in nuclearity and pyrazolate binding, which cause pronounced changes in color and magnetic properties. Antiferromagnetic coupling between the copper(II) ions is switched on or off depending on the pyrazole binding mode. PMID:17425304

Prokofieva, Angelina; Prikhod'ko, Alexander I; Enyedy, Eva Anna; Farkas, Etelka; Maringgele, Walter; Demeshko, Serhiy; Dechert, Sebastian; Meyer, Franc

2007-05-14

350

Macromolecular and morphological evolution of poly(styrene sulfonate) complexes with tetradecyltrimethylammonium bromide.  

PubMed

Macromolecular characteristics and morphology of water-soluble complexes between sodium poly(styrene sulfonate) (PSS) and tetradecyltrimethylammonium bromide have been followed as a function of surfactant-to-polymer charge ratio (S/P) to elicit possible changes in the complexation mechanism. As revealed by light scattering, shorter PSS (30 and 150 repeat units) yield multichain complexes while longer PSS (450 and 5000 repeat units) form single-chain species throughout 0 < S/P < 0.9. Irrespective of PSS chain length, the complexes exist in solution in a swollen coil conformation and undergo a compaction with S/P but never collapse into a globule. Even when the free PSS chain is too short to coil (30 repeat units), the complexes adopt a coiled conformation due to multichain aggregation. Morphological changes (manifested by a hypochromic shift in UV spectra of the complexes at S/P < 0.5 and an increase in the local surfactant mobility observed at S/P > 0.5 by ESR) strongly suggest a change in the formation mechanism of the complexes with a transition near S/P = 0.5. PMID:22992169

Popov, Alexey; Zakharova, Julia; Wasserman, Alexander; Motyakin, Mikhail; Kasaikin, Victor

2012-10-11

351

Hydrolysis of macromolecular components of primary and secondary wastewater sludge by thermal hydrolytic pretreatment.  

PubMed

A laboratory simulation of the thermal hydrolytic pretreatment (THP) process was performed on wastewater sludge, as well as key macromolecular components: proteins, lipids, and polysaccharides. Hydrolysis temperatures from 130 to 220 degrees C were investigated. The objectives of this study were to determine how and over which temperature range THP specifically affects sludge components, and whether hydrolysis temperature can be used to minimize the previously reported drawbacks of THP such as high total ammonia nitrogen (TAN) loads and the production of highly-colored recalcitrant organics. In addition, the applicability of THP to primary sludge (PS) was investigated. The breakdown of proteins, lipids, and polysaccharides was determined to be temperature dependent, and both waste activated sludge (WAS) and PS responded similarly to THP apart from intrinsic differences in lipid and protein content. Pure carbohydrate solutions were not largely converted to mono- or dimeric reducing sugar units at temperatures below 220 degrees C, however significant caramelization of starch and production of dextrose and maltose was observed to occur at 220 degrees C. Volatile fatty acid production during thermal hydrolysis was largely attributed to the breakdown of unsaturated lipids, and long-chain fatty acid production was not significant in terms of previous reports of methanogenic inhibition. Ammonia was produced from protein during thermal hydrolysis, however solids loading rather than thermal hydrolysis temperature appeared to be a more meaningful control for ammonia levels in downstream anaerobic digestion. PMID:19695659

Wilson, Christopher A; Novak, John T

2009-10-01

352

NMR Solution Structure and Condition-Dependent Oligomerization of the Antimicrobial Peptide Human Defensin 5  

PubMed Central

Human defensin 5 (HD5) is a 32-residue host-defense peptide expressed in the gastrointestinal, reproductive, and urinary tracts that has antimicrobial activity. It exhibits six cysteine residues that are regiospecifically oxidized to form three disulfide bonds (Cys3—Cys31, Cys5—Cys20, and Cys10—Cys30) in the oxidized form (HD5ox). To probe the solution structure and oligomerization properties of HD5ox, and select mutant peptides lacking one or more disulfide bonds, NMR solution studies and analytical ultracentrifugation experiments are reported in addition to in vitro peptide stability assays. The NMR solution structure of HD5ox, solved at pH 4 in 90:10 H2O/D2O, is presented (PDB: 2LXZ). Relaxation T1/T2 measurements and the rotational correlation time (Tc) estimated from a [15N,1H]-TRACT experiment demonstrate that HD5ox is dimeric under these experimental conditions. Exchange broadening of the H? signals in the NMR spectra suggests that residues 19-21 (Val19-Cys20-Glu21) contribute to the dimer interface in solution. Exchange broadening is also observed for residues 7-14 comprising the loop. Sedimentation velocity and equilibrium studies conducted in buffered aqueous solution reveal that the oligomerization state of HD5ox is pH-dependent. Sedimentation coefficients of ca. 1.8 S and a molecular weight of 14,363 Da were determined for HD5ox at pH 7, supporting a tetrameric form ([HD5ox] ? 30 ?M). At pH 2, a sedimentation coefficient of ca. 1.0 S and a molecular weight of 7,079 Da, corresponding to a HD5ox dimer, were obtained. Millimolar concentrations of NaCl, CaCl2, and MgCl2 have negligible effect on the HD5ox sedimentation coefficients in buffered aqueous solution at neutral pH. Removal of a single disulfide bond results in a loss of peptide fold and quaternary structure. These biophysical investigations highlight the dynamic and environment-sensitive behavior of HD5ox in solution, and provide important insights into HD5ox structure/activity relationships and the requirements for antimicrobial action. PMID:23163963

Wommack, Andrew J.; Robson, Scott A.; Wanniarachchi, Yoshitha A.; Wan, Andrea; Turner, Christopher J.; Wagner, Gerhard; Nolan, Elizabeth M.

2012-01-01

353

Theoretical study of mixing energetics in homovalent fluorite-structured oxide solid solutions  

NASA Astrophysics Data System (ADS)

Mixing energies (?Hmix) for fluorite-structured (Zr1-xCex)O2 and (Th1-xCex)O2 solid solutions are computed from density functional theory (DFT), employing cluster-expansion (CE), special-quasirandom-structure (SQS), and continuum-elasticity approaches. These systems are of interest as models for actinide-dioxide mixtures, due to the availability of calorimetric data which allows a direct assessment of the accuracy of the different computational methods for calculating ?Hmix in such fluorite-structured solid solutions. The DFT-based SQS and CE results for solid solutions with random configurational disorder are in very good agreement, and are used along with the calorimetry data to test the accuracy of a linear-elasticity model which allows predictions of the ?Hmix under the assumption that the dominant contribution in these homovalent solid solutions arises from elastic strain energy. The linear-elasticity models describe the mixing energies to within an accuracy of approximately 2 and 0.1 kJ/mol for the Zr and Th based systems, respectively. The excellent accuracy for the ThO2-based system is interpreted to result from the smaller size mismatch, and corresponding high accuracy of the linear elasticity approximation. We thus apply elasticity theory to estimate the magnitudes of ?Hmix for (Th1-xMx)O2 and (U1-xMx)O2 actinide-dioxide solid solutions, with M = U, Th, Ce, Np, Pu and Am, for which the degree of size mismatch is comparable to that in (Th1-xCex)O2; the results yield elastic contributions to ?Hmix with a maximum magnitude of 3 kJ/mol.

Alexandrov, Vitaly; Grønbech-Jensen, Niels; Navrotsky, Alexandra; Asta, Mark

2014-01-01

354

The local structure of Pd(x)Ce(1-x)O(2-x-?) solid solutions.  

PubMed

PdxCe1-xO2-x-? solid solutions, which are highly efficient catalysts for the low-temperature oxidation of carbon monoxide, were examined using a set of structural (XRD-PDF, HRTEM, XRD) and spectral (XPS, Raman spectroscopy) methods in combination with quantum-chemical calculations. A comparison of the experimental results and pair distribution function (PDF) modeling data enabled reliable verification of the model of non-isomorphic substitution of Ce(4+) ions by Pd(2+) ions in PdxCe1-xO2-x-? solid solutions. Palladium ions were shown to be in a near square planar environment with C4v symmetry, which is typical for Pd(2+) ions. Such a near square planar environment was revealed by Raman spectroscopy due to the appearance of the band at ? = 187 cm(-1), which corresponds to the A1 vibrational mode of Pd(2+) ions in [PdO4] subunits. The binding energy of Pd3d5/2 (Eb(Pd3d5/2)) for the Pd(2+) ion in the CeO2 lattice is 1 eV higher than that of Eb(Pd3d5/2) for PdO oxide due to a decrease in the Pd-O distances and the formation of more ionic bonds because of the displacement of Pd(2+) ions with respect to the position of Ce(4+) ions in the fluorite structure. Five structural models of solid solutions are considered in this work. As demonstrated by the DFT calculations, the most realistic model is based on the displacement of palladium ions leading to a near square planar PdO4 environment, which includes water molecules stabilizing the region of anion vacancies in their dissociated state as two hydroxyl groups. The introduction of water molecules in the composition of the PdxCe1-xO2-x-? solution leads to a decrease in the formation energy and to additional stabilization of palladium in the CeO2 matrix. The formation of PdxCe1-xO2-x-? solid solutions is accompanied by the dispersing effect caused by distortions of the fluorite structure induced by Pd(2+) ions. The coprecipitation method, which allows Pd(2+) ions to be introduced at the stage of fluorite structure formation, was demonstrated to be the optimal method for the synthesis of a homogeneous PdxCe1-xO2-x-? solid solution. PMID:24894189

Gulyaev, R V; Kardash, T Yu; Malykhin, S E; Stonkus, O A; Ivanova, A S; Boronin, A I

2014-07-14

355

Solution structures of purine base analogues 6-chloroguanine, 8-azaguanine and allopurinol.  

PubMed

Analogues of purine bases are highly relevant in the biological context and have been implicated as drug molecules for therapy against a number of diseases. Additionally, these molecules have been implicated to have a role in the prebiotic RNA world. However, experimental data on the structures of these molecules in aqueous solution is lacking. In this work, we report the ultraviolet resonance Raman spectra of 6-chloroguanine, 8-azaguanine and allopurinol, obtained with 260?nm excitation. The reported spectra have been assigned to normal modes computed from density functional theory (B3LYP/6-31G (d,p)) calculations. This work has been useful in identifying the solution-state structures of these molecules at neutral pH. We find that the guanine analogues 6-chloroguanine and 8-azaguanine exist as keto-N9H and keto-N7H tautomers in solution, respectively. On the other hand, the hypoxanthine analogue allopurinol exists as a mixture of keto-N9H and keto-N8H tautomers in solution. We predict that this work would be particularly useful in future vibrational studies where these molecules are present in complexes with their target proteins. PMID:23384120

Gogia, Spriha; Puranik, Mrinalini

2014-01-01

356

Structure and growth of bis(2-ethylhexyl) sulfosuccinate micelles in aqueous solutions  

SciTech Connect

The structure and growth of micelles formed by anionic surfactant sodium bis(2-ethylhexyl) sulfosuccinate (AOT) in aqueous solutions have been studied by small angle neutron scattering (SANS). They used the contrast variation technique to determine the aggregation number, the effective charge, and two molecular parameters of the micelles in solutions of 0.8 g/dL surfactant concentration. They then used these two molecular parameters to analyze micellar solutions at other concentrations. Two micellar parameters, the mean aggregation number n and the effective charge z0, have been extracted from experimental data for solutions with surfactant concentrations ranging from 0.2 to 1.0 g/dL. The minimum micellar aggregation number is predicted to be 15 at the critical micellar concentration (cmc) and the structure is a compact spherical aggregate having well-defined hydrophobic and hydrophilic regions. The micelles grow moderately as the surfactant concentration increases, transforming from a spherical to an oblate spheroidal shape in a manner describable by the ladder model.

Sheu, E.Y.; Chen, S.; Huang, J.S.

1987-06-04

357

Numerical Solutions and Structures of Double Quantum Jet Solving by an Upwind Scheme  

NASA Astrophysics Data System (ADS)

The solutions of a double quantum jet are analyzed by solving the quantum fluid dynamical formulation (QFD) of the Schr"odinger equation. The QFD equations are obtained by expressing the Schr"odinger wave function as =?^1/2(iS/)and u=(u,v). In QFD, Q=-?-1/2??^1/2 is called as quantum potential. An upwind method is developed to solve the QFD equations. The method use a third-order upwind method to discrete convection terms and the central finite difference method to discrete the quantum potential. A fourth-order Runge-Kutta method is used for time marching. Two cases, one-dimensional free particle with external potential and two-dimensional free particle with external potential, are presented to illustrate the accuracy of the QFD solver. The computational results are compared well with the results obtained by solving the Schr"odinger equation. Finally, the QFD solver is applied to solve the solutions of a double quantum jet and to investigate its structures. First, a mathematical formulation is derived to describe the double quantum jet. The jet has the probability density equals 2 and the velocity equals 2 at the inlet of the jet. Then, the solutions are computed by the QFD solver. The structures of the solutions are affected by the strength of the quantum potential. The interesting phenomena of quantum clustering are found.

Lin, San-Yih

2005-11-01

358

Solution spectroelectrochemical cell for in situ X-ray absorption fine structure  

SciTech Connect

A purpose-built spectroelectrochemical cell for in situ fluorescence XAFS (X-ray Absorption Fine Structure) measurements of bulk solution species during constant-potential electrolysis is described. The cell performance was demonstrated by the collection of europium L{sub 3}-edge XANES (X-ray Absorption Near Edge Structure) throughout the course of electrolysis of an aqueous solution of EuCl{sub 3}{center_dot}6H{sub 2}O in 1 M H{sub 2}SO{sub 4}. The europium L{sub 3}-edge resonances reported here for the Eu{sup III} and Eu{sup II} ions demonstrate that their 2p{sub 3/2} {yields} 5d electronic transition probabilities are not the same.

Antonio, M.R.; Soderholm, L. [Argonne National Lab., IL (United States). Chemistry Div.; Song, I. [Case Western Reserve Univ., Cleveland, OH (United States)

1995-06-12

359

AR-NE3A, a New Macromolecular Crystallography Beamline for Pharmaceutical Applications at the Photon Factory  

SciTech Connect

Recent advances in high-throughput techniques for macromolecular crystallography have highlighted the importance of structure-based drug design (SBDD), and the demand for synchrotron use by pharmaceutical researchers has increased. Thus, in collaboration with Astellas Pharma Inc., we have constructed a new high-throughput macromolecular crystallography beamline, AR-NE3A, which is dedicated to SBDD. At AR-NE3A, a photon flux up to three times higher than those at existing high-throughput beams at the Photon Factory, AR-NW12A and BL-5A, can be realized at the same sample positions. Installed in the experimental hutch are a high-precision diffractometer, fast-readout, high-gain CCD detector, and sample exchange robot capable of handling more than two hundred cryo-cooled samples stored in a Dewar. To facilitate high-throughput data collection required for pharmaceutical research, fully automated data collection and processing systems have been developed. Thus, sample exchange, centering, data collection, and data processing are automatically carried out based on the user's pre-defined schedule. Although Astellas Pharma Inc. has a priority access to AR-NE3A, the remaining beam time is allocated to general academic and other industrial users.

Yamada, Yusuke; Hiraki, Masahiko; Sasajima, Kumiko; Matsugaki, Naohiro; Igarashi, Noriyuki; Kikuchi, Takashi; Mori, Takeharu; Toyoshima, Akio; Kishimoto, Shunji; Wakatsuki, Soichi [Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba, Ibaraki, 305-0801 (Japan); Amano, Yasushi; Warizaya, Masaichi; Sakashita, Hitoshi [Drug Discovery Research, Astellas Pharma Inc., 21, Miyukigaoka, Tukuba, Ibaraki, 300-8585 (Japan)

2010-06-23

360

Macromolecular crowding: chemistry and physics meet biology (Ascona, Switzerland, 10-14 June 2012)  

NASA Astrophysics Data System (ADS)

More than 60 years of biochemical and biophysical studies have accustomed us to think of proteins as highly purified entities that act in isolation, more or less freely diffusing until they find their cognate partner to bind to. While in vitro experiments that reproduce these conditions largely remain the only way to investigate the intrinsic properties of molecules, this approach ignores an important factor: in their natural milieu , proteins are surrounded by several other molecules of different chemical nature, and this crowded environment can considerably modify their behaviour. About 40% of the cellular volume on average is occupied by all sorts of molecules. Furthermore, biological macromolecules live and operate in an extremely structured and complex environment within the cell (endoplasmic reticulum, Golgi apparatus, cytoskeletal structures, etc). Hence, to further complicate the picture, the interior of the cell is by no means a simply crowded medium, rather, a most crowded and confining one. In recent times, several approaches have been developed in the attempt to take into account important factors such as the ones mentioned above, at both theoretical and experimental levels, so that this field of research is now emerging as one of the most thriving in molecular and cell biology (see figure 1). Figure 1. Figure 1. Left: number of articles containing the word 'crowding' as a keyword limited to the biological and chemical science domains (source: ISI Web of Science). The arrow flags the 2003 'EMBO Workshop on Biological Implications of Macromolecular Crowding' (Embo, 2012). Right: number of citations to articles containing the word 'crowding' limited to the same domains (bars) and an exponential regression curve (source: Elsevier Scopus). To promote the importance of molecular crowding and confinement and provide researchers active in this field an interdisciplinary forum for meeting and exchanging ideas, we recently organized an international conference held in Ascona from 10 to 14 June 2012. In the unique scenario of the Maggiore lake and absorbed in the magic atmosphere of the Centro Stefano Franscini (CSF) at Monte Verità, we enjoyed three-and-a-half days of intense and inspiring activity, where not only many of the most prominent scientists working on macromolecular crowding, but also experts in closely related fields such as colloids and soft matter presented their work. The meeting was intended and has been organized to bring theoreticians and experimentalists together in the attempt to promote an active dialogue. Moreover, we wanted different disciplines to be represented, notably physics and chemistry, besides biology, as cross-fertilization is proving an increasingly fundamental source of inspiration and advancement. This issue of Physical Biology (PB) features a selection of the oral contributions presented at the conference, expanded in the form of research or review articles. PB, one of the scientific journals of the Institute of Physics (IOP), is one of the most dynamic and lively forums active at the interface between biology on one side, and physics and mathematics on the other. As its mission is stated by IOP, PB 'focuses on research in which physics-based approaches lead to new insights into biological systems at all scales of space and time, and all levels of complexity'. For these reasons, and also in view of its high reputation and broad readership, PB appears to be the ideal place for disseminating the thriving pieces of research presented at the conference. We are extremely grateful to PB and its kind and efficient editorial staff who helped make this issue a great scientific follow-up to the conference. The opening lecture of the conference, the first of four day-opening keynote lectures, was given by Allen P Minton from NIH (USA), possibly the most influential among the pioneers in the field. He provided a lucid and well-thought-out overview of the concept of macromolecular crowding through an exhaustive chronological account of the major milestones. It is clear that the concept of excl

Foffi, G.; Pastore, A.; Piazza, F.; Temussi, P. A.

2013-08-01

361

Direct Observation of Protein Unfolded State Compaction in the Presence of Macromolecular Crowding  

PubMed Central

Proteins fold and function in cellular environments that are crowded with other macromolecules. As a consequence of excluded volume effects, compact folded states of proteins should be indirectly stabilized due to destabilization of extended unfolded conformations. Here, we assess the role of excluded volume in terms of protein stability, structural dimensions and folding dynamics using a sugar-based crowding agent, dextran 20, and the small ribosomal protein S16 as a model system. To specifically address dimensions, we labeled the protein with BODIPY at two positions and measured Trp-BODIPY distances under different conditions. As expected, we found that dextran 20 (200 mg/ml) stabilized the variants against urea-induced unfolding. At conditions where the protein is unfolded, Förster resonance energy transfer measurements reveal that in the presence of dextran, the unfolded ensemble is more compact and there is residual structure left as probed by far-ultraviolet circular dichroism. In the presence of a crowding agent, folding rates are faster in the two-state regime, and at low denaturant concentrations, a kinetic intermediate is favored. Our study provides direct evidence for protein unfolded-state compaction in the presence of macromolecular crowding along with its energetic and kinetic consequences. PMID:23442920

Mikaelsson, Therese; Aden, Jorgen; Johansson, Lennart B.-A.; Wittung-Stafshede, Pernilla

2013-01-01

362

Solution Structure of the Integral Human Membrane Protein VDAC-1 in Detergent Micelles  

Microsoft Academic Search

The voltage-dependent anion channel (VDAC) mediates trafficking of small molecules and ions across the eukaryotic outer mitochondrial membrane. VDAC also interacts with antiapoptotic proteins from the Bcl-2 family, and this interaction inhibits release of apoptogenic proteins from the mitochondrion. We present the nuclear magnetic resonance (NMR) solution structure of recombinant human VDAC-1 reconstituted in detergent micelles. It forms a 19-stranded

Sebastian Hiller; Robert G. Garces; Thomas J. Malia; Vladislav Y. Orekhov; Marco Colombini; Gerhard Wagner

2008-01-01

363

Intramolecular Structural Change of PAMAM Dendrimers in Aqueous Solutions Revealed by Small Angle Neutron Scattering  

Microsoft Academic Search

Small-angle neutron scattering (SANS) experiments were carried out to investigate the structure of aqueous (D2O) G4 PAMAM dendrimer solutions as a function of molecular protonation and dendrimer concentration. Our results indicate unambiguously that, although the radius of gyration RG remains nearly invariant, the dendrimer radial density profile (r) decreases in the dendrimer core with a continuous increase in protonation. This

L. Porcar; Kunlun Hong; Paul D Butler; Kenneth W Herwig; Gregory Scott Smith; Yun Liu; Wei-Ren Chen

2010-01-01

364

Analytical Solution for the Bending of a Plate on a Functionally Graded Layer of Complex Structure  

Microsoft Academic Search

\\u000a The problem of interaction between an asymmetrically loaded thin circular plate and a supporting elastic foundation is reduced\\u000a to the solution of system of the dual integral equations for the unknown normal contact pressure and differential equation\\u000a of plate bending. The supporting medium is an isotropic elastic functionally graded layer of complex structure of constant\\u000a thickness lying, with or without

Sergey Aizikovich; Andrey Vasiliev; Igor Sevostianov; Irina Trubchik; Ludmila Evich; Elena Ambalova

365

Insight into the Structure of Light Harvesting Complex II and its Stabilization in Detergent Solution  

Microsoft Academic Search

The structure of spinach light-harvesting complex II (LHC II), stabilized in a solution of the detergent n-octyl--d-glucoside (BOG), was investigated by small-angle neutron scattering (SANS). Physicochemical characterization of the isolated complex indicated that it was pure (>95%) and also in its native trimeric state. SANS with contrast variation was used to investigate the properties of the protein-detergent complex at three

Mateus B. Cardoso; Dmitriy Smolensky; William T. Heller; Hugh Michael ONeill

2009-01-01

366

Formation of [b (n?1) +OH+H] + ion structural analogs by solution-phase chemistry  

Microsoft Academic Search

Derivatization of a variety of peptides by a method known to enhance anhydride formation is demonstrated by mass spectrometry\\u000a to yield ions that have elemental composition and fragmentation properties identical to [b(n?1)+OH +H]+ ions formed by gas-phase rearrangement and fragmentation. The [b(n?1) +OH +H]+ ions formed by gas-phase rearrangement and fragmentation and the solution-phase [b(n?1) +OH +H]+ ion structural analogs

Joshua S. Sharp; Kenneth B. Tomer

2005-01-01

367

NMR solution structures of adducts derived from the binding of polycyclic aromatic diol epoxides to DNA  

SciTech Connect

Site-specifically modified oligonucleotides were derived from the reactions of stereoisomeric polycyclic aromatic diol epoxide metabolite model compounds with oligonucleotides of defined base composition and sequence. The NMR solution structures of ten different adducts studied so far are briefly described, and it is shown that stereochemical factors and the nature of the oligonucleotide context of the complementary strands, exert a powerful influence on the conformational features of these adducts.

Cosman, M.; Patel, D.J. [Memorial Sloan Kettering Cancer Center, New York, NY (United States). Cellular Biochemistry and Biophysics Program; Hingerty, B.E. [Oak Ridge National Lab., TN (United States). Health and Safety Research Div.; Amin, S. [American Health Foundation, Valhalla, NY (United States); Broyde, S.; Geacintov, N.E. [New York Univ., NY (United States)

1995-12-31

368

Water molecules effect on pure Ti passive film structure in methanol solution  

NASA Astrophysics Data System (ADS)

To understand the role of water on titanium SCC properties in methanol solutions, composition and structure of the passive film were studied using X-ray photoelectron and electrochemical impedance spectroscopies. The passive film consists of the inner compact layer and a porous outer layer. The inner layer thickness is less than 4 nm and decreases with the increasing water content. Water improves the passive film properties, thus changes SCC susceptibility by altering the hydrogen bonding of methanol and reacting with titanium preferentially.

Qin, Zhi; Pang, Xiaolu; Qiao, Lijie; Khodayari, Mehdi; Volinsky, Alex A.

2014-06-01

369

Solution structure of the bacterial chemotaxis adaptor protein CheW from Escherichia coli  

Microsoft Academic Search

The bacterial chemotaxis adaptor protein CheW physically links the chemoreceptors (MCPs) and the histidine kinase CheA. Extensive investigations using bacterium Escherichia coli have established the central role of CheW in the MCP-modulated activation of CheA. Here we report the solution structure of CheW from E. coli determined by NMR spectroscopy. The results show that E. coli CheW shares an overall

You Li; Yunfei Hu; Wenyu Fu; Bin Xia; Changwen Jin

2007-01-01

370

Effective protein-protein interaction from structure factor data of a lysozyme solution  

SciTech Connect

We report the determination of an effective protein-protein central potential for a lysozyme solution, obtained from the direct inversion of the total structure factor of the system, as extracted from small angle neutron scattering. The inversion scheme rests on a hypernetted-chain relationship between the effective potential and the structural functions, and is preliminarily tested for the case of a Lennard-Jones interaction. The characteristics of our potential are discussed in comparison with current models of effective interactions in complex fluids. The phase behavior predictions are also investigated.

Abramo, M. C.; Caccamo, C.; Costa, D.; Ruberto, R.; Wanderlingh, U. [Dipartimento di Fisica e di Scienze della Terra, Università degli Studi di Messina and CNISM (Consorzio Nazionale Interuniversitario di Struttura della Materia) Viale F. Stagno d'Alcontres 31, 98166 Messina (Italy)] [Dipartimento di Fisica e di Scienze della Terra, Università degli Studi di Messina and CNISM (Consorzio Nazionale Interuniversitario di Struttura della Materia) Viale F. Stagno d'Alcontres 31, 98166 Messina (Italy); Cavero, M. [School of Chemistry and Physics, University of Kwazulu-Natal, Private Bag X01, Scottsville 3209, Pietermaritzburg (South Africa)] [School of Chemistry and Physics, University of Kwazulu-Natal, Private Bag X01, Scottsville 3209, Pietermaritzburg (South Africa); Pellicane, G. [School of Chemistry and Physics, University of Kwazulu-Natal, Private Bag X01, Scottsville 3209, Pietermaritzburg (South Africa) [School of Chemistry and Physics, University of Kwazulu-Natal, Private Bag X01, Scottsville 3209, Pietermaritzburg (South Africa); National Institute for Theoretical Physics (NITheP), KZN node, Pietermaritzburg (South Africa)

2013-08-07

371

Effective protein-protein interaction from structure factor data of a lysozyme solution  

NASA Astrophysics Data System (ADS)

We report the determination of an effective protein-protein central potential for a lysozyme solution, obtained from the direct inversion of the total structure factor of the system, as extracted from small angle neutron scattering. The inversion scheme rests on a hypernetted-chain relationship between the effective potential and the structural functions, and is preliminarily tested for the case of a Lennard-Jones interaction. The characteristics of our potential are discussed in comparison with current models of effective interactions in complex fluids. The phase behavior predictions are also investigated.

Abramo, M. C.; Caccamo, C.; Cavero, M.; Costa, D.; Pellicane, G.; Ruberto, R.; Wanderlingh, U.

2013-08-01

372

Reversible pressure-induced structure changes in turbostratic BN-C solid solutions.  

PubMed

The results obtained by Rietveld analysis and numerical modeling of B-C-N layered clusters with various types of lattice defects explain the evolution of diffraction patterns of turbostratic graphite-like BN-C solid solutions which are experimentally observed at room temperature at pressures up to 30 GPa. Above 20 GPa a reversible diffusionless transformation of the initial turbostratic structure takes place, giving a high-pressure phase formed by close-packed buckled layers having a diamond-like structure. PMID:16186650

Solozhenko, Vladimir L; Kurakevych, Oleksandr O

2005-10-01

373

Nuclear Magnetic Dipole Interactions in Field-Oriented Proteins: Information for Structure Determination in Solution  

NASA Astrophysics Data System (ADS)

The measurement of dipolar contributions to the splitting of 15N resonances of ^1H-15N amide pairs in multidimensional high-field NMR spectra of field-oriented cyanometmyoglobin is reported. The splittings appear as small field-dependent perturbations of normal scalar couplings. Assignment of more than 90 resonances to specific sequential sites in the protein allows correlation of the dipolar contributions with predictions based on the known susceptibility and known structure of the protein. Implications as an additional source of information for protein structure determination in solution are discussed.

Tolman, J. R.; Flanagan, J. M.; Kennedy, M. A.; Prestegard, J. H.

1995-09-01

374

Nuclear magnetic dipole interactions in field-oriented proteins: information for structure determination in solution.  

PubMed Central

The measurement of dipolar contributions to the splitting of 15N resonances of 1H-15N amide pairs in multidimensional high-field NMR spectra of field-oriented cyanometmyoglobin is reported. The splittings appear as small field-dependent perturbations of normal scalar couplings. Assignment of more than 90 resonances to specific sequential sites in the protein allows correlation of the dipolar contributions with predictions based on the known susceptibility and known structure of the protein. Implications as an additional source of information for protein structure determination in solution are discussed. PMID:7568117

Tolman, J R; Flanagan, J M; Kennedy, M A; Prestegard, J H

1995-01-01

375

Molecular structure of dibenzoylmethylphosphonyl-14-crown-5 in the crystalline state and in solution  

SciTech Connect

Progress in the chemistry of synthetic macrocyclic compounds has been related to the use of these compounds as complexing agents. The phosphoryl group has significant electron-donor properties. Thus, interest is found in the study of the structures of macrocyclic compounds containing the phosphoryl group. In the authors previous work, they studied dibenzoadamantylphosphonyl-17-crown-6 (I) and dibenzomethylphosphonyl-20-crown-7 (II) in the crystalline state and in solution. In the present communication, results are given for a structural study of dibenzomethylphosphonyl-14-crown-5 (III) by means of x-ray diffraction structural analysis and dipole moment (DM) measurements. The atom-atom potential method was used for calculating the energy of the nonbonding interactions of the macrocycle atoms. The three-dimensional structures of (I)-(III) were considered relative to the ionophore and antiarrhythmic properties established for these compounds in their previous work.

Raevskii, O.A.; Umarova, I.O.; Tkachev, V.V.; Atovmyan, L.O.; Shtepanek, A.S.; Kudrya, T.N.

1987-03-10

376

Thorium nanochemistry: the solution structure of the Th(IV)?hydroxo pentamer  

SciTech Connect

Tetravalent thorium exhibits a strong tendency towards hydrolysis and subsequent polymerization. Polymeric species play a crucial role in understanding thorium solution chemistry, since their presence causes apparent solubility several orders of magnitude higher than predicted by thermodynamic data bases. Although electrospray mass spectrometry (ESI MS) identifies Th(IV) dimers and pentamers unequivocally as dominant species close to the solubility limit, the molecular structure of Th{sub 5}(OH){sub y} polymers was hitherto unknown. In the present study, X-ray absorption fine structure (XAFS) spectroscopy, high energy X-ray scattering (HEXS) measurements, and quantum chemical calculations are combined to solve the pentamer structure. The most favourable structure is represented by two Th(IV) dimers linked by a central Th(IV) cation through hydroxide bridges.

Walther, Clemens; Rothe, Jörg; Schimmelpfennig, Bernd; Fuss, Markus (Karlsruher)

2012-10-10

377

The cytoplasmic cage domain of the mechanosensitive channel MscS is a sensor of macromolecular crowding  

PubMed Central

Cells actively regulate the macromolecular excluded volume of the cytoplasm to maintain the reciprocal fraction of free aqueous solution that is optimal for intracellular processes. However, the mechanisms whereby cells sense this critical parameter remain unclear. The mechanosensitive channel of small conductance (MscS channel), which is the major regulator of turgor in bacteria, mediates efflux of small osmolytes in response to increased membrane tension. At moderate sustained tensions produced by a decrease in external osmolarity, MscS undergoes slow adaptive inactivation; however, it inactivates abruptly in the presence of cytoplasmic crowding agents. To understand the mechanism underlying this rapid inactivation, we combined extrapolated and equilibrium molecular dynamics simulations with electrophysiological analyses of MscS mutants to explore possible transitions of MscS and generated models of the resting and inactivated states. Our models suggest that the coupling of the gate formed by TM3 helices to the peripheral TM1–TM2 pairs depends on the axial position of the core TM3 barrel relative to the TM1–TM2 shaft and the state of the associated hollow cytoplasmic domain (“cage”). They also indicate that the tension-driven inactivation transition separates the gate from the peripheral helices and promotes kinks in TM3s at G113 and that this conformation is stabilized by association of the TM3b segment with the ? domain of the cage. We found that mutations destabilizing the TM3b–? interactions preclude inactivation and make the channel insensitive to crowding agents and voltage; mutations that strengthen this association result in a stable closed state and silent inactivation. Steered simulations showed that pressure exerted on the cage bottom in the inactivated state reduces the volume of the cage in the cytoplasm and at the same time increases the footprint of the transmembrane domain in the membrane, implying coupled sensitivity to both membrane tension and crowding pressure. The cage, therefore, provides feedback on the increasing crowding that disengages the gate and prevents excessive draining and condensation of the cytoplasm. We discuss the structural mechanics of cells surrounded by an elastic cell wall where this MscS-specific feedback mechanism may be necessary. PMID:24778428

Rowe, Ian; Anishkin, Andriy; Kamaraju, Kishore; Yoshimura, Kenjiro

2014-01-01

378

Structure and dimerization of translation initiation factor aIF5B in solution  

SciTech Connect

Translation initiation factor 5B (IF5B) is required for initiation of protein synthesis. The solution structure of archaeal IF5B (aIF5B) was analysed by small-angle X-ray scattering (SAXS) and dynamic light scattering (DLS) and was indicated to be in both monomeric and dimeric form. Sedimentation equilibrium (SE) analytical ultracentrifugation (AUC) of aIF5B indicated that aIF5B forms irreversible dimers in solution but only to a maximum of 5.0-6.8% dimer. Sedimentation velocity (SV) AUC at higher speed also indicated the presence of two species, and the sedimentation coefficients s{sub 20,w}{sup 0} were determined to be 3.64 and 5.51 {+-} 0.29 S for monomer and dimer, respectively. The atomic resolution (crystallographic) structure of aIF5B (Roll-Mecak et al. [6]) was used to model monomer and dimer, and theoretical sedimentation coefficients for these models were computed (3.89 and 5.63 S, respectively) in good agreement with the sedimentation coefficients obtained from SV analysis. Thus, the structure of aIF5B in solution must be very similar to the atomic resolution structure of aIF5B. SAXS data were acquired in the same buffer with the addition of 2% glycerol to inhibit dimerization, and the resultant monomeric aIF5B in solution did indeed adopt a structure very similar to the one reported earlier for the protein in crystalline form. The p(r) function indicated an elongated conformation supported by a radius of gyration of 37.5 {+-} 0.2 {angstrom} and a maximum dimension of {approx}130 {angstrom}. The effects of glycerol on the formation of dimers are discussed. This new model of aIF5B in solution shows that there are universal structural differences between aIF5B and the homologous protein IF2 from Escherichia coli.

Carø VohlanderRasmussen, Louise; Oliveira, Cristiano Luis Pinto; Byron, Olwyn; Jensen, Janni Mosgaard; Pedersen, Jan Skov; Sperling-Petersen, Hans Uffe; Mortensen, Kim Kusk (Aarhus); (Glasgow)

2012-02-07

379

Solution structure studies of monomeric human TIP47/perilipin-3 reveal a highly extended conformation  

PubMed Central

Tail-interacting protein of 47 kDa (TIP47) has two putative functions: lipid biogenesis and mannose 6-phosphate receptor recycling. Progress in understanding the molecular details of these two functions has been hampered by the lack of structural data on TIP47, with a crystal structure of the C-terminal domain of the mouse homologue constituting the only structural data in the literature so far. Our studies have first provided a strategy to obtain pure monodisperse preparations of the full-length TIP47/perilipin-3 protein, as well as a series of N-terminal truncation mutants with no exogenous sequences. These constructs have then enabled us to obtain the first structural characterization of the full-length protein in solution. Our work demonstrates that the N-terminal region of TIP47/perilipin-3, in contrast to the largely helical C-terminal region, is predominantly ?-structure with turns and bends. Moreover, we show that full-length TIP47/perilipin-3 adopts an extended conformation in solution, with considerable spatial separation of the N- and C-termini that would likely translate into a separation of functional domains. PMID:22508559

Hynson, Robert M. G.; Jeffries, Cy M.; Trewhella, Jill; Cocklin, Simon

2012-01-01

380

A Method for Solution NMR Structural Studies of Large Integral Membrane Proteins: Reverse Micelle Encapsulation  

PubMed Central

The structural study of membrane proteins perhaps represents one of the greatest challenges of the post-genomic era. While membrane proteins comprise over 50% of current and potential drug targets, their structural characterization lags far behind that of soluble proteins. Nuclear magnetic resonance (NMR) offers great potential not only with respect to structural characterization of integral membrane proteins but may also provide the ability to study the details of small ligand interactions. However, the size limitations of solution NMR have restricted comprehensive structural characterization of membrane protein NMR structures to the relatively small ?-barrel proteins or helical proteins of relatively simple topology. In an effort to escape the barriers presented by slow molecular reorientation of large integral membrane proteins solubilized by detergent micelles in water, we have adapted the reverse micelle encapsulation strategy originally developed for the study of large soluble proteins by solution NMR methods. Here we review a novel approach to the solubilization of large integral membrane proteins in reverse micelle surfactants dissolved in low viscosity alkane solvents. The procedure is illustrated with a 54 kDa construct of the homotetrameric KcsA potassium channel. PMID:19665988

Kielec, Joseph M.; Valentine, Kathleen G.; Wand, A. Joshua

2009-01-01

381

Solution structure and calcium-binding properties of EF-hands 3 and 4 of calsenilin  

PubMed Central

Calsenilin is a member of the recoverin branch of the EF-hand superfamily that is reported to interact with presenilins, regulate prodynorphin gene expression, modulate voltage-gated Kv4 potassium channel function, and bind to neurotoxins. Calsenilin is a Ca+2-binding protein and plays an important role in calcium signaling. Despite its importance in numerous neurological functions, the structure of this protein has not been reported. In the absence of Ca+2, the protein has limited spectral resolution that increases upon the addition of Ca+2. Here, we describe the three-dimensional solution structure of EF-hands 3 and 4 of calsenilin in the Ca+2-bound form. The Ca+2-bound structure consists of five ?-helices and one two-stranded antiparallel ?-sheet. The long loop that connects EF hands 3 and 4 is highly disordered in solution. In addition to its structural effects, Ca+2 binding also increases the protein's propensity to dimerize. These changes in structure and oligomerization state induced upon Ca+2 binding may play important roles in molecular recognition during calcium signaling. PMID:17962406

Yu, Liping; Sun, Chaohong; Mendoza, Renaldo; Wang, Jie; Matayoshi, Edmund D.; Hebert, Eric; Pereda-Lopez, Ana; Hajduk, Philip J.; Olejniczak, Edward T.

2007-01-01

382

Solution structure of the extraterminal domain of the bromodomain-containing protein BRD4  

PubMed Central

BRD4, which is a member of the BET (bromodomains and extraterminal) protein family, interacts preferentially with acetylated chromatin and possesses multiple cellular functions in meiosis, embryonic development, the cell cycle, and transcription. BRD4 and its family members contain two bromodomains known to bind acetylated lysine, and a conserved ET domain whose function is unclear. Here we show the solution structure of the ET domain of mouse BRD4, which provides the first three-dimensional structure of an ET domain in the BET family. We determined the NMR structure of BRD4-ET with a root-mean-square deviation of 0.41 Å for the backbone atoms in the structured region of residues 608–676 on the basis of 1793 upper distance limits derived from NOE intensities measured in three-dimensional NOESY spectra. The structure of the BRD4-ET domain comprises three ?-helices and a characteristic loop region of an irregular but well-defined structure. A DALI search revealed no close structural homologs in the current Protein Data Bank. The BRD4-ET structure has an acidic patch that forms a continuous ridge with a hydrophobic cleft, which may interact with other proteins and/or DNA. PMID:18815416

Lin, Yi-Jan; Umehara, Takashi; Inoue, Makoto; Saito, Kohei; Kigawa, Takanori; Jang, Moon-Kyoo; Ozato, Keiko; Yokoyama, Shigeyuki; Padmanabhan, Balasundaram; Guntert, Peter

2008-01-01

383

Electronic structure of hemin in solution studied by resonant X-ray emission spectroscopy and electronic structure calculations.  

PubMed

Resonant inelastic X-ray scattering spectra at the iron L-edge from hemin in dimethyl sulfoxide liquid solution are reported. Our experiments, which are interpreted with the help of electronic structure calculations, support earlier assignments of hemin-solvent interactions, including the iron spin state and the role of the chloride ligand obtained from a total fluorescence yield study. The analysis of the explicit radiative relaxation channels of 2p core-level excited iron, explored in the present work, allows for a rather quantitative assignment of the orbitals involved in the excitation-deexcitation process of the core-excited hemin in solution. We specifically distinguish between contributions of partially and fully occupied valence orbitals to the broad X-ray emission band. In addition, our calculations reveal a detailed picture of the character of these orbitals. PMID:25068599

Atak, Kaan; Golnak, Ronny; Xiao, Jie; Suljoti, Edlira; Pflüger, Mika; Brandenburg, Tim; Winter, Bernd; Aziz, Emad F

2014-08-21

384

Quantitative influence of macromolecular crowding on gene regulation kinetics.  

PubMed

We introduce macromolecular crowding quantitatively into the model for kinetics of gene regulation in Escherichia coli. We analyse and compute the specific-site searching time for 180 known transcription factors (TFs) regulating 1300 operons. The time is between 160 s (e.g. for SoxS Mw = 12.91 kDa) and 1550 s (e.g. for PepA6 of Mw = 329.28 kDa). Diffusion coefficients for one-dimensional sliding are between for large proteins up to for small monomers or dimers. Three-dimensional diffusion coefficients in the cytoplasm are 2 orders of magnitude larger than 1D sliding coefficients, nevertheless the sliding enhances the binding rates of TF to specific sites by 1-2 orders of magnitude. The latter effect is due to ubiquitous non-specific binding. We compare the model to experimental data for LacI repressor and find that non-specific binding of the protein to DNA is activation- and not diffusion-limited. We show that the target location rate by LacI repressor is optimized with respect to microscopic rate constant for association to non-specific sites on DNA. We analyse the effect of oligomerization of TFs and DNA looping effects on searching kinetics. We show that optimal searching strategy depends on TF abundance. PMID:24121687

Tabaka, Marcin; Kalwarczyk, Tomasz; Ho?yst, Robert

2014-01-01

385

Quantitative influence of macromolecular crowding on gene regulation kinetics  

PubMed Central

We introduce macromolecular crowding quantitatively into the model for kinetics of gene regulation in Escherichia coli. We analyse and compute the specific-site searching time for 180 known transcription factors (TFs) regulating 1300 operons. The time is between 160 s (e.g. for SoxS Mw = 12.91 kDa) and 1550 s (e.g. for PepA6 of Mw = 329.28 kDa). Diffusion coefficients for one-dimensional sliding are between for large proteins up to for small monomers or dimers. Three-dimensional diffusion coefficients in the cytoplasm are 2 orders of magnitude larger than 1D sliding coefficients, nevertheless the sliding enhances the binding rates of TF to specific sites by 1–2 orders of magnitude. The latter effect is due to ubiquitous non-specific binding. We compare the model to experimental data for LacI repressor and find that non-specific binding of the protein to DNA is activation- and not diffusion-limited. We show that the target location rate by LacI repressor is optimized with respect to microscopic rate constant for association to non-specific sites on DNA. We analyse the effect of oligomerization of TFs and DNA looping effects on searching kinetics. We show that optimal searching strategy depends on TF abundance. PMID:24121687

Tabaka, Marcin; Kalwarczyk, Tomasz; Holyst, Robert

2014-01-01

386

Thermodynamic and Structural Properties of Methanol-Water Solutions Using Non-Additive Interaction Models  

PubMed Central

We study bulk structural and thermodynamic properties of methanol-water solutions via molecular dynamics simulations using novel interaction potentials based on the charge equilibration (fluctuating charge) formalism to explicitly account for molecular polarization at the atomic level. The study uses the TIP4P-FQ potential for water-water interactions, and the CHARMM-based (Chemistry at HARvard Molecular Mechanics) fluctuating charge potential for methanol-methanol and methanol-water interactions. In terms of bulk solution properties, we discuss liquid densities, enthalpies of mixing, dielectric constants, self-diffusion constants, as well as structural properties related to local hydrogen bonding structure as manifested in radial distribution functions and cluster analysis. We further explore the electronic response of water and methanol in the differing local environments established by the interaction of each species predominantly with molecules of the other species. The current force field for the alcohol-water interaction performs reasonably well for most properties, with the greatest deviation from experiment observed for the excess mixing enthalpies, which are predicted to be too favorable. This is qualitatively consistent with the overestimation of the methanol-water gas-phase interaction energy for the lowest-energy conformer (methanol as proton donor). Hydration free energies for methanol in TIP4P-FQ water are predicted to be ?5.6±0.2 kcal/mole, in respectable agreement with the experimental value of ?5.1 kcal/mole. With respect to solution micro-structure, the present cluster analysis suggests that the micro-scale environment for concentrations where select thermodynamic quantities reach extremal values is described by a bi-percolating network structure. PMID:18074339

Zhong, Yang; Warren, G. Lee; Patel, Sandeep

2014-01-01

387

Ceruloplasmin: Macromolecular Assemblies with Iron-Containing Acute Phase Proteins  

PubMed Central

Copper-containing ferroxidase ceruloplasmin (Cp) forms binary and ternary complexes with cationic proteins lactoferrin (Lf) and myeloperoxidase (Mpo) during inflammation. We present an X-ray crystal structure of a 2Cp-Mpo complex at 4.7 Å resolution. This structure allows one to identify major protein–protein interaction areas and provides an explanation for a competitive inhibition of Mpo by Cp and for the activation of p-phenylenediamine oxidation by Mpo. Small angle X-ray scattering was employed to construct low-resolution models of the Cp-Lf complex and, for the first time, of the ternary 2Cp-2Lf-Mpo complex in solution. The SAXS-based model of Cp-Lf supports the predicted 1?1 stoichiometry of the complex and demonstrates that both lobes of Lf contact domains 1 and 6 of Cp. The 2Cp-2Lf-Mpo SAXS model reveals the absence of interaction between Mpo and Lf in the ternary complex, so Cp can serve as a mediator of protein interactions in complex architecture. Mpo protects antioxidant properties of Cp by isolating its sensitive loop from proteases. The latter is important for incorporation of Fe3+ into Lf, which activates ferroxidase activity of Cp and precludes oxidation of Cp substrates. Our models provide the structural basis for possible regulatory role of these complexes in preventing iron-induced oxidative damage. PMID:23843990

Samygina, Valeriya R.; Sokolov, Alexey V.; Bourenkov, Gleb; Petoukhov, Maxim V.; Pulina, Maria O.; Zakharova, Elena T.; Vasilyev, Vadim B.; Bartunik, Hans; Svergun, Dmitri I.

2013-01-01

388

Solution structure and lipid binding of a nonspecific lipid transfer protein extracted from maize seeds.  

PubMed Central

The three-dimensional solution structure of a nonspecific lipid transfer protein extracted from maize seeds determined by 1H NMR spectroscopy is described. This cationic protein consists of 93 amino acid residues. Its structure was determined from 1,091 NOE-derived distance restraints, including 929 interresidue connectivities and 197 dihedral restraints (phi, psi, chi 1) derived from NOEs and 3J coupling constants. The global fold involving four helical fragments connected by three loops and a C-terminal tail without regular secondary structures is stabilized by four disulfide bridges. The most striking feature of this structure is the existence of an internal hydrophobic cavity running through the whole molecule. The global fold of this protein, very similar to that of a previously described lipid transfer protein extracted from wheat seeds (Gincel E et al., 1994, Eur J Biochem 226:413-422) constitutes a new architecture for alpha-class proteins. 1H NMR and fluorescence studies show that this protein forms well-defined complexes in aqueous solution with lysophosphatidylcholine. Dissociation constants, Kd, of 1.9 +/- 0.6 x 10(-6) M and > 10(-3) M were obtained with lyso-C16 and -C12, respectively. A structure model for a lipid-protein complex is proposed in which the aliphatic chain of the phospholipid is inserted in the internal cavity and the polar head interacts with the charged side chains located at one end of this cavity. Our model for the lipid-protein complex is qualitatively very similar to the recently published crystal structure (Shin DH et al., 1995, Structure 3:189-199). PMID:8845747

Gomar, J.; Petit, M. C.; Sodano, P.; Sy, D.; Marion, D.; Kader, J. C.; Vovelle, F.; Ptak, M.

1996-01-01

389

Ion aggregation in high salt solutions. II. Spectral graph analysis of water hydrogen-bonding network and ion aggregate structures  

NASA Astrophysics Data System (ADS)

Graph theory in mathematics and computer science is the study of graphs that are structures with pairwise connections between any objects. Here, the spectral graph theory and molecular dynamics simulation method are used to describe both morphological variation of ion aggregates in high salt solutions and ion effects on water hydrogen-bonding network structure. From the characteristic value analysis of the adjacency matrices that are graph theoretical representations of ion clusters, ion networks, and water H-bond structures, we obtained the ensemble average eigenvalue spectra revealing intricate connectivity and topology of ion aggregate structure that can be classified as either ion cluster or ion network. We further show that there is an isospectral relationship between the eigenvalue spectra of ion networks in high KSCN solutions and those of water H-bonding networks. This reveals the isomorphic relationship between water H-bond structure and ion-ion network structure in KSCN solution. On the other hand, the ion clusters formed in high NaCl solutions are shown to be graph-theoretically and morphologically different from the ion network structures in KSCN solutions. These observations support the bifurcation hypothesis on large ion aggregate growth mechanism via either ion cluster or ion network formation. We thus anticipate that the present spectral graph analyses of ion aggregate structures and their effects on water H-bonding network structures in high salt solutions can provide important information on the specific ion effects on water structures and possibly protein stability resulting from protein-water interactions.

Choi, Jun-Ho; Cho, Minhaeng

2014-10-01

390

Insights into substrate recognition by the Escherichia coli Orf135 protein through its solution structure.  

PubMed

Escherichia coli Orf135 hydrolyzes oxidatively damaged nucleotides such as 2-hydroxy-dATP, 8-oxo-dGTP and 5-hydroxy-CTP, in addition to 5-methyl-dCTP, dCTP and CTP. Nucleotide pool sanitization by Orf135 is important since nucleotides are continually subjected to potential damage by reactive oxygen species produced during respiration. Orf135 is a member of the Nudix family of proteins which hydrolyze nucleoside diphosphate derivatives. Nudix hydrolases are characterized by the presence of a conserved motif, even though they recognize various substrates and possess a variety of substrate binding pockets. We investigated the tertiary structure of Orf135 and its interaction with a 2-hydroxy-dATP analog using NMR. We report on the solution structure of Orf135, which should contribute towards a structural understanding of Orf135 and its interaction with substrates. PMID:22414689

Kawasaki, Kumiko; Kanaba, Teppei; Yoneyama, Momoko; Murata-Kamiya, Naoko; Kojima, Chojiro; Ito, Yutaka; Kamiya, Hiroyuki; Mishima, Masaki

2012-04-01

391

The structure and bonding of solid solutions of transition and p-elements in ?-rhombohedral boron  

NASA Astrophysics Data System (ADS)

Recent research on the structure and bonding of solid solutions in ?-rhombohedral boron is reviewed. The structure of ?-rhombohedral boron consists mainly of boron icosahedra, which form an open although rigid three-dimensional network. The interstices between the icosahedra accommodate atoms of the transition elements (Sc, Cr, Mn, Fe, Ni, Cu, Zr) and atoms with partially filled p-levels (Si, Ge, Se). The structure accommodates up to 5 atomic percent interstitial atoms. In a few cases substitutional replacements of boron by metal or non-metal atoms have been estalished. The interstitial positions are never completely occupied by the dissolved atoms. Pure ?-rhombohedral boron is an electron-deficient covalent solid. It is in pure, single-crystalline form a p-type semiconductor due to electron-deficiency and the fact that two of the boron positions are invariably only partially occupied. By doping ?-rhombohedral boron with three atomic percent iron an n-type semiconductor can be prepared.

Lundström, Torsten

1986-04-01

392

Structure and aggregation proclivity of C12E3 in aqueous solution  

NASA Astrophysics Data System (ADS)

Olygo(ethylene glycol) alkyl ethers - CxEy are well known for their high surface activity and rich phase behavior. These substances exhibit some unusual aggregation characteristics in aqueous solution even at concentrations well below CMC attributed to the formation of pre-aggregates of small size, e.g., dimers. To verify this, a series of C12E3 dimers with initial geometries taken from coarse-grained molecular dynamics simulations is subject to geometry optimization with two quantum chemical methods: DFT and ONIOM in implicit water solvent. The resulting structures are classified into groups based on structural parameters. Their stability is assessed by relative and binding energy and rationalized in terms of molecular characteristics. All studied dimers are stable and various mutual alignments of the surfactants therein are feasible. The loss of surface area is outlined as the predominant stabilizing factor. Substantial number of the structures is suitable for further aggregation.

Zahariev, Ts.; Ivanova, A.; Velinova, M.; Tadjer, A.

2013-01-01

393

NMR characterization and solution structure determination of the oxidized cytochrome c7 from Desulfuromonas?acetoxidans  

PubMed Central

The solution structure of the three-heme electron transfer protein cytochrome c7 from Desulfuromonas acetoxidans is reported. The determination of the structure is obtained through NMR spectroscopy on the fully oxidized, paramagnetic form. The richness of structural motifs and the presence of three prosthetic groups in a protein of 68 residues is discussed in comparison with the four-heme cytochromes c3 already characterized through x-ray crystallography. In particular, the orientation of the three hemes present in cytochrome c7 is similar to that of three out of four hemes of cytochromes c3. The reduction potentials of the individual hemes, which have been obtained through the sequence-specific assignment of the heme resonances, are discussed with respect to the properties of the protein matrix. This information is relevant for any attempt to understand the electron transfer pathway. PMID:8962062

Banci, Lucia; Bertini, Ivano; Bruschi, Mireille; Sompornpisut, Pornthep; Turano, Paola

1996-01-01

394

Structure and interaction in protein solutions as studied by small-angle neutron scattering  

SciTech Connect

Small-angle neutron scattering (SANS) measurements have been performed to compare the effect of the salts KF, KCl, and KBr on crystallization in aqueous solution of lysozyme protein. It is found that the propensity of the salt to crystallize protein follows the Hoffmeister series (KFsolution, lysozyme macromolecules are prolate ellipsoidal with semimajor and semiminor axes as 22 and 13.5 A, respectively. SANS also gives that the effective (structural+counterion) charge (Z) on the protein as obtained by taking into account screened Coulomb interaction between the protein macromolecules is found to be much smaller than the structural charge. There is decrease in Z suggesting the higher counterion condensation on protein with the increase in the concentration. The counterion condensation seems to be responsible for the differences in the effect of different salts. It is also found that with the addition of salts, lysozyme macromolecules convert to dimers, and for the same salt concentration the comparative effect of different salts follows the Hoffmeister series. Time evolved measurements prior to and after the crystallization show that the protein solution mostly consists of monomers and dimers. Interestingly, higher-mers are not observed in these measurements as perhaps they are formed in very small numbers towards the process that leads to the crystallization. The time dependent data have been used to obtain the fraction of crystallization as a function of time.

Chodankar, S.; Aswal, V.K. [Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai-400 085 (India)

2005-10-01

395

Structural and Optical Properties Thin Film Copper Oxides Formed by Chemical Solution Deposition Process Technique  

NASA Astrophysics Data System (ADS)

Cu2O films were prepared by chemical deposition process (CSD) using solutions of copper nitrate, dip-coated onto glass substrates. The precursor solutions were altered in an effort to seek the best solution for successful deposition. Organic additive of ethanolamine (EA) and (poly)ethylene glycol (PEG, H(OCH2CH2)nOH) was added to the solution and had shown positive effect in terms of the wetability and hence homogenous films resulted. Most films characterised by XRD gave (002) Cu2O, cuprite structure. To avoid films cracking and inhomogeneous coverage, multiple coatings were done with drying in between the successive coatings. Five to eight coatings were carried out for better coverage to ensure surface homogeneity. The microstructure of the surface oxides consisted of nanostructured oxides with uniform size distribution of 60-80nm. The optical transmittance of optimized Cu2O film reaches around 80% at wavelength of ˜ 700nm and the calculated direct optical band gaps were ˜ 2eV for the Cu2O films.

Lockman, Zainovia; Abidin, Noor Rehan Zainal; Hutagalung, Sabar Derita

2007-05-01

396

A simple quantitative model of macromolecular crowding effects on protein folding: Application to the murine prion protein(121-231)  

NASA Astrophysics Data System (ADS)

A model of protein folding kinetics is applied to study the effects of macromolecular crowding on protein folding rate and stability. Macromolecular crowding is found to promote a decrease of the entropic cost of folding of proteins that produces an increase of both the stability and the folding rate. The acceleration of the folding rate due to macromolecular crowding is shown to be a topology-dependent effect. The model is applied to the folding dynamics of the murine prion protein (121-231). The differential effect of macromolecular crowding as a function of protein topology suffices to make non-native configurations relatively more accessible.

Bergasa-Caceres, Fernando; Rabitz, Herschel A.

2013-06-01

397

Macromolecular delivery of 5-aminolaevulinic acid for photodynamic therapy using dendrimer conjugates.  

PubMed

Intracellular porphyrin generation following administration of 5-aminolaevulinic acid (5-ALA) has been widely used in photodynamic therapy. However, cellular uptake of 5-ALA is limited by its hydrophilicity, and improved means of delivery are therefore being sought. Highly branched polymeric drug carriers known as dendrimers present a promising new approach to drug delivery because they have a well-defined structure capable of incorporating a high drug payload. In this work, a dendrimer conjugate was investigated, which incorporated 18 aminolaevulinic acid residues attached via ester linkages to a multipodent aromatic core. The ability of the dendrimer to deliver and release 5-ALA intracellularly for metabolism to the photosensitizer, protoporphyrin IX, was studied in the transformed PAM 212 murine keratinocyte and A431 human epidermoid carcinoma cell lines. Up to an optimum concentration of 0.1 mmol/L, the dendrimer was significantly more efficient compared with 5-ALA for porphyrin synthesis. The intracellular porphyrin fluorescence levels showed good correlation with cellular phototoxicity following light exposure, together with minimal dark toxicity. Cellular uptake of the dendrimer occurs through endocytic routes predominantly via a macropinocytosis pathway. In conclusion, macromolecular dendritic derivatives are capable of delivering 5-ALA efficiently to cells for sustained porphyrin synthesis. PMID:17363482

Battah, Sinan; Balaratnam, Sherina; Casas, Adriana; O'Neill, Sophie; Edwards, Christine; Batlle, Alcira; Dobbin, Paul; MacRobert, Alexander J

2007-03-01

398

Protein Modelling: What Happened to the "Protein Structure Gap"?  

PubMed Central

Computational modeling and prediction of three-dimensional macromolecular structures and complexes from their sequence has been a long standing vision in structural biology as it holds the promise to bypass part of the laborious process of experimental structure solution. Over the last two decades, a paradigm shift has occurred: starting from a situation where the “structure knowledge gap” between the huge number of protein sequences and small number of known structures has hampered the widespread use of structure-based approaches in life science research, today some form of structural information – either experimental or computational – is available for the majority of amino acids encoded by common model organism genomes. Template based homology modeling techniques have matured to a point where they are now routinely used to complement experimental techniques. With the scientific focus of interest moving towards larger macromolecular complexes and dynamic networks of interactions, the integration of computational modeling methods with low-resolution experimental techniques allows studying large and complex molecular machines. Computational modeling and prediction techniques are still facing a number of challenges which hamper the more widespread use by the non-expert scientist. For example, it is often difficult to convey the underlying assumptions of a computational technique, as well as the expected accuracy and structural variability of a specific model. However, these aspects are crucial to understand the limitations of a model, and to decide which interpretations and conclusions can be supported. PMID:24010712

Schwede, Torsten

2013-01-01

399

Solution and Crystallographic Structures of the Central Region of the Phosphoprotein from Human Metapneumovirus  

PubMed Central

Human metapneumovirus (HMPV) of the family Paramyxoviridae is a major cause of respiratory illness worldwide. Phosphoproteins (P) from Paramyxoviridae are essential co-factors of the viral RNA polymerase that form tetramers and possess long intrinsically disordered regions (IDRs). We located the central region of HMPV P (Pced) which is involved in tetramerization using disorder analysis and modeled its 3D structure ab initio using Rosetta fold-and-dock. We characterized the solution-structure of Pced using small angle X-ray scattering (SAXS) and carried out direct fitting to the scattering data to filter out incorrect models. Molecular dynamics simulations (MDS) and ensemble optimization were employed to select correct models and capture the dynamic character of Pced. Our analysis revealed that oligomerization involves a compact central core located between residues 169-194 (Pcore), that is surrounded by flexible regions with ?-helical propensity. We crystallized this fragment and solved its structure at 3.1 Å resolution by molecular replacement, using the folded core from our SAXS-validated ab initio model. The RMSD between modeled and experimental tetramers is as low as 0.9 Å, demonstrating the accuracy of the approach. A comparison of the structure of HMPV P to existing mononegavirales Pced structures suggests that Pced evolved under weak selective pressure. Finally, we discuss the advantages of using SAXS in combination with ab initio modeling and MDS to solve the structure of small, homo-oligomeric protein complexes. PMID:24224051

Leyrat, Cedric; Renner, Max; Harlos, Karl; Grimes, Jonathan M.

2013-01-01

400

Thermomechanical effects of co-solute on the structure formation of bovine serum albumin.  

PubMed

The effect of glucose syrup on the structural properties of bovine serum albumin has been addressed in preparations from low to high solids. Fifteen percent protein was mixed with the co-solute at concentrations up to 65% and subjected to thermal treatment to examine the changes in phase and state transitions. Thermomechanics were the working protocol being carried out with micro differential scanning calorimetry and small deformation dynamic oscillation. Results argue that protein molecules have been extensively stabilised by the addition of a co-solute, recorded via a delayed thermal denaturation. Further, increasing the glucose syrup enhanced polymer-polymer interactions leading to stronger networks following thermal denaturation of the globular protein. Condensed BSA/glucose syrup mixtures, i.e. at 80% solids, were cooled at subzero temperatures to exhibit a considerable state of vitrification. Molecular relaxation phenomena were successfully followed using theoretical concepts from synthetic polymer research to yield the mechanical glass transition temperature. PMID:24679784

George, Paul; Lundin, Leif; Kasapis, Stefan