Science.gov

Sample records for proton crystallography station

  1. Neutron proton crystallography station (PCS)

    SciTech Connect

    Fisher, Zoe; Kovalevsky, Andrey; Johnson, Hannah; Mustyakimov, Marat

    2009-01-01

    The PCS (Protein Crystallography Station) at Los Alamos Neutron Science Center (LANSCE) is a unique facility in the USA that is designed and optimized for detecting and collecting neutron diffraction data from macromolecular crystals. PCS utilizes the 20 Hz spallation neutron source at LANSCE to enable time-of-flight measurements using 0.6-7.0 {angstrom} neutrons. This increases the neutron flux on the sample by using a wavelength range that is optimal for studying macromolecular crystal structures. The diagram below show a schematic of PCS and photos of the detector and instrument cave.

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

    PubMed Central

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

    2010-01-01

    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

  3. The crystallography stations at the Alba synchrotron

    NASA Astrophysics Data System (ADS)

    Fauth, François; Boer, Roeland; Gil-Ortiz, Fernando; Popescu, Catalin; Vallcorba, Oriol; Peral, Inma; Fullà, Daniel; Benach, Jordi; Juanhuix, Jordi

    2015-08-01

    Alba is a 3rd-generation 3 GeV synchrotron facility with an emittance of 4.6nm·rad which has been operational since 2011 and has recently started top-up operation. Photons in a broad energy range of 0.08-80 keV are served to seven beamlines dedicated to a large variety of scientific fields. The portfolio includes two beamlines, XALOC and MSPD, fully dedicated to X-ray crystallography. BL13-XALOC is currently the only macromolecular crystallography beamline. The end-station includes a high-accuracy single-axis diffractometer with a removable minikappa stage, a sample-mounting robot and a large-area, photon-counting detector. The beamline optics, fed by an in-vacuum undulator, deliver a tunable photon beam between 5.5 and 22 keV. The beam size at the sample position can be adjusted by defocusing the mirrors in a range of 50-300μm in the horizontal direction and 5.5-300μm in the vertical direction. Beamline BL04-MSPD, which is fed by a superconducting wiggler, has two in-line end-stations. The first station is devoted to high-pressure/microdiffraction. It offers a μm beam in the range 20-50 keV, particularly suited for powder diffraction studies requiring a very small beam, e.g. mapping of cultural heritage samples and high-pressures studies. The second station is dedicated to high-resolution/high-throughput powder diffraction. It covers the 8-50 keV range and includes a heavy-duty 3-circle diffractometer equipped with a 13-channel multianalyzer detector with high-angular resolution ( FWHM) and a high-throughput, position-sensitive detector spanning in 2 range allowing millisecond data acquisitions.

  4. Fifteen years of the Protein Crystallography Station: The coming of age of macromolecular neutron crystallography

    SciTech Connect

    Chen, Julian C.-H.; Unkefer, Clifford Jay

    2017-01-01

    The Protein Crystallography Station (PCS), located at the Los Alamos Neutron Scattering Center (LANSCE), was the first macromolecular crystallography beamline to be built at a spallation neutron source. Following testing and commissioning, the PCS user program was funded by the Biology and Environmental Research program of the Department of Energy Office of Science (DOE-OBER) for 13 years (2002–2014). The PCS remained the only dedicated macromolecular neutron crystallography station in North America until the construction and commissioning of the MaNDi and IMAGINE instruments at Oak Ridge National Laboratory, which started in 2012. The instrument produced a number of research and technical outcomes that have contributed to the field, clearly demonstrating the power of neutron crystallography in helping scientists to understand enzyme reaction mechanisms, hydrogen bonding and visualization of H-atom positions, which are critical to nearly all chemical reactions. During this period, neutron crystallography became a technique that increasingly gained traction, and became more integrated into macromolecular crystallography through software developments led by investigators at the PCS. As a result, this review highlights the contributions of the PCS to macromolecular neutron crystallography, and gives an overview of the history of neutron crystallography and the development of macromolecular neutron crystallography from the 1960s to the 1990s and onwards through the 2000s.

  5. Fifteen years of the Protein Crystallography Station: the coming of age of macromolecular neutron crystallography.

    PubMed

    Chen, Julian C-H; Unkefer, Clifford J

    2017-01-01

    The Protein Crystallography Station (PCS), located at the Los Alamos Neutron Scattering Center (LANSCE), was the first macromolecular crystallography beamline to be built at a spallation neutron source. Following testing and commissioning, the PCS user program was funded by the Biology and Environmental Research program of the Department of Energy Office of Science (DOE-OBER) for 13 years (2002-2014). The PCS remained the only dedicated macromolecular neutron crystallography station in North America until the construction and commissioning of the MaNDi and IMAGINE instruments at Oak Ridge National Laboratory, which started in 2012. The instrument produced a number of research and technical outcomes that have contributed to the field, clearly demonstrating the power of neutron crystallo-graphy in helping scientists to understand enzyme reaction mechanisms, hydrogen bonding and visualization of H-atom positions, which are critical to nearly all chemical reactions. During this period, neutron crystallography became a technique that increasingly gained traction, and became more integrated into macromolecular crystallography through software developments led by investigators at the PCS. This review highlights the contributions of the PCS to macromolecular neutron crystallography, and gives an overview of the history of neutron crystallography and the development of macromolecular neutron crystallography from the 1960s to the 1990s and onwards through the 2000s.

  6. Fifteen years of the Protein Crystallography Station: The coming of age of macromolecular neutron crystallography

    DOE PAGES

    Chen, Julian C.-H.; Unkefer, Clifford Jay

    2017-01-01

    The Protein Crystallography Station (PCS), located at the Los Alamos Neutron Scattering Center (LANSCE), was the first macromolecular crystallography beamline to be built at a spallation neutron source. Following testing and commissioning, the PCS user program was funded by the Biology and Environmental Research program of the Department of Energy Office of Science (DOE-OBER) for 13 years (2002–2014). The PCS remained the only dedicated macromolecular neutron crystallography station in North America until the construction and commissioning of the MaNDi and IMAGINE instruments at Oak Ridge National Laboratory, which started in 2012. The instrument produced a number of research and technicalmore » outcomes that have contributed to the field, clearly demonstrating the power of neutron crystallography in helping scientists to understand enzyme reaction mechanisms, hydrogen bonding and visualization of H-atom positions, which are critical to nearly all chemical reactions. During this period, neutron crystallography became a technique that increasingly gained traction, and became more integrated into macromolecular crystallography through software developments led by investigators at the PCS. As a result, this review highlights the contributions of the PCS to macromolecular neutron crystallography, and gives an overview of the history of neutron crystallography and the development of macromolecular neutron crystallography from the 1960s to the 1990s and onwards through the 2000s.« less

  7. Fifteen years of the Protein Crystallography Station: the coming of age of macromolecular neutron crystallography

    PubMed Central

    Chen, Julian C.-H.

    2017-01-01

    The Protein Crystallography Station (PCS), located at the Los Alamos Neutron Scattering Center (LANSCE), was the first macromolecular crystallography beamline to be built at a spallation neutron source. Following testing and commissioning, the PCS user program was funded by the Biology and Environmental Research program of the Department of Energy Office of Science (DOE-OBER) for 13 years (2002–2014). The PCS remained the only dedicated macromolecular neutron crystallography station in North America until the construction and commissioning of the MaNDi and IMAGINE instruments at Oak Ridge National Laboratory, which started in 2012. The instrument produced a number of research and technical outcomes that have contributed to the field, clearly demonstrating the power of neutron crystallo­graphy in helping scientists to understand enzyme reaction mechanisms, hydrogen bonding and visualization of H-atom positions, which are critical to nearly all chemical reactions. During this period, neutron crystallography became a technique that increasingly gained traction, and became more integrated into macromolecular crystallography through software developments led by investigators at the PCS. This review highlights the contributions of the PCS to macromolecular neutron crystallography, and gives an overview of the history of neutron crystallography and the development of macromolecular neutron crystallography from the 1960s to the 1990s and onwards through the 2000s. PMID:28250943

  8. X-ray crystallography facility for the international space station

    NASA Astrophysics Data System (ADS)

    McDdonald, William T.; Lewis, Johanna L.; Smith, Craig D.; Delucas, Lawrence J.

    1997-01-01

    Directed by NASA's Office of Space Access and Technology (OSAT), the University of Alabama at Birmingham (UAB) Center for Macromolecular Crystallography (CMC) recently completed a Design Feasibility Study for the X-ray Crystallography Facility (XCF) for the International Space Station (ISS). The XCF is a facility for growing macromolecular protein crystals; harvesting, selecting, and mounting sample crystals, and snap-freezing the samples, if necessary; performing x-ray diffraction; and downlinking the diffraction data to the ground. Knowledge of the structure of protein molecules is essential for the development of pharmaceuticals by structure-based drug design techniques. Currently, x-ray diffraction of high quality protein crystals is the only method of determining the structure of these macromolecules. High quality protein crystals have been grown in microgravity onboard the Space Shuttle Orbiter for more than 10 years, but these crystals always have been returned to Earth for x-ray diffraction. The XCF will allow crystal growth, harvesting, mounting, and x-ray diffraction onboard the ISS, maximizing diffraction data quality and timeliness. This paper presents the XCF design concept, describing key feasibility issues for the ISS application and advanced technologies and operational features which resolve those issues. The conclusion is that the XCF design is feasible and can be operational onboard the ISS by early in 2002.

  9. X-ray crystallography facility for the international space station

    SciTech Connect

    McdDonald, William T.; Lewis, Johanna L.; Smith, Craig D.; DeLucas, Lawrence J.

    1997-01-10

    Directed by NASA's Office of Space Access and Technology (OSAT), the University of Alabama at Birmingham (UAB) Center for Macromolecular Crystallography (CMC) recently completed a Design Feasibility Study for the X-ray Crystallography Facility (XCF) for the International Space Station (ISS). The XCF is a facility for growing macromolecular protein crystals; harvesting, selecting, and mounting sample crystals, and snap-freezing the samples, if necessary; performing x-ray diffraction; and downlinking the diffraction data to the ground. Knowledge of the structure of protein molecules is essential for the development of pharmaceuticals by structure-based drug design techniques. Currently, x-ray diffraction of high quality protein crystals is the only method of determining the structure of these macromolecules. High quality protein crystals have been grown in microgravity onboard the Space Shuttle Orbiter for more than 10 years, but these crystals always have been returned to Earth for x-ray diffraction. The XCF will allow crystal growth, harvesting, mounting, and x-ray diffraction onboard the ISS, maximizing diffraction data quality and timeliness. This paper presents the XCF design concept, describing key feasibility issues for the ISS application and advanced technologies and operational features which resolve those issues. The conclusion is that the XCF design is feasible and can be operational onboard the ISS by early in 2002.

  10. The New Macromolecular Crystallography Stations At MAX-lab: The MAD Station

    SciTech Connect

    Ursby, Thomas; Svensson, Christer; Sommarin, Bengt; Mammen, Christian B.; Als-Nielsen, Jens; Cerenius, Yngve; Fodje, Michel N.; Logan, Derek T.; Thunnissen, Marjolein M. G. M.; Liljas, Anders; Larsen, Sine

    2004-05-12

    A new beamline, Cassiopeia, at MAX II is about to come into operation. It consists of an energy-tunable station and four side stations intended for macromolecular crystallography. The X-ray source is a 3.5 T superconducting multipole wiggler installed in the 1.5 GeV MAX II storage ring. The energy-tunable station use grazing incidence Rh-coated silicon mirrors and an internally water-cooled Si(111) double-crystal monochromator while the four side stations use bent diamond and germanium monochromators and multilayer mirrors. This paper concentrates on the optics design of the energy-tunable station and also briefly describes other beamline components.

  11. Long-range electrostatics-induced two-proton transfer captured by neutron crystallography in an enzyme catalytic site

    DOE PAGES

    Gerlits, Oksana; Wymore, Troy; Das, Amit; ...

    2016-03-09

    Neutron crystallography was used to directly locate two protons before and after a pH-induced two-proton transfer between catalytic aspartic acid residues and the hydroxy group of the bound clinical drug darunavir, located in the catalytic site of enzyme HIV-1 protease. The two-proton transfer is triggered by electrostatic effects arising from protonation state changes of surface residues far from the active site. The mechanism and pH effect are supported by quantum mechanics/molecular mechanics (QM/MM) calculations. The low-pH proton configuration in the catalytic site is deemed critical for the catalytic action of this enzyme and may apply more generally to other asparticmore » proteases. Neutrons therefore represent a superb probe to obtain structural details for proton transfer reactions in biological systems at a truly atomic level.« less

  12. Long-range electrostatics-induced two-proton transfer captured by neutron crystallography in an enzyme catalytic site

    SciTech Connect

    Gerlits, Oksana; Wymore, Troy; Das, Amit; Shen, Chen -Hsiang; Parks, Jerry M.; Smith, Jeremy C.; Weiss, Kevin L.; Keen, David A.; Blakeley, Matthew P.; Louis, John M.; Langan, Paul; Weber, Irene T.; Kovalevsky, Andrey

    2016-03-09

    Neutron crystallography was used to directly locate two protons before and after a pH-induced two-proton transfer between catalytic aspartic acid residues and the hydroxy group of the bound clinical drug darunavir, located in the catalytic site of enzyme HIV-1 protease. The two-proton transfer is triggered by electrostatic effects arising from protonation state changes of surface residues far from the active site. The mechanism and pH effect are supported by quantum mechanics/molecular mechanics (QM/MM) calculations. The low-pH proton configuration in the catalytic site is deemed critical for the catalytic action of this enzyme and may apply more generally to other aspartic proteases. Neutrons therefore represent a superb probe to obtain structural details for proton transfer reactions in biological systems at a truly atomic level.

  13. Long-Range Electrostatics-Induced Two-Proton Transfer Captured by Neutron Crystallography in an Enzyme Catalytic Site.

    PubMed

    Gerlits, Oksana; Wymore, Troy; Das, Amit; Shen, Chen-Hsiang; Parks, Jerry M; Smith, Jeremy C; Weiss, Kevin L; Keen, David A; Blakeley, Matthew P; Louis, John M; Langan, Paul; Weber, Irene T; Kovalevsky, Andrey

    2016-04-11

    Neutron crystallography was used to directly locate two protons before and after a pH-induced two-proton transfer between catalytic aspartic acid residues and the hydroxy group of the bound clinical drug darunavir, located in the catalytic site of enzyme HIV-1 protease. The two-proton transfer is triggered by electrostatic effects arising from protonation state changes of surface residues far from the active site. The mechanism and pH effect are supported by quantum mechanics/molecular mechanics (QM/MM) calculations. The low-pH proton configuration in the catalytic site is deemed critical for the catalytic action of this enzyme and may apply more generally to other aspartic proteases. Neutrons therefore represent a superb probe to obtain structural details for proton transfer reactions in biological systems at a truly atomic level. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  14. Compact measurement station for low energy proton beams

    NASA Astrophysics Data System (ADS)

    Yildiz, H.; Ozbey, A.; Oz, S.; Yasatekin, B.; Turemen, G.; Ogur, S.; Sunar, E.; Aydin, Y. O.; Dimov, V. A.; Unel, G.; Alacakir, A.

    2017-02-01

    A compact, remote controlled, cost efficient diagnostic station has been developed to measure the charge, the profile and the emittance for low energy proton beams. It has been installed and tested in the proton beam line of the Project Prometheus at SANAEM of the Turkish Atomic Energy Authority.

  15. Direct determination of protonation states and visualization of hydrogen bonding in a glycoside hydrolase with neutron crystallography

    PubMed Central

    Wan, Qun; Parks, Jerry M.; Hanson, B. Leif; Fisher, Suzanne Zoe; Ostermann, Andreas; Schrader, Tobias E.; Graham, David E.; Coates, Leighton; Langan, Paul; Kovalevsky, Andrey

    2015-01-01

    Glycoside hydrolase (GH) enzymes apply acid/base chemistry to catalyze the decomposition of complex carbohydrates. These ubiquitous enzymes accept protons from solvent and donate them to substrates at close to neutral pH by modulating the pKa values of key side chains during catalysis. However, it is not known how the catalytic acid residue acquires a proton and transfers it efficiently to the substrate. To better understand GH chemistry, we used macromolecular neutron crystallography to directly determine protonation and ionization states of the active site residues of a family 11 GH at multiple pD (pD = pH + 0.4) values. The general acid glutamate (Glu) cycles between two conformations, upward and downward, but is protonated only in the downward orientation. We performed continuum electrostatics calculations to estimate the pKa values of the catalytic Glu residues in both the apo- and substrate-bound states of the enzyme. The calculated pKa of the Glu increases substantially when the side chain moves down. The energy barrier required to rotate the catalytic Glu residue back to the upward conformation, where it can protonate the glycosidic oxygen of the substrate, is 4.3 kcal/mol according to free energy simulations. These findings shed light on the initial stage of the glycoside hydrolysis reaction in which molecular motion enables the general acid catalyst to obtain a proton from the bulk solvent and deliver it to the glycosidic oxygen. PMID:26392527

  16. A pKa calculation of residues in a proton pump, bacteriorhodopsin, from structures determined by electron crystallography.

    PubMed

    Mitsuoka, Kaoru

    2014-11-01

    Bacteriorhodopsin (bR) is a light-driven proton pump, which is a membrane protein found in halophilic archeae like Halobacterium salinarum and in eubacteria [1]. When the covalently bound retinal chromophore absorbs the light energy, it changes the conformation from all-trans to 13-cis. This configuration change initiates ion translocation across the cell membrane and a proton moves from inside to outside of the cell. The bR molecules are forming two-dimensional crystals on the membranes of halophilic archeae, and therefore the atomic model of bR was first determined by electron crystallography. The determined structure can be used to determine the pKa values, through which the charge states of ionizable residues in bR determine their pH-dependent properties. The pH-dependent properties are crucial for proton translocation from ionizable residues or to ionizable residues. Detection of the intermediate states of the reaction cycle (photocycle) produced spectroscopic information, which can predict the ionization state of the ionozable residues. In the transition from the L intermediate to the M intermediate, it is known that a proton moves from the Shiff base on the retinal chromophore to Asp85, while a proton is released to the extracellar side from proton-releasing groups including Glu194 and Glu204. Experimentally the pKa value of the proton release is determined to be about 9.7, while the pKa value of Asp85 was measured to change from 2.6 to 7.5 by the proton release from the proton-releasing groups [2]. Here we used the PROPKA program [3] to calculate the pKa values of Asp85 and the proton-releasing groups from the structures at pH 5.5 and at pH 10.0 determined by electron crystallography. The calculation showed that the pKa value of Asp85 changes from 5.3 to 6.1, which qualitatively show the similar changes with the measured difference. The largest change between the structures is the shift of Arg82 by the proton release from the proton-releasing groups

  17. Bent Diamond Crystals and Multilayer Based Optics at the new 5-Station Protein Crystallography Beamline 'Cassiopeia' at MAX-lab

    SciTech Connect

    Mammen, Christian B.; Als-Nielsen, Jens; Ursby, Thomas; Thunnissen, Marjolein

    2004-05-12

    A new 5-station beamline for protein crystallography is being commissioned at the Swedish synchrotron light source MAX-II at Lund University. Of the 2K/{gamma} = 14 mrad horizontal wiggler fan, the central 2 mrad are used and split in three parts. The central 1 mrad will be used for a station optimized for MAD experiments and on each side of the central fan, from 0.5 mrad to 1 mrad, there are two fixed energy stations using different energies of the same part of the beam. These, in total five stations, can be used simultaneously and independently for diffraction data collection. The two upstream monochromators for the side stations are meridionally bent asymmetric diamond(111) crystals in Laue transmission geometry. The monochromators for the downstream side stations are bent Ge(111) crystals in asymmetric Bragg reflection geometry. Curved multilayer mirrors inserted in the monochromatic beams provide focusing in the vertical plane. The first side station is under commissioning, and a preliminary test protein data set has been collected.

  18. Protonation states of histidine and other key residues in deoxy normal human adult hemoglobin by neutron protein crystallography

    SciTech Connect

    Kovalevsky, Andrey; Chatake, Toshiyuki; Shibayama, Naoya; Park, Sam-Yong; Ishikawa, Takuya; Mustyakimov, Marat; Fisher, S. Zoe; Langan, Paul; Morimoto, Yukio

    2010-11-01

    Using neutron diffraction analysis, the protonation states of 35 of 38 histidine residues were determined for the deoxy form of normal human adult hemoglobin. Distal and buried histidines may contribute to the increased affinity of the deoxy state for hydrogen ions and its decreased affinity for oxygen compared with the oxygenated form. The protonation states of the histidine residues key to the function of deoxy (T-state) human hemoglobin have been investigated using neutron protein crystallography. These residues can reversibly bind protons, thereby regulating the oxygen affinity of hemoglobin. By examining the OMIT F{sub o} − F{sub c} and 2F{sub o} − F{sub c} neutron scattering maps, the protonation states of 35 of the 38 His residues were directly determined. The remaining three residues were found to be disordered. Surprisingly, seven pairs of His residues from equivalent α or β chains, αHis20, αHis50, αHis58, αHis89, βHis63, βHis143 and βHis146, have different protonation states. The protonation of distal His residues in the α{sub 1}β{sub 1} heterodimer and the protonation of αHis103 in both subunits demonstrates that these residues may participate in buffering hydrogen ions and may influence the oxygen binding. The observed protonation states of His residues are compared with their ΔpK{sub a} between the deoxy and oxy states. Examination of inter-subunit interfaces provided evidence for interactions that are essential for the stability of the deoxy tertiary structure.

  19. The Vector Field Proton Magnetometer for IGY Satellite Ground Stations

    NASA Technical Reports Server (NTRS)

    Shapiro, I. R.; Stolarik, J. D.; Heppner, J. P.

    1960-01-01

    The application of homogeneous-bias fields to a proton precessional magnetometer allows the measurement of the vector field by measuring the absolute scalar field F, declination variations (Delta)D, and inclination variations (Delta)I. The absolute scalar field can be measured to an accuracy of +/- 1 gamma and absolute declination and inclination to an accuracy of +/- 2 minutes. This paper describes a vector proton magnetometer that has been in operation at nine Minitrack stations since the spring of 1958.

  20. Direct determination of protonation states and visualization of hydrogen bonding in a glycoside hydrolase with neutron crystallography

    SciTech Connect

    Wan, Qun; Parks, Jerry M.; Hanson, B. Leif; Fisher, Suzanne Zoe; Ostermann, Andreas; Schrader, Tobias E.; Graham, David E.; Coates, Leighton; Langan, Paul; Kovalevsky, Andrey

    2015-09-21

    Glycoside hydrolase (GH) enzymes apply acid/base chemistry to catalyze the decomposition of complex carbohydrates. These ubiquitous enzymes accept protons from solvent and donate them to substrates at close to neutral pH by modulating the pKa values of key side chains during catalysis. However, it is not known how the catalytic acid residue acquires a proton and transfers it efficiently to the substrate. To better understand GH chemistry, we used macromolecular neutron crystallography to directly determine protonation and ionization states of the active site residues of a family 11 GH at multiple pD (pD = pH + 0.4) values. The general acid glutamate (Glu) cycles between two conformations, upward and downward, but is protonated only in the downward orientation. We performed continuum electrostatics calculations to estimate the pKa values of the catalytic Glu residues in both the apo- and substrate-bound states of the enzyme. The calculated pKa of the Glu increases substantially when the side chain moves down. The energy barrier required to rotate the catalytic Glu residue back to the upward conformation, where it can protonate the glycosidic oxygen of the substrate, is 4.3 kcal/mol according to free energy simulations. Lastly, these findings shed light on the initial stage of the glycoside hydrolysis reaction in which molecular motion enables the general acid catalyst to obtain a proton from the bulk solvent and deliver it to the glycosidic oxygen.

  1. Direct determination of protonation states and visualization of hydrogen bonding in a glycoside hydrolase with neutron crystallography

    DOE PAGES

    Wan, Qun; Parks, Jerry M.; Hanson, B. Leif; ...

    2015-09-21

    Glycoside hydrolase (GH) enzymes apply acid/base chemistry to catalyze the decomposition of complex carbohydrates. These ubiquitous enzymes accept protons from solvent and donate them to substrates at close to neutral pH by modulating the pKa values of key side chains during catalysis. However, it is not known how the catalytic acid residue acquires a proton and transfers it efficiently to the substrate. To better understand GH chemistry, we used macromolecular neutron crystallography to directly determine protonation and ionization states of the active site residues of a family 11 GH at multiple pD (pD = pH + 0.4) values. The generalmore » acid glutamate (Glu) cycles between two conformations, upward and downward, but is protonated only in the downward orientation. We performed continuum electrostatics calculations to estimate the pKa values of the catalytic Glu residues in both the apo- and substrate-bound states of the enzyme. The calculated pKa of the Glu increases substantially when the side chain moves down. The energy barrier required to rotate the catalytic Glu residue back to the upward conformation, where it can protonate the glycosidic oxygen of the substrate, is 4.3 kcal/mol according to free energy simulations. Lastly, these findings shed light on the initial stage of the glycoside hydrolysis reaction in which molecular motion enables the general acid catalyst to obtain a proton from the bulk solvent and deliver it to the glycosidic oxygen.« less

  2. Characteristics of trapped proton anisotropy at Space Station Freedom altitudes

    SciTech Connect

    Armstrong, T.W.; Colborn, B.L.; Watts, J.W.

    1990-10-01

    The ionizing radiation dose for spacecraft in low-Earth orbit (LEO) is produced mainly by protons trapped in the Earth's magnetic field. Current data bases describing this trapped radiation environment assume the protons to have an isotropic angular distribution, although the fluxes are actually highly anisotropic in LEO. The anisotropy of the trapped proton exposure has not been an important practical consideration for most previous LEO missions because the random spacecraft orientation during passage through the radiation belt averages out the anisotropy. Thus, in spite of the actual exposure anisotropy, cumulative radiation effects over many orbits can be predicted as if the environment were isotropic when the spacecraft orientation is variable during exposure. However, Space Station Freedom will be gravity gradient stabilized to reduce drag, and, due to this fixed orientation, the cumulative incident proton flux will remain anisotropic. The anisotropy could potentially influence several aspects of Space Station design and operation, such as the appropriate location for radiation sensitive components and experiments, location of workstations and sleeping quarters, and the design and placement of radiation monitors. Also, on-board mass could possible be utilized to counteract the anisotropy effects and reduce the dose exposure. Until recently only omnidirectional data bases for the trapped proton environment were available. However, a method to predict orbit-average, angular dependent (vector) trapped proton flux spectra has been developed from the standard omnidirectional trapped proton data bases.

  3. Characteristics of trapped proton anisotropy at Space Station Freedom altitudes

    NASA Technical Reports Server (NTRS)

    Armstrong, T. W.; Colborn, B. L.; Watts, J. W.

    1990-01-01

    The ionizing radiation dose for spacecraft in low-Earth orbit (LEO) is produced mainly by protons trapped in the Earth's magnetic field. Current data bases describing this trapped radiation environment assume the protons to have an isotropic angular distribution, although the fluxes are actually highly anisotropic in LEO. The general nature of this directionality is understood theoretically and has been observed by several satellites. The anisotropy of the trapped proton exposure has not been an important practical consideration for most previous LEO missions because the random spacecraft orientation during passage through the radiation belt 'averages out' the anisotropy. Thus, in spite of the actual exposure anisotropy, cumulative radiation effects over many orbits can be predicted as if the environment were isotropic when the spacecraft orientation is variable during exposure. However, Space Station Freedom will be gravity gradient stabilized to reduce drag, and, due to this fixed orientation, the cumulative incident proton flux will remain anisotropic. The anisotropy could potentially influence several aspects of Space Station design and operation, such as the appropriate location for radiation sensitive components and experiments, location of workstations and sleeping quarters, and the design and placement of radiation monitors. Also, on-board mass could possible be utilized to counteract the anisotropy effects and reduce the dose exposure. Until recently only omnidirectional data bases for the trapped proton environment were available. However, a method to predict orbit-average, angular dependent ('vector') trapped proton flux spectra has been developed from the standard omnidirectional trapped proton data bases. This method was used to characterize the trapped proton anisotropy for the Space Station orbit (28.5 degree inclination, circular) in terms of its dependence on altitude, solar cycle modulation (solar minimum vs. solar maximum), shielding thickness

  4. Characteristics of trapped proton anisotropy at Space Station Freedom altitudes

    NASA Astrophysics Data System (ADS)

    Armstrong, T. W.; Colborn, B. L.; Watts, J. W.

    1990-10-01

    The ionizing radiation dose for spacecraft in low-Earth orbit (LEO) is produced mainly by protons trapped in the Earth's magnetic field. Current data bases describing this trapped radiation environment assume the protons to have an isotropic angular distribution, although the fluxes are actually highly anisotropic in LEO. The general nature of this directionality is understood theoretically and has been observed by several satellites. The anisotropy of the trapped proton exposure has not been an important practical consideration for most previous LEO missions because the random spacecraft orientation during passage through the radiation belt 'averages out' the anisotropy. Thus, in spite of the actual exposure anisotropy, cumulative radiation effects over many orbits can be predicted as if the environment were isotropic when the spacecraft orientation is variable during exposure. However, Space Station Freedom will be gravity gradient stabilized to reduce drag, and, due to this fixed orientation, the cumulative incident proton flux will remain anisotropic. The anisotropy could potentially influence several aspects of Space Station design and operation, such as the appropriate location for radiation sensitive components and experiments, location of workstations and sleeping quarters, and the design and placement of radiation monitors. Also, on-board mass could possible be utilized to counteract the anisotropy effects and reduce the dose exposure. Until recently only omnidirectional data bases for the trapped proton environment were available. However, a method to predict orbit-average, angular dependent ('vector') trapped proton flux spectra has been developed from the standard omnidirectional trapped proton data bases. This method was used to characterize the trapped proton anisotropy for the Space Station orbit (28.5 degree inclination, circular) in terms of its dependence on altitude, solar cycle modulation (solar minimum vs. solar maximum), shielding thickness

  5. Neutron crystallography of photoactive yellow protein reveals unusual protonation state of Arg52 in the crystal.

    PubMed

    Yonezawa, Kento; Shimizu, Nobutaka; Kurihara, Kazuo; Yamazaki, Yoichi; Kamikubo, Hironari; Kataoka, Mikio

    2017-08-24

    Because of its high pKa, arginine (Arg) is believed to be protonated even in the hydrophobic environment of the protein interior. However, our neutron crystallographic structure of photoactive yellow protein, a light sensor, demonstrated that Arg52 adopts an electrically neutral form. We also showed that the hydrogen bond between the chromophore and Glu46 is a so-called low barrier hydrogen bond (LBHB). Because both the neutral Arg and LBHB are unusual in proteins, these observations remain controversial. To validate our findings, we carried out neutron crystallographic analysis of the E46Q mutant of PYP. The resultant structure revealed that the proportion of the cationic form is higher in E46Q than in WT, although the cationic and neutral forms of Arg52 coexist in E46Q. These observations were confirmed by the occupancy of the deuterium atom bound to the N η1 atom combined with an alternative conformation of the N(η2)D2 group comprising sp(2) hybridisation. Based on these results, we propose that the formation of the LBHB decreases the proton affinity of Arg52, stabilizing the neutral form in the crystal.

  6. A New High-Flux Chemical and Materials Crystallography Station at the SRS Daresbury. 1. Design, Construction and Test Results.

    PubMed

    Cernik, R J; Clegg, W; Catlow, C R; Bushnell-Wye, G; Flaherty, J V; Greaves, G N; Burrows, I; Taylor, D J; Teat, S J; Hamichi, M

    1997-09-01

    A new single-crystal diffraction facility has been constructed on beamline 9 of the SRS at Daresbury Laboratory for the study of structural problems in chemistry and materials science. The station utilizes up to 3.8 mrad horizontally from the 5 T wiggler magnet which can be focused horizontally and vertically. The horizontal focusing is provided by a choice of gallium-cooled triangular bent Si (111) or Si (220) monochromators, giving a wavelength range from 0.3 to 1.5 A. Focusing in the vertical plane is achieved by a cylindrically bent zerodur mirror with a 300 mum-thick palladium coating. The station is equipped with a modified Enraf-Nonius CAD-4 four-circle diffractometer and a Siemens SMART CCD area-detector system. High- and low-temperature facilities are available to cover the temperature range from about 80 to 1000 K. Early results on test compounds without optimization of the beam optics demonstrate that excellent refined structures can be obtained from samples giving diffraction patterns too weak to be measured with conventional laboratory X-ray sources, fulfilling a major objective of the project.

  7. Preliminary time-of-flight neutron diffraction studies of Escherichia coli ABC transport receptor phosphate-binding protein at the Protein Crystallography Station.

    PubMed

    Sippel, K H; Bacik, J; Quiocho, F A; Fisher, S Z

    2014-06-01

    Inorganic phosphate is an essential molecule for all known life. Organisms have developed many mechanisms to ensure an adequate supply, even in low-phosphate conditions. In prokaryotes phosphate transport is instigated by the phosphate-binding protein (PBP), the initial receptor for the ATP-binding cassette (ABC) phosphate transporter. In the crystal structure of the PBP-phosphate complex, the phosphate is completely desolvated and sequestered in a deep cleft and is bound by 13 hydrogen bonds: 12 to protein NH and OH donor groups and one to a carboxylate acceptor group. The carboxylate plays a key recognition role by accepting a phosphate hydrogen. PBP phosphate affinity is relatively consistent across a broad pH range, indicating the capacity to bind monobasic (H2PO4-) and dibasic (HPO4(2-)) phosphate; however, the mechanism by which it might accommodate the second hydrogen of monobasic phosphate is unclear. To answer this question, neutron diffraction studies were initiated. Large single crystals with a volume of 8 mm3 were grown and subjected to hydrogen/deuterium exchange. A 2.5 Å resolution data set was collected on the Protein Crystallography Station at the Los Alamos Neutron Science Center. Initial refinement of the neutron data shows significant nuclear density, and refinement is ongoing. This is the first report of a neutron study from this superfamily.

  8. Preliminary time-of-flight neutron diffraction studies of Escherichia coli ABC transport receptor phosphate-binding protein at the Protein Crystallography Station

    PubMed Central

    Sippel, K. H.; Bacik, J.; Quiocho, F. A.; Fisher, S. Z.

    2014-01-01

    Inorganic phosphate is an essential molecule for all known life. Organisms have developed many mechanisms to ensure an adequate supply, even in low-phosphate conditions. In prokaryotes phosphate transport is instigated by the phosphate-binding protein (PBP), the initial receptor for the ATP-binding cassette (ABC) phosphate transporter. In the crystal structure of the PBP–phosphate complex, the phosphate is completely desolvated and sequestered in a deep cleft and is bound by 13 hydrogen bonds: 12 to protein NH and OH donor groups and one to a carboxylate acceptor group. The carboxylate plays a key recognition role by accepting a phosphate hydrogen. PBP phosphate affinity is relatively consistent across a broad pH range, indicating the capacity to bind monobasic (H2PO4 −) and dibasic (HPO4 2−) phosphate; however, the mechanism by which it might accommodate the second hydrogen of monobasic phosphate is unclear. To answer this question, neutron diffraction studies were initiated. Large single crystals with a volume of 8 mm3 were grown and subjected to hydrogen/deuterium exchange. A 2.5 Å resolution data set was collected on the Protein Crystallography Station at the Los Alamos Neutron Science Center. Initial refinement of the neutron data shows significant nuclear density, and refinement is ongoing. This is the first report of a neutron study from this superfamily. PMID:24915101

  9. “Newton’s cradle” proton relay with amide–imidic acid tautomerization in inverting cellulase visualized by neutron crystallography

    PubMed Central

    Nakamura, Akihiko; Ishida, Takuya; Kusaka, Katsuhiro; Yamada, Taro; Fushinobu, Shinya; Tanaka, Ichiro; Kaneko, Satoshi; Ohta, Kazunori; Tanaka, Hiroaki; Inaka, Koji; Higuchi, Yoshiki; Niimura, Nobuo; Samejima, Masahiro; Igarashi, Kiyohiko

    2015-01-01

    Hydrolysis of carbohydrates is a major bioreaction in nature, catalyzed by glycoside hydrolases (GHs). We used neutron diffraction and high-resolution x-ray diffraction analyses to investigate the hydrogen bond network in inverting cellulase PcCel45A, which is an endoglucanase belonging to subfamily C of GH family 45, isolated from the basidiomycete Phanerochaete chrysosporium. Examination of the enzyme and enzyme-ligand structures indicates a key role of multiple tautomerizations of asparagine residues and peptide bonds, which are finally connected to the other catalytic residue via typical side-chain hydrogen bonds, in forming the “Newton’s cradle”–like proton relay pathway of the catalytic cycle. Amide–imidic acid tautomerization of asparagine has not been taken into account in recent molecular dynamics simulations of not only cellulases but also general enzyme catalysis, and it may be necessary to reconsider our interpretation of many enzymatic reactions. PMID:26601228

  10. "Newton's cradle" proton relay with amide-imidic acid tautomerization in inverting cellulase visualized by neutron crystallography.

    PubMed

    Nakamura, Akihiko; Ishida, Takuya; Kusaka, Katsuhiro; Yamada, Taro; Fushinobu, Shinya; Tanaka, Ichiro; Kaneko, Satoshi; Ohta, Kazunori; Tanaka, Hiroaki; Inaka, Koji; Higuchi, Yoshiki; Niimura, Nobuo; Samejima, Masahiro; Igarashi, Kiyohiko

    2015-08-01

    Hydrolysis of carbohydrates is a major bioreaction in nature, catalyzed by glycoside hydrolases (GHs). We used neutron diffraction and high-resolution x-ray diffraction analyses to investigate the hydrogen bond network in inverting cellulase PcCel45A, which is an endoglucanase belonging to subfamily C of GH family 45, isolated from the basidiomycete Phanerochaete chrysosporium. Examination of the enzyme and enzyme-ligand structures indicates a key role of multiple tautomerizations of asparagine residues and peptide bonds, which are finally connected to the other catalytic residue via typical side-chain hydrogen bonds, in forming the "Newton's cradle"-like proton relay pathway of the catalytic cycle. Amide-imidic acid tautomerization of asparagine has not been taken into account in recent molecular dynamics simulations of not only cellulases but also general enzyme catalysis, and it may be necessary to reconsider our interpretation of many enzymatic reactions.

  11. Protein structures by spallation neutron crystallography

    PubMed Central

    Langan, Paul; Fisher, Zoë; Kovalevsky, Andrii; Mustyakimov, Marat; Sutcliffe Valone, Amanda; Unkefer, Cliff; Waltman, Mary Jo; Coates, Leighton; Adams, Paul D.; Afonine, Pavel V.; Bennett, Brad; Dealwis, Chris; Schoenborn, Benno P.

    2008-01-01

    The Protein Crystallography Station 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. This capability also includes the Macromolecular Neutron Crystallography (MNC) consortium between Los Alamos (LANL) and Lawrence Berkeley National Laboratories for developing computational tools for neutron protein crystallography, a biological deuteration laboratory, the National Stable Isotope Production Facility, and an MNC drug design consortium between LANL and Case Western Reserve University. PMID:18421142

  12. ⁵¹V NMR Crystallography of Vanadium Chloroperoxidase and Its Directed Evolution P395D/L241V/T343A Mutant: Protonation Environments of the Active Site.

    PubMed

    Gupta, Rupal; Hou, Guangjin; Renirie, Rokus; Wever, Ron; Polenova, Tatyana

    2015-04-29

    Vanadium-dependent haloperoxidases (VHPOs) perform two-electron oxidation of halides using hydrogen peroxide. Their mechanism, including the factors determining the substrate specificity and the pH-dependence of the catalytic rates, is poorly understood. The vanadate cofactor in the active site of VHPOs contains "spectroscopically silent" V(V), which does not change oxidation state during the reaction. We employed an NMR crystallography approach based on (51)V magic angle spinning NMR spectroscopy and Density Functional Theory, to gain insights into the structure and coordination environment of the cofactor in the resting state of vanadium-dependent chloroperoxidases (VCPO). The cofactor environments in the wild-type VCPO and its P395D/L241V/T343A mutant exhibiting 5-100-fold improved catalytic activity are examined at various pH values. Optimal sensitivity attained due to the fast MAS probe technologies enabled the assignment of the location and number of protons on the vanadate as a function of pH. The vanadate cofactor changes its protonation from quadruply protonated at pH 6.3 to triply protonated at pH 7.3 to doubly protonated at pH 8.3. In contrast, in the mutant, the vanadate protonation is the same at pH 5.0 and 8.3, and the cofactor is doubly protonated. This methodology to identify the distinct protonation environments of the cofactor, which are also pH-dependent, could help explain the different reactivities of the wild-type and mutant VCPO and their pH-dependence. This study demonstrates that (51)V-based NMR crystallography can be used to derive the detailed coordination environments of vanadium centers in large biological molecules.

  13. The high-energy proton fluxes in the SAA observed with REM aboard the MIR orbital station

    NASA Technical Reports Server (NTRS)

    Buhler, P.; Zehnder, A.; Kruglanski, M.; Daly, E.; Adams, L.

    2002-01-01

    During two years, from November 1994 to 1996, the particle detector REM measured the highly energetic electron and proton environment at the outside of the MIR orbital station. Using mission averaged data we investigate various aspects of the proton fluxes in the SAA. Comparison with the radiation belt model AP8 reveal important differences. c2002 Elsevier Science Ltd. All rights reserved.

  14. The high-energy proton fluxes in the SAA observed with REM aboard the MIR orbital station

    NASA Technical Reports Server (NTRS)

    Buhler, P.; Zehnder, A.; Kruglanski, M.; Daly, E.; Adams, L.

    2002-01-01

    During two years, from November 1994 to 1996, the particle detector REM measured the highly energetic electron and proton environment at the outside of the MIR orbital station. Using mission averaged data we investigate various aspects of the proton fluxes in the SAA. Comparison with the radiation belt model AP8 reveal important differences. c2002 Elsevier Science Ltd. All rights reserved.

  15. Toward resolving the catalytic mechanism of dihydrofolate reductase using neutron and ultrahigh-resolution X-ray crystallography [Neutron and ultrahigh resolution X-ray crystallography reveals water as the proton donor in the catalytic mechanism of dihydrofolate reductase

    SciTech Connect

    Wan, Qun; Bennett, Brad C.; Wilson, Mark A.; Kovalevsky, Andrey; Langan, Paul; Howell, Elizabeth E.; Dealwis, Chris

    2014-12-01

    Dihydrofolate reductase (DHFR) catalyzes the NADPH-dependent reduction of dihydrofolate (DHF) to tetrahydrofolate (THF). An important step in the mechanism involves proton donation to the N5 atom of DHF. The inability to determine the protonation states of active site residues and substrate has led to the lack of consensus on a catalytic mechanism. To resolve this ambiguity, we conducted neutron and ultrahigh resolution X-ray crystallographic studies of the pseudo-Michaelis ternary complex of DHFR with folate and NADP+ from E. coli. The neutron data were collected to 2.0 Å resolution using a 3.6 mm3 crystal with the quasi-Laue technique, and the structure reveals that the N3 atom of folate is protonated while Asp27 is negatively charged. Previous mechanisms have proposed a keto-to-enol tautomerization of the substrate to facilitate protonation of the N5 atom. The structure supports the existence of the keto tautomer due to protonation of the N3 atom, suggesting tautomerization is unnecessary for catalysis. In the 1.05 Å resolution X-ray structure of the ternary complex, conformational disorder of the Met20 side chain is coupled to electron density for a partially occupied water within hydrogen-bonding distance of the N5 atom of folate; this suggests direct protonation of substrate by solvent. We propose a catalytic mechanism for DHFR that involves stabilization of the keto tautomer of the substrate, elevation of the pKa of the N5 atom of DHF by Asp27, and protonation of N5 by water whose access to the active site is gated by fluctuation of the Met20 side chain even though the Met-20 loop is closed.

  16. Toward resolving the catalytic mechanism of dihydrofolate reductase using neutron and ultrahigh-resolution X-ray crystallography [Neutron and ultrahigh resolution X-ray crystallography reveals water as the proton donor in the catalytic mechanism of dihydrofolate reductase

    DOE PAGES

    Wan, Qun; Bennett, Brad C.; Wilson, Mark A.; ...

    2014-12-01

    Dihydrofolate reductase (DHFR) catalyzes the NADPH-dependent reduction of dihydrofolate (DHF) to tetrahydrofolate (THF). An important step in the mechanism involves proton donation to the N5 atom of DHF. The inability to determine the protonation states of active site residues and substrate has led to the lack of consensus on a catalytic mechanism. To resolve this ambiguity, we conducted neutron and ultrahigh resolution X-ray crystallographic studies of the pseudo-Michaelis ternary complex of DHFR with folate and NADP+ from E. coli. The neutron data were collected to 2.0 Å resolution using a 3.6 mm3 crystal with the quasi-Laue technique, and the structuremore » reveals that the N3 atom of folate is protonated while Asp27 is negatively charged. Previous mechanisms have proposed a keto-to-enol tautomerization of the substrate to facilitate protonation of the N5 atom. The structure supports the existence of the keto tautomer due to protonation of the N3 atom, suggesting tautomerization is unnecessary for catalysis. In the 1.05 Å resolution X-ray structure of the ternary complex, conformational disorder of the Met20 side chain is coupled to electron density for a partially occupied water within hydrogen-bonding distance of the N5 atom of folate; this suggests direct protonation of substrate by solvent. We propose a catalytic mechanism for DHFR that involves stabilization of the keto tautomer of the substrate, elevation of the pKa of the N5 atom of DHF by Asp27, and protonation of N5 by water whose access to the active site is gated by fluctuation of the Met20 side chain even though the Met-20 loop is closed.« less

  17. Protein crystallography with spallation neutrons

    SciTech Connect

    Langan, P.; Schoenborn, Benno P.

    2003-01-01

    proteins and oriented molecular complexes. With spallation neutrons and their time dependent wavelength structure, one can select data with an optimal wavelength bandwidth and cover the whole Laue spectrum as time (wavelength) resolved diffraction data. This optimizes data quality with best peak to background ratios and provides spatial and energy resolution to eliminate peak overlaps. Such a Protein Crystallography Station (PCS) has been built and tested at Los Alamos Neutron Science Center. A partially coupled moderator is used to increase flux and data are collected by a Cylindrical He3 detector covering 120' with 200mm height. The PCS is described along with examples of data collected from a number of proteins.

  18. Design and performance of U7B beamline and X-ray diffraction and scattering station at NSRL and its preliminary experiments in protein crystallography

    NASA Astrophysics Data System (ADS)

    Pan, Guoqiang; Xu, Chaoyin; Fan, Rong; Gao, Chen; Lou, Xiaohua; Teng, Maikun; Huang, Qingqiu; Niu, Liwen

    2005-03-01

    This publication describes the design and performance of the U7B beamline and X-ray diffraction and diffuse scattering station at National Synchrotron Radiation Laboratory (NSRL). The beamline optics comprise a Pt-coated toroidal focusing mirror and a double-crystal Si(1 1 1) monochromator. A preliminary experiment of diffraction data collection and processing was carried out using a commercial imaging plate detector system (Mar345). The data collected from one single crystal of acutohaemolysin, a Lys49-type PLA2 from Agkistrodon acutus venom, are of high quality.

  19. Mannobiose Binding Induces Changes in Hydrogen Bonding and Protonation States of Acidic Residues in Concanavalin A As Revealed by Neutron Crystallography.

    PubMed

    Gerlits, Oksana O; Coates, Leighton; Woods, Robert J; Kovalevsky, Andrey

    2017-08-30

    Plant lectins are carbohydrate-binding proteins with various biomedical applications. Concanavalin A (Con A) holds promise in treating cancerous tumors. To better understand the Con A carbohydrate binding specificity, we obtained a room-temperature neutron structure of this legume lectin in complex with a disaccharide Manα1-2Man, mannobiose. The neutron structure afforded direct visualization of the hydrogen bonding between the protein and ligand, showing that the ligand is able to alter both protonation states and interactions for residues located close to and distant from the binding site. An unprecedented low-barrier hydrogen bond was observed forming between the carboxylic side chains of Asp28 and Glu8, with the D atom positioned equidistant from the oxygen atoms having an O···D···O angle of 101.5°.

  20. Exploring the Mechanism of β-Lactam Ring Protonation in the Class A β-lactamase Acylation Mechanism Using Neutron and X-ray Crystallography

    SciTech Connect

    Vandavasi, Venu Gopal; Weiss, Kevin L.; Cooper, Jonathan B.; Erskine, Peter T.; Tomanicek, Stephen J.; Ostermann, Andreas; Schrader, Tobias E.; Ginell, Stephan L.; Coates, Leighton

    2016-01-14

    The catalytic mechanism of class A beta-lactamases is often debated due in part to the large number of amino acids that interact with bound beta-lactam substrates. The role and function of the conserved residue Lys 73 in the catalytic mechanism of class A type beta-lactamase enzymes is still not well understood after decades of scientific research. To better elucidate the functions of this vital residue, we used both neutron and high-resolution X-ray diffraction to examine both the structures of the ligand free protein and the acyl-enzyme complex of perdeuterated E166A Toho-1 beta-lactamase with the antibiotic cefotaxime. The E166A mutant lacks a critical glutamate residue that has a key role in the deacylation step of the catalytic mechanism, allowing the acyl-enzyme adduct to be captured for study. In our ligand free structures, Lys 73 is present in a single conformation, however in all of our acyl-enzyme structures, Lys 73 is present in two different conformations, in which one conformer is closer to Ser 70 while the other conformer is positioned closer to Ser 130, which supports the existence of a possible pathway by which proton transfer from Lys 73 to Ser 130 can occur. This and further clarifications of the role of Lys 73 in the acylation mechanism may facilitate the design of inhibitors that capitalize on the enzymes native machinery.

  1. Exploring the Mechanism of β-Lactam Ring Protonation in the Class A β-lactamase Acylation Mechanism Using Neutron and X-ray Crystallography

    SciTech Connect

    Vandavasi, Venu Gopal; Weiss, Kevin L.; Cooper, Jonathan B.; Erskine, Peter T.; Tomanicek, Stephen J.; Ostermann, Andreas; Schrader, Tobias E.; Ginell, Stephan L.; Coates, Leighton

    2015-12-02

    The catalytic mechanism of class A beta-lactamases is often debated due in part to the large number of amino acids that interact with bound beta-lactam substrates. The role and function of the conserved residue Lys 73 in the catalytic mechanism of class A type beta-lactamase enzymes is still not well understood after decades of scientific research. To better elucidate the functions of this vital residue, we used both neutron and high-resolution X-ray diffraction to examine both the structures of the ligand free protein and the acyl-enzyme complex of perdeuterated E166A Toho-1 beta-lactamase with the antibiotic cefotaxime. The E166A mutant lacks a critical glutamate residue that has a key role in the deacylation step of the catalytic mechanism, allowing the acyl-enzyme adduct to be captured for study. In our ligand free structures, Lys 73 is present in a single conformation, however in all of our acyl-enzyme structures, Lys 73 is present in two different conformations, in which one conformer is closer to Ser 70 while the other conformer is positioned closer to Ser 130, which supports the existence of a possible pathway by which proton transfer from Lys 73 to Ser 130 can occur. This and further clarifications of the role of Lys 73 in the acylation mechanism may facilitate the design of inhibitors that capitalize on the enzymes native machinery.

  2. Exploring the Mechanism of β-Lactam Ring Protonation in the Class A β-lactamase Acylation Mechanism Using Neutron and X-ray Crystallography

    DOE PAGES

    Vandavasi, Venu Gopal; Weiss, Kevin L.; Cooper, Jonathan B.; ...

    2015-12-02

    The catalytic mechanism of class A beta-lactamases is often debated due in part to the large number of amino acids that interact with bound beta-lactam substrates. The role and function of the conserved residue Lys 73 in the catalytic mechanism of class A type beta-lactamase enzymes is still not well understood after decades of scientific research. To better elucidate the functions of this vital residue, we used both neutron and high-resolution X-ray diffraction to examine both the structures of the ligand free protein and the acyl-enzyme complex of perdeuterated E166A Toho-1 beta-lactamase with the antibiotic cefotaxime. The E166A mutant lacksmore » a critical glutamate residue that has a key role in the deacylation step of the catalytic mechanism, allowing the acyl-enzyme adduct to be captured for study. In our ligand free structures, Lys 73 is present in a single conformation, however in all of our acyl-enzyme structures, Lys 73 is present in two different conformations, in which one conformer is closer to Ser 70 while the other conformer is positioned closer to Ser 130, which supports the existence of a possible pathway by which proton transfer from Lys 73 to Ser 130 can occur. This and further clarifications of the role of Lys 73 in the acylation mechanism may facilitate the design of inhibitors that capitalize on the enzymes native machinery.« less

  3. Neutron Nucleic Acid Crystallography.

    PubMed

    Chatake, Toshiyuki

    2016-01-01

    The hydration shells surrounding nucleic acids and hydrogen-bonding networks involving water molecules and nucleic acids are essential interactions for the structural stability and function of nucleic acids. Water molecules in the hydration shells influence various conformations of DNA and RNA by specific hydrogen-bonding networks, which often contribute to the chemical reactivity and molecular recognition of nucleic acids. However, X-ray crystallography could not provide a complete description of structural information with respect to hydrogen bonds. Indeed, X-ray crystallography is a powerful tool for determining the locations of water molecules, i.e., the location of the oxygen atom of H2O; however, it is very difficult to determine the orientation of the water molecules, i.e., the orientation of the two hydrogen atoms of H2O, because X-ray scattering from the hydrogen atom is very small.Neutron crystallography is a specialized tool for determining the positions of hydrogen atoms. Neutrons are not diffracted by electrons, but are diffracted by atomic nuclei; accordingly, neutron scattering lengths of hydrogen and its isotopes are comparable to those of non-hydrogen atoms. Therefore, neutron crystallography can determine both of the locations and orientations of water molecules. This chapter describes the current status of neutron nucleic acid crystallographic research as well as the basic principles of neutron diffraction experiments performed on nucleic acid crystals: materials, crystallization, diffraction experiments, and structure determination.

  4. Crystallography: Sources of inspiration

    NASA Astrophysics Data System (ADS)

    McSweeney, Sean; Fromme, Petra

    2014-01-01

    Synchrotrons have long been the preferred X-ray sources for crystallography, but competition has arrived with the advent of X-ray free-electron lasers. A synchrotron expert and an advocate of free-electron lasers discuss the prospects of the respective source types for applications in structural biology.

  5. Radiation tests of the EMU spacesuit for the International SpaceStation using energetic protons

    SciTech Connect

    Zeitlin, C.; Heilbronn, L.; Miller, J.; Shavers, M.

    2001-06-04

    Measurements using silicon detectors to characterize theradiation transmitted through the EMU spacesuit and a human phantom havebeen performed using 155 and 250 MeV proton beams at the Loma LindaUniversity Medical Center (LLUMC). The beams simulate radiationencountered in space, where trapped protons having kinetic energies onthe order of 100 MeV are copious. Protons with 100 MeV kinetic energy andabove can penetrate many centimeters of water of other light materials,so that astronauts exposed to such energetic particles will receive dosesto their internal organs. This dose can be enhanced or reduced byshielding - either from the spacesuit or the self-shielding of the body -but minimization of the risk depends on details of the incident particleflux (in particular the energy spectrum) and on the dose responses of thevarious critical organs.

  6. Five-dimensional crystallography

    PubMed Central

    Schmidt, Marius; Graber, Tim; Henning, Robert; Srajer, Vukica

    2010-01-01

    A method for determining a comprehensive chemical kinetic mechanism in macromolecular reactions is presented. The method is based on five-dimensional crystallography, where, in addition to space and time, temperature is also taken into consideration and an analysis based on singular value decomposition is applied. First results of such a time-resolved crystallographic study are presented. Temperature-dependent time-resolved X-ray diffraction measurements were conducted on the newly upgraded BioCARS 14-ID-B beamline at the Advanced Photon Source and aimed at elucidating a comprehensive kinetic mechanism of the photoactive yellow protein photocycle. Extensive time series of crystallographic data were collected at two temperatures, 293 K and 303 K. Relaxation times of the reaction extracted from these time series exhibit measurable differences for the two temperatures, hence demonstrating that five-dimensional crystallography is feasible. PMID:20164643

  7. Digital data-acquisition system for use with a proton-precession base-station magnetometer

    SciTech Connect

    McPherron, R.L.

    1982-08-26

    At UCLA the base station magnetometer is a Scintrex MB -2 which uses a two inch wide chart record scaled to 100 nT. The magnetometer is also equipped with a digital readout. This is available in BCD format on a 37 pin connector at the back of the instrument. This reading may be recorded digitally if an appropriate data acquisition and storage system is available. The recent development of inexpensive microcomputers and audio cassette recorders provided motivation for our exploration group to develop a digital data acquisition system for the existing base station magnetometer. A block diagram of the data acquisition system is presented. The microcomputer utilizes a R6502 as the central processor. Data are entered into the computer via a 12 key keypad and are displayed on a 6 digit liquid crystal display. Data from the Scintrex base magnetometer is passed to the microcomputer via a 37 line connector. One line of this connector is used to signal the status of the internally controlled sampling circuit in the base station magnetometer. Digital data are stored temporarily in RAM memory until an output buffer is filled. When this occurs power is applied to the audio cassette tape transport mechanism and after a short delay a block of data is written onto tape. The tape interface implements the Kansas City standard which is nearly universally used for microcomputer recording on audio cassette recorders. The entire system is powered by the same 12V dc battery used by the base station magnetometer. (WHK)

  8. Inner magnetosphere variations after solar proton events. Observations on Mir space station in 1989-1994 time period.

    PubMed

    Dachev TsP; Semkova, J V; Matviichuk YuN; Tomov, B T; Koleva, R T; Baynov, P T; Petrov, V M; Shurshakov, V V; Ivanov, Y u

    1998-01-01

    Measurements on board the Mir space station have been used to study the dose rate and the particle flux distribution in the inner magnetosphere. The measurements have been performed with the Bulgarian-Russian dosimeter-radiometer Liulin. The paper concentrates on the dynamics of the observed "new" and "second" maxima which were created after Solar Proton Events (SPE) in the 1989-1994 time. The "second" belt was first observed after the SPE on October 20, 1989, and the last observation was after the SPE on February 20, 1994. The creation of the "new" belt is a unique phenomena seen in the Liulin data set after the SPE on March 23, 1991 and relates to the magnetic storm on March 24. The new belt fully disappears in the middle of 1993.

  9. Crystallography: past and present

    NASA Astrophysics Data System (ADS)

    Hodeau, J.-L.; Guinebretiere, R.

    2007-12-01

    In the 19th century, crystallography referred to the study of crystal shapes. Such studies by Haüy and Bravais allowed the establishment of important hypotheses such as (i) “les molécules intégrantes qui sont censées être les plus petits solides que l’on puisse extraire d’un minéral” [1], (ii) the definition of the crystal lattice and (iii) “le cristal est clivable parallèlement à deux ou trois formes cristallines” [2]. This morphological crystallography defined a crystal like “a chemically homogeneous solid, wholly or partly bounded by natural planes that intersect at predetermined angles” [3]. It described the main symmetry elements and operations, nomenclatures of different crystal forms and also the theory of twinning. A breakthrough appeared in 1912 with the use of X-rays by M. von Laue and W.H. and W.L. Bragg. This experimental development allowed the determination of the atomic content of each unit cell constituting the crystal and defined a crystal as “any solid in which an atomic pattern is repeated periodically in three dimensions, that is, any solid that “diffracts” an incident X-ray beam” [3]. Mathematical tools like the Patterson methods, the direct methods, were developed. The way for solving crystalline structure was opened first for simple compounds and at that time crystallography was associated mainly with perfect crystals. In the fifties, crystallographers already had most apparatus and fundamental methods at their disposal; however, we had to wait for the development of computers to see the full use of these tools. Furthermore the development of new sources of neutrons, electrons and synchrotron X-rays allowed the studies of complex compounds like large macromolecules in biology. Nowadays, one of the new frontiers for crystallographers is to relate the crystal structure to its physical-chemical-biological properties, this means that an accurate structural determination is needed to focus on a selective part of the

  10. Precision measurement of the proton and helium flux in primary cosmic rays with the Alpha Magnetic Spectrometer on the International Space Station

    NASA Astrophysics Data System (ADS)

    Heil, M.

    2016-11-01

    The precise measurements of the proton and helium flux in primary cosmic rays based on on data collected by the Alpha Magnetic Spectrometer during the first 30 months of operation (May 19, 2012 to November 26, 2013) onboard the International Space Station are presented. Knowledge of the rigidity dependence of the proton and helium flux is important in understanding the origin, acceleration, and propagation of cosmic rays in our galaxy. The high statistics of the measurements (300 mio. protons, 50 mio. helium) allow to study the detailed variations with rigidity of the fluxes spectral index. The spectral index of both the proton and the helium flux progressively hardens at rigidities larger than 100 GV. The rigidity dependence of the helium flux spectral index is similar to that of the proton spectral index though the magnitudes are different. Remarkably, the spectral index of the proton to helium flux ratio increases with rigidity up to 45 GV and then becomes constant; the flux ratio above 45 GV is well described by a single power law.

  11. From crystallography to life

    NASA Astrophysics Data System (ADS)

    Allen, Roland E.

    2014-06-01

    2014 is the International Year of Crystallography, an extremely broad field which has had enormous impact in biology and materials science. Both experimental facilities and methods for interpreting the data have become increasingly sophisticated during the past century, and many highly complex systems have now been characterized, including large proteins and other biological macromolecules. A very few representative examples are mentioned here, including crystallographic studies of proteins that regulate programmed cell death (apoptosis), and structure determinations of G-protein coupled receptors (GPCRs), respectively the subjects of the 2014 Aminoff Prize and the 2012 Nobel Prize in chemistry. Normal apoptosis is essential for human embryonic development, prevention of cancer, and other processes within multicellular organisms. GPCRs are the targets of about half of all modern medicinal drugs, since they are responsible for the majority of cellular responses to hormones and neurotransmitters, as well as the senses of sight, taste, and smell. In materials, the behavior of electrons (both ordinary and exotic) is largely determined by the arrangement of the atoms. As examples, we mention carbon-based materials (diamond, buckyballs, nanotubes, and graphene) and high-temperature superconductors (cuprate and iron-based).

  12. Infrared Protein Crystallography

    SciTech Connect

    J Sage; Y Zhang; J McGeehan; R Ravelli; M Weik; J van Thor

    2011-12-31

    We consider the application of infrared spectroscopy to protein crystals, with particular emphasis on exploiting molecular orientation through polarization measurements on oriented single crystals. Infrared microscopes enable transmission measurements on individual crystals using either thermal or nonthermal sources, and can accommodate flow cells, used to measure spectral changes induced by exposure to soluble ligands, and cryostreams, used for measurements of flash-cooled crystals. Comparison of unpolarized infrared measurements on crystals and solutions probes the effects of crystallization and can enhance the value of the structural models refined from X-ray diffraction data by establishing solution conditions under which they are most relevant. Results on several proteins are consistent with similar equilibrium conformational distributions in crystal and solutions. However, the rates of conformational change are often perturbed. Infrared measurements also detect products generated by X-ray exposure, including CO{sub 2}. Crystals with favorable symmetry exhibit infrared dichroism that enhances the synergy with X-ray crystallography. Polarized infrared measurements on crystals can distinguish spectral contributions from chemically similar sites, identify hydrogen bonding partners, and, in opportune situations, determine three-dimensional orientations of molecular groups. This article is part of a Special Issue entitled: Protein Structure and Function in the Crystalline State.

  13. Warm dense crystallography

    NASA Astrophysics Data System (ADS)

    Valenza, Ryan A.; Seidler, Gerald T.

    2016-03-01

    The intense femtosecond-scale pulses from x-ray free electron lasers (XFELs) are able to create and interrogate interesting states of matter characterized by long-lived nonequilibrium semicore or core electron occupancies or by the heating of dense phases via the relaxation cascade initiated by the photoelectric effect. We address here the latter case of "warm dense matter" (WDM) and investigate the observable consequences of x-ray heating of the electronic degrees of freedom in crystalline systems. We report temperature-dependent density functional theory calculations for the x-ray diffraction from crystalline LiF, graphite, diamond, and Be. We find testable, strong signatures of condensed-phase effects that emphasize the importance of wide-angle scattering to study nonequilibrium states. These results also suggest that the reorganization of the valence electron density at eV-scale temperatures presents a confounding factor to achieving atomic resolution in macromolecular serial femtosecond crystallography (SFX) studies at XFELs, as performed under the "diffract before destroy" paradigm.

  14. Lipidic cubic phase serial millisecond crystallography using synchrotron radiation

    PubMed Central

    Nogly, Przemyslaw; James, Daniel; Wang, Dingjie; White, Thomas A.; Zatsepin, Nadia; Shilova, Anastasya; Nelson, Garrett; Liu, Haiguang; Johansson, Linda; Heymann, Michael; Jaeger, Kathrin; Metz, Markus; Wickstrand, Cecilia; Wu, Wenting; Båth, Petra; Berntsen, Peter; Oberthuer, Dominik; Panneels, Valerie; Cherezov, Vadim; Chapman, Henry; Schertler, Gebhard; Neutze, Richard; Spence, John; Moraes, Isabel; Burghammer, Manfred; Standfuss, Joerg; Weierstall, Uwe

    2015-01-01

    Lipidic cubic phases (LCPs) have emerged as successful matrixes for the crystallization of membrane proteins. Moreover, the viscous LCP also provides a highly effective delivery medium for serial femtosecond crystallography (SFX) at X-ray free-electron lasers (XFELs). Here, the adaptation of this technology to perform serial millisecond crystallography (SMX) at more widely available synchrotron microfocus beamlines is described. Compared with conventional microcrystallography, LCP-SMX eliminates the need for difficult handling of individual crystals and allows for data collection at room temperature. The technology is demonstrated by solving a structure of the light-driven proton-pump bacteriorhodopsin (bR) at a resolution of 2.4 Å. The room-temperature structure of bR is very similar to previous cryogenic structures but shows small yet distinct differences in the retinal ligand and proton-transfer pathway. PMID:25866654

  15. Sub-atomic resolution X-ray crystallography and neutron crystallography: promise, challenges and potential

    PubMed Central

    Blakeley, Matthew P.; Hasnain, Samar S.; Antonyuk, Svetlana V.

    2015-01-01

    The International Year of Crystallography saw the number of macromolecular structures deposited in the Protein Data Bank cross the 100000 mark, with more than 90000 of these provided by X-ray crystallography. The number of X-ray structures determined to sub-atomic resolution (i.e. ≤1 Å) has passed 600 and this is likely to continue to grow rapidly with diffraction-limited synchrotron radiation sources such as MAX-IV (Sweden) and Sirius (Brazil) under construction. A dozen X-ray structures have been deposited to ultra-high resolution (i.e. ≤0.7 Å), for which precise electron density can be exploited to obtain charge density and provide information on the bonding character of catalytic or electron transfer sites. Although the development of neutron macromolecular crystallography over the years has been far less pronounced, and its application much less widespread, the availability of new and improved instrumentation, combined with dedicated deuteration facilities, are beginning to transform the field. Of the 83 macromolecular structures deposited with neutron diffraction data, more than half (49/83, 59%) were released since 2010. Sub-mm3 crystals are now regularly being used for data collection, structures have been determined to atomic resolution for a few small proteins, and much larger unit-cell systems (cell edges >100 Å) are being successfully studied. While some details relating to H-atom positions are tractable with X-ray crystallography at sub-atomic resolution, the mobility of certain H atoms precludes them from being located. In addition, highly polarized H atoms and protons (H+) remain invisible with X-rays. Moreover, the majority of X-ray structures are determined from cryo-cooled crystals at 100 K, and, although radiation damage can be strongly controlled, especially since the advent of shutterless fast detectors, and by using limited doses and crystal translation at micro-focus beams, radiation damage can still take place. Neutron

  16. Sub-atomic resolution X-ray crystallography and neutron crystallography: promise, challenges and potential.

    PubMed

    Blakeley, Matthew P; Hasnain, Samar S; Antonyuk, Svetlana V

    2015-07-01

    The International Year of Crystallography saw the number of macromolecular structures deposited in the Protein Data Bank cross the 100000 mark, with more than 90000 of these provided by X-ray crystallography. The number of X-ray structures determined to sub-atomic resolution (i.e. ≤1 Å) has passed 600 and this is likely to continue to grow rapidly with diffraction-limited synchrotron radiation sources such as MAX-IV (Sweden) and Sirius (Brazil) under construction. A dozen X-ray structures have been deposited to ultra-high resolution (i.e. ≤0.7 Å), for which precise electron density can be exploited to obtain charge density and provide information on the bonding character of catalytic or electron transfer sites. Although the development of neutron macromolecular crystallography over the years has been far less pronounced, and its application much less widespread, the availability of new and improved instrumentation, combined with dedicated deuteration facilities, are beginning to transform the field. Of the 83 macromolecular structures deposited with neutron diffraction data, more than half (49/83, 59%) were released since 2010. Sub-mm(3) crystals are now regularly being used for data collection, structures have been determined to atomic resolution for a few small proteins, and much larger unit-cell systems (cell edges >100 Å) are being successfully studied. While some details relating to H-atom positions are tractable with X-ray crystallography at sub-atomic resolution, the mobility of certain H atoms precludes them from being located. In addition, highly polarized H atoms and protons (H(+)) remain invisible with X-rays. Moreover, the majority of X-ray structures are determined from cryo-cooled crystals at 100 K, and, although radiation damage can be strongly controlled, especially since the advent of shutterless fast detectors, and by using limited doses and crystal translation at micro-focus beams, radiation damage can still take place. Neutron

  17. Microgravity and Macromolecular Crystallography

    NASA Technical Reports Server (NTRS)

    Kundrot, Craig E.; Judge, Russell A.; Pusey, Marc L.; Snell, Edward H.; Rose, M. Franklin (Technical Monitor)

    2000-01-01

    Macromolecular crystal growth has been seen as an ideal experiment to make use of the reduced acceleration environment provided by an orbiting spacecraft. The experiments are small, simply operated and have a high potential scientific and economic impact. In this review we examine the theoretical reasons why microgravity should be a beneficial environment for crystal growth and survey the history of experiments on the Space Shuttle Orbiter, on unmanned spacecraft, and on the Mir space station. Finally we outline the direction for optimizing the future use of orbiting platforms.

  18. Microgravity and Macromolecular Crystallography

    NASA Technical Reports Server (NTRS)

    Kundrot, Craig E.; Judge, Russell A.; Pusey, Marc L.; Snell, Edward H.; Rose, M. Franklin (Technical Monitor)

    2000-01-01

    Macromolecular crystal growth has been seen as an ideal experiment to make use of the reduced acceleration environment provided by an orbiting spacecraft. The experiments are small, simply operated and have a high potential scientific and economic impact. In this review we examine the theoretical reasons why microgravity should be a beneficial environment for crystal growth and survey the history of experiments on the Space Shuttle Orbiter, on unmanned spacecraft, and on the Mir space station. Finally we outline the direction for optimizing the future use of orbiting platforms.

  19. NMR crystallography: the use of chemical shifts

    NASA Astrophysics Data System (ADS)

    Harris, Robin K.

    2004-10-01

    Measurements of chemical shifts obtained from magic-angle spinning NMR spectra (together with quantum mechanical computations of shielding) can provide valuable information on crystallography. Examples are given of the determination of crystallographic asymmetric units, of molecular symmetry in the solid-state environment, and of crystallographic space group assignment. Measurements of full tensor components for 199Hg have given additional coordination information. The nature of intermolecular hydrogen bonding in cortisone acetate polymorphs and solvates is obtained from chemical shift information, also involving measurement of the full tensor parameters. The resulting data have been used as restraints, built into the computation algorithm, in the analysis of powder diffraction patterns to give full crystal structures. A combination of quantum mechanical computation of shielding and measurement of proton chemical shifts (obtained by high-speed MAS) leads to the determination of the position of a proton in an intermolecular hydrogen bond. A recently-developed computer program specifically based on crystallographic repetition has been shown to give acceptable results. Moreover, NMR chemical shifts can distinguish between static and dynamic disorder in crystalline materials and can be used to determine modes and rates of molecular exchange motion.

  20. Neutron crystallography for the study of hydrogen bonds in macromolecules

    DOE PAGES

    Oksanen, Esko; Chen, Julian C.; Fisher, Zoe

    2017-04-07

    The hydrogen bond (H bond) is one of the most important interactions that form the foundation of secondary and tertiary protein structure. Beyond holding protein structures together, H bonds are also intimately involved in solvent coordination, ligand binding, and enzyme catalysis. The H bond by definition involves the light atom, H, and it is very difficult to study directly, especially with X-ray crystallographic techniques, due to the poor scattering power of H atoms. Neutron protein crystallography provides a powerful, complementary tool that can give unambiguous information to structural biologists on solvent organization and coordination, the electrostatics of ligand binding, themore » protonation states of amino acid side chains and catalytic water species. The method is complementary to X-ray crystallography and the dynamic data obtainable with NMR spectroscopy. Also, as it gives explicit H atom positions, it can be very valuable to computational chemistry where exact knowledge of protonation and solvent orientation can make a large difference in modeling. Finally, this article gives general information about neutron crystallography and shows specific examples of how the method has contributed to structural biology, structure-based drug design; and the understanding of fundamental questions of reaction mechanisms.« less

  1. Neutron Crystallography for the Study of Hydrogen Bonds in Macromolecules.

    PubMed

    Oksanen, Esko; Chen, Julian C-H; Fisher, Suzanne Zoë

    2017-04-07

    Abstract: The hydrogen bond (H bond) is one of the most important interactions that form the foundation of secondary and tertiary protein structure. Beyond holding protein structures together, H bonds are also intimately involved in solvent coordination, ligand binding, and enzyme catalysis. The H bond by definition involves the light atom, H, and it is very difficult to study directly, especially with X-ray crystallographic techniques, due to the poor scattering power of H atoms. Neutron protein crystallography provides a powerful, complementary tool that can give unambiguous information to structural biologists on solvent organization and coordination, the electrostatics of ligand binding, the protonation states of amino acid side chains and catalytic water species. The method is complementary to X-ray crystallography and the dynamic data obtainable with NMR spectroscopy. Also, as it gives explicit H atom positions, it can be very valuable to computational chemistry where exact knowledge of protonation and solvent orientation can make a large difference in modeling. This article gives general information about neutron crystallography and shows specific examples of how the method has contributed to structural biology, structure-based drug design; and the understanding of fundamental questions of reaction mechanisms.

  2. Direct methods in protein crystallography.

    PubMed

    Karle, J

    1989-11-01

    It is pointed out that the 'direct methods' of phase determination for small-structure crystallography do not have immediate applicability to macromolecular structures. The term 'direct methods in macromolecular crystallography' is suggested to categorize a spectrum of approaches to macromolecular structure determination in which the analyses are characterized by the use of two-phase and higher-order-phase invariants. The evaluation of the invariants is generally obtained by the use of heavy-atom techniques. The results of a number of the more recent algebraic and probabilistic studies involving isomorphous replacement and anomalous dispersion thus become valid subjects for discussion here. These studies are described and suggestions are also presented concerning future applicability. Additional discussion concerns the special techniques of filtering, the use of non-crystallographic symmetry, some features of maximum entropy and attempts to apply phase-determining formulas to the refinement of macromolecular structure. It is noted that, in addition to the continuing remarkable progress in macromolecular crystallography based on the traditional applications of isomorphous replacement and anomalous dispersion, recent valuable advances have been made in the application of non-crystallographic symmetry, in particular, to virus structures and in applications of filtering. Good progress has also been reported in the application of exact linear algebra to multiple-wavelength anomalous-dispersion investigations of structures containing anomalous scatterers of only moderate scattering power.

  3. Micro-crystallography comes of age

    PubMed Central

    Smith, Janet L.; Fischetti, Robert F.; Yamamoto, Masaki

    2012-01-01

    The latest revolution in macromolecular crystallography was incited by the development of dedicated, user friendly, micro-crystallography beamlines. Brilliant X-ray beams of diameter 20 microns or less, now available at most synchrotron sources, enable structure determination from samples that previously were inaccessible. Relative to traditional crystallography, crystals with one or more small dimensions have diffraction patterns with vastly improved signal-to-noise when recorded with an appropriately matched beam size. Structures can be solved from isolated, well diffracting regions within inhomogeneous samples. This review summarizes the technological requirements and approaches to producing micro-beams and how they continue to change the practice of crystallography. PMID:23021872

  4. Radiation Tests of the Extravehicular Mobility Unit Space Suit for the International Space Station Using Energetic Protons. Chapter 3

    NASA Technical Reports Server (NTRS)

    Zeitlin, C.; Heilbronn, L.; Miller, J.; Shavers, M.

    2003-01-01

    Measurements using silicon detectors to characterize the radiation transmitted through the EMU space suit and a human phantom have been performed using 155 and 250 MeV proton beams at LLUMC. The beams simulate radiation encountered in space, where trapped protons having kinetic energies on the order of 100 MeV are copious. Protons with 100 MeV kinetic energy and above can penetrate many centimeters of water or other light materials, so that astronauts exposed to such energetic particles will receive doses to their internal organs. This dose can be enhanced or reduced by shielding - either from the space suit or the self-shielding of the body - but minimization of the risk depends on details of the incident particle flux (in particular the energy spectrum) and on the dose responses of the various critical organs. Data were taken to characterize the beams and to calibrate the detectors using the beam in a treatment room at LLUPTF, in preparation for an experiment with the same beams incident on detectors placed in a human phantom within the EMU suit. Nuclear interactions of high-energy protons in various materials produce a small flux of highly ionizing, low-energy secondary radiation. Secondaries are of interest for their biological effects, since they cause doses and especially dose-equivalents to increase relative to the values expected simply from ionization energy loss along the Bragg curve. Because many secondaries have very short ranges, they are best measured in passive track detectors such as CR-39. The silicon detector data presented here are intended to supplement the CR-39 data in regions where silicon has greater sensitivity, in particular the portion of the LET spectrum below 5 keV/micron. The results obtained in this study suggest that optimizing the radiation shielding properties of space suits is a formidable task. The naive assumption that adding mass can reduce risk is not supported by the data, which show that reducing the dose delivered at or

  5. Wrinkling crystallography on spherical surfaces.

    PubMed

    Brojan, Miha; Terwagne, Denis; Lagrange, Romain; Reis, Pedro M

    2015-01-06

    We present the results of an experimental investigation on the crystallography of the dimpled patterns obtained through wrinkling of a curved elastic system. Our macroscopic samples comprise a thin hemispherical shell bound to an equally curved compliant substrate. Under compression, a crystalline pattern of dimples self-organizes on the surface of the shell. Stresses are relaxed by both out-of-surface buckling and the emergence of defects in the quasi-hexagonal pattern. Three-dimensional scanning is used to digitize the topography. Regarding the dimples as point-like packing units produces spherical Voronoi tessellations with cells that are polydisperse and distorted, away from their regular shapes. We analyze the structure of crystalline defects, as a function of system size. Disclinations are observed and, above a threshold value, dislocations proliferate rapidly with system size. Our samples exhibit striking similarities with other curved crystals of charged particles and colloids. Differences are also found and attributed to the far-from-equilibrium nature of our patterns due to the random and initially frozen material imperfections which act as nucleation points, the presence of a physical boundary which represents an additional source of stress, and the inability of dimples to rearrange during crystallization. Even if we do not have access to the exact form of the interdimple interaction, our experiments suggest a broader generality of previous results of curved crystallography and their robustness on the details of the interaction potential. Furthermore, our findings open the door to future studies on curved crystals far from equilibrium.

  6. The success story of crystallography.

    PubMed

    Schwarzenbach, Dieter

    2012-01-01

    Diffractionists usually place the birth of crystallography in 1912 with the first X-ray diffraction experiment of Friedrich, Knipping and Laue. This discovery propelled the mathematical branch of mineralogy to global importance and enabled crystal structure determination. Knowledge of the geometrical structure of matter at atomic resolution had revolutionary consequences for all branches of the natural sciences: physics, chemistry, biology, earth sciences and material science. It is scarcely possible for a single person in a single article to trace and appropriately value all of these developments. This article presents the limited, subjective view of its author and a limited selection of references. The bulk of the article covers the history of X-ray structure determination from the NaCl structure to aperiodic structures and macromolecular structures. The theoretical foundations were available by 1920. The subsequent success of crystallography was then due to the development of diffraction equipment, the theory of the solution of the phase problem, symmetry theory and computers. The many structures becoming known called for the development of crystal chemistry and of data banks. Diffuse scattering from disordered structures without and with partial long-range order allows determination of short-range order. Neutron and electron scattering and diffraction are also mentioned.

  7. Microfluidic Tools for Protein Crystallography

    NASA Astrophysics Data System (ADS)

    Abdallah, Bahige G.

    X-ray crystallography is the most widely used method to determine the structure of proteins, providing an understanding of their functions in all aspects of life to advance applications in fields such as drug development and renewable energy. New techniques, namely serial femtosecond crystallography (SFX), have unlocked the ability to unravel the structures of complex proteins with vital biological functions. A key step and major bottleneck of structure determination is protein crystallization, which is very arduous due to the complexity of proteins and their natural environments. Furthermore, crystal characteristics govern data quality, thus need to be optimized to attain the most accurate reconstruction of the protein structure. Crystal size is one such characteristic in which narrowed distributions with a small modal size can significantly reduce the amount of protein needed for SFX. A novel microfluidic sorting platform was developed to isolate viable ~200 nm -- ~600 nm photosystem I (PSI) membrane protein crystals from ~200 nm -- ~20 ?m crystal samples using dielectrophoresis, as confirmed by fluorescence microscopy, second-order nonlinear imaging of chiral crystals (SONICC), and dynamic light scattering. The platform was scaled-up to rapidly provide 100s of microliters of sorted crystals necessary for SFX, in which similar crystal size distributions were attained. Transmission electron microscopy was used to view the PSI crystal lattice, which remained well-ordered postsorting, and SFX diffraction data was obtained, confirming a high-quality, viable crystal sample. Simulations indicated sorted samples provided accurate, complete SFX datasets with 3500-fold less protein than unsorted samples. Microfluidic devices were also developed for versatile, rapid protein crystallization screening using nanovolumes of sample. Concentration gradients of protein and precipitant were generated to crystallize PSI, phycocyanin, and lysozyme using modified counterdiffusion

  8. Sample mounts for microcrystal crystallography

    NASA Technical Reports Server (NTRS)

    Thorne, Robert E. (Inventor); Stum, Zachary (Inventor); O'Neill, Kevin (Inventor); Kmetko, Jan (Inventor)

    2009-01-01

    Sample mounts (10) for mounting microcrystals of biological macromolecules for X-ray crystallography are prepared by using patterned thin polyimide films (12) that have curvature imparted thereto, for example, by being attached to a curved outer surface of a small metal rod (16). The patterned film (12) preferably includes a tip end (24) for holding a crystal. Preferably, a small sample aperture is disposed in the film for reception of the crystal. A second, larger aperture can also be provided that is connected to the sample aperture by a drainage channel, allowing removal of excess liquid and easier manipulation in viscous solutions. The curvature imparted to the film (12) increases the film's rigidity and allows a convenient scoop-like action for retrieving crystals. The polyimide contributes minimally to background and absorption, and can be treated to obtain desired hydrophobicity or hydrophilicity.

  9. Phase retrieval in protein crystallography.

    PubMed

    Liu, Zhong Chuan; Xu, Rui; Dong, Yu Hui

    2012-03-01

    Solution of the phase problem is central to crystallographic structure determination. An oversampling method is proposed, based on the hybrid input-output algorithm (HIO) [Fienup (1982). Appl. Opt. 21, 2758-2769], to retrieve the phases of reflections in crystallography. This method can extend low-resolution structures to higher resolution for structure determination of proteins without additional sample preparation. The method requires an envelope of the protein which divides a unit cell into the density region where the proteins are located and the non-density region occupied by solvents. After a few hundred to a few thousand iterations, the correct phases and density maps are recovered. The method has been used successfully in several cases to retrieve the phases from the experimental X-ray diffraction data and the envelopes of proteins constructed from structure files downloaded from the Protein Data Bank. It is hoped that this method will greatly facilitate the ab initio structure determination of proteins.

  10. Sample mounts for microcrystal crystallography

    NASA Technical Reports Server (NTRS)

    Thorne, Robert E. (Inventor); Stum, Zachary (Inventor); O'Neill, Kevin (Inventor); Kmetko, Jan (Inventor)

    2007-01-01

    Sample mounts (10) for mounting microcrystals of biological macromolecules for X-ray crystallography are prepared by using patterned thin polyimide films (12) that have curvature imparted thereto, for example, by being attached to a curved outer surface of a small metal rod (16). The patterned film (12) preferably includes a tapered tip end (24) for holding a crystal. Preferably, a small sample aperture is disposed in the film for reception of the crystal. A second, larger aperture can also be provided that is connected to the sample aperture by a drainage channel, allowing removal of excess liquid and easier manipulation in viscous solutions. The curvature imparted to the film (12) increases the film's rigidity and allows a convenient scoop-like action for retrieving crystals. The polyimide contributes minimally to background and absorption, and can be treated to obtain desired hydrophobicity or hydrophilicity.

  11. Wrinkling crystallography on spherical surfaces

    PubMed Central

    Brojan, Miha; Terwagne, Denis; Lagrange, Romain; Reis, Pedro M.

    2015-01-01

    We present the results of an experimental investigation on the crystallography of the dimpled patterns obtained through wrinkling of a curved elastic system. Our macroscopic samples comprise a thin hemispherical shell bound to an equally curved compliant substrate. Under compression, a crystalline pattern of dimples self-organizes on the surface of the shell. Stresses are relaxed by both out-of-surface buckling and the emergence of defects in the quasi-hexagonal pattern. Three-dimensional scanning is used to digitize the topography. Regarding the dimples as point-like packing units produces spherical Voronoi tessellations with cells that are polydisperse and distorted, away from their regular shapes. We analyze the structure of crystalline defects, as a function of system size. Disclinations are observed and, above a threshold value, dislocations proliferate rapidly with system size. Our samples exhibit striking similarities with other curved crystals of charged particles and colloids. Differences are also found and attributed to the far-from-equilibrium nature of our patterns due to the random and initially frozen material imperfections which act as nucleation points, the presence of a physical boundary which represents an additional source of stress, and the inability of dimples to rearrange during crystallization. Even if we do not have access to the exact form of the interdimple interaction, our experiments suggest a broader generality of previous results of curved crystallography and their robustness on the details of the interaction potential. Furthermore, our findings open the door to future studies on curved crystals far from equilibrium. PMID:25535355

  12. X-rays and solar proton event induced changes in the first mode Schumann resonance frequency observed at a low latitude station Agra, India

    NASA Astrophysics Data System (ADS)

    Singh, Birbal; Tyagi, Rajesh; Hobara, Yasuhide; Hayakawa, Masashi

    2014-06-01

    Effects of two events of X-ray bursts followed by solar proton events (SPEs) occurred on 22 September, 2011 and 06 July, 2012 on the variation of first mode Schumann resonance (SR) frequency monitored at a low latitude station, Agra (Geograph. lat. 27.2°N, long. 78°E) India are examined. The variation of average first mode SR frequency shows a sudden increase in coincidence with the X-ray bursts and a decrease associated with the peak flux of SPE. The increases in the frequency in the two cases are 8.4% and 10.9% and corresponding decreases are 4.3% and 3.3% respectively. The increases in the frequency are interpreted in terms of growth of ionization in the upper part of D-region ionosphere due to X-ray bursts and decreases during SPE are caused by the high ionization in the lower D-region (altitude about 50-60 km) in the polar region. The variation of SR frequency is observed to be consistent with other observatories at middle and high latitudes. The effects of X-ray flares on the D-region of the ionosphere at low and equatorial latitudes are also examined by analyzing the amplitude data of VLF transmitter signal (NWC, f=19.8 kHz) monitored at Agra. The flare effect observed prior to sun-set hours shows increase of electron density above 60 km in the ionosphere.

  13. History of protein crystallography in China.

    PubMed

    Rao, Zihe

    2007-06-29

    China has a strong background in X-ray crystallography dating back to the 1920s. Protein crystallography research in China was first developed following the successful synthesis of insulin in China in 1966. The subsequent determination of the three-dimensional structure of porcine insulin made China one of the few countries which could determine macromolecular structures by X-ray diffraction methods in the late 1960s and early 1970s. After a slow period during the 1970s and 1980s, protein crystallography in China has reached a new climax with a number of outstanding accomplishments. Here, I review the history and progress of protein crystallography in China and detail some of the recent research highlights, including the crystal structures of two membrane proteins as well as the structural genomics initiative in China.

  14. Automated data collection for macromolecular crystallography.

    PubMed

    Winter, Graeme; McAuley, Katherine E

    2011-09-01

    An overview, together with some practical advice, is presented of the current status of the automation of macromolecular crystallography (MX) data collection, with a focus on MX beamlines at Diamond Light Source, UK.

  15. X-ray crystallography of viruses.

    PubMed

    Verdaguer, Nuria; Garriga, Damià; Fita, Ignacio

    2013-01-01

    For about 30 years X-ray crystallography has been by far the most powerful approach for determining virus structures at close to atomic resolutions. Information provided by these studies has deeply and extensively enriched and shaped our vision of the virus world. In turn, the ever increasing complexity and size of the virus structures being investigated have constituted a major driving force for methodological and conceptual developments in X-ray macromolecular crystallography. Landmarks of new virus structures determinations, such as the ones from the first animal viruses or from the first membrane-containing viruses, have often been associated to methodological breakthroughs in X-ray crystallography. In this chapter we present the common ground of proteins and virus crystallography with an emphasis in the peculiarities of virus studies. For example, the solution of the phase problem, a central issue in X-ray diffraction, has benefited enormously from the presence of non-crystallographic symmetry in virus crystals.

  16. Statistical learning for chemical crystallography

    NASA Astrophysics Data System (ADS)

    Balachandran, Prasanna V.

    A novel computational approach is developed for the study of chemical crystallography in materials science using the tools of information theory and data science. By integrating the information derived from phase homologies, electronic structure calculations and known crystal structure data, a high-dimensional data space is created. From this data space, we seek to extract statistically robust and yet physically meaningful relationships linking structure with chemistry and property in the form of chemical design rules that identifies the exact role of key structure governing factors without any a priori assumptions. The powerful role of data dimensionality reduction, clustering analysis and data mining methods for both classification and prediction of structure-property relationships in materials is discussed. Using examples from two different crystal chemistry families, apatites and perovskite oxides, it is shown how high-dimensional data can be used to assess patterns of behavior as well as establish predictive Quantitative Structure-Activity Relationships (QSARs). A library of potentially new "virtual" stoichiometric and non-stoichiometric apatites and high TC piezoelectric perovskite materials chemistries were identified, thereby reinforcing the value of statistical learning methods in rational materials design.

  17. Structure validation in chemical crystallography

    PubMed Central

    Spek, Anthony L.

    2009-01-01

    Automated structure validation was introduced in chemical crystallography about 12 years ago as a tool to assist practitioners with the exponential growth in crystal structure analyses. Validation has since evolved into an easy-to-use checkCIF/PLATON web-based IUCr service. The result of a crystal structure determination has to be supplied as a CIF-formatted computer-readable file. The checking software tests the data in the CIF for completeness, quality and consistency. In addition, the reported structure is checked for incomplete analysis, errors in the analysis and relevant issues to be verified. A validation report is generated in the form of a list of ALERTS on the issues to be corrected, checked or commented on. Structure validation has largely eliminated obvious problems with structure reports published in IUCr journals, such as refinement in a space group of too low symmetry. This paper reports on the current status of structure validation and possible future extensions. PMID:19171970

  18. Asymmetry in serial femtosecond crystallography data

    PubMed Central

    Sharma, Amit; Johansson, Linda; Dunevall, Elin; Wahlgren, Weixiao Y.; Neutze, Richard

    2017-01-01

    Serial crystallography is an increasingly important approach to protein crystallography that exploits both X-ray free-electron laser (XFEL) and synchrotron radiation. Serial crystallography recovers complete X-ray diffraction data by processing and merging diffraction images from thousands of randomly oriented non-uniform microcrystals, of which all observations are partial Bragg reflections. Random fluctuations in the XFEL pulse energy spectrum, variations in the size and shape of microcrystals, integrating over millions of weak partial observations and instabilities in the XFEL beam position lead to new types of experimental errors. The quality of Bragg intensity estimates deriving from serial crystallography is therefore contingent upon assumptions made while modeling these data. Here it is observed that serial femtosecond crystallography (SFX) Bragg reflections do not follow a unimodal Gaussian distribution and it is recommended that an idealized assumption of single Gaussian peak profiles be relaxed to incorporate apparent asymmetries when processing SFX data. The phenomenon is illustrated by re-analyzing data collected from microcrystals of the Blastochloris viridis photosynthetic reaction center and comparing these intensity observations with conventional synchrotron data. The results show that skewness in the SFX observations captures the essence of the Wilson plot and an empirical treatment is suggested that can help to separate the diffraction Bragg intensity from the background. PMID:28248658

  19. Canadian macromolecular crystallography facility: a suite of fully automated beamlines.

    PubMed

    Grochulski, Pawel; Fodje, Michel; Labiuk, Shaunivan; Gorin, James; Janzen, Kathryn; Berg, Russ

    2012-06-01

    The Canadian light source is a 2.9 GeV national synchrotron radiation facility located on the University of Saskatchewan campus in Saskatoon. The small-gap in-vacuum undulator illuminated beamline, 08ID-1, together with the bending magnet beamline, 08B1-1, constitute the Canadian Macromolecular Crystallography Facility (CMCF). The CMCF provides service to more than 50 Principal Investigators in Canada and the United States. Up to 25% of the beam time is devoted to commercial users and the general user program is guaranteed up to 55% of the useful beam time through a peer-review process. CMCF staff provides "Mail-In" crystallography service to users with the highest scored proposals. Both beamlines are equipped with very robust end-stations including on-axis visualization systems, Rayonix 300 CCD series detectors and Stanford-type robotic sample auto-mounters. MxDC, an in-house developed beamline control system, is integrated with a data processing module, AutoProcess, allowing full automation of data collection and data processing with minimal human intervention. Sample management and remote monitoring of experiments is enabled through interaction with a Laboratory Information Management System developed at the facility.

  20. E-Science and Protein Crystallography

    SciTech Connect

    Miller, Laniece E.; Powell, James E. Jr.

    2012-08-09

    Dr. Zoe Fisher is the instrument scientist for the Protein Crystallography Station (PCS) at the Los Alamos Neutron Science Center's (LANSC) Lujan Neutron Scattering Center. She helps schedule researchers who intend to use the instrument to collect data, and provides in depth support for their activities. Users submit proposals for beam/instrument time via LANSCE proposal review system. In 2012, there were about 20 proposals submitted for this instrument. The instrument scientists review the proposals online. Accepted proposals are scheduled via an aggregate calendar which takes into account staff and resource availability, and the scientist is notified via email when their proposal is accepted and their requested time is scheduled. The entire PCS data acquisition and processing workflow is streamlined through various locally developed and commercial software packages. One 24 hour period produces one 200 Mb file, giving a total of maybe 2-5 Gb of data for the entire run. This data is then transferred to a hard disk in Dr. Fisher's office where she views the data with the customer and compresses the data to a text format which she sends them. This compression translates the data from an electron density to structural coordinates, which are the products submitted to a protein structure database. As noted above, the raw experimental data is stored onsite at LANSCE on workstations maintained by the instrument scientist. It is extraordinarily rare for anyone to request this data, although the remote possibility of an audit by a funding organization motivates its limited preservation. The raw data is not rigorously backed up, but only stored on a single hard drive. Interestingly, only about 50% of the experimental data actually ends up deposited and described in peer reviewed publications; the data that is not published tends to either not be viable structures or is calibration data. Dr. Fisher does protein crystallography research using both neutron and x-ray scattering

  1. Fragment screening using X-ray crystallography.

    PubMed

    Davies, Thomas G; Tickle, Ian J

    2012-01-01

    The fragment-based approach is now well established as an important component of modern drug discovery. A key part in establishing its position as a viable technique has been the development of a range of biophysical methodologies with sufficient sensitivity to detect the binding of very weakly binding molecules. X-ray crystallography was one of the first techniques demonstrated to be capable of detecting such weak binding, but historically its potential for screening was under-appreciated and impractical due to its relatively low throughput. In this chapter we discuss the various benefits associated with fragment-screening by X-ray crystallography, and describe the technical developments we have implemented to allow its routine use in drug discovery. We emphasize how this approach has allowed a much greater exploitation of crystallography than has traditionally been the case within the pharmaceutical industry, with the rapid and timely provision of structural information having maximum impact on project direction.

  2. Ab-initio phasing in protein crystallography

    NASA Astrophysics Data System (ADS)

    van der Plas, J. L.; Millane, Rick P.

    2000-11-01

    The central problem in the determination of protein structures form x-ray diffraction dada (x-ray crystallography) corresponds to a phase retrieval problem with undersampled amplitude data. Algorithms for this problem that have an increased radius of convergence have the potential for reducing the amount of experimental work, and cost, involved in determining protein structures. We describe such an algorithm. Application of the algorithm to a simulated crystallographic problem shows that it converges to the correct solution, with no initial phase information, where currently used algorithms fail. The results lend support to the possibility of ab initio phasing in protein crystallography.

  3. 10 years of protein crystallography at AR-NW12A beamline

    NASA Astrophysics Data System (ADS)

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

    2013-03-01

    The exponential growth of protein crystallography can be observed in the continuously increasing demand for synchrotron beam time, both from academic and industrial users. Nowadays, the screening of a profusion of sample crystals for more and more projects is being implemented by taking advantage of fully automated procedures at every level of the experiments. The insertion device AR-NW12A beamline is one of the five macromolecular crystallography (MX) beamlines at the Photon Factory (PF). Currently the oldest MX beamline operational at the High Energy Accelerator Research Organization (KEK), the end-station was launched in 2001 as part of an upgrade of the PF Advanced Ring. Since its commissioning, AR-NW12A has been operating as a high-throughput beamline, slowly evolving to a multipurpose end-station for MX experiments. The development of the beamline took place about a decade ago, in parallel with a drastic development of protein crystallography and more general synchrotron technology. To keep the beamline up-to-date and competitive with other MX stations in Japan and worldwide, new features have been constantly added, with the goal of user friendliness of the various beamline optics and other instruments. Here we describe the evolution of AR-NW12A for its tenth anniversary. We also discuss the plans for upgrades for AR-NW12A, the future objectives in terms of the beamline developments, and especially the strong desire to open the beamline to a larger user community.

  4. Protein Crystallography in Vaccine Research and Development

    PubMed Central

    Malito, Enrico; Carfi, Andrea; Bottomley, Matthew J.

    2015-01-01

    The use of protein X-ray crystallography for structure-based design of small-molecule drugs is well-documented and includes several notable success stories. However, it is less well-known that structural biology has emerged as a major tool for the design of novel vaccine antigens. Here, we review the important contributions that protein crystallography has made so far to vaccine research and development. We discuss several examples of the crystallographic characterization of vaccine antigen structures, alone or in complexes with ligands or receptors. We cover the critical role of high-resolution epitope mapping by reviewing structures of complexes between antigens and their cognate neutralizing, or protective, antibody fragments. Most importantly, we provide recent examples where structural insights obtained via protein crystallography have been used to design novel optimized vaccine antigens. This review aims to illustrate the value of protein crystallography in the emerging discipline of structural vaccinology and its impact on the rational design of vaccines. PMID:26068237

  5. High-throughput Crystallography for Structural Genomics

    PubMed Central

    Joachimiak, Andrzej

    2009-01-01

    Protein X-ray crystallography recently celebrated its 50th anniversary. The structures of myoglobin and hemoglobin determined by Kendrew and Perutz provided the first glimpses into the complex protein architecture and chemistry. Since then, the field of structural molecular biology has experienced extraordinary progress and now over 53,000 proteins structures have been deposited into the Protein Data Bank. In the past decade many advances in macromolecular crystallography have been driven by world-wide structural genomics efforts. This was made possible because of third-generation synchrotron sources, structure phasing approaches using anomalous signal and cryo-crystallography. Complementary progress in molecular biology, proteomics, hardware and software for crystallographic data collection, structure determination and refinement, computer science, databases, robotics and automation improved and accelerated many processes. These advancements provide the robust foundation for structural molecular biology and assure strong contribution to science in the future. In this report we focus mainly on reviewing structural genomics high-throughput X-ray crystallography technologies and their impact. PMID:19765976

  6. Resolution of structural heterogeneity in dynamic crystallography.

    PubMed

    Ren, Zhong; Chan, Peter W Y; Moffat, Keith; Pai, Emil F; Royer, William E; Šrajer, Vukica; Yang, Xiaojing

    2013-06-01

    Dynamic behavior of proteins is critical to their function. X-ray crystallography, a powerful yet mostly static technique, faces inherent challenges in acquiring dynamic information despite decades of effort. Dynamic `structural changes' are often indirectly inferred from `structural differences' by comparing related static structures. In contrast, the direct observation of dynamic structural changes requires the initiation of a biochemical reaction or process in a crystal. Both the direct and the indirect approaches share a common challenge in analysis: how to interpret the structural heterogeneity intrinsic to all dynamic processes. This paper presents a real-space approach to this challenge, in which a suite of analytical methods and tools to identify and refine the mixed structural species present in multiple crystallographic data sets have been developed. These methods have been applied to representative scenarios in dynamic crystallography, and reveal structural information that is otherwise difficult to interpret or inaccessible using conventional methods.

  7. In situ macromolecular crystallography using microbeams

    PubMed Central

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

    2012-01-01

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

  8. Resolution of structural heterogeneity in dynamic crystallography

    PubMed Central

    Ren, Zhong; Chan, Peter W. Y.; Moffat, Keith; Pai, Emil F.; Royer, William E.; Šrajer, Vukica; Yang, Xiaojing

    2013-01-01

    Dynamic behavior of proteins is critical to their function. X-­ray crystallography, a powerful yet mostly static technique, faces inherent challenges in acquiring dynamic information despite decades of effort. Dynamic ‘structural changes’ are often indirectly inferred from ‘structural differences’ by comparing related static structures. In contrast, the direct observation of dynamic structural changes requires the initiation of a biochemical reaction or process in a crystal. Both the direct and the indirect approaches share a common challenge in analysis: how to interpret the structural heterogeneity intrinsic to all dynamic processes. This paper presents a real-space approach to this challenge, in which a suite of analytical methods and tools to identify and refine the mixed structural species present in multiple crystallographic data sets have been developed. These methods have been applied to representative scenarios in dynamic crystallography, and reveal structural information that is otherwise difficult to interpret or inaccessible using conventional methods. PMID:23695239

  9. In situ macromolecular crystallography using microbeams.

    PubMed

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

    2012-05-01

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

  10. Neutron Crystallography for Macromolecular Structure Analysis

    NASA Astrophysics Data System (ADS)

    Kuroki, Ryota

    Hydrogen atoms in proteins as well as protein-bound water molecules play a significant role in many chemical reaction processes in living systems, such as catalytic reaction and molecular recognition. Neutron crystallography is a powerful tool to identify locations of light atoms like hydrogen. In the field of neutron crystallography, the development of diffractometers and techniques for preparation and crystallization of target samples has been developed to complement the low flux of neutron sources. In Japan, single-crystal diffractometers named BIX-3 and BIX-4 have been developed, and contribute to the effective collection of neutron diffraction data. Recent developments on the complementary use of neutron and X-ray diffraction data have begun solving previously undetermined problems of protein function. Further efforts to acquire higher measurement performance are now in progress to increase the application of neutron crystallographic studies.

  11. Graphical tools for macromolecular crystallography in PHENIX

    PubMed Central

    Echols, Nathaniel; Grosse-Kunstleve, Ralf W.; Afonine, Pavel V.; Bunkóczi, Gábor; Chen, Vincent B.; Headd, Jeffrey J.; McCoy, Airlie J.; Moriarty, Nigel W.; Read, Randy J.; Richardson, David C.; Richardson, Jane S.; Terwilliger, Thomas C.; Adams, Paul D.

    2012-01-01

    A new Python-based graphical user interface for the PHENIX suite of crystallography software is described. This interface unifies the command-line programs and their graphical displays, simplifying the development of new interfaces and avoiding duplication of function. With careful design, graphical interfaces can be displayed automatically, instead of being manually constructed. The resulting package is easily maintained and extended as new programs are added or modified. PMID:22675231

  12. High-Throughput Methods for Electron Crystallography

    PubMed Central

    Stokes, David L.; Ubarretxena-Belandia, Iban; Gonen, Tamir; Engel, Andreas

    2013-01-01

    Membrane proteins play a tremendously important role in cell physiology and serve as a target for an increasing number of drugs. Structural information is key to understanding their function and for developing new strategies for combating disease. However, the complex physical chemistry associated with membrane proteins has made them more difficult to study than their soluble cousins. Electron crystallography has historically been a successful method for solving membrane protein structures and has the advantage of providing the natural environment of a lipid membrane. Specifically, when membrane proteins form two-dimensional arrays within a lipid bilayer, images and diffraction can be recorded by electron microscopy. The corresponding data can be combined to produce a three-dimensional reconstruction which, under favorable conditions, can extend to atomic resolution. Like X-ray crystallography, the quality of the structures are very much dependent on the order and size of the crystals. However, unlike X-ray crystallography, high-throughput methods for screening crystallization trials for electron crystallography are not in general use. In this chapter, we describe two alternative and potentially complementary methods for high-throughput screening of membrane protein crystallization within the lipid bilayer. The first method relies on the conventional use of dialysis for removing detergent and thus reconstituting the bilayer; an array of dialysis wells in the standard 96-well format allows the use of a liquid-handling robot and greatly increases throughput. The second method relies on detergent complexation by cyclodextrin; a specialized pipetting robot has been designed not only to titrate cyclodextrin, but to use light scattering to monitor the reconstitution process. In addition, the use of liquid-handling robots for making negatively stained grids and methods for automatically imaging samples in the electron microscope are described. PMID:23132066

  13. Peculiarities of the solar proton events of 19 October 1989 and 23 March 1991 according to the measurements onboard the Mir space station.

    PubMed

    Petrov, V M; Mahkmtov, V S; Panova, N A; Shurshakov, V A; Dachev TsP; Semkova, J V; Matvijchuk YuP

    1994-10-01

    Flux and dose rate dynamics of solar cosmic rays were measured by the Lyulin dosimeter during the events 19 October 1989 and 23 March 1991. The maximum dose rate registered was 0.4, 0.12 and 0.01 cGy/hour, respectively. Based on the latitude distribution of particle flux a power law form for the energy spectra of solar protons in the anisotropic phase of the events on 19 October 1989 and 23 March 1991 was determined. It was obtained that after the development of geomagnetic storm protons with energies more than 1 GeV were registered.

  14. NMR Crystallography of a Carbanionic Intermediate in Tryptophan Synthase: Chemical Structure, Tautomerization, and Reaction Specificity

    PubMed Central

    2016-01-01

    Carbanionic intermediates play a central role in the catalytic transformations of amino acids performed by pyridoxal-5′-phosphate (PLP)-dependent enzymes. Here, we make use of NMR crystallography—the synergistic combination of solid-state nuclear magnetic resonance, X-ray crystallography, and computational chemistry—to interrogate a carbanionic/quinonoid intermediate analogue in the β-subunit active site of the PLP-requiring enzyme tryptophan synthase. The solid-state NMR chemical shifts of the PLP pyridine ring nitrogen and additional sites, coupled with first-principles computational models, allow a detailed model of protonation states for ionizable groups on the cofactor, substrates, and nearby catalytic residues to be established. Most significantly, we find that a deprotonated pyridine nitrogen on PLP precludes formation of a true quinonoid species and that there is an equilibrium between the phenolic and protonated Schiff base tautomeric forms of this intermediate. Natural bond orbital analysis indicates that the latter builds up negative charge at the substrate Cα and positive charge at C4′ of the cofactor, consistent with its role as the catalytic tautomer. These findings support the hypothesis that the specificity for β-elimination/replacement versus transamination is dictated in part by the protonation states of ionizable groups on PLP and the reacting substrates and underscore the essential role that NMR crystallography can play in characterizing both chemical structure and dynamics within functioning enzyme active sites. PMID:27779384

  15. The future of crystallography in drug discovery

    PubMed Central

    Zheng, Heping; Hou, Jing; Zimmerman, Matthew D; Wlodawer, Alexander; Minor, Wladek

    2014-01-01

    Introduction X-ray crystallography plays an important role in structure-based drug design (SBDD), and accurate analysis of crystal structures of target macromolecules and macromolecule–ligand complexes is critical at all stages. However, whereas there has been significant progress in improving methods of structural biology, particularly in X-ray crystallography, corresponding progress in the development of computational methods (such as in silico high-throughput screening) is still on the horizon. Crystal structures can be overinterpreted and thus bias hypotheses and follow-up experiments. As in any experimental science, the models of macromolecular structures derived from X-ray diffraction data have their limitations, which need to be critically evaluated and well understood for structure-based drug discovery. Areas covered This review describes how the validity, accuracy and precision of a protein or nucleic acid structure determined by X-ray crystallography can be evaluated from three different perspectives: i) the nature of the diffraction experiment; ii) the interpretation of an electron density map; and iii) the interpretation of the structural model in terms of function and mechanism. The strategies to optimally exploit a macromolecular structure are also discussed in the context of ‘Big Data’ analysis, biochemical experimental design and structure-based drug discovery. Expert opinion Although X-ray crystallography is one of the most detailed ‘microscopes’ available today for examining macromolecular structures, the authors would like to re-emphasize that such structures are only simplified models of the target macromolecules. The authors also wish to reinforce the idea that a structure should not be thought of as a set of precise coordinates but rather as a framework for generating hypotheses to be explored. Numerous biochemical and biophysical experiments, including new diffraction experiments, can and should be performed to verify or falsify

  16. A technique for determining the deuterium/hydrogen contrast map in neutron macromolecular crystallography.

    PubMed

    Chatake, Toshiyuki; Fujiwara, Satoru

    2016-01-01

    A difference in the neutron scattering length between hydrogen and deuterium leads to a high density contrast in neutron Fourier maps. In this study, a technique for determining the deuterium/hydrogen (D/H) contrast map in neutron macromolecular crystallography is developed and evaluated using ribonuclease A. The contrast map between the D2O-solvent and H2O-solvent crystals is calculated in real space, rather than in reciprocal space as performed in previous neutron D/H contrast crystallography. The present technique can thus utilize all of the amplitudes of the neutron structure factors for both D2O-solvent and H2O-solvent crystals. The neutron D/H contrast maps clearly demonstrate the powerful detectability of H/D exchange in proteins. In fact, alternative protonation states and alternative conformations of hydroxyl groups are observed at medium resolution (1.8 Å). Moreover, water molecules can be categorized into three types according to their tendency towards rotational disorder. These results directly indicate improvement in the neutron crystal structure analysis. This technique is suitable for incorporation into the standard structure-determination process used in neutron protein crystallography; consequently, more precise and efficient determination of the D-atom positions is possible using a combination of this D/H contrast technique and standard neutron structure-determination protocols.

  17. Facilities for small-molecule crystallography at synchrotron sources.

    PubMed

    Barnett, Sarah A; Nowell, Harriott; Warren, Mark R; Wilcox, Andrian; Allan, David R

    2016-01-01

    Although macromolecular crystallography is a widely supported technique at synchrotron radiation facilities throughout the world, there are, in comparison, only very few beamlines dedicated to small-molecule crystallography. This limited provision is despite the increasing demand for beamtime from the chemical crystallography community and the ever greater overlap between systems that can be classed as either small macromolecules or large small molecules. In this article, a very brief overview of beamlines that support small-molecule single-crystal diffraction techniques will be given along with a more detailed description of beamline I19, a dedicated facility for small-molecule crystallography at Diamond Light Source.

  18. NMR crystallography of enzyme active sites: probing chemically detailed, three-dimensional structure in tryptophan synthase.

    PubMed

    Mueller, Leonard J; Dunn, Michael F

    2013-09-17

    NMR crystallography--the synergistic combination of X-ray diffraction, solid-state NMR spectroscopy, and computational chemistry--offers unprecedented insight into three-dimensional, chemically detailed structure. Initially, researchers used NMR crystallography to refine diffraction data from organic and inorganic solids. Now we are applying this technique to explore active sites in biomolecules, where it reveals chemically rich detail concerning the interactions between enzyme site residues and the reacting substrate. Researchers cannot achieve this level of detail from X-ray, NMR,or computational methodologies in isolation. For example, typical X-ray crystal structures (1.5-2.5 Å resolution) of enzyme-bound intermediates identify possible hydrogen-bonding interactions between site residues and substrate but do not directly identify the protonation states. Solid-state NMR can provide chemical shifts for selected atoms of enzyme-substrate complexes, but without a larger structural framework in which to interpret them only empirical correlations with local chemical structure are possible. Ab initio calculations and molecular mechanics can build models for enzymatic processes, but they rely on researcher-specified chemical details. Together, however, X-ray diffraction, solid-state NMR spectroscopy, and computational chemistry can provide consistent and testable models for structure and function of enzyme active sites: X-ray crystallography provides a coarse framework upon which scientists can develop models of the active site using computational chemistry; they can then distinguish these models by comparing calculated NMR chemical shifts with the results of solid-state NMR spectroscopy experiments. Conceptually, each technique is a puzzle piece offering a generous view of the big picture. Only when correctly pieced together, however, can they reveal the big picture at the highest possible resolution. In this Account, we detail our first steps in the development of

  19. Ultrafast X-Ray Crystallography and Liquidography

    NASA Astrophysics Data System (ADS)

    Ki, Hosung; Oang, Key Young; Kim, Jeongho; Ihee, Hyotcherl

    2017-05-01

    Time-resolved X-ray diffraction provides direct information on three-dimensional structures of reacting molecules and thus can be used to elucidate structural dynamics of chemical and biological reactions. In this review, we discuss time-resolved X-ray diffraction on small molecules and proteins with particular emphasis on its application to crystalline (crystallography) and liquid-solution (liquidography) samples. Time-resolved X-ray diffraction has been used to study picosecond and slower dynamics at synchrotrons and can now access even femtosecond dynamics with the recent arrival of X-ray free-electron lasers.

  20. Statistical crystallography of surface micelle spacing

    NASA Technical Reports Server (NTRS)

    Noever, David A.

    1992-01-01

    The aggregation of the recently reported surface micelles of block polyelectrolytes is analyzed using techniques of statistical crystallography. A polygonal lattice (Voronoi mosaic) connects center-to-center points, yielding statistical agreement with crystallographic predictions; Aboav-Weaire's law and Lewis's law are verified. This protocol supplements the standard analysis of surface micelles leading to aggregation number determination and, when compared to numerical simulations, allows further insight into the random partitioning of surface films. In particular, agreement with Lewis's law has been linked to the geometric packing requirements of filling two-dimensional space which compete with (or balance) physical forces such as interfacial tension, electrostatic repulsion, and van der Waals attraction.

  1. Ultrafast X-Ray Crystallography and Liquidography.

    PubMed

    Ki, Hosung; Oang, Key Young; Kim, Jeongho; Ihee, Hyotcherl

    2017-05-05

    Time-resolved X-ray diffraction provides direct information on three-dimensional structures of reacting molecules and thus can be used to elucidate structural dynamics of chemical and biological reactions. In this review, we discuss time-resolved X-ray diffraction on small molecules and proteins with particular emphasis on its application to crystalline (crystallography) and liquid-solution (liquidography) samples. Time-resolved X-ray diffraction has been used to study picosecond and slower dynamics at synchrotrons and can now access even femtosecond dynamics with the recent arrival of X-ray free-electron lasers.

  2. The Construction of Group Theory in Crystallography

    NASA Astrophysics Data System (ADS)

    Maitte, Bernard

    This article sets out to retrace the manner in which Group Theory evolved in crystallography. To engage in this study it is necessary to select, amongst all the approaches to crystals, those which, from the point of view of modern science, mark a step towards the establishment of our current understanding. In this way it favours our current perspective. To compensate this distortion, we recall the context in which each explanation that marks history appears. It so becomes clear that notions of triperiodic assemblages and the crystallographic laws of crystal systems and symmetrical classes do not derive from "natural" observations but were compiled and belong to precise theories.

  3. Metalloprotein Crystallography: More than a Structure

    PubMed Central

    2016-01-01

    Conspectus Metal ions and metallocofactors play important roles in a broad range of biochemical reactions. Accordingly, it has been estimated that as much as 25–50% of the proteome uses transition metal ions to carry out a variety of essential functions. The metal ions incorporated within metalloproteins fulfill functional roles based on chemical properties, the diversity of which arises as transition metals can adopt different redox states and geometries, dictated by the identity of the metal and the protein environment. The coupling of a metal ion with an organic framework in metallocofactors, such as heme and cobalamin, further expands the chemical functionality of metals in biology. The three-dimensional visualization of metal ions and complex metallocofactors within a protein scaffold is often a starting point for enzymology, highlighting the importance of structural characterization of metalloproteins. Metalloprotein crystallography, however, presents a number of implicit challenges including correctly incorporating the relevant metal or metallocofactor, maintaining the proper environment for the protein to be purified and crystallized (including providing anaerobic, cold, or aphotic environments), and being mindful of the possibility of X-ray induced damage to the proteins or incorporated metal ions. Nevertheless, the incorporated metals or metallocofactors also present unique advantages in metalloprotein crystallography. The significant resonance that metals undergo with X-ray photons at wavelengths used for protein crystallography and the rich electronic properties of metals, which provide intense and spectroscopically unique signatures, allow a metalloprotein crystallographer to use anomalous dispersion to determine phases for structure solution and to use simultaneous or parallel spectroscopic techniques on single crystals. These properties, coupled with the improved brightness of beamlines, the ability to tune the wavelength of the X-ray beam, the

  4. Does crystallography need a new name?

    DOE PAGES

    Argryriou, Dimitri

    2017-07-01

    The discovery of X-rays and their use in the observation of diffraction from crystals placed crystallography at the forefront of science at the beginning of the last century. The combination of this new tool, together with the emerging understanding of the symmetry of crystals, exposed the locations of atoms in matter and allowed us to start understanding macroscopic properties from an atomic perspective for the first time. These discoveries transformed physics and chemistry bringing to light new scientific fields such as materials science and structural biology.

  5. Automated High Throughput Drug Target Crystallography

    SciTech Connect

    Rupp, B

    2005-02-18

    The molecular structures of drug target proteins and receptors form the basis for 'rational' or structure guided drug design. The majority of target structures are experimentally determined by protein X-ray crystallography, which as evolved into a highly automated, high throughput drug discovery and screening tool. Process automation has accelerated tasks from parallel protein expression, fully automated crystallization, and rapid data collection to highly efficient structure determination methods. A thoroughly designed automation technology platform supported by a powerful informatics infrastructure forms the basis for optimal workflow implementation and the data mining and analysis tools to generate new leads from experimental protein drug target structures.

  6. EIGER detector: application in macromolecular crystallography

    PubMed Central

    Casanas, Arnau; Warshamanage, Rangana; Finke, Aaron D.; Panepucci, Ezequiel; Olieric, Vincent; Nöll, Anne; Tampé, Robert; Brandstetter, Stefan; Förster, Andreas; Mueller, Marcus; Schulze-Briese, Clemens; Bunk, Oliver; Wang, Meitian

    2016-01-01

    The development of single-photon-counting detectors, such as the PILATUS, has been a major recent breakthrough in macromolecular crystallography, enabling noise-free detection and novel data-acquisition modes. The new EIGER detector features a pixel size of 75 × 75 µm, frame rates of up to 3000 Hz and a dead time as low as 3.8 µs. An EIGER 1M and EIGER 16M were tested on Swiss Light Source beamlines X10SA and X06SA for their application in macromolecular crystallography. The combination of fast frame rates and a very short dead time allows high-quality data acquisition in a shorter time. The ultrafine φ-slicing data-collection method is introduced and validated and its application in finding the optimal rotation angle, a suitable rotation speed and a sufficient X-ray dose are presented. An improvement of the data quality up to slicing at one tenth of the mosaicity has been observed, which is much finer than expected based on previous findings. The influence of key data-collection parameters on data quality is discussed. PMID:27599736

  7. Structural physiology based on electron crystallography

    PubMed Central

    Fujiyoshi, Yoshinori

    2011-01-01

    There are many questions in brain science, which are extremely interesting but very difficult to answer. For example, how do education and other experiences during human development influence the ability and personality of the adult? The molecular mechanisms underlying such phenomena are still totally unclear. However, technological and instrumental advancements of electron microscopy have facilitated comprehension of the structures of biological components, cells, and organelles. Electron crystallography is especially good for studying the structure and function of membrane proteins, which are key molecules of signal transduction in neural and other cells. Electron crystallography is now an established technique to analyze the structures of membrane proteins in lipid bilayers, which are close to their natural biological environment. By utilizing cryo-electron microscopes with helium cooled specimen stages, which were developed through a personal motivation to understand functions of neural systems from a structural point of view, structures of membrane proteins were analyzed at a resolution higher than 3 Å. This review has four objectives. First, it is intended to introduce the new research field of structural physiology. Second, it introduces some of the personal struggles, which were involved in developing the cryo-electron microscope. Third, it discusses some of the technology for the structural analysis of membrane proteins based on cryo-electron microscopy. Finally, it reviews structural and functional analyses of membrane proteins. PMID:21416541

  8. EIGER detector: application in macromolecular crystallography.

    PubMed

    Casanas, Arnau; Warshamanage, Rangana; Finke, Aaron D; Panepucci, Ezequiel; Olieric, Vincent; Nöll, Anne; Tampé, Robert; Brandstetter, Stefan; Förster, Andreas; Mueller, Marcus; Schulze-Briese, Clemens; Bunk, Oliver; Wang, Meitian

    2016-09-01

    The development of single-photon-counting detectors, such as the PILATUS, has been a major recent breakthrough in macromolecular crystallography, enabling noise-free detection and novel data-acquisition modes. The new EIGER detector features a pixel size of 75 × 75 µm, frame rates of up to 3000 Hz and a dead time as low as 3.8 µs. An EIGER 1M and EIGER 16M were tested on Swiss Light Source beamlines X10SA and X06SA for their application in macromolecular crystallography. The combination of fast frame rates and a very short dead time allows high-quality data acquisition in a shorter time. The ultrafine ϕ-slicing data-collection method is introduced and validated and its application in finding the optimal rotation angle, a suitable rotation speed and a sufficient X-ray dose are presented. An improvement of the data quality up to slicing at one tenth of the mosaicity has been observed, which is much finer than expected based on previous findings. The influence of key data-collection parameters on data quality is discussed.

  9. CLIMS: crystallography laboratory information management system.

    PubMed

    Fulton, Kate F; Ervine, Shaun; Faux, Noel; Forster, Richard; Jodun, Rachel A; Ly, Wayson; Robilliard, Lee; Sonsini, Jai; Whelan, Dan; Whisstock, James C; Buckle, Ashley M

    2004-09-01

    Macromolecular crystallography requires simple yet effective means of organizing and managing the large amounts of data generated by crystallization experiments. There are several freely available web-based Laboratory Information Management Systems (LIMS) that assist in these tasks. These, however, rely on the limited user interfaces allowed in HTML-based web pages. To address this limitation, a new LIMS for protein crystallization, which features a novel rich graphical user interface (GUI) to a relational database, has been developed. This application, which is called CLIMS (Crystallography LIMS), assists in all aspects of protein-crystallization projects: protein expression, handling, crystallization optimization, visualization of results and preliminary diffraction data. Extensive use of templates, particularly for commercial screens and common optimization grid screens, exploits the redundancy in experimental setups. The crystallization tray is the central focus of the graphical interface, thus facilitating rapid visualization and annotation of results. CLIMS was developed specifically to cater for the needs of individual laboratories requiring an intuitive and robust system for managing crystallization experiments and is freely available.

  10. Graphene-based microfluidics for serial crystallography.

    PubMed

    Sui, Shuo; Wang, Yuxi; Kolewe, Kristopher W; Srajer, Vukica; Henning, Robert; Schiffman, Jessica D; Dimitrakopoulos, Christos; Perry, Sarah L

    2016-08-02

    Microfluidic strategies to enable the growth and subsequent serial crystallographic analysis of micro-crystals have the potential to facilitate both structural characterization and dynamic structural studies of protein targets that have been resistant to single-crystal strategies. However, adapting microfluidic crystallization platforms for micro-crystallography requires a dramatic decrease in the overall device thickness. We report a robust strategy for the straightforward incorporation of single-layer graphene into ultra-thin microfluidic devices. This architecture allows for a total material thickness of only ∼1 μm, facilitating on-chip X-ray diffraction analysis while creating a sample environment that is stable against significant water loss over several weeks. We demonstrate excellent signal-to-noise in our X-ray diffraction measurements using a 1.5 μs polychromatic X-ray exposure, and validate our approach via on-chip structure determination using hen egg white lysozyme (HEWL) as a model system. Although this work is focused on the use of graphene for protein crystallography, we anticipate that this technology should find utility in a wide range of both X-ray and other lab on a chip applications.

  11. Implications of the focal beam profile in serial femtosecond crystallography

    SciTech Connect

    Galli, Lorenzo; Chapman, Henry N.; Metcalf, Peter

    2015-05-12

    The photon density profile of an X-ray free-electron laser (XFEL) beam at the focal position is a critical parameter for serial femtosecond crystallography (SFX), but is difficult to measure because of the destructive power of the beam. A novel high intensity radiation induced phasing method (HIRIP) has been proposed as a general experimental approach for protein structure determination, but has proved to be sensitive to variations of the X-ray intensity, with uniform incident fluence desired for best performance. Here we show that experimental SFX data collected at the nano-focus chamber of the Coherent X-ray Imaging end-station at the Linac Coherent Light Source using crystals with a limited size distribution suggests an average profile of the X-ray beam that has a large variation of intensity. We propose a new method to improve the quality of high fluence data for HI-RIP, by identifying and removing diffraction patterns from crystals exposed to the low intensity region of the beam. The method requires crystals of average size comparable to the width of the focal spot.

  12. 3D shape reconstruction of loop objects in X-ray protein crystallography.

    PubMed

    Strutz, Tilo

    2011-01-01

    Knowledge of the shape of crystals can benefit data collection in X-ray crystallography. A preliminary step is the determination of the loop object, i.e., the shape of the loop holding the crystal. Based on the standard set-up of experimental X-ray stations for protein crystallography, the paper reviews a reconstruction method merely requiring 2D object contours and presents a dedicated novel algorithm. Properties of the object surface (e.g., texture) and depth information do not have to be considered. The complexity of the reconstruction task is significantly reduced by slicing the 3D object into parallel 2D cross-sections. The shape of each cross-section is determined using support lines forming polygons. The slicing technique allows the reconstruction of concave surfaces perpendicular to the direction of projection. In spite of the low computational complexity, the reconstruction method is resilient to noisy object projections caused by imperfections in the image-processing system extracting the contours. The algorithm developed here has been successfully applied to the reconstruction of shapes of loop objects in X-ray crystallography.

  13. A Compact X-Ray System for Support of High Throughput Crystallography

    NASA Technical Reports Server (NTRS)

    Ciszak, Ewa; Gubarev, Mikhail; Gibson, Walter M.; Joy, Marshall K.; Whitaker, Ann F. (Technical Monitor)

    2001-01-01

    Standard x-ray systems for crystallography rely on massive generators coupled with optics that guide X-ray beams onto the crystal sample. Optics for single-crystal diffractometry include total reflection mirrors, polycapillary optics or graded multilayer monochromators. The benefit of using polycapillary optic is that it can collect x-rays over tile greatest solid angle, and thus most efficiently, utilize the greatest portion of X-rays emitted from the Source, The x-ray generator has to have a small anode spot, and thus its size and power requirements can be substantially reduced We present the design and results from the first high flux x-ray system for crystallography that combine's a microfocus X-ray generator (40microns FWHM Spot size at a power of 45 W) and a collimating, polycapillary optic. Diffraction data collected from small test crystals with cell dimensions up to 160A (lysozyme and thaumatin) are of high quality. For example, diffraction data collected from a lysozyme crystal at RT yielded R=5.0% for data extending to 1.70A. We compare these results with measurements taken from standard crystallographic systems. Our current microfocus X-ray diffraction system is attractive for supporting crystal growth research in the standard crystallography laboratory as well as in remote, automated crystal growth laboratory. Its small volume, light-weight, and low power requirements are sufficient to have it installed in unique environments, i.e.. on-board International Space Station.

  14. Dynamically polarized samples for neutron protein crystallography at the Spallation Neutron Source

    NASA Astrophysics Data System (ADS)

    Zhao, Jinkui; Pierce, Josh; Myles, Dean; Robertson, J. L.; Herwig, Kenneth W.; Standaert, Bob; Cuneo, Matt; Li, Le; Meilleur, Flora

    2016-09-01

    To prepare for the next generation neutron scattering instruments for the planned second target station at the Spallation Neutron Source (SNS) and to broaden the scientific impact of neutron protein crystallography at the Oak Ridge National Laboratory, we have recently ramped up our efforts to develop a dynamically polarized target for neutron protein crystallography at the SNS. Proteins contain a large amount of hydrogen which contributes to incoherent diffraction background and limits the sensitivity of neutron protein crystallography. This incoherent background can be suppressed by using polarized neutron diffraction, which in the same time also improves the coherent diffraction signal. Our plan is to develop a custom Dynamic Nuclear Polarization (DNP) setup tailored to neutron protein diffraction instruments. Protein crystals will be polarized at a magnetic field of 5 T and temperatures of below 1 K. After the dynamic polarization process, the sample will be brought to a frozen-spin mode in a 0.5 T holding field and at temperatures below 100 mK. In a parallel effort, we are also investigating various ways of incorporating polarization agents needed for DNP, such as site specific spin labels, into protein crystals.

  15. X-Ray Crystallography: One Century of Nobel Prizes

    ERIC Educational Resources Information Center

    Galli, Simona

    2014-01-01

    In 2012, the United Nations General Assembly declared 2014 the International Year of Crystallography. Throughout the year 2014 and beyond, all the crystallographic associations and societies active all over the world are organizing events to attract the wider public toward crystallography and the numerous topics to which it is deeply interlinked.…

  16. X-Ray Crystallography: One Century of Nobel Prizes

    ERIC Educational Resources Information Center

    Galli, Simona

    2014-01-01

    In 2012, the United Nations General Assembly declared 2014 the International Year of Crystallography. Throughout the year 2014 and beyond, all the crystallographic associations and societies active all over the world are organizing events to attract the wider public toward crystallography and the numerous topics to which it is deeply interlinked.…

  17. New micro-beam beamline at SPring-8, targeting at protein micro-crystallography

    SciTech Connect

    Hirata, Kunio; Ueno, Go; Nisawa, Atsushi; Kawano, Yoshiaki; Hikima, Takaaki; Tanaka, Takashi; Kitamura, Hideo; Yamamoto, Masaki; Shimizu, Nobutaka; Kumasaka, Takashi; Takeshita, Kunikazu; Ohashi, Haruhiko; Goto, Shunji

    2010-06-23

    A new protein micro-crystallography beamline BL32XU at SPring-8 is under construction and scheduled to start operation in 2010. The beamline is designed to provide the stabilized and brilliant micro-beam to collect high-quality data from micro-crystals. The beamline consists of a hybrid in-vacuum undulator, a liquid-nitrogen cooled double crystal monochromator, and K-B focusing mirrors with large magnification factor. Development of data acquisition system and end station consists of high-precision diffractometer, high-efficiency area detector, sample auto-changer etc. are also in progress.

  18. Neutron structure of human carbonic anhydrase II: implications for proton transfer.

    PubMed

    Fisher, S Zoë; Kovalevsky, Andrey Y; Domsic, John F; Mustyakimov, Marat; McKenna, Robert; Silverman, David N; Langan, Paul A

    2010-01-26

    Human carbonic anhydrase II (HCA II) catalyzes the reversible hydration of carbon dioxide to form bicarbonate and a proton. Despite many high-resolution X-ray crystal structures, mutagenesis, and kinetic data, the structural details of the active site, especially the proton transfer pathway, are unclear. A large HCA II crystal was prepared at pH 9.0 and subjected to vapor H-D exchange to replace labile hydrogens with deuteriums. Neutron diffraction studies were conducted at the Protein Crystallography Station at Los Alamos National Laboratory. The structure to 2.0 A resolution reveals several interesting active site features: (1) the Zn-bound solvent appearing to be predominantly a D(2)O molecule, (2) the orientation and hydrogen bonding pattern of solvent molecules in the active site cavity, (3) the side chain of His64 being unprotonated (neutral) and predominantly in an inward conformation pointing toward the zinc, and (4) the phenolic side chain of Tyr7 appearing to be unprotonated. The implications of these details are discussed, and a proposed mechanism for proton transfer is presented.

  19. Neutron Structure of Human Carbonic Anhydrase II: Implications for Proton Transfer†

    PubMed Central

    Fisher, S. Zoë; Kovalevsky, Andrey Y.; Domsic, John F.; Mustyakimov, Marat; McKenna, Robert; Silverman, David N.; Langan, Paul A.

    2010-01-01

    Human carbonic anhydrase II (HCA II) catalyzes the reversible hydration of carbon dioxide to form bicarbonate and a proton. Despite many high-resolution X-ray crystal structures, mutagenesis, and kinetic data, the structural details of the active site, especially the proton transfer pathway, are unclear. A large HCA II crystal was prepared at pH 9.0 and subjected to vapor H–D exchange to replace labile hydrogens with deuteriums. Neutron diffraction studies were conducted at the Protein Crystallography Station at Los Alamos National Laboratory. The structure to 2.0 Å resolution reveals several interesting active site features: (1) the Zn-bound solvent appearing to be predominantly a D2O molecule, (2) the orientation and hydrogen bonding pattern of solvent molecules in the active site cavity, (3) the side chain of His64 being unprotonated (neutral) and predominantly in an inward conformation pointing toward the zinc, and (4) the phenolic side chain of Tyr7 appearing to be unprotonated. The implications of these details are discussed, and a proposed mechanism for proton transfer is presented. PMID:20025241

  20. Report on Proton and Ion Beam measurements at the Matter in Extreme Condition (MCC) end station at SLAC National Accelerator Laboratory

    SciTech Connect

    Gauthier, Maxence

    2016-02-16

    We report on MeV ion beams produced with high-repetition rates of 1 Hz at the MEC end station at SLAC National Accelerator Laboratory. These data were obtained during the commissioning beam time of the new 30TW laser. After describing the experimental set-up, the laser conditions and the target diagnostics, ion beam spectra measured for different foil thicknesses and laser intensities will be presented and discussed. These results are subsequently compared with results from cryogenic hydrogen jets at MEC in January 2015.

  1. Crystallography of Alumina-YAG-Eutectic

    NASA Technical Reports Server (NTRS)

    Farmer, Serene C.; Sayir, Ali; Dickerson, Robert M.; Matson, Lawrence E.

    2000-01-01

    Multiple descriptions of the alumina-YAG eutectic crystallography appear in the ceramic literature. The orientation between two phases in a eutectic system has direct impact on residual stress, morphology, microstructural stability, and high temperature mechanical properties. A study to demonstrate that the different crystallographic relationships can be correlated with different growth constraints was undertaken. Fibers produced by Laser-Heated Float Zone (LHFZ) and Edge-defined Film-fed Growth (EFG) were examined. A map of the orientation relationship between Al2O3 and Y3Al5O12 and their relationship to the fiber growth axis as a function of pull rate are presented. Regions in which a single orientation predominates are identified.

  2. Neutron crystallography: opportunities, challenges, and limitations.

    PubMed

    Blakeley, Matthew P; Langan, Paul; Niimura, Nobuo; Podjarny, Alberto

    2008-10-01

    Neutron crystallography has had an important, but relatively small role in structural biology over the years. In this review of recently determined neutron structures, a theme emerges of a field currently expanding beyond its traditional boundaries, to address larger and more complex problems, with smaller samples and shorter data collection times, and employing more sophisticated structure determination and refinement methods. The origin of this transformation can be found in a number of advances including first, the development of neutron image-plates and quasi-Laue methods at nuclear reactor neutron sources and the development of time-of-flight Laue methods and electronic detectors at spallation neutron sources; second, new facilities and methods for sample perdeuteration and crystallization; third, new approaches and computational tools for structure determination.

  3. CIF: the computer language of crystallography.

    PubMed

    Brown, I David; McMahon, Brian

    2002-06-01

    The Crystallographic Information File (CIF) was adopted in 1990 by the International Union of Crystallography as a file structure for the archiving and distribution of crystallographic information. The CIF standard is now well established and is in regular use for reporting crystal structure determinations to Acta Crystallographica and other journals. The structure of CIF is flexible and extensible and is compatible with other evolving standards. It is well suited to relational and object-oriented models, and is being adopted by the crystallographic databases. This paper reviews the development of CIF and describes its salient features. Future extension of the standard to include implementation of methods will allow CIF to exploit the potential of advanced information-handling software.

  4. Busting out of crystallography's Sisyphean prison

    NASA Astrophysics Data System (ADS)

    Cranswick, L. M. D.

    2008-01-01

    The history of crystallographic computing and use of crystallographic software is one which traces the escape from the drudgery of manual human calculations to a world where the user delegates most of the travail to electronic computers. This review traces the development of small-molecule single-crystal and powder diffraction hardware, starting with the use of Hollerith tabulators of the late 1930's through to today's use of high-performance personal computers. It also emphasizes that the main challenge for current and future crystallography computing is not that of hardware development, or even specific scientific challenges, but rather in maintaining a critical mass of human expertise with which these computational challenges can be undertaken.

  5. Viscous hydrophilic injection matrices for serial crystallography

    PubMed Central

    Kovácsová, Gabriela; Grünbein, Marie Luise; Kloos, Marco; Barends, Thomas R. M.; Heberle, Joachim; Kabsch, Wolfgang; Shoeman, Robert L.; Doak, R. Bruce; Schlichting, Ilme

    2017-01-01

    Serial (femtosecond) crystallography at synchrotron and X-ray free-electron laser (XFEL) sources distributes the absorbed radiation dose over all crystals used for data collection and therefore allows measurement of radiation damage prone systems, including the use of microcrystals for room-temperature measurements. Serial crystallography relies on fast and efficient exchange of crystals upon X-ray exposure, which can be achieved using a variety of methods, including various injection techniques. The latter vary significantly in their flow rates – gas dynamic virtual nozzle based injectors provide very thin fast-flowing jets, whereas high-viscosity extrusion injectors produce much thicker streams with flow rates two to three orders of magnitude lower. High-viscosity extrusion results in much lower sample consumption, as its sample delivery speed is commensurate both with typical XFEL repetition rates and with data acquisition rates at synchrotron sources. An obvious viscous injection medium is lipidic cubic phase (LCP) as it is used for in meso membrane protein crystallization. However, LCP has limited compatibility with many crystallization conditions. While a few other viscous media have been described in the literature, there is an ongoing need to identify additional injection media for crystal embedding. Critical attributes are reliable injection properties and a broad chemical compatibility to accommodate samples as heterogeneous and sensitive as protein crystals. Here, the use of two novel hydro­gels as viscous injection matrices is described, namely sodium carb­oxy­methyl cellulose and the thermo-reversible block polymer Pluronic F-127. Both are compatible with various crystallization conditions and yield acceptable X-ray background. The stability and velocity of the extruded stream were also analysed and the dependence of the stream velocity on the flow rate was measured. In contrast with previously characterized injection media, both new matrices

  6. Kinetic protein crystallography: a tool to watch proteins in action

    SciTech Connect

    Bourgeois, D.; Weik, M.

    2009-04-14

    Many proteins function in the crystalline state, making crystallography a tool that, beside structure, can address mechanism. By initiating biological turnover in the crystal, transient structural species form, which may be filmed 'on the fly' by Laue diffraction or captured by trapping methods. These strategies are jointly referred to as 'kinetic crystallography'. In this article, we review the general concepts of kinetic crystallography in the context of the conformational energy landscape of a protein. Whereas Laue diffraction is best suited to the investigation of cyclic, ultra-fast and light-triggered reactions, trapping approaches, on the other hand, are applicable to a wider range of biological systems but require care to avoid artefacts. Complementary methods - mainly UV/visible single-crystal spectroscopy - have proven essential to design, interpret and validate kinetic crystallography experiments. Achievements in the field as well as remaining puzzling questions are considered through the examination of recently published work: real-time-resolved crystallography of dimeric haemoglobin based on pump-probe Laue diffraction, temperature-trapping crystallography of acetylcholinesterase based on photo- and radio-induced ligand cleavage, and lattice-trapping crystallography of superoxide reductase based on product soaking and the combined use of X-ray diffraction and Raman spectroscopy.

  7. The status of the macromolecular crystallography beamlines at the European Synchrotron Radiation Facility

    NASA Astrophysics Data System (ADS)

    Mueller-Dieckmann, Christoph; Bowler, Matthew W.; Carpentier, Philippe; Flot, David; McCarthy, Andrew A.; Nanao, Max H.; Nurizzo, Didier; Pernot, Petra; Popov, Alexander; Round, Adam; Royant, Antoine; de Sanctis, Daniele; von Stetten, David; Leonard, Gordon A.

    2015-04-01

    The European Synchrotron Radiation Facility (ESRF) is the oldest and most powerful 3rd generation synchrotron in Europe, providing X-rays to more than 40 experimental stations welcoming several thousand researchers per year. A major success story has been the ESRF's facilities for macromolecular crystallography (MX). These are grouped around 3 straight sections: On ID23 canted undulators accommodate ID23-1, a mini-focus tuneable energy end station and ID23-2, the world's first micro-focus beamline dedicated to MX; ID29 houses a single, mini-focus, tuneable energy end station; ID30 will provide three end stations for MX due in operation from mid-2014 to early 2015. Here, one branch of a canted X-ray source feeds two fixed-energy end stations (MASSIF-1, MASSIF-3). The second feeds ID30B, a variable focus, tuneable energy beamline. MASSIF-1 is optimised for automatic high-throughput experiments requiring a relatively large beam size at the sample position, MASSIF-3 is a high-intensity, micro-focus facility designed to complement ID23-2. All end stations are highly automated, equipped with sample mounting robots and large area, fast-readout photon-counting detectors. Experiment control and tracking is achieved via a combination of the MXCuBE2 graphical user interface and the ISPyB database, the former allowing user-friendly control of all beamline components, the latter providing data tracking before, after and during experiments.

  8. Apparatus for proton radiography

    DOEpatents

    Martin, Ronald L.

    1976-01-01

    An apparatus for effecting diagnostic proton radiography of patients in hospitals comprises a source of negative hydrogen ions, a synchrotron for accelerating the negative hydrogen ions to a predetermined energy, a plurality of stations for stripping extraction of a radiography beam of protons, means for sweeping the extracted beam to cover a target, and means for measuring the residual range, residual energy, or percentage transmission of protons that pass through the target. The combination of information identifying the position of the beam with information about particles traversing the subject and the back absorber is performed with the aid of a computer to provide a proton radiograph of the subject. In an alternate embodiment of the invention, a back absorber comprises a plurality of scintillators which are coupled to detectors.

  9. The macromolecular crystallography beamline I911-3 at the MAX IV laboratory

    PubMed Central

    Ursby, Thomas; Unge, Johan; Appio, Roberto; Logan, Derek T.; Fredslund, Folmer; Svensson, Christer; Larsson, Krister; Labrador, Ana; Thunnissen, Marjolein M. G. M.

    2013-01-01

    The macromolecular crystallography beamline I911-3, part of the Cassiopeia/I911 suite of beamlines, is based on a superconducting wiggler at the MAX II ring of the MAX IV Laboratory in Lund, Sweden. The beamline is energy-tunable within a range between 6 and 18 keV. I911-3 opened for users in 2005. In 2010–2011 the experimental station was completely rebuilt and refurbished such that it has become a state-of-the-art experimental station with better possibilities for rapid throughput, crystal screening and work with smaller samples. This paper describes the complete I911-3 beamline and how it is embedded in the Cassiopeia suite of beamlines. PMID:23765310

  10. Fragment-Based Screening by Protein Crystallography: Successes and Pitfalls

    PubMed Central

    Chilingaryan, Zorik; Yin, Zhou; Oakley, Aaron J.

    2012-01-01

    Fragment-based drug discovery (FBDD) concerns the screening of low-molecular weight compounds against macromolecular targets of clinical relevance. These compounds act as starting points for the development of drugs. FBDD has evolved and grown in popularity over the past 15 years. In this paper, the rationale and technology behind the use of X-ray crystallography in fragment based screening (FBS) will be described, including fragment library design and use of synchrotron radiation and robotics for high-throughput X-ray data collection. Some recent uses of crystallography in FBS will be described in detail, including interrogation of the drug targets β-secretase, phenylethanolamine N-methyltransferase, phosphodiesterase 4A and Hsp90. These examples provide illustrations of projects where crystallography is straightforward or difficult, and where other screening methods can help overcome the limitations of crystallography necessitated by diffraction quality. PMID:23202926

  11. Phase Equilibria and Crystallography of Ceramic Oxides

    PubMed Central

    Wong-Ng, W.; Roth, R. S.; Vanderah, T. A.; McMurdie, H. F.

    2001-01-01

    Research in phase equilibria and crystallography has been a tradition in the Ceramics Division at National Bureau of Standards/National Institute of Standatrds and Technology (NBS/NIST) since the early thirties. In the early years, effort was concentrated in areas of Portland cement, ceramic glazes and glasses, instrument bearings, and battery materials. In the past 40 years, a large portion of the work was related to electronic materials, including ferroelectrics, piezoelectrics, ionic conductors, dielectrics, microwave dielectrics, and high-temperature superconductors. As a result of the phase equilibria studies, many new compounds have been discovered. Some of these discoveries have had a significant impact on US industry. Structure determinations of these new phases have often been carried out as a joint effort among NBS/NIST colleagues and also with outside collaborators using both single crystal and neutron and x-ray powder diffraction techniques. All phase equilibria diagrams were included in Phase Diagrams for Ceramists, which are collaborative publications between The American Ceramic Society (ACerS) and NBS/NIST. All x-ray powder diffraction patterns have been included in the Powder Diffraction File (PDF). This article gives a brief account of the history of the development of the phase equilibria and crystallographic research on ceramic oxides in the Ceramics Division. Represented systems, particularly electronic materials, are highlighted. PMID:27500068

  12. Fourier-Space Crystallography as Group Cohomology

    NASA Astrophysics Data System (ADS)

    Rabson, David; Fisher, Benji

    2001-03-01

    David Mermin has argued persuasively that the theoretical significance of quasicrystals lies not so much in relaxing the requirement of periodicity as in replacing exact identity of a density function (e.g., electronic or mass) under symmetry operations with indistinguishability of correlation functions, as expressed in Fourier space.(N.D. Mermin, Phys. Stat. Sol. (a) 151), 275 (1995) and references. After reviewing the formalism of Fourier-space crystallography (phase functions and gauge transformations), we present a new formulation in the language of cohomology of groups. First we reexpress the classification of space groups in terms of a first cohomology group; we then show how recent work by König and Mermin(A. König and N.D. Mermin, Am. J. Phys. 68), 525 (2000). on band sticking in nonsymmorphic crystals derives naturally from a first homology group and discuss its connection to a second cohomology group. The new language lets us prove generally several theorems previously known only in special cases. Finally, we let the listener decide whether we're just ``speaking prose.''(N.D. Mermin, Rev. Mod. Phys. 64), 3 (1992).

  13. Phase Equilibria and Crystallography of Ceramic Oxides.

    PubMed

    Wong-Ng, W; Roth, R S; Vanderah, T A; McMurdie, H F

    2001-01-01

    Research in phase equilibria and crystallography has been a tradition in the Ceramics Division at National Bureau of Standards/National Institute of Standatrds and Technology (NBS/NIST) since the early thirties. In the early years, effort was concentrated in areas of Portland cement, ceramic glazes and glasses, instrument bearings, and battery materials. In the past 40 years, a large portion of the work was related to electronic materials, including ferroelectrics, piezoelectrics, ionic conductors, dielectrics, microwave dielectrics, and high-temperature superconductors. As a result of the phase equilibria studies, many new compounds have been discovered. Some of these discoveries have had a significant impact on US industry. Structure determinations of these new phases have often been carried out as a joint effort among NBS/NIST colleagues and also with outside collaborators using both single crystal and neutron and x-ray powder diffraction techniques. All phase equilibria diagrams were included in Phase Diagrams for Ceramists, which are collaborative publications between The American Ceramic Society (ACerS) and NBS/NIST. All x-ray powder diffraction patterns have been included in the Powder Diffraction File (PDF). This article gives a brief account of the history of the development of the phase equilibria and crystallographic research on ceramic oxides in the Ceramics Division. Represented systems, particularly electronic materials, are highlighted.

  14. Crystallography, Evolution, and the Structure of Viruses

    PubMed Central

    Rossmann, Michael G.

    2012-01-01

    My undergraduate education in mathematics and physics was a good grounding for graduate studies in crystallographic studies of small organic molecules. As a postdoctoral fellow in Minnesota, I learned how to program an early electronic computer for crystallographic calculations. I then joined Max Perutz, excited to use my skills in the determination of the first protein structures. The results were even more fascinating than the development of techniques and provided inspiration for starting my own laboratory at Purdue University. My first studies on dehydrogenases established the conservation of nucleotide-binding structures. Having thus established myself as an independent scientist, I could start on my most cherished ambition of studying the structure of viruses. About a decade later, my laboratory had produced the structure of a small RNA plant virus and then, in another six years, the first structure of a human common cold virus. Many more virus structures followed, but soon it became essential to supplement crystallography with electron microscopy to investigate viral assembly, viral infection of cells, and neutralization of viruses by antibodies. A major guide in all these studies was the discovery of evolution at the molecular level. The conservation of three-dimensional structure has been a recurring theme, from my experiences with Max Perutz in the study of hemoglobin to the recognition of the conserved nucleotide-binding fold and to the recognition of the jelly roll fold in the capsid protein of a large variety of viruses. PMID:22318719

  15. Crystallography, evolution, and the structure of viruses.

    PubMed

    Rossmann, Michael G

    2012-03-16

    My undergraduate education in mathematics and physics was a good grounding for graduate studies in crystallographic studies of small organic molecules. As a postdoctoral fellow in Minnesota, I learned how to program an early electronic computer for crystallographic calculations. I then joined Max Perutz, excited to use my skills in the determination of the first protein structures. The results were even more fascinating than the development of techniques and provided inspiration for starting my own laboratory at Purdue University. My first studies on dehydrogenases established the conservation of nucleotide-binding structures. Having thus established myself as an independent scientist, I could start on my most cherished ambition of studying the structure of viruses. About a decade later, my laboratory had produced the structure of a small RNA plant virus and then, in another six years, the first structure of a human common cold virus. Many more virus structures followed, but soon it became essential to supplement crystallography with electron microscopy to investigate viral assembly, viral infection of cells, and neutralization of viruses by antibodies. A major guide in all these studies was the discovery of evolution at the molecular level. The conservation of three-dimensional structure has been a recurring theme, from my experiences with Max Perutz in the study of hemoglobin to the recognition of the conserved nucleotide-binding fold and to the recognition of the jelly roll fold in the capsid protein of a large variety of viruses.

  16. Identification of rogue datasets in serial crystallography.

    PubMed

    Assmann, Greta; Brehm, Wolfgang; Diederichs, Kay

    2016-06-01

    Advances in beamline optics, detectors and X-ray sources allow new techniques of crystallographic data collection. In serial crystallography, a large number of partial datasets from crystals of small volume are measured. Merging of datasets from different crystals in order to enhance data completeness and accuracy is only valid if the crystals are isomorphous, i.e. sufficiently similar in cell parameters, unit-cell contents and molecular structure. Identification and exclusion of non-isomorphous datasets is therefore indispensable and must be done by means of suitable indicators. To identify rogue datasets, the influence of each dataset on CC1/2 [Karplus & Diederichs (2012 ▸). Science, 336, 1030-1033], the correlation coefficient between pairs of intensities averaged in two randomly assigned subsets of observations, is evaluated. The presented method employs a precise calculation of CC1/2 that avoids the random assignment, and instead of using an overall CC1/2, an average over resolution shells is employed to obtain sensible results. The selection procedure was verified by measuring the correlation of observed (merged) intensities and intensities calculated from a model. It is found that inclusion and merging of non-isomorphous datasets may bias the refined model towards those datasets, and measures to reduce this effect are suggested.

  17. Protein Crystallography from the Perspective of Technology Developments

    PubMed Central

    Su, Xiao-Dong; Zhang, Heng; Terwilliger, Thomas C.; Liljas, Anders; Xiao, Junyu; Dong, Yuhui

    2015-01-01

    Early on, crystallography was a domain of mineralogy and mathematics and dealt mostly with symmetry properties and imaginary crystal lattices. This changed when Wilhelm Conrad Röntgen discovered X-rays in 1895, and in 1912 Max von Laue and his associates discovered X-ray irradiated salt crystals would produce diffraction patterns that could reveal the internal atomic periodicity of the crystals. In the same year the father-and-son team, Henry and Lawrence Bragg successfully solved the first crystal structure of sodium chloride and the era of modern crystallography began. Protein crystallography (PX) started some 20 years later with the pioneering work of British crystallographers. In the past 50-60 years, the achievements of modern crystallography and particularly those in protein crystallography have been due to breakthroughs in theoretical and technical advancements such as phasing and direct methods; to more powerful X-ray sources such as synchrotron radiation (SR); to more sensitive and efficient X-ray detectors; to ever faster computers and to improvements in software. The exponential development of protein crystallography has been accelerated by the invention and applications of recombinant DNA technology that can yield nearly any protein of interest in large amounts and with relative ease. Novel methods, informatics platforms, and technologies for automation and high-throughput have allowed the development of large-scale, high efficiency macromolecular crystallography efforts in the field of structural genomics (SG). Very recently, the X-ray free-electron laser (XFEL) sources and its applications in protein crystallography have shown great potential for revolutionizing the whole field again in the near future. PMID:25983389

  18. Space Station

    NASA Image and Video Library

    1991-01-01

    In 1982, the Space Station Task Force was formed, signaling the initiation of the Space Station Freedom Program, and eventually resulting in the Marshall Space Flight Center's responsibilities for Space Station Work Package 1.

  19. NSLS-II biomedical beamlines for micro-crystallography, FMX, and for highly automated crystallography, AMX: New opportunities for advanced data collection

    SciTech Connect

    Fuchs, Martin R. Bhogadi, Dileep K.; Jakoncic, Jean; Myers, Stuart; Sweet, Robert M.; Berman, Lonny E.; Skinner, John; Idir, Mourad; Chubar, Oleg; McSweeney, Sean; Schneider, Dieter K.

    2016-07-27

    We present the final design of the x-ray optics and experimental stations of two macromolecular crystallography (MX) beamlines at the National Synchrotron Light Source-II. The microfocusing FMX beamline will deliver a flux of ∼5×10{sup 12} ph/s at 1 Å into a 1 – 20 µm spot, its flux density surpassing current MX beamlines by up to two orders of magnitude. It covers an energy range from 5 – 30 keV. The highly automated AMX beamline is optimized for high throughput, with beam sizes from 4 – 100 µm, an energy range of 5 – 18 keV and a flux at 1 Å of ∼10{sup 13} ph/s. A focus in designing the beamlines lay on achieving high beam stability, for example by implementing a horizontal bounce double crystal monochromator at FMX. A combination of compound refractive lenses and bimorph mirror optics at FMX supports rapid beam size changes. Central components of the in-house developed experimental stations are horizontal axis goniometers with a target sphere of confusion of 100 nm, piezo-slits for dynamic beam size changes during diffraction experiments, dedicated secondary goniometers for data collection from specimen in crystallization plates, and next generation pixel array detectors. FMX and AMX will support a broad range of biomedical structure determination methods from serial crystallography on micron-sized crystals, to structure determination of complexes in large unit cells, to rapid sample screening and room temperature data collection of crystals in trays.

  20. Serial Femtosecond Crystallography and Ultrafast Absorption Spectroscopy of the Photoswitchable Fluorescent Protein IrisFP.

    PubMed

    Colletier, Jacques-Philippe; Sliwa, Michel; Gallat, François-Xavier; Sugahara, Michihiro; Guillon, Virginia; Schirò, Giorgio; Coquelle, Nicolas; Woodhouse, Joyce; Roux, Laure; Gotthard, Guillaume; Royant, Antoine; Uriarte, Lucas Martinez; Ruckebusch, Cyril; Joti, Yasumasa; Byrdin, Martin; Mizohata, Eiichi; Nango, Eriko; Tanaka, Tomoyuki; Tono, Kensuke; Yabashi, Makina; Adam, Virgile; Cammarata, Marco; Schlichting, Ilme; Bourgeois, Dominique; Weik, Martin

    2016-03-03

    Reversibly photoswitchable fluorescent proteins find growing applications in cell biology, yet mechanistic details, in particular on the ultrafast photochemical time scale, remain unknown. We employed time-resolved pump-probe absorption spectroscopy on the reversibly photoswitchable fluorescent protein IrisFP in solution to study photoswitching from the nonfluorescent (off) to the fluorescent (on) state. Evidence is provided for the existence of several intermediate states on the pico- and microsecond time scales that are attributed to chromophore isomerization and proton transfer, respectively. Kinetic modeling favors a sequential mechanism with the existence of two excited state intermediates with lifetimes of 2 and 15 ps, the second of which controls the photoswitching quantum yield. In order to support that IrisFP is suited for time-resolved experiments aiming at a structural characterization of these ps intermediates, we used serial femtosecond crystallography at an X-ray free electron laser and solved the structure of IrisFP in its on state. Sample consumption was minimized by embedding crystals in mineral grease, in which they remain photoswitchable. Our spectroscopic and structural results pave the way for time-resolved serial femtosecond crystallography aiming at characterizing the structure of ultrafast intermediates in reversibly photoswitchable fluorescent proteins.

  1. International Space Station (ISS)

    NASA Image and Video Library

    1997-10-03

    In this photograph, Russians are working on the aft portion of the United States-funded, Russian-built Functional Cargo Bay (FGB) also known as Zarya (Russian for sunrise). Built at Khrunichev, the FGB began pre-launch testing shortly after this photo was taken. Launched by a Russian Proton rocket from the Baikonu Cosmodrome on November 20, 1998, Zarya was the first element of the International Space Station (ISS) followed by the U.S. Unity Node. The aft docking mechanism, Pirs, on the far right with ventilation ducting rurning through it, will be docked with the third Station element, the Russian Service Module, or Zvezda.

  2. JBlulce Data Acquisition Software for Macromolecular Crystallography

    SciTech Connect

    2010-06-01

    JBlulce (Java Beam Line Universal Integrated Configuration Environment is a data acquisition software for macromolecular crystallography conforming user interface of the SSRL Blulce that has become a de-factor standard in the field. Besides this interface conformity, JBlulce is a unique system in terms of architecture, speec, capability and osftware implementation. It features only two software layers, the JBlulce clients and the EPICS servers, as compared to three layers present in Blulc and most of similar systems. This layers reduction provides a faster communication with hardware and an easier access to advanced hardware capabilities like on-the-fly scanning. Then JBlulc clients are designed to operate in parallel with the other beamline controls which streamlines the tasks performed by staff such as beamline preparation, maitenance, audting and user assistance. Another distinction is the deployment of multiple plugins that can be written in any programming languag thus involving more staff into the development. further on, JBlulce makes use of unified motion controls allowing for easy scanning and optimizing of any beamline component. Finally, the graphic interface is implemented in Java making full use of rich Java libraries and Jave IDE for debugging. to compare, Blulce user interface is implemented with aging Tcl/tk language providing very restricted capabilities. JBlulce makes full use of the industrial power and wide drivers selection of EPICS in controlling hardware; all hardware commuication is routed via multiple EPICS servers residing on local area network. JBlulce also includes several EPICS State Notation servers aimed at making hardware communication more robust. Besides using EPICS for controlling hardware, JBlulce extensively uses EPICS databases for efficien communications between multiple instances of JBlulce clients and JBlulce pplugins that can run in parallel on different computers. All of the above makes JBlulce one of the biggest and most

  3. Fluorescent Approaches to High Throughput Crystallography

    NASA Technical Reports Server (NTRS)

    Pusey, Marc L.; Forsythe, Elizabeth; Achari, Amiruddha

    2005-01-01

    X-ray crystallography remains the primary method for determining the structure of macromolecules. The first requirement is to have crystals, and obtaining them is often the rate-limiting step. The numbers of crystallization trials that are set up for any one protein for structural genomics, and the rate at which they are being set up, now overwhelm the ability for strictly human analysis of the results. Automated analysis methods are now being implemented with varying degrees of success, but these typically cannot reliably extract intermediate results. By covalently modifying a subpopulation, less than or = 1 %, of a macromolecule solution with a fluorescent probe, the labeled material will add to a growing crystal as a microheterogeneous growth unit. Labeling procedures can be readily incorporated into the final stages of purification. The covalently attached probe will concentrate in the crystal relative to the solution, and under fluorescent illumination the crystals show up as bright objects against a dark background. As crystalline packing is more dense than amorphous precipitate, the fluorescence intensity can be used as a guide in distinguishing different types of precipitated phases, even in the absence of obvious crystalline features, widening the available potential lead conditions in the absence of clear "hits." Non-protein structures, such as salt crystals, will not incorporate the probe and will not show up under fluorescent illumination. Also, brightly fluorescent crystals are readily found against less fluorescent precipitated phases, which under white light illumination may serve to obscure the crystals. Automated image analysis to find crystals should be greatly facilitated, without having to first define crystallization drop boundaries and by having the protein or protein structures all that show up. The trace fluorescently labeled crystals will also emit with sufficient intensity to aid in the automation of crystal alignment using relatively low

  4. Fluorescent Approaches to High Throughput Crystallography

    NASA Technical Reports Server (NTRS)

    Pusey, Marc L.; Forsythe, Elizabeth

    2005-01-01

    X-ray crystallography remains the primary method for determining the structure of macromolecules. The first requirement is to have crystals, and obtaining them is often the rate-limiting step. The numbers of crystallization trials that are set up for any one protein for structural genomics, and the rate at which they are being set up, now overwhelm the ability for strictly human analysis of the results. Automated analysis methods are now being implemented with varying degrees of success, but these typically cannot reliably extract intermediate results. By covalently modifying a subpopulation, 51%, of a macromolecule solution with a fluorescent probe, the labeled material will add to a growing crystal as a microheterogeneous growth unit. Labeling procedures can be readily incorporated into the final stages of purification. The covalently attached probe will concentrate in the crystal relative to the solution, and under fluorescent illumination the crystals show up as bright objects against a dark background. As crystalline packing is more dense than amorphous precipitate, the fluorescence intensity can be used as a guide in distinguishing different types of precipitated phases, even in the absence of obvious crystalline features, widening the available potential lead conditions in the absence of clear hits. Non-protein structures, such as salt crystals, will not incorporate the probe and will not show up under fluorescent illumination. Also, brightly fluorescent crystals are readily found against less fluorescent precipitated phases, which under white light illumination may serve to obscure the crystals. Automated image analysis to find crystals should be greatly facilitated, without having to first define crystallization drop boundaries and by having the protein or protein structures all that show up. The trace fluorescently labeled crystals will also emit with sufficient intensity to aid in the automation of crystal alignment using relatively low cost optics

  5. Fluorescent Approaches to High Throughput Crystallography

    NASA Technical Reports Server (NTRS)

    Minamitani, Elizabeth Forsythe; Pusey, Marc L.

    2004-01-01

    X-ray crystallography remains the primary method for determining the structure of macromolecules. The first requirement is to have crystals, and obtaining them is often the rate-limiting step. The numbers of crystallization trials that are set up for any one protein for structural genomics, and the rate at which they are being set up, now overwhelm the ability for strictly human analysis of the results. Automated analysis methods are now being implemented with varying degrees of success, but these typically cannot reliably extract intermediate results. By covalently modifying a subpopulation, less than or = 1%, of a macromolecule solution with a fluorescent probe, the labeled material will add to a growing crystal as a microheterogeneous growth unit. Labeling procedures can be readily incorporated into the final stages of a macromolecules purification. The covalently attached probe will concentrate in the crystal relative to the solution, and under fluorescent illumination the crystals will show up as bright objects against a dark background. As crystalline packing is more dense than amorphous precipitate, the fluorescence intensity can be used as a guide in distinguishing different types of precipitated phases, even in the absence of obvious crystalline features, widening the available potential lead conditions in the absence of clear "bits." Non-protein structures, such as salt crystals, will not incorporate the probe and will not show up under fluorescent illumination. Also, brightly fluorescent crystals are readily found against less fluorescent precipitated phases, which under white light illumination may serve to obscure the crystals. Automated image analysis to find crystals should be greatly facilitated, without having to first define crystallization drop boundaries and by having the protein or protein structures all that show up. The trace fluorescently labeled crystals will also emit with sufficient intensity to aid in the automation of crystal alignment

  6. Fluorescent Approaches to High Throughput Crystallography

    NASA Technical Reports Server (NTRS)

    Pusey, Marc L.; Forsythe, Elizabeth

    2004-01-01

    X-ray crystallography remains the primary method for determining the structure of macromolecules. The first requirement is to have crystals, and obtaining them is often the rate-limiting step. The numbers of crystallization trials that are set up for any one protein for structural genomics, and the rate at which they are being set up, now overwhelm the ability for strictly human analysis of the results. Automated analysis methods are now being implemented with varying degrees of success, but these typically can not reliably extract intermediate results. By covalently modifying a subpopulation, less than or = 1%, of a macromolecule solution with a fluorescent probe, the labeled material will add to a growing crystal as a microheterogeneous growth unit. Labeling procedures can be readily incorporated into the final stages of purification. The covalently attached probe will concentrate in the crystal relative to the solution, and under fluorescent illumination the crystals show up as bright objects against a dark background. As crystalline packing is more dense than amorphous precipitate, the fluorescence intensity can be used as a guide in distinguishing different types of precipitated phases, even in the absence of obvious crystalline features, widening the available potential lead conditions in the absence of clear "hits." Non-protein structures, such as salt crystals, will not incorporate the probe and will not show up under fluorescent illumination. Also, brightly fluorescent crystals are readily found against less fluorescent precipitated phases, which under white light illumination may serve to obscure the crystals. Automated image analysis to find crystals should be greatly facilitated, without having to first define crystallization drop boundaries and by having the protein or protein structures all that show up. The trace fluorescently labeled crystals will also emit with sufficient intensity to aid in the automation of crystal alignment using relatively low

  7. International Space Station (ISS)

    NASA Image and Video Library

    2001-06-08

    Astronaut Susan J. Helms, Expedition Two flight engineer, mounts a video camera onto a bracket in the Russian Zarya or Functional Cargo Block (FGB) of the International Space Station (ISS). Launched by a Russian Proton rocket from the Baikonu Cosmodrome on November 20, 1998, the Unites States-funded and Russian-built Zarya was the first element of the ISS, followed by the U.S. Unity Node.

  8. Proton Therapy

    MedlinePlus

    ... Proton Therapy Alternative & Integrative Medicine Clinical Trials GBM AGILE TTFields – Optune™ Brain Tumor Treatment Locations Treatment Side ... Proton Therapy Alternative & Integrative Medicine Clinical Trials GBM AGILE TTFields – Optune™ Brain Tumor Treatment Locations Treatment Side ...

  9. Beamline X29: a novel undulator source for X-ray crystallography.

    PubMed

    Shi, Wuxian; Robinson, Howard; Sullivan, Michael; Abel, Don; Toomey, John; Berman, Lonny E; Lynch, Don; Rosenbaum, Gerd; Rakowsky, George; Rock, Larry; Nolan, Bill; Shea-McCarthy, Grace; Schneider, Dieter; Johnson, Erik; Sweet, Robert M; Chance, Mark R

    2006-09-01

    A high-flux insertion device and beamline for macromolecular crystallography has been built at the National Synchrotron Light Source (NSLS) that employs a mini-gap undulator source developed by the NSLS. The mini-gap undulator at beamline X29 is a hybrid-magnet device of period 12.5 mm operating at proven gaps of 3.3-10 mm. The beamline provides hard X-rays for macromolecular crystallography experiments from the second and third harmonics over an energy range of 5-15 keV. The X-ray optics is designed to deliver intense and highly collimated X-rays. Horizontal focusing is achieved by a cryogenically cooled sagittally focusing double-crystal monochromator with approximately 4.1:1 demagnification. A vertical focusing mirror downstream of the monochromator is used for harmonic rejection and vertical focusing. The experimental station hosts an Area Detector Systems Quantum 315 CCD detector with 2.2 s readout time between exposures and Crystal Logic goniostat for crystal rotation and detector positioning. An auto-mounter crystal changer has been installed to facilitate the high-throughput data collection required by the major users, which includes structural genomics projects and the Macromolecular Crystallography Research Resource mail-in program. X29 is 10(3) times brighter than any existing bending-magnet beamline at NSLS with an actual flux of 2.5 x 10(11) photons s(-1) through a 0.12 mm square aperture at 11.271 keV.

  10. Enantioselective Protonation

    PubMed Central

    Mohr, Justin T.; Hong, Allen Y.; Stoltz, Brian M.

    2010-01-01

    Enantioselective protonation is a common process in biosynthetic sequences. The decarboxylase and esterase enzymes that effect this valuable transformation are able to control both the steric environment around the proton acceptor (typically an enolate) and the proton donor (typically a thiol). Recently, several chemical methods to achieve enantioselective protonation have been developed by exploiting various means of enantiocontrol in different mechanisms. These laboratory transformations have proven useful for the preparation of a number of valuable organic compounds. PMID:20428461

  11. Optimized beamline design for macromolecular crystallography at the Cornell High Energy Synchrotron Source (CHESS) (abstract)

    NASA Astrophysics Data System (ADS)

    Schildkamp, Wilfried; Bilderback, Donald; Moffat, Keith

    1989-07-01

    The A1 station on the CHESS wiggler beamline has been the workhorse for most macromolecular crystallographic experiments. This station is equipped with a fixed energy focusing germanium (111) monochromator and a focusing total reflection mirror. Our macromolecular crystallographers made full use of the high flux of more than 1012 photons/s/mm2 and the stable beam conditions, both in position and energy resolution. As a result, the A1 station was heavily oversubscribed. CHESS is presently expanding its capabilities and a new diffraction station for macromolecular crystallography is under construction. This beamline will be powered by a 24-pole hybrid permanent magnet wiggler with a critical energy of 25 keV. A focusing monochromator, which handles a specific heat load of 10 W/mm2, will have a range of tunability which covers all relevant absorption edges from 7 to 15 keV using a Ge(111) crystal. The energy resolution and the focusing properties remain constant within a factor of 2 over the entire tunability range. We expect a brilliance of about 1013 photons/s/mm2/mrad2/0.1% bandpass. The diffraction station will be equipped with an oscillation camera which can be used with x-ray film of 5×5 or 8×10 in. size or alternatively with Kodak storage phosphors. A wide variety of clamp-on accessories, like crystal coolers, fast shutters, helium pathways, polarimeter, etc. are available. The station will contain a beampipe system, which can also be used for small angle scattering experiments with sample-to-detector distances of up to 3000 mm. The entire diffraction station, its control area, a biological preparation area, and a darkroom are to be embedded in a biological safety containment of the level BL3. This will allow diffraction studies of virulent strains of viruses and other biohazards, which could not previously be studied at synchrotron radiation sources before without causing major disruption to the normal laboratory procedure.

  12. NMR Crystallography of Enzyme Active Sites: Probing Chemically-Detailed, Three-Dimensional Structure in Tryptophan Synthase

    PubMed Central

    Dunn, Michael F.

    2013-01-01

    Conspectus NMR crystallography – the synergistic combination of X-ray diffraction, solid-state NMR spectroscopy, and computational chemistry – offers unprecedented insight into three-dimensional, chemically-detailed structure. From its initial role in refining diffraction data of organic and inorganic solids, NMR crystallography is now being developed for application to active sites in biomolecules, where it reveals chemically-rich detail concerning the interactions between enzyme site residues and the reacting substrate that is not achievable when X-ray, NMR, or computational methodologies are applied in isolation. For example, typical X-ray crystal structures (1.5 to 2.5 Å resolution) of enzyme-bound intermediates identify possible hydrogen-bonding interactions between site residues and substrate, but do not directly identify the protonation state of either. Solid-state NMR can provide chemical shifts for selected atoms of enzyme-substrate complexes, but without a larger structural framework in which to interpret them, only empirical correlations with local chemical structure are possible. Ab initio calculations and molecular mechanics can build models for enzymatic processes, but rely on chemical details that must be specified. Together, however, X-ray diffraction, solid-state NMR spectroscopy, and computational chemistry can provide consistent and testable models for structure and function of enzyme active sites: X-ray crystallography provides a coarse framework upon which models of the active site can be developed using computational chemistry; these models can be distinguished by comparison of their calculated NMR chemical shifts with the results of solid-state NMR spectroscopy experiments. Conceptually, each technique is a puzzle piece offering a generous view of the big picture. Only when correctly pieced together, however, can they reveal the big picture at highest resolution. In this Account, we detail our first steps in the development of NMR

  13. International Space Station (ISS)

    NASA Image and Video Library

    1999-01-01

    The International Space Station (ISS) is an unparalleled international scientific and technological cooperative venture that will usher in a new era of human space exploration and research and provide benefits to people on Earth. On-Orbit assembly began on November 20, 1998, with the launch of the first ISS component, Zarya, on a Russian Proton rocket. The Space Shuttle followed on December 4, 1998, carrying the U.S.-built Unity cornecting Module. Sixteen nations are participating in the ISS program: the United States, Canada, Japan, Russia, Brazil, Belgium, Denmark, France, Germany, Italy, the Netherlands, Norway, Spain, Sweden, Switzerland, and the United Kingdom. The ISS will include six laboratories and be four times larger and more capable than any previous space station. The United States provides two laboratories (United States Laboratory and Centrifuge Accommodation Module) and a habitation module. There will be two Russian research modules, one Japanese laboratory, referred to as the Japanese Experiment Module (JEM), and one European Space Agency (ESA) laboratory called the Columbus Orbital Facility (COF). The station's internal volume will be roughly equivalent to the passenger cabin volume of two 747 jets. Over five years, a total of more than 40 space flights by at least three different vehicles - the Space Shuttle, the Russian Proton Rocket, and the Russian Soyuz rocket - will bring together more than 100 different station components and the ISS crew. Astronauts will perform many spacewalks and use new robotics and other technologies to assemble ISS components in space.

  14. Applied Crystallography - Proceedings of the XVth Conference

    NASA Astrophysics Data System (ADS)

    Morawiec, H.; Ströż, D.

    1993-06-01

    The Table of Contents for the full book PDF is as follows: * Foreword * The International Centre for Diffraction Data and Its Future Developments * The Rietveld Method - A Historical Perspective * Real Structure in Quantitative Powder Diffraction Phase Analysis * Neutron Focusing Optics in Applied Crystallography * The Crystal Structures of Oxygen Deficient Rare Earth Oxides * Short-Range Order in Layer-Structured Ba1-xSrxBi2Nb2O9 Ferroelectrics * Radial Distribution Function as a Tool of Structural Studies on Noncrystalline Materials * Determination of Radial Distribution Function (RDF) of Electrodeposited Cu-Cd Alloys After Annealing * Spheres Packing as a Factor Describing the Local Environment and Structure Stability * X-Ray Stress Measurement of Samples Combined with Diffraction Line Analysis * Phase Stability and Martensitic Transformation in Cu-Zn and Cu-Zn-Al Single Crystals * Order, Defects, Precipitates and the Martensitic Transformation in β Cu-Zn-Al * Effect of γ Precipitates on the Martensitic Transformation in Cu-Zn-Al Alloys * Phase Transitions and Shape Memory Effect in a Thermomechanically Treated NiTi Alloy * Structure of Martensite and Bainite in CuAlMn Alloys * Glass-Ceramics * Mechanism of Texture Formation at the Rolling of Low Stacking Fault Energy Metals and Alloys * Shear Texture of Zinc and the Conditions of Its Occuring * The Development of Texture of ZnAlMg Sheets Depending on Deformation Geometry * Texture Stability of the D.S. NiAlMoCrTi Alloy After Heat Treatment * X-Ray Diffraction Method for Controlling of Texture Evolution in Layers * Texture and Lattice Imperfections Study of Some Low Alloyed Copper Alloys * Selected Examples of the Calculation of the Orientation Distribution Function for Low Crystal and Sample Symmetries * Automatical X-Ray Quantitative Phase Analysis * Application of a PC Computer for Crystallographic Calculations * Electron Diffraction Analysis using a Personal Computer * CA.R.INE Crystallography Version 2

  15. Cleavage crystallography of liquid metal embrittled aluminum alloys

    NASA Technical Reports Server (NTRS)

    Reynolds, A. P.; Stoner, G. E.

    1991-01-01

    The crystallography of liquid metal-induced transgranular cleavage in six aluminum alloys having a variety of microstructures has been determined via Laue X-ray back reflection. The cleavage crystallography was independent of alloy microstructure, and the cleavage plane was 100-plane oriented in all cases. It was further determined that the cleavage crystallography was not influenced by alloy texture. Examination of the fracture surface indicated that there was not a unique direction of crack propagation. In addition, the existence of 100-plane cleavage on alloy 2024 fracture surfaces was inferred by comparison of secondary cleavage crack intersection geometry on the 2024 surfaces with the geometry of secondary cleavage crack intersections on the test alloys.

  16. Status of the crystallography beamlines at PETRA III

    NASA Astrophysics Data System (ADS)

    Burkhardt, Anja; Pakendorf, Tim; Reime, Bernd; Meyer, Jan; Fischer, Pontus; Stübe, Nicolas; Panneerselvam, Saravanan; Lorbeer, Olga; Stachnik, Karolina; Warmer, Martin; Rödig, Philip; Göries, Dennis; Meents, Alke

    2016-03-01

    Since 2013, three beamlines for macromolecular crystallography are available to users at the third-generation synchrotron PETRA III in Hamburg: P11, P13 and P14, the latter two operated by EMBL. Beamline P11 is operated by DESY and is equipped with a Pilatus 6M detector. Together with the photon flux of 2× 10^{13} ph/s provided by the very brilliant X-ray source of PETRA III, a full data set can be typically collected in less than 2min. P11 provides state-of-the-art microfocusing capabilities with beam sizes down to 1× 1 μ m2, which makes the beamline ideally suited for investigation of microcrystals and serial crystallography experiments. An automatic sample changer allows fast sample exchange in less than 20s, which enables high-throughput crystallography and fast crystal screening. For sample preparation, an S2 biosafety laboratory is available in close proximity to the beamline.

  17. Temperature-dependent macromolecular X-ray crystallography

    SciTech Connect

    Weik, Martin Colletier, Jacques-Philippe

    2010-04-01

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

  18. Native sulfur/chlorine SAD phasing for serial femtosecond crystallography

    SciTech Connect

    Nakane, Takanori; Song, Changyong; Suzuki, Mamoru; Nango, Eriko; Kobayashi, Jun; Masuda, Tetsuya; Inoue, Shigeyuki; Mizohata, Eiichi; Nakatsu, Toru; Tanaka, Tomoyuki; Tanaka, Rie; Shimamura, Tatsuro; Tono, Kensuke; Joti, Yasumasa; Kameshima, Takashi; Hatsui, Takaki; Yabashi, Makina; Nureki, Osamu; Iwata, So; Sugahara, Michihiro

    2015-11-27

    Sulfur SAD phasing facilitates the structure determination of diverse native proteins using femtosecond X-rays from free-electron lasers via serial femtosecond crystallography. Serial femtosecond crystallography (SFX) allows structures to be determined with minimal radiation damage. However, phasing native crystals in SFX is not very common. Here, the structure determination of native lysozyme from single-wavelength anomalous diffraction (SAD) by utilizing the anomalous signal of sulfur and chlorine at a wavelength of 1.77 Å is successfully demonstrated. This sulfur SAD method can be applied to a wide range of proteins, which will improve the determination of native crystal structures.

  19. Macromolecular crystallography beamline X25 at the NSLS.

    PubMed

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

    2014-05-01

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

  20. Crystallography Open Databases and Preservation: a World-wide Initiative

    NASA Astrophysics Data System (ADS)

    Chateigner, Daniel

    In 2003, an international team of crystallographers proposed the Crystallography Open Database (COD), a fully-free collection of crystal structure data, in the aim of ensuring their preservation. With nearly 250000 entries, this database represents a large open set of data for crystallographers, academics and industrials, located at five different places world-wide, and included in Thomson-Reuters’ ISI. As a large step towards data preservation, raw data can now be uploaded along with «digested» structure files, and COD can be questioned by most of the crystallography-linked industrial software. The COD initiative work deserves several other open developments.

  1. Macromolecular crystallography beamline X25 at the NSLS

    PubMed Central

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

    2014-01-01

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

  2. Cryo-crystallography: diffraction at low temperature and more.

    PubMed

    Macchi, Piero

    2012-01-01

    This chapter comments on the motivations and the methods of crystallographic studies at low temperature. Cry-crystallography is a brunch of Crystallography, a science that is too often confused with a technique. On the other hand, the scientific background to study crystal phases at low temperature is here provided, together with a survey of many possible techniques that provide complementary or supplementary information. Several applications are discussed, in particular in relation with highly accurate studies like electron density determination or phase transition mechanisms.

  3. Tinker Toys, Crystallography, and the Introductory Mineralogy Course

    ERIC Educational Resources Information Center

    Buseck, Peter R.

    1970-01-01

    Describes the use of Tinker Toys to construct three dimensional models of crystals useful in illustrating many concepts of crystallography. Space lattices representing all of the Bravais types can be constructed. Also discusses the use of appropriate models to demonstrate the various symmetry operations. Bibliography. (LC)

  4. Tinker Toys, Crystallography, and the Introductory Mineralogy Course

    ERIC Educational Resources Information Center

    Buseck, Peter R.

    1970-01-01

    Describes the use of Tinker Toys to construct three dimensional models of crystals useful in illustrating many concepts of crystallography. Space lattices representing all of the Bravais types can be constructed. Also discusses the use of appropriate models to demonstrate the various symmetry operations. Bibliography. (LC)

  5. Models as an Aid to Courses in Crystallography and Mineralogy.

    ERIC Educational Resources Information Center

    Brady, K. T.

    1983-01-01

    Three models used in teaching crystallography/mineralogy at the University of Technology (Papua, New Guinea) are described. These include stereographic projection model, optical indicatrix models for Istropic/Anisotropic minerals, and model showing effect of anisotropic minerals under crossed polars. Photographs of the models are also included.…

  6. Two-Dimensional Crystallography Introduced by the Sprinkler Watering Problem

    ERIC Educational Resources Information Center

    De Toro, Jose A.; Calvo, Gabriel F.; Muniz, Pablo

    2012-01-01

    The problem of optimizing the number of circular sprinklers watering large fields is used to introduce, from a purely elementary geometrical perspective, some basic concepts in crystallography and comment on a few size effects in condensed matter physics. We examine square and hexagonal lattices to build a function describing the, so-called, dry…

  7. Using Two-Dimensional Colloidal Crystals to Understand Crystallography

    ERIC Educational Resources Information Center

    Bosse, Stephanie A.; Loening, Nikolaus M.

    2008-01-01

    X-ray crystallography is an essential technique for modern chemistry and biochemistry, but it is infrequently encountered by undergraduate students owing to lack of access to equipment, the time-scale for generating diffraction-quality molecular crystals, and the level of mathematics involved in analyzing the resulting diffraction patterns.…

  8. Two-Dimensional Crystallography Introduced by the Sprinkler Watering Problem

    ERIC Educational Resources Information Center

    De Toro, Jose A.; Calvo, Gabriel F.; Muniz, Pablo

    2012-01-01

    The problem of optimizing the number of circular sprinklers watering large fields is used to introduce, from a purely elementary geometrical perspective, some basic concepts in crystallography and comment on a few size effects in condensed matter physics. We examine square and hexagonal lattices to build a function describing the, so-called, dry…

  9. Fab Chaperone-Assisted RNA Crystallography (Fab CARC).

    PubMed

    Sherman, Eileen; Archer, Jennifer; Ye, Jing-Dong

    2016-01-01

    Recent discovery of structured RNAs such as ribozymes and riboswitches shows that there is still much to learn about the structure and function of RNAs. Knowledge learned can be employed in both biochemical research and clinical applications. X-ray crystallography gives unparalleled atomic-level structural detail from which functional inferences can be deduced. However, the difficulty in obtaining high-quality crystals and their phasing information make it a very challenging task. RNA crystallography is particularly arduous due to several factors such as RNA's paucity of surface chemical diversity, lability, repetitive anionic backbone, and flexibility, all of which are counterproductive to crystal packing. Here we describe Fab chaperone assisted RNA crystallography (CARC), a systematic technique to increase RNA crystallography success by facilitating crystal packing as well as expediting phase determination through molecular replacement of conserved Fab domains. Major steps described in this chapter include selection of a synthetic Fab library displayed on M13 phage against a structured RNA crystallization target, ELISA for initial choice of binding Fabs, Fab expression followed by protein A affinity then cation exchange chromatography purification, final choice of Fab by binding specificity and affinity as determined by a dot blot assay, and lastly gel filtration purification of a large quantity of chosen Fabs for crystallization.

  10. Facilitating structure determination: workshop on robotics andautomation in macromolecular crystallography

    SciTech Connect

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

    2006-03-28

    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.

  11. Using Two-Dimensional Colloidal Crystals to Understand Crystallography

    ERIC Educational Resources Information Center

    Bosse, Stephanie A.; Loening, Nikolaus M.

    2008-01-01

    X-ray crystallography is an essential technique for modern chemistry and biochemistry, but it is infrequently encountered by undergraduate students owing to lack of access to equipment, the time-scale for generating diffraction-quality molecular crystals, and the level of mathematics involved in analyzing the resulting diffraction patterns.…

  12. International Space Station (ISS)

    NASA Image and Video Library

    2001-12-12

    Astronauts Frank L. Culbertson, Jr. (left), Expedition Three mission commander, and Daniel W. Bursch, Expedition Four flight engineer, work in the Russian Zvezda Service Module on the International Space Station (ISS). Zvezda is linked to the Russian built Functional Cargo Block (FGB), or Zarya, the first component of the ISS. Zarya was launched on a Russian Proton rocket prior to the launch of Unity. The third component of the ISS, Zvezda (Russian word for star), the primary Russian contribution to the ISS, was launched by a three-stage Proton rocket on July 12, 2000. Zvezda serves as the cornerstone for early human habitation of the Station, providing living quarters, a life support system, electrical power distribution, a data processing system, a flight control system, and a propulsion system. It also provides a communications system that includes remote command capabilities from ground flight controllers. The 42,000 pound module measures 43 feet in length and has a wing span of 98 feet. Similar in layout to the core module of Russia's Mir space station, it contains 3 pressurized compartments and 13 windows that allow ultimate viewing of Earth and space.

  13. International Space Station (ISS)

    NASA Image and Video Library

    2001-09-16

    Aboard the International Space Station (ISS), Cosmonaut and Expedition Three flight engineer Vladimir N. Dezhurov, representing Rosaviakosmos, talks with flight controllers from the Zvezda Service Module. Russian-built Zvezda is linked to the Functional Cargo Block (FGB), or Zarya, the first component of the ISS. Zarya was launched on a Russian Proton rocket prior to the launch of Unity. The third component of the ISS, Zvezda (Russian word for star), the primary Russian contribution to the ISS, was launched by a three-stage Proton rocket on July 12, 2000. Zvezda serves as the cornerstone for early human habitation of the Station, providing living quarters, a life support system, electrical power distribution, a data processing system, flight control system, and propulsion system. It also provides a communications system that includes remote command capabilities from ground flight controllers. The 42,000-pound module measures 43 feet in length and has a wing span of 98 feet. Similar in layout to the core module of Russia's Mir space station, it contains 3 pressurized compartments and 13 windows that allow ultimate viewing of Earth and space.

  14. International Space Station (ISS)

    NASA Image and Video Library

    2001-03-30

    Astronaut James S. Voss, Expedition Two flight engineer, performs an electronics task in the Russian Zvezda Service Module on the International Space Station (ISS). Zvezda is linked to the Russian-built Functional Cargo Block (FGB), or Zarya, the first component of the ISS. Zarya was launched on a Russian Proton rocket prior to the launch of Unity, the first U.S.-built component to the ISS. Zvezda (Russian word for star), the third component of the ISS and the primary Russian contribution to the ISS, was launched by a three-stage Proton rocket on July 12, 2000. Zvezda serves as the cornerstone for early human habitation of the station, providing living quarters, a life support system, electrical power distribution, a data processing system, a flight control system, and a propulsion system. It also provides a communications system that includes remote command capabilities from ground flight controllers. The 42,000-pound module measures 43 feet in length and has a wing span of 98 feet. Similar in layout to the core module of Russia's Mir space station, it contains 3 pressurized compartments and 13 windows that allow ultimate viewing of Earth and space.

  15. International Space Station (ISS)

    NASA Image and Video Library

    2002-03-25

    Cosmonaut Yury I. Onufrienko, Expedition Four mission commander, uses a communication system in the Russian Zvezda Service Module on the International Space Station (ISS). The Zvezda is linked to the Russian-built Functional Cargo Block (FGB) or Zarya, the first component of the ISS. Zarya was launched on a Russian Proton rocket prior to the launch of Unity. The third component of the ISS, Zvezda (Russian word for star), the primary Russian contribution to the ISS, was launched by a three-stage Proton rocket on July 12, 2000. Zvezda serves as the cornerstone for early human habitation of the station, providing living quarters, a life support system, electrical power distribution, a data processing system, flight control system, and propulsion system. It also provides a communications system that includes remote command capabilities from ground flight controllers. The 42,000-pound module measures 43 feet in length and has a wing span of 98 feet. Similar in layout to the core module of Russia's Mir space station, it contains 3 pressurized compartments and 13 windows that allow ultimate viewing of Earth and space.

  16. Proton Transport

    NASA Technical Reports Server (NTRS)

    Pohorille, Andrew; DeVincenzi, Donald L. (Technical Monitor)

    2001-01-01

    The transport of protons across membranes is an essential process for both bioenergetics of modern cells and the origins of cellular life. All living systems make use of proton gradients across cell walls to convert environmental energy into a high-energy chemical compound, adenosine triphosphate (ATP), synthesized from adenosine diphosphate. ATP, in turn, is used as a source of energy to drive many cellular reactions. The ubiquity of this process in biology suggests that even the earliest cellular systems were relying on proton gradient for harvesting environmental energy needed to support their survival and growth. In contemporary cells, proton transfer is assisted by large, complex proteins embedded in membranes. The issue addressed in this Study was: how the same process can be accomplished with the aid of similar but much simpler molecules that could have existed in the protobiological milieu? The model system used in the study contained a bilayer membrane made of phospholipid, dimyristoylphosphatidylcholine (DMPC) which is a good model of the biological membranes forming cellular boundaries. Both sides of the bilayer were surrounded by water which simulated the environment inside and outside the cell. Embedded in the membrane was a fragment of the Influenza-A M$_2$ protein and enough sodium counterions to maintain system neutrality. This protein has been shown to exhibit remarkably high rates of proton transport and, therefore, is an excellent model to study the formation of proton gradients across membranes. The Influenza M$_2$ protein is 97 amino acids in length, but a fragment 25 amino acids long. which contains a transmembrane domain of 19 amino acids flanked by three amino acids on each side. is sufficient to transport protons. Four identical protein fragments, each folded into a helix, aggregate to form small channels spanning the membrane. Protons are conducted through a narrow pore in the middle of the channel in response to applied voltage. This

  17. Space Station

    NASA Image and Video Library

    1972-01-01

    This is an artist's concept of a modular space station. In 1970 the Marshall Space Flight Center arnounced the completion of a study concerning a modular space station that could be launched by the planned-for reusable Space Shuttle. The study envisioned a space station composed of cylindrical sections 14 feet in diameter and of varying lengths joined to form any one of a number of possible shapes. The sections were restricted to 14 feet in diameter and 58 feet in length to be consistent with a shuttle cargo bay size of 15 by 60 feet. Center officials said that the first elements of the space station could be in orbit by about 1978 and could be manned by three or six men. This would be an interim space station with sections that could be added later to form a full 12-man station by the early 1980s.

  18. Space station

    NASA Technical Reports Server (NTRS)

    Stewart, Donald F.; Hayes, Judith

    1989-01-01

    The history of American space flight indicates that a space station is the next logical step in the scientific pursuit of greater knowledge of the universe. The Space Station and its complement of space vehicles, developed by NASA, will add new dimensions to an already extensive space program in the United States. The Space Station offers extraordinary benefits for a comparatively modest investment (currently estimated at one-ninth the cost of the Apollo Program). The station will provide a permanent multipurpose facility in orbit necessary for the expansion of space science and technology. It will enable significant advancements in life sciences research, satellite communications, astronomy, and materials processing. Eventually, the station will function in support of the commercialization and industrialization of space. Also, as a prerequisite to manned interplanetary exploration, the long-duration space flights typical of Space Station missions will provide the essential life sciences research to allow progressively longer human staytime in space.

  19. Space Station

    NASA Technical Reports Server (NTRS)

    Anderton, D. A.

    1985-01-01

    The official start of a bold new space program, essential to maintain the United States' leadership in space was signaled by a Presidential directive to move aggressively again into space by proceeding with the development of a space station. Development concepts for a permanently manned space station are discussed. Reasons for establishing an inhabited space station are given. Cost estimates and timetables are also cited.

  20. Characterizing the proton loading site in cytochrome c oxidase.

    PubMed

    Lu, Jianxun; Gunner, M R

    2014-08-26

    Cytochrome c oxidase (CcO) uses the energy released by reduction of O2 to H2O to drive eight charges from the high pH to low pH side of the membrane, increasing the electrochemical gradient. Four electrons and protons are used for chemistry, while four more protons are pumped. Proton pumping requires that residues on a pathway change proton affinity through the reaction cycle to load and then release protons. The protonation states of all residues in CcO are determined in MultiConformational Continuum Electrostatics simulations with the protonation and redox states of heme a, a3, Cu(B), Y288, and E286 used to define the catalytic cycle. One proton is found to be loaded and released from residues identified as the proton loading site (PLS) on the P-side of the protein in each of the four CcO redox states. Thus, the same proton pumping mechanism can be used each time CcO is reduced. Calculations with structures of Rhodobacter sphaeroides, Paracoccus denitrificans, and bovine CcO derived by crystallography and molecular dynamics show the PLS functions similarly in different CcO species. The PLS is a cluster rather than a single residue, as different structures show 1-4 residues load and release protons. However, the proton affinity of the heme a3 propionic acids primarily determines the number of protons loaded into the PLS; if their proton affinity is too low, less than one proton is loaded.

  1. Characterizing the proton loading site in cytochrome c oxidase

    PubMed Central

    Lu, Jianxun; Gunner, M. R.

    2014-01-01

    Cytochrome c oxidase (CcO) uses the energy released by reduction of O2 to H2O to drive eight charges from the high pH to low pH side of the membrane, increasing the electrochemical gradient. Four electrons and protons are used for chemistry, while four more protons are pumped. Proton pumping requires that residues on a pathway change proton affinity through the reaction cycle to load and then release protons. The protonation states of all residues in CcO are determined in MultiConformational Continuum Electrostatics simulations with the protonation and redox states of heme a, a3, CuB, Y288, and E286 used to define the catalytic cycle. One proton is found to be loaded and released from residues identified as the proton loading site (PLS) on the P-side of the protein in each of the four CcO redox states. Thus, the same proton pumping mechanism can be used each time CcO is reduced. Calculations with structures of Rhodobacter sphaeroides, Paracoccus denitrificans, and bovine CcO derived by crystallography and molecular dynamics show the PLS functions similarly in different CcO species. The PLS is a cluster rather than a single residue, as different structures show 1–4 residues load and release protons. However, the proton affinity of the heme a3 propionic acids primarily determines the number of protons loaded into the PLS; if their proton affinity is too low, less than one proton is loaded. PMID:25114210

  2. International Space Station (ISS)

    NASA Image and Video Library

    1997-01-01

    This photograph, taken by the Boeing Company,shows Boeing technicians preparing to install one of six hatches or doors to the Node 1 (also called Unity), the first U.S. Module for the International Space Station (ISS). The Node 1, or Unity, serves as a cornecting passageway to Space Station modules and was manufactured by the Boeing Company at the Marshall Space Flight Center from 1994 to 1997. The U.S. built Unity module was launched aboard the orbiter Endeavour (STS-88 mission) on December 4, 1998 and connected to the Zarya, the Russian-built Functional Energy Block (FGB). The Zarya was launched on a Russian proton rocket prior to the launch of the Unity. The ISS is a multidisciplinary laboratory, technology test bed, and observatory that will provide unprecedented undertakings in scientific, technological, and international experimentation.

  3. International Space Station (ISS)

    NASA Image and Video Library

    1997-01-01

    This photograph, taken by the Boeing Company, shows Boeing technicians preparing to install one of six hatches or doors to the Node 1 (also called Unity), the first U.S. Module for the International Space Station (ISS). The Node 1, or Unity, serves as a cornecting passageway to Space Station modules and was manufactured by the Boeing Company at the Marshall Space Flight Center from 1994 to 1997. The U.S. built Unity module was launched aboard the orbiter Endeavour (STS-88 mission) on December 4, 1998 and connected to the Zarya, the Russian-built Functional Energy Block (FGB). The Zarya was launched on a Russian proton rocket prior to the launch of the Unity. The ISS is a multidisciplinary laboratory, technology test bed, and observatory that will provide unprecedented undertakings in scientific, technological, and international experimentation.

  4. Precision Measurement of the Proton Flux in Primary Cosmic Rays from Rigidity 1 GV to 1.8 TV with the Alpha Magnetic Spectrometer on the International Space Station

    NASA Astrophysics Data System (ADS)

    Aguilar, M.; Aisa, D.; Alpat, B.; Alvino, A.; Ambrosi, G.; Andeen, K.; Arruda, L.; Attig, N.; Azzarello, P.; Bachlechner, A.; Barao, F.; Barrau, A.; Barrin, L.; Bartoloni, A.; Basara, L.; Battarbee, M.; Battiston, R.; Bazo, J.; Becker, U.; Behlmann, M.; Beischer, B.; Berdugo, J.; Bertucci, B.; Bigongiari, G.; Bindi, V.; Bizzaglia, S.; Bizzarri, M.; Boella, G.; de Boer, W.; Bollweg, K.; Bonnivard, V.; Borgia, B.; Borsini, S.; Boschini, M. J.; Bourquin, M.; Burger, J.; Cadoux, F.; Cai, X. D.; Capell, M.; Caroff, S.; Casaus, J.; Cascioli, V.; Castellini, G.; Cernuda, I.; Cerreta, D.; Cervelli, F.; Chae, M. J.; Chang, Y. H.; Chen, A. I.; Chen, H.; Cheng, G. M.; Chen, H. S.; Cheng, L.; Chou, H. Y.; Choumilov, E.; Choutko, V.; Chung, C. H.; Clark, C.; Clavero, R.; Coignet, G.; Consolandi, C.; Contin, A.; Corti, C.; Gil, E. Cortina; Coste, B.; Creus, W.; Crispoltoni, M.; Cui, Z.; Dai, Y. M.; Delgado, C.; Della Torre, S.; Demirköz, M. B.; Derome, L.; Di Falco, S.; Di Masso, L.; Dimiccoli, F.; Díaz, C.; von Doetinchem, P.; Donnini, F.; Du, W. J.; Duranti, M.; D'Urso, D.; Eline, A.; Eppling, F. J.; Eronen, T.; Fan, Y. Y.; Farnesini, L.; Feng, J.; Fiandrini, E.; Fiasson, A.; Finch, E.; Fisher, P.; Galaktionov, Y.; Gallucci, G.; García, B.; García-López, R.; Gargiulo, C.; Gast, H.; Gebauer, I.; Gervasi, M.; Ghelfi, A.; Gillard, W.; Giovacchini, F.; Goglov, P.; Gong, J.; Goy, C.; Grabski, V.; Grandi, D.; Graziani, M.; Guandalini, C.; Guerri, I.; Guo, K. H.; Haas, D.; Habiby, M.; Haino, S.; Han, K. C.; He, Z. H.; Heil, M.; Hoffman, J.; Hsieh, T. H.; Huang, Z. C.; Huh, C.; Incagli, M.; Ionica, M.; Jang, W. Y.; Jinchi, H.; Kanishev, K.; Kim, G. N.; Kim, K. S.; Kirn, Th.; Kossakowski, R.; Kounina, O.; Kounine, A.; Koutsenko, V.; Krafczyk, M. S.; La Vacca, G.; Laudi, E.; Laurenti, G.; Lazzizzera, I.; Lebedev, A.; Lee, H. T.; Lee, S. C.; Leluc, C.; Levi, G.; Li, H. L.; Li, J. Q.; Li, Q.; Li, Q.; Li, T. X.; Li, W.; Li, Y.; Li, Z. H.; Li, Z. Y.; Lim, S.; Lin, C. H.; Lipari, P.; Lippert, T.; Liu, D.; Liu, H.; Lolli, M.; Lomtadze, T.; Lu, M. J.; Lu, S. Q.; Lu, Y. S.; Luebelsmeyer, K.; Luo, J. Z.; Lv, S. S.; Majka, R.; Mañá, C.; Marín, J.; Martin, T.; Martínez, G.; Masi, N.; Maurin, D.; Menchaca-Rocha, A.; Meng, Q.; Mo, D. C.; Morescalchi, L.; Mott, P.; Müller, M.; Ni, J. Q.; Nikonov, N.; Nozzoli, F.; Nunes, P.; Obermeier, A.; Oliva, A.; Orcinha, M.; Palmonari, F.; Palomares, C.; Paniccia, M.; Papi, A.; Pauluzzi, M.; Pedreschi, E.; Pensotti, S.; Pereira, R.; Picot-Clemente, N.; Pilo, F.; Piluso, A.; Pizzolotto, C.; Plyaskin, V.; Pohl, M.; Poireau, V.; Postaci, E.; Putze, A.; Quadrani, L.; Qi, X. M.; Qin, X.; Qu, Z. Y.; Räihä, T.; Rancoita, P. G.; Rapin, D.; Ricol, J. S.; Rodríguez, I.; Rosier-Lees, S.; Rozhkov, A.; Rozza, D.; Sagdeev, R.; Sandweiss, J.; Saouter, P.; Sbarra, C.; Schael, S.; Schmidt, S. M.; von Dratzig, A. Schulz; Schwering, G.; Scolieri, G.; Seo, E. S.; Shan, B. S.; Shan, Y. H.; Shi, J. Y.; Shi, X. Y.; Shi, Y. M.; Siedenburg, T.; Son, D.; Spada, F.; Spinella, F.; Sun, W.; Sun, W. H.; Tacconi, M.; Tang, C. P.; Tang, X. W.; Tang, Z. C.; Tao, L.; Tescaro, D.; Ting, Samuel C. C.; Ting, S. M.; Tomassetti, N.; Torsti, J.; Türkoǧlu, C.; Urban, T.; Vagelli, V.; Valente, E.; Vannini, C.; Valtonen, E.; Vaurynovich, S.; Vecchi, M.; Velasco, M.; Vialle, J. P.; Vitale, V.; Vitillo, S.; Wang, L. Q.; Wang, N. H.; Wang, Q. L.; Wang, R. S.; Wang, X.; Wang, Z. X.; Weng, Z. L.; Whitman, K.; Wienkenhöver, J.; Wu, H.; Wu, X.; Xia, X.; Xie, M.; Xie, S.; Xiong, R. Q.; Xin, G. M.; Xu, N. S.; Xu, W.; Yan, Q.; Yang, J.; Yang, M.; Ye, Q. H.; Yi, H.; Yu, Y. J.; Yu, Z. Q.; Zeissler, S.; Zhang, J. H.; Zhang, M. T.; Zhang, X. B.; Zhang, Z.; Zheng, Z. M.; Zhuang, H. L.; Zhukov, V.; Zichichi, A.; Zimmermann, N.; Zuccon, P.; Zurbach, C.; AMS Collaboration

    2015-05-01

    A precise measurement of the proton flux in primary cosmic rays with rigidity (momentum/charge) from 1 GV to 1.8 TV is presented based on 300 million events. Knowledge of the rigidity dependence of the proton flux is important in understanding the origin, acceleration, and propagation of cosmic rays. We present the detailed variation with rigidity of the flux spectral index for the first time. The spectral index progressively hardens at high rigidities.

  5. Precision Measurement of the Proton Flux in Primary Cosmic Rays from Rigidity 1 GV to 1.8 TV with the Alpha Magnetic Spectrometer on the International Space Station.

    PubMed

    Aguilar, M; Aisa, D; Alpat, B; Alvino, A; Ambrosi, G; Andeen, K; Arruda, L; Attig, N; Azzarello, P; Bachlechner, A; Barao, F; Barrau, A; Barrin, L; Bartoloni, A; Basara, L; Battarbee, M; Battiston, R; Bazo, J; Becker, U; Behlmann, M; Beischer, B; Berdugo, J; Bertucci, B; Bigongiari, G; Bindi, V; Bizzaglia, S; Bizzarri, M; Boella, G; de Boer, W; Bollweg, K; Bonnivard, V; Borgia, B; Borsini, S; Boschini, M J; Bourquin, M; Burger, J; Cadoux, F; Cai, X D; Capell, M; Caroff, S; Casaus, J; Cascioli, V; Castellini, G; Cernuda, I; Cerreta, D; Cervelli, F; Chae, M J; Chang, Y H; Chen, A I; Chen, H; Cheng, G M; Chen, H S; Cheng, L; Chou, H Y; Choumilov, E; Choutko, V; Chung, C H; Clark, C; Clavero, R; Coignet, G; Consolandi, C; Contin, A; Corti, C; Cortina Gil, E; Coste, B; Creus, W; Crispoltoni, M; Cui, Z; Dai, Y M; Delgado, C; Della Torre, S; Demirköz, M B; Derome, L; Di Falco, S; Di Masso, L; Dimiccoli, F; Díaz, C; von Doetinchem, P; Donnini, F; Du, W J; Duranti, M; D'Urso, D; Eline, A; Eppling, F J; Eronen, T; Fan, Y Y; Farnesini, L; Feng, J; Fiandrini, E; Fiasson, A; Finch, E; Fisher, P; Galaktionov, Y; Gallucci, G; García, B; García-López, R; Gargiulo, C; Gast, H; Gebauer, I; Gervasi, M; Ghelfi, A; Gillard, W; Giovacchini, F; Goglov, P; Gong, J; Goy, C; Grabski, V; Grandi, D; Graziani, M; Guandalini, C; Guerri, I; Guo, K H; Haas, D; Habiby, M; Haino, S; Han, K C; He, Z H; Heil, M; Hoffman, J; Hsieh, T H; Huang, Z C; Huh, C; Incagli, M; Ionica, M; Jang, W Y; Jinchi, H; Kanishev, K; Kim, G N; Kim, K S; Kirn, Th; Kossakowski, R; Kounina, O; Kounine, A; Koutsenko, V; Krafczyk, M S; La Vacca, G; Laudi, E; Laurenti, G; Lazzizzera, I; Lebedev, A; Lee, H T; Lee, S C; Leluc, C; Levi, G; Li, H L; Li, J Q; Li, Q; Li, Q; Li, T X; Li, W; Li, Y; Li, Z H; Li, Z Y; Lim, S; Lin, C H; Lipari, P; Lippert, T; Liu, D; Liu, H; Lolli, M; Lomtadze, T; Lu, M J; Lu, S Q; Lu, Y S; Luebelsmeyer, K; Luo, J Z; Lv, S S; Majka, R; Mañá, C; Marín, J; Martin, T; Martínez, G; Masi, N; Maurin, D; Menchaca-Rocha, A; Meng, Q; Mo, D C; Morescalchi, L; Mott, P; Müller, M; Ni, J Q; Nikonov, N; Nozzoli, F; Nunes, P; Obermeier, A; Oliva, A; Orcinha, M; Palmonari, F; Palomares, C; Paniccia, M; Papi, A; Pauluzzi, M; Pedreschi, E; Pensotti, S; Pereira, R; Picot-Clemente, N; Pilo, F; Piluso, A; Pizzolotto, C; Plyaskin, V; Pohl, M; Poireau, V; Postaci, E; Putze, A; Quadrani, L; Qi, X M; Qin, X; Qu, Z Y; Räihä, T; Rancoita, P G; Rapin, D; Ricol, J S; Rodríguez, I; Rosier-Lees, S; Rozhkov, A; Rozza, D; Sagdeev, R; Sandweiss, J; Saouter, P; Sbarra, C; Schael, S; Schmidt, S M; Schulz von Dratzig, A; Schwering, G; Scolieri, G; Seo, E S; Shan, B S; Shan, Y H; Shi, J Y; Shi, X Y; Shi, Y M; Siedenburg, T; Son, D; Spada, F; Spinella, F; Sun, W; Sun, W H; Tacconi, M; Tang, C P; Tang, X W; Tang, Z C; Tao, L; Tescaro, D; Ting, Samuel C C; Ting, S M; Tomassetti, N; Torsti, J; Türkoğlu, C; Urban, T; Vagelli, V; Valente, E; Vannini, C; Valtonen, E; Vaurynovich, S; Vecchi, M; Velasco, M; Vialle, J P; Vitale, V; Vitillo, S; Wang, L Q; Wang, N H; Wang, Q L; Wang, R S; Wang, X; Wang, Z X; Weng, Z L; Whitman, K; Wienkenhöver, J; Wu, H; Wu, X; Xia, X; Xie, M; Xie, S; Xiong, R Q; Xin, G M; Xu, N S; Xu, W; Yan, Q; Yang, J; Yang, M; Ye, Q H; Yi, H; Yu, Y J; Yu, Z Q; Zeissler, S; Zhang, J H; Zhang, M T; Zhang, X B; Zhang, Z; Zheng, Z M; Zhuang, H L; Zhukov, V; Zichichi, A; Zimmermann, N; Zuccon, P; Zurbach, C

    2015-05-01

    A precise measurement of the proton flux in primary cosmic rays with rigidity (momentum/charge) from 1 GV to 1.8 TV is presented based on 300 million events. Knowledge of the rigidity dependence of the proton flux is important in understanding the origin, acceleration, and propagation of cosmic rays. We present the detailed variation with rigidity of the flux spectral index for the first time. The spectral index progressively hardens at high rigidities.

  6. Space Station

    NASA Image and Video Library

    1952-01-01

    This is a von Braun 1952 space station concept. In a 1952 series of articles written in Collier's, Dr. Wernher von Braun, then Technical Director of the Army Ordnance Guided Missiles Development Group at Redstone Arsenal, wrote of a large wheel-like space station in a 1,075-mile orbit. This station, made of flexible nylon, would be carried into space by a fully reusable three-stage launch vehicle. Once in space, the station's collapsible nylon body would be inflated much like an automobile tire. The 250-foot-wide wheel would rotate to provide artificial gravity, an important consideration at the time because little was known about the effects of prolonged zero-gravity on humans. Von Braun's wheel was slated for a number of important missions: a way station for space exploration, a meteorological observatory and a navigation aid. This concept was illustrated by artist Chesley Bonestell.

  7. Proton Therapy

    MedlinePlus

    ... effects of the treatment. top of page What equipment is used? Proton beam therapy uses special machines, ... tumor cells. top of page Who operates the equipment? With backgrounds in mechanical, electrical, software, hardware and ...

  8. Structure of ATP synthase from Paracoccus denitrificans determined by X-ray crystallography at 4.0 Å resolution

    PubMed Central

    Morales-Rios, Edgar; Montgomery, Martin G.; Leslie, Andrew G. W.; Walker, John E.

    2015-01-01

    The structure of the intact ATP synthase from the α-proteobacterium Paracoccus denitrificans, inhibited by its natural regulatory ζ-protein, has been solved by X-ray crystallography at 4.0 Å resolution. The ζ-protein is bound via its N-terminal α-helix in a catalytic interface in the F1 domain. The bacterial F1 domain is attached to the membrane domain by peripheral and central stalks. The δ-subunit component of the peripheral stalk binds to the N-terminal regions of two α-subunits. The stalk extends via two parallel long α-helices, one in each of the related b and b′ subunits, down a noncatalytic interface of the F1 domain and interacts in an unspecified way with the a-subunit in the membrane domain. The a-subunit lies close to a ring of 12 c-subunits attached to the central stalk in the F1 domain, and, together, the central stalk and c-ring form the enzyme’s rotor. Rotation is driven by the transmembrane proton-motive force, by a mechanism where protons pass through the interface between the a-subunit and c-ring via two half-channels in the a-subunit. These half-channels are probably located in a bundle of four α-helices in the a-subunit that are tilted at ∼30° to the plane of the membrane. Conserved polar residues in the two α-helices closest to the c-ring probably line the proton inlet path to an essential carboxyl group in the c-subunit in the proton uptake site and a proton exit path from the proton release site. The structure has provided deep insights into the workings of this extraordinary molecular machine. PMID:26460036

  9. Quantification of detergent using colorimetric methods in membrane protein crystallography.

    PubMed

    Prince, Chelsy; Jia, Zongchao

    2015-01-01

    Membrane protein crystallography has the potential to greatly aid our understanding of membrane protein biology. Yet, membrane protein crystals remain challenging to produce. Although robust methods for the expression and purification of membrane proteins continue to be developed, the detergent component of membrane protein samples is equally important to crystallization efforts. This chapter describes the development of three colorimetric assays for the quantitation of detergent in membrane protein samples and provides detailed protocols. All of these techniques use small sample volumes and have potential applications in crystallography. The application of these techniques in crystallization prescreening, detergent concentration modification, and detergent exchange experiments is demonstrated. It has been observed that the concentration of detergent in a membrane protein sample can be just as important as the protein concentration when attempting to reproduce crystallization lead conditions. © 2015 Elsevier Inc. All rights reserved.

  10. Raman Crystallography and Other Biochemical Applications of Raman Microscopy

    NASA Astrophysics Data System (ADS)

    Carey, Paul R.

    2006-05-01

    Recent studies using a Raman microscope have shown that single protein crystals provide an ideal platform to undertake Raman difference spectroscopic analyses under nonresonance conditions. This approach, termed Raman crystallography, provides a means of characterizing chemical events within the crystal such as ligand binding and enzyme reactions. In many cases Raman crystallography goes hand in hand with X-ray crystallographic studies because the Raman results can inform the X-ray crystallographer about the status of chemical events in the crystal prior to flash freezing and X-ray analysis. In turn, the combined data from the Raman and X-ray analyses are highly synergistic and offer novel perspectives on structure and dynamics in enzyme active sites. In a related area, protein misfolding, Raman microscopy can provide detailed insights into the chemistry of the amyloid plaques associated with Alzheimer's disease and into the intermediates on the α-synuclein protein misfolding pathway implicated in Parkinson's disease.

  11. Rapid visualization of hydrogen positions in neutron protein crystallography structures

    SciTech Connect

    Blakeley, Matthew P.; Meilleur, Flora; Myles, Dean A A; Weiss, Kevin L; Munshi, Parthapratim; Shang-Lin, Chung

    2012-01-01

    Neutron crystallography is a powerful technique to visualize experimentally the position of light atoms, including hydrogen and its isotope deuterium. Over the last several years, structural biologists have shown an increasing interest for the technique as it uniquely complements X-ray crystallographic data by revealing the position of hydrogen/deuterium atoms in macromolecules. With this regained interest, access to macromolecule neutron crystallography beam lines is becoming a limiting step. In this report we show that rapid data collection could be a valuable alternative to long data collection time when appropriate. Comparison of perdeuterated Rubredoxin structures refined against neutron data sets collected over hours and up to five days shows that rapid neutron data collection in just 14 hours is sufficient to provide the position of 262 hydrogen positions atoms without ambiguity.

  12. Liquid sample delivery techniques for serial femtosecond crystallography

    PubMed Central

    Weierstall, Uwe

    2014-01-01

    X-ray free-electron lasers overcome the problem of radiation damage in protein crystallography and allow structure determination from micro- and nanocrystals at room temperature. To ensure that consecutive X-ray pulses do not probe previously exposed crystals, the sample needs to be replaced with the X-ray repetition rate, which ranges from 120 Hz at warm linac-based free-electron lasers to 1 MHz at superconducting linacs. Liquid injectors are therefore an essential part of a serial femtosecond crystallography experiment at an X-ray free-electron laser. Here, we compare different techniques of injecting microcrystals in solution into the pulsed X-ray beam in vacuum. Sample waste due to mismatch of the liquid flow rate to the X-ray repetition rate can be addressed through various techniques. PMID:24914163

  13. Oil-free hyaluronic acid matrix for serial femtosecond crystallography

    PubMed Central

    Sugahara, Michihiro; Song, Changyong; Suzuki, Mamoru; Masuda, Tetsuya; Inoue, Shigeyuki; Nakane, Takanori; Yumoto, Fumiaki; Nango, Eriko; Tanaka, Rie; Tono, Kensuke; Joti, Yasumasa; Kameshima, Takashi; Hatsui, Takaki; Yabashi, Makina; Nureki, Osamu; Numata, Keiji; Iwata, So

    2016-01-01

    The grease matrix was originally introduced as a microcrystal-carrier for serial femtosecond crystallography and has been expanded to applications for various types of proteins, including membrane proteins. However, the grease-based matrix has limited application for oil-sensitive proteins. Here we introduce a grease-free, water-based hyaluronic acid matrix. Applications for proteinase K and lysozyme proteins were able to produce electron density maps at 2.3-Å resolution. PMID:27087008

  14. Oil-free hyaluronic acid matrix for serial femtosecond crystallography

    NASA Astrophysics Data System (ADS)

    Sugahara, Michihiro; Song, Changyong; Suzuki, Mamoru; Masuda, Tetsuya; Inoue, Shigeyuki; Nakane, Takanori; Yumoto, Fumiaki; Nango, Eriko; Tanaka, Rie; Tono, Kensuke; Joti, Yasumasa; Kameshima, Takashi; Hatsui, Takaki; Yabashi, Makina; Nureki, Osamu; Numata, Keiji; Iwata, So

    2016-04-01

    The grease matrix was originally introduced as a microcrystal-carrier for serial femtosecond crystallography and has been expanded to applications for various types of proteins, including membrane proteins. However, the grease-based matrix has limited application for oil-sensitive proteins. Here we introduce a grease-free, water-based hyaluronic acid matrix. Applications for proteinase K and lysozyme proteins were able to produce electron density maps at 2.3-Å resolution.

  15. PRIGo: a new multi-axis goniometer for macromolecular crystallography.

    PubMed

    Waltersperger, Sandro; Olieric, Vincent; Pradervand, Claude; Glettig, Wayne; Salathe, Marco; Fuchs, Martin R; Curtin, Adrian; Wang, Xiaoqiang; Ebner, Simon; Panepucci, Ezequiel; Weinert, Tobias; Schulze-Briese, Clemens; Wang, Meitian

    2015-07-01

    The Parallel Robotics Inspired Goniometer (PRIGo) is a novel compact and high-precision goniometer providing an alternative to (mini-)kappa, traditional three-circle goniometers and Eulerian cradles used for sample reorientation in macromolecular crystallography. Based on a combination of serial and parallel kinematics, PRIGo emulates an arc. It is mounted on an air-bearing stage for rotation around ω and consists of four linear positioners working synchronously to achieve x, y, z translations and χ rotation (0-90°), followed by a ϕ stage (0-360°) for rotation around the sample holder axis. Owing to the use of piezo linear positioners and active correction, PRIGo features spheres of confusion of <1 µm, <7 µm and <10 µm for ω, χ and ϕ, respectively, and is therefore very well suited for micro-crystallography. PRIGo enables optimal strategies for both native and experimental phasing crystallographic data collection. Herein, PRIGo hardware and software, its calibration, as well as applications in macromolecular crystallography are described.

  16. PRIGo: a new multi-axis goniometer for macromolecular crystallography

    PubMed Central

    Waltersperger, Sandro; Olieric, Vincent; Pradervand, Claude; Glettig, Wayne; Salathe, Marco; Fuchs, Martin R.; Curtin, Adrian; Wang, Xiaoqiang; Ebner, Simon; Panepucci, Ezequiel; Weinert, Tobias; Schulze-Briese, Clemens; Wang, Meitian

    2015-01-01

    The Parallel Robotics Inspired Goniometer (PRIGo) is a novel compact and high-precision goniometer providing an alternative to (mini-)kappa, traditional three-circle goniometers and Eulerian cradles used for sample reorientation in macromolecular crystallography. Based on a combination of serial and parallel kinematics, PRIGo emulates an arc. It is mounted on an air-bearing stage for rotation around ω and consists of four linear positioners working synchronously to achieve x, y, z translations and χ rotation (0–90°), followed by a ϕ stage (0–360°) for rotation around the sample holder axis. Owing to the use of piezo linear positioners and active correction, PRIGo features spheres of confusion of <1 µm, <7 µm and <10 µm for ω, χ and ϕ, respectively, and is therefore very well suited for micro-crystallography. PRIGo enables optimal strategies for both native and experimental phasing crystallographic data collection. Herein, PRIGo hardware and software, its calibration, as well as applications in macromolecular crystallography are described. PMID:26134792

  17. X-ray crystallography at the heart of life science.

    PubMed

    Yonath, Ada

    2011-10-01

    X-ray crystallography is the fundamental research tool that shaped our notion on biological structure & function at the molecular level. It generates the information vital to understand life processes by providing the information required for creating accurate three-dimensional models (namely mapping the position of each and every atom that makes up the studied object). The use of this method begun in the middle of last century following Max von Laue discovery of the phenomenon of diffraction of X-rays by crystals, and the successful application of this discovery for the determination of the electronic distribution within simple inorganic molecules by Sir William Henry Bragg and his son, William Lawrence Bragg. The idea of extension of this method to biological molecules met initially with considerable skepticism. For over two decades many respected scientists doubted whether it could be done. Yet, despite its bottlenecks (some of which are described below), the superiority of X-ray crystallography over all other approaches for shedding light on functional aspects at the molecular level became evident once the first structure was determined. The power of this method inspired continuous efforts and spectacular innovations, which vastly accelerated its incredible expansion. Consequently, over the last six decades biological crystallography has produced a constantly growing number of structures, some of which were considered formidable. This remarkable advance yielded numerous new insights into intricate functional aspects. Owing to space limitation this article focuses on selected studies performed recently and highlights some recent exciting developments. Copyright © 2011. Published by Elsevier Ltd.

  18. The macromolecular crystallography facility at the advanced light source

    NASA Astrophysics Data System (ADS)

    Earnest, Thomas; Padmore, Howard; Cork, Carl; Behrsing, Rolf; Kim, Sung-Hou

    1996-10-01

    Synchrotron radiation offers several advantages over the use of rotating anode sources for biological crystallography, which allow for the collection of higher-resolution data, substantially more rapid data collection, phasing by multiwavelength anomalous diffraction (MAD) techniques, and time-resolved experiments using polychromatic radiation (Laue diffraction). The use of synchrotron radiation is often necessary to record useful data from crystals which diffract weakly or have very large unit cells. The high brightness and stability characteristics of the advanced light source (ALS) at Lawrence Berkeley National Laboratory, along with the low emittance and long straight sections to accommodate insertion devices present in third generation synchrotrons like the ALS, lead to several advantages in the field of macromolecular crystallography. We are presently constructing a macromolecular crystallography facility at the ALS which is optimized for user-friendliness and high-throughput data collection, with advanced capabilities for MAD and Laue experiments. The X-rays will be directed to three branchlines. A well-equipped support lab will be available for biochemistry, crystal mounting and sample storage, as well as computer hardware and software available, along with staff support, allowing for the complete processing of data on site.

  19. Space Station

    NASA Image and Video Library

    1969-01-01

    This picture illustrates a concept of a 33-Foot-Diameter Space Station Leading to a Space Base. In-house work of the Marshall Space Flight Center, as well as a Phase B contract with the McDornel Douglas Astronautics Company, resulted in a preliminary design for a space station in 1969 and l970. The Marshall-McDonnel Douglas approach envisioned the use of two common modules as the core configuration of a 12-man space station. Each common module was 33 feet in diameter and 40 feet in length and provided the building blocks, not only for the space station, but also for a 50-man space base. Coupled together, the two modules would form a four-deck facility: two decks for laboratories and two decks for operations and living quarters. Zero-gravity would be the normal mode of operation, although the station would have an artificial gravity capability. This general-purpose orbital facility was to provide wide-ranging research capabilities. The design of the facility was driven by the need to accommodate a broad spectrum of activities in support of astronomy, astrophysics, aerospace medicine, biology, materials processing, space physics, and space manufacturing. To serve the needs of Earth observations, the station was to be placed in a 242-nautical-mile orbit at a 55-degree inclination. An Intermediate-21 vehicle (comprised of Saturn S-IC and S-II stages) would have launched the station in 1977.

  20. Space Station

    NASA Image and Video Library

    1991-01-01

    This artist's concept depicts the Space Station Freedom as it would look orbiting the Earth, illustrated by Marshall Space Flight Center artist, Tom Buzbee. Scheduled to be completed in late 1999, this smaller configuration of the Space Station featured a horizontal truss structure that supported U.S., European, and Japanese Laboratory Modules; the U.S. Habitation Module; and three sets of solar arrays. The Space Station Freedom was an international, permanently marned, orbiting base to be assembled in orbit by a series of Space Shuttle missions that were to begin in the mid-1990's.

  1. Space Station

    NASA Image and Video Library

    1991-01-01

    This artist's concept depicts the Space Station Freedom as it would look orbiting the Earth; illustrated by Marshall Space Flight Center artist, Tom Buzbee. Scheduled to be completed in late 1999, this smaller configuration of the Space Station features a horizontal truss structure that supported U.S., European, and Japanese Laboratory Modules; the U.S. Habitation Module; and three sets of solar arrays. The Space Station Freedom was an international, permanently marned, orbiting base to be assembled in orbit by a series of Space Shuttle missions that were to begin in the mid-1990's.

  2. Three-dimensional protonic conductivity in porous organic cage solids

    NASA Astrophysics Data System (ADS)

    Liu, Ming; Chen, Linjiang; Lewis, Scott; Chong, Samantha Y.; Little, Marc A.; Hasell, Tom; Aldous, Iain M.; Brown, Craig M.; Smith, Martin W.; Morrison, Carole A.; Hardwick, Laurence J.; Cooper, Andrew I.

    2016-09-01

    Proton conduction is a fundamental process in biology and in devices such as proton exchange membrane fuel cells. To maximize proton conduction, three-dimensional conduction pathways are preferred over one-dimensional pathways, which prevent conduction in two dimensions. Many crystalline porous solids to date show one-dimensional proton conduction. Here we report porous molecular cages with proton conductivities (up to 10-3 S cm-1 at high relative humidity) that compete with extended metal-organic frameworks. The structure of the organic cage imposes a conduction pathway that is necessarily three-dimensional. The cage molecules also promote proton transfer by confining the water molecules while being sufficiently flexible to allow hydrogen bond reorganization. The proton conduction is explained at the molecular level through a combination of proton conductivity measurements, crystallography, molecular simulations and quasi-elastic neutron scattering. These results provide a starting point for high-temperature, anhydrous proton conductors through inclusion of guests other than water in the cage pores.

  3. Three-dimensional protonic conductivity in porous organic cage solids.

    PubMed

    Liu, Ming; Chen, Linjiang; Lewis, Scott; Chong, Samantha Y; Little, Marc A; Hasell, Tom; Aldous, Iain M; Brown, Craig M; Smith, Martin W; Morrison, Carole A; Hardwick, Laurence J; Cooper, Andrew I

    2016-09-13

    Proton conduction is a fundamental process in biology and in devices such as proton exchange membrane fuel cells. To maximize proton conduction, three-dimensional conduction pathways are preferred over one-dimensional pathways, which prevent conduction in two dimensions. Many crystalline porous solids to date show one-dimensional proton conduction. Here we report porous molecular cages with proton conductivities (up to 10(-3) S cm(-1) at high relative humidity) that compete with extended metal-organic frameworks. The structure of the organic cage imposes a conduction pathway that is necessarily three-dimensional. The cage molecules also promote proton transfer by confining the water molecules while being sufficiently flexible to allow hydrogen bond reorganization. The proton conduction is explained at the molecular level through a combination of proton conductivity measurements, crystallography, molecular simulations and quasi-elastic neutron scattering. These results provide a starting point for high-temperature, anhydrous proton conductors through inclusion of guests other than water in the cage pores.

  4. Three-dimensional protonic conductivity in porous organic cage solids

    PubMed Central

    Liu, Ming; Chen, Linjiang; Lewis, Scott; Chong, Samantha Y.; Little, Marc A.; Hasell, Tom; Aldous, Iain M.; Brown, Craig M.; Smith, Martin W.; Morrison, Carole A.; Hardwick, Laurence J.; Cooper, Andrew I.

    2016-01-01

    Proton conduction is a fundamental process in biology and in devices such as proton exchange membrane fuel cells. To maximize proton conduction, three-dimensional conduction pathways are preferred over one-dimensional pathways, which prevent conduction in two dimensions. Many crystalline porous solids to date show one-dimensional proton conduction. Here we report porous molecular cages with proton conductivities (up to 10−3 S cm−1 at high relative humidity) that compete with extended metal-organic frameworks. The structure of the organic cage imposes a conduction pathway that is necessarily three-dimensional. The cage molecules also promote proton transfer by confining the water molecules while being sufficiently flexible to allow hydrogen bond reorganization. The proton conduction is explained at the molecular level through a combination of proton conductivity measurements, crystallography, molecular simulations and quasi-elastic neutron scattering. These results provide a starting point for high-temperature, anhydrous proton conductors through inclusion of guests other than water in the cage pores. PMID:27619230

  5. Structural studies of Neurospora crassa LPMO9D and redox partner CDHIIA using neutron crystallography and small-angle scattering.

    PubMed

    Bodenheimer, Annette M; O'Dell, William B; Stanley, Christopher B; Meilleur, Flora

    2017-08-07

    Sensitivity to hydrogen/deuterium and lack of observable radiation damage makes cold neutrons an ideal probe the structural studies of proteins with highly photosensitive groups such as the copper center of lytic polysaccharide monooxygenases (LPMOs) and flavin adenine dinucleotide (FAD) and heme redox cofactors of cellobiose dehydrogenases (CDHs). Here, neutron crystallography and small-angle neutron scattering are used to investigate Neurospora crassa LPMO9D (NcLPMO9D) and CDHIIA (NcCDHIIA), respectively. The presence of LPMO greatly enhances the efficiency of commercial glycoside hydrolase cocktails in the depolymerization of cellulose. LPMOs can receive electrons from CDHs to activate molecular dioxygen for the oxidation of cellulose resulting in chain cleavage and disruption of local crystallinity. Using neutron protein crystallography, the hydrogen/deuterium atoms of NcLPMO9D could be located throughout the structure. At the copper active site, the protonation states of the side chains of His1, His84, His157 and Tyr168, and the orientation of water molecules could be determined. Small-angle neutron scattering measurements provided low resolution models of NcCDHIIA with both the dehydrogenase and cytochrome domains in oxidized states that exhibited elongated conformations. This work demonstrates the suitability of neutron diffraction and scattering for characterizing enzymes critical to oxidative cellulose deconstruction. Copyright © 2017 Elsevier Ltd. All rights reserved.

  6. Stations Outdoors

    ERIC Educational Resources Information Center

    Madison, John P.; And Others

    1976-01-01

    Described is a program of outdoor education utilizing activity-oriented learning stations. Described are 13 activities including: a pond study, orienteering, nature crafts, outdoor mathematics, linear distance measurement, and area measurement. (SL)

  7. Space Station

    NASA Image and Video Library

    1970-01-01

    This is an illustration of the Space Base concept. In-house work of the Marshall Space Flight Center, as well as a Phase B contract with the McDornel Douglas Astronautics Company, resulted in a preliminary design for a space station in 1969 and l970. The Marshall-McDonnel Douglas approach envisioned the use of two common modules as the core configuration of a 12-man space station. Each common module was 33 feet in diameter and 40 feet in length and provided the building blocks, not only for the space station, but also for a 50-man space base. Coupled together, the two modules would form a four-deck facility: two decks for laboratories and two decks for operations and living quarters. Zero-gravity would be the normal mode of operation, although the station would have an artificial-gravity capability. This general-purpose orbital facility was to provide wide-ranging research capabilities. The design of the facility was driven by the need to accommodate a broad spectrum of activities in support of astronomy, astrophysics, aerospace medicine, biology, materials processing, space physics, and space manufacturing. To serve the needs of Earth observations, the station was to be placed in a 242-nautical-mile orbit at a 55-degree inclination. An Intermediate-21 vehicle (comprised of Saturn S-IC and S-II stages) would have launched the station in 1977.

  8. Lipidic cubic phase injector is a viable crystal delivery system for time-resolved serial crystallography

    SciTech Connect

    Nogly, Przemyslaw; Panneels, Valerie; Nelson, Garrett; Gati, Cornelius; Kimura, Tetsunari; Milne, Christopher; Milathianaki, Despina; Kubo, Minoru; Wu, Wenting; Conrad, Chelsie; Coe, Jesse; Bean, Richard; Zhao, Yun; Bath, Petra; Dods, Robert; Harimoorthy, Rajiv; Beyerlein, Kenneth R.; Rheinberger, Jan; James, Daniel; DePonte, Daniel; Li, Chufeng; Sala, Leonardo; Williams, Garth J.; Hunter, Mark S.; Koglin, Jason E.; Berntsen, Peter; Nango, Eriko; Chapman, Henry N.; Fromme, Petra; Frank, Matthias; Abela, Rafael; Boutet, Sebastien; Barty, Anton; White, Thomas A.; Weierstall, Uwe; Spence, John; Neutze, Richard; Schertler, Gebhard; Standfuss, Jorg

    2016-08-22

    Serial femtosecond crystallography (SFX) using X-ray free-electron laser sources is an emerging method with considerable potential for time-resolved pump-probe experiments. Here we present a lipidic cubic phase SFX structure of the light-driven proton pump bacteriorhodopsin (bR) to 2.3 Å resolution and a method to investigate protein dynamics with modest sample requirement. Time-resolved SFX (TR-SFX) with a pump-probe delay of 1 ms yields difference Fourier maps compatible with the dark to M state transition of bR. Importantly, the method is very sample efficient and reduces sample consumption to about 1 mg per collected time point. Accumulation of M intermediate within the crystal lattice is confirmed by time-resolved visible absorption spectroscopy. Furthermore, this study provides an important step towards characterizing the complete photocycle dynamics of retinal proteins and demonstrates the feasibility of a sample efficient viscous medium jet for TR-SFX.

  9. Lipidic cubic phase injector is a viable crystal delivery system for time-resolved serial crystallography

    PubMed Central

    Nogly, Przemyslaw; Panneels, Valerie; Nelson, Garrett; Gati, Cornelius; Kimura, Tetsunari; Milne, Christopher; Milathianaki, Despina; Kubo, Minoru; Wu, Wenting; Conrad, Chelsie; Coe, Jesse; Bean, Richard; Zhao, Yun; Båth, Petra; Dods, Robert; Harimoorthy, Rajiv; Beyerlein, Kenneth R.; Rheinberger, Jan; James, Daniel; DePonte, Daniel; Li, Chufeng; Sala, Leonardo; Williams, Garth J.; Hunter, Mark S.; Koglin, Jason E.; Berntsen, Peter; Nango, Eriko; Iwata, So; Chapman, Henry N.; Fromme, Petra; Frank, Matthias; Abela, Rafael; Boutet, Sébastien; Barty, Anton; White, Thomas A.; Weierstall, Uwe; Spence, John; Neutze, Richard; Schertler, Gebhard; Standfuss, Jörg

    2016-01-01

    Serial femtosecond crystallography (SFX) using X-ray free-electron laser sources is an emerging method with considerable potential for time-resolved pump-probe experiments. Here we present a lipidic cubic phase SFX structure of the light-driven proton pump bacteriorhodopsin (bR) to 2.3 Å resolution and a method to investigate protein dynamics with modest sample requirement. Time-resolved SFX (TR-SFX) with a pump-probe delay of 1 ms yields difference Fourier maps compatible with the dark to M state transition of bR. Importantly, the method is very sample efficient and reduces sample consumption to about 1 mg per collected time point. Accumulation of M intermediate within the crystal lattice is confirmed by time-resolved visible absorption spectroscopy. This study provides an important step towards characterizing the complete photocycle dynamics of retinal proteins and demonstrates the feasibility of a sample efficient viscous medium jet for TR-SFX. PMID:27545823

  10. Lipidic cubic phase injector is a viable crystal delivery system for time-resolved serial crystallography

    DOE PAGES

    Nogly, Przemyslaw; Panneels, Valerie; Nelson, Garrett; ...

    2016-08-22

    Serial femtosecond crystallography (SFX) using X-ray free-electron laser sources is an emerging method with considerable potential for time-resolved pump-probe experiments. Here we present a lipidic cubic phase SFX structure of the light-driven proton pump bacteriorhodopsin (bR) to 2.3 Å resolution and a method to investigate protein dynamics with modest sample requirement. Time-resolved SFX (TR-SFX) with a pump-probe delay of 1 ms yields difference Fourier maps compatible with the dark to M state transition of bR. Importantly, the method is very sample efficient and reduces sample consumption to about 1 mg per collected time point. Accumulation of M intermediate within themore » crystal lattice is confirmed by time-resolved visible absorption spectroscopy. Furthermore, this study provides an important step towards characterizing the complete photocycle dynamics of retinal proteins and demonstrates the feasibility of a sample efficient viscous medium jet for TR-SFX.« less

  11. Lipidic cubic phase injector is a viable crystal delivery system for time-resolved serial crystallography.

    PubMed

    Nogly, Przemyslaw; Panneels, Valerie; Nelson, Garrett; Gati, Cornelius; Kimura, Tetsunari; Milne, Christopher; Milathianaki, Despina; Kubo, Minoru; Wu, Wenting; Conrad, Chelsie; Coe, Jesse; Bean, Richard; Zhao, Yun; Båth, Petra; Dods, Robert; Harimoorthy, Rajiv; Beyerlein, Kenneth R; Rheinberger, Jan; James, Daniel; DePonte, Daniel; Li, Chufeng; Sala, Leonardo; Williams, Garth J; Hunter, Mark S; Koglin, Jason E; Berntsen, Peter; Nango, Eriko; Iwata, So; Chapman, Henry N; Fromme, Petra; Frank, Matthias; Abela, Rafael; Boutet, Sébastien; Barty, Anton; White, Thomas A; Weierstall, Uwe; Spence, John; Neutze, Richard; Schertler, Gebhard; Standfuss, Jörg

    2016-08-22

    Serial femtosecond crystallography (SFX) using X-ray free-electron laser sources is an emerging method with considerable potential for time-resolved pump-probe experiments. Here we present a lipidic cubic phase SFX structure of the light-driven proton pump bacteriorhodopsin (bR) to 2.3 Å resolution and a method to investigate protein dynamics with modest sample requirement. Time-resolved SFX (TR-SFX) with a pump-probe delay of 1 ms yields difference Fourier maps compatible with the dark to M state transition of bR. Importantly, the method is very sample efficient and reduces sample consumption to about 1 mg per collected time point. Accumulation of M intermediate within the crystal lattice is confirmed by time-resolved visible absorption spectroscopy. This study provides an important step towards characterizing the complete photocycle dynamics of retinal proteins and demonstrates the feasibility of a sample efficient viscous medium jet for TR-SFX.

  12. Hydrogen Filling Station

    SciTech Connect

    Boehm, Robert F; Sabacky, Bruce; Anderson II, Everett B; Haberman, David; Al-Hassin, Mowafak; He, Xiaoming; Morriseau, Brian

    2010-02-24

    future. Project partners also conducted a workshop on hydrogen safety and permitting. This provided an opportunity for the various permitting agencies and end users to gather to share experiences and knowledge. As a result of this workshop, the permitting process for the hydrogen filling station on the Las Vegas Valley Water District’s land was done more efficiently and those who would be responsible for the operation were better educated on the safety and reliability of hydrogen production and storage. The lessons learned in permitting the filling station and conducting this workshop provided a basis for future hydrogen projects in the region. Continuing efforts to increase the working pressure of electrolysis and efficiency have been pursued. Research was also performed on improving the cost, efficiency and durability of Proton Exchange Membrane (PEM) hydrogen technology. Research elements focused upon PEM membranes, electrodes/catalysts, membrane-electrode assemblies, seals, bipolar plates, utilization of renewable power, reliability issues, scale, and advanced conversion topics. Additionally, direct solar-to-hydrogen conversion research to demonstrate stable and efficient photoelectrochemistry (PEC) hydrogen production systems based on a number of optional concepts was performed. Candidate PEC concepts included technical obstacles such as inefficient photocatalysis, inadequate photocurrent due to non-optimal material band gap energies, rapid electron-hole recombination, reduced hole mobility and diminished operational lifetimes of surface materials exposed to electrolytes. Project Objective 1: Design, build, operate hydrogen filling station Project Objective 2: Perform research and development for utilizing solar technologies on the hydrogen filling station and convert two utility vehicles for use by the station operators Project Objective 3: Increase capacity of hydrogen filling station; add additional vehicle; conduct safety workshop; develop a roadmap for

  13. International Space Station (ISS)

    NASA Image and Video Library

    1997-10-01

    The Zvezda Service Module, the first Russian contribution and third element to the International Space Station (ISS), is shown under construction in the Krunichev State Research and Production Facility (KhSC) in Moscow. Russian technicians work on the module shortly after it completed a pressurization test. In the foreground is the forward portion of the module, including the spherical transfer compartment and its three docking ports. The forward port docked with the cornected Functional Cargo Block, followed by Node 1. Launched via a three-stage Proton rocket on July 12, 2000, the Zvezda Service Module serves as the cornerstone for early human habitation of the Station, providing living quarters, life support system, electrical power distribution, data processing system, flight control system, and propulsion system. It also provides a communications system that includes remote command capabilities from ground flight controllers. The 42,000-pound module measures 43 feet in length and has a wing span of 98 feet. Similar in layout to the core module of Russia's Mir space station, it contains 3 pressurized compartments and 13 windows that allow ultimate viewing of Earth and space.

  14. Proton Therapy

    MedlinePlus

    ... Liver Breast Esophagus Rectum Skull base sarcomas Pediatric brain tumors Head and neck - see the Head and Neck Cancer page Eye ... Intensity-Modulated Radiation Therapy (IMRT) Brain Tumor Treatment Brain Tumors Prostate Cancer Lung Cancer ... related to Proton Therapy Videos related ...

  15. Proton geriatrics

    NASA Astrophysics Data System (ADS)

    Kephart, Thomas W.; Nakagawa, Norio

    1984-07-01

    An SO(10) model with particle spectrum and low energy gauge group identical to that of minimal SU (5) below MX but with a nonstandard charge assignment is shown to agree with the experimental best value of sin2θw(Mw) and the lower bound on the proton lifetime.

  16. Proton Radiobiology

    PubMed Central

    Tommasino, Francesco; Durante, Marco

    2015-01-01

    In addition to the physical advantages (Bragg peak), the use of charged particles in cancer therapy can be associated with distinct biological effects compared to X-rays. While heavy ions (densely ionizing radiation) are known to have an energy- and charge-dependent increased Relative Biological Effectiveness (RBE), protons should not be very different from sparsely ionizing photons. A slightly increased biological effectiveness is taken into account in proton treatment planning by assuming a fixed RBE of 1.1 for the whole radiation field. However, data emerging from recent studies suggest that, for several end points of clinical relevance, the biological response is differentially modulated by protons compared to photons. In parallel, research in the field of medical physics highlighted how variations in RBE that are currently neglected might actually result in deposition of significant doses in healthy organs. This seems to be relevant in particular for normal tissues in the entrance region and for organs at risk close behind the tumor. All these aspects will be considered and discussed in this review, highlighting how a re-discussion of the role of a variable RBE in proton therapy might be well-timed. PMID:25686476

  17. Space Station

    NASA Image and Video Library

    1971-01-01

    This is an artist's concept of the Research and Applications Modules (RAM). Evolutionary growth was an important consideration in space station plarning, and another project was undertaken in 1971 to facilitate such growth. The RAM study, conducted through a Marshall Space Flight Center contract with General Dynamics Convair Aerospace, resulted in the conceptualization of a series of RAM payload carrier-sortie laboratories, pallets, free-flyers, and payload and support modules. The study considered two basic manned systems. The first would use RAM hardware for sortie mission, where laboratories were carried into space and remained attached to the Shuttle for operational periods up to 7 days. The second envisioned a modular space station capability that could be evolved by mating RAM modules to the space station core configuration. The RAM hardware was to be built by Europeans, thus fostering international participation in the space program.

  18. Space Station

    NASA Image and Video Library

    1986-08-01

    In response to President Reagan's directive to NASA to develop a permanent marned Space Station within a decade, part of the State of the Union message to Congress on January 25, 1984, NASA and the Administration adopted a phased approach to Station development. This approach provided an initial capability at reduced costs, to be followed by an enhanced Space Station capability in the future. This illustration depicts a configuration with enhanced capabilities. It builds on the horizontal boom and module pattern of the revised baseline. This configuration would feature dual keels, two vertical spines 105-meters long joined by upper and lower booms. The structure carrying the modules would become a transverse boom of a basically rectangular structure. The two new booms, 45-meters in length, would provide extensive accommodations for attached payloads, and would offer a wide field of view. Power would be increased significantly, with the addition if a 50-kW solar dynamic power system.

  19. From crystal morphology to molecular and scale crystallography

    NASA Astrophysics Data System (ADS)

    Janner, A.; Janssen, T.

    2015-08-01

    A number of topics, ranging from morphology of aperiodic crystals to indexed enclosing forms of axial-symmetric proteins, nucleic acids and viruses, have been selected among those investigated by the authors in 50 years of research. The basic symmetries involved in fields like superspace, molecular and scale crystallography, are considered from a personal point of view in their time evolution. A number of specific subjects follow, chosen among a few highlights and presented according to the experience of the authors: snow crystals, calaverite {{AuTe}}2, the incommensurately modulated crystals {{Rb}}2{{ZnBr}}4, {[{N}{({{CH}}3)}4]}2{{ZnCl}}4 and the mitochondrial ferritin.

  20. High-Resolution Protein Structure Determination by Serial Femtosecond Crystallography

    PubMed Central

    Boutet, Sébastien; Lomb, Lukas; Williams, Garth J.; Barends, Thomas R. M.; Aquila, Andrew; Doak, R. Bruce; Weierstall, Uwe; DePonte, Daniel P.; Steinbrener, Jan; Shoeman, Robert L.; Messerschmidt, Marc; Barty, Anton; White, Thomas A.; Kassemeyer, Stephan; Kirian, Richard A.; Seibert, M. Marvin; Montanez, Paul A.; Kenney, Chris; Herbst, Ryan; Hart, Philip; Pines, Jack; Haller, Gunther; Gruner, Sol M.; Philipp, Hugh T.; Tate, Mark W.; Hromalik, Marianne; Koerner, Lucas J.; van Bakel, Niels; Morse, John; Ghonsalves, Wilfred; Arnlund, David; Bogan, Michael J.; Caleman, Carl; Fromme, Raimund; Hampton, Christina Y.; Hunter, Mark S.; Johansson, Linda C.; Katona, Gergely; Kupitz, Christopher; Liang, Mengning; Martin, Andrew V.; Nass, Karol; Redecke, Lars; Stellato, Francesco; Timneanu, Nicusor; Wang, Dingjie; Zatsepin, Nadia A.; Schafer, Donald; Defever, James; Neutze, Richard; Fromme, Petra; Spence, John C. H.; Chapman, Henry N.; Schlichting, Ilme

    2013-01-01

    Structure determination of proteins and other macromolecules has historically required the growth of high-quality crystals sufficiently large to diffract x-rays efficiently while withstanding radiation damage. We applied serial femtosecond crystallography (SFX) using an x-ray free-electron laser (XFEL) to obtain high-resolution structural information from microcrystals (less than 1 micrometer by 1 micrometer by 3 micrometers) of the well-characterized model protein lysozyme. The agreement with synchrotron data demonstrates the immediate relevance of SFX for analyzing the structure of the large group of difficult-to-crystallize molecules. PMID:22653729

  1. High-resolution protein structure determination by serial femtosecond crystallography.

    PubMed

    Boutet, Sébastien; Lomb, Lukas; Williams, Garth J; Barends, Thomas R M; Aquila, Andrew; Doak, R Bruce; Weierstall, Uwe; DePonte, Daniel P; Steinbrener, Jan; Shoeman, Robert L; Messerschmidt, Marc; Barty, Anton; White, Thomas A; Kassemeyer, Stephan; Kirian, Richard A; Seibert, M Marvin; Montanez, Paul A; Kenney, Chris; Herbst, Ryan; Hart, Philip; Pines, Jack; Haller, Gunther; Gruner, Sol M; Philipp, Hugh T; Tate, Mark W; Hromalik, Marianne; Koerner, Lucas J; van Bakel, Niels; Morse, John; Ghonsalves, Wilfred; Arnlund, David; Bogan, Michael J; Caleman, Carl; Fromme, Raimund; Hampton, Christina Y; Hunter, Mark S; Johansson, Linda C; Katona, Gergely; Kupitz, Christopher; Liang, Mengning; Martin, Andrew V; Nass, Karol; Redecke, Lars; Stellato, Francesco; Timneanu, Nicusor; Wang, Dingjie; Zatsepin, Nadia A; Schafer, Donald; Defever, James; Neutze, Richard; Fromme, Petra; Spence, John C H; Chapman, Henry N; Schlichting, Ilme

    2012-07-20

    Structure determination of proteins and other macromolecules has historically required the growth of high-quality crystals sufficiently large to diffract x-rays efficiently while withstanding radiation damage. We applied serial femtosecond crystallography (SFX) using an x-ray free-electron laser (XFEL) to obtain high-resolution structural information from microcrystals (less than 1 micrometer by 1 micrometer by 3 micrometers) of the well-characterized model protein lysozyme. The agreement with synchrotron data demonstrates the immediate relevance of SFX for analyzing the structure of the large group of difficult-to-crystallize molecules.

  2. A prototype direct-detection CCD for protein crystallography.

    PubMed

    Green, Katherine S; Szebenyi, Doletha M E; Boggs, Kasey; Bredthauer, Richard; Tate, Mark W; Gruner, Sol M

    2013-08-01

    The fabrication and testing of a prototype deep-depletion direct-conversion X-ray CCD detector are described. The device is fabricated on 600 µm-thick high-resistivity silicon, with 24 × 24 µm pixels in a 4k × 4k pixel format. Calibration measurements and the results of initial protein crystallography experiments at the Cornell High Energy Synchrotron Source (CHESS) F1 beamline are described, as well as suggested improvements for future versions of the detector.

  3. Crystallography of lath martensite and stabilization of retained austenite

    SciTech Connect

    Sarikaya. M.

    1982-10-01

    TEM was used to study the morphology and crystallography of lath martensite in low and medium carbon steels in the as-quenched and 200/sup 0/C tempered conditions. The steels have microduplex structures of dislocated lath martensite and continuous thin films of retained austenite at the lath interfaces. Stacks of laths form the packets which are derived from different (111) variants of the same austenite grain. The residual parent austenite enables microdiffraction experiments with small electron beam spot sizes for the orientation relationships (OR) between austenite and martensite. All three most commonly observed ORs, namely Kurdjumov-Sachs, Nishiyama-Wassermann, and Greninger-Troiano, operate within the same sample.

  4. Low-dose fixed-target serial synchrotron crystallography

    PubMed Central

    Owen, Robin L.; Axford, Danny; Sherrell, Darren A.; Kuo, Anling; Ernst, Oliver P.; Schulz, Eike C.; Miller, R. J. Dwayne; Mueller-Werkmeister, Henrike M.

    2017-01-01

    The development of serial crystallography has been driven by the sample requirements imposed by X-ray free-electron lasers. Serial techniques are now being exploited at synchrotrons. Using a fixed-target approach to high-throughput serial sampling, it is demonstrated that high-quality data can be collected from myoglobin crystals, allowing room-temperature, low-dose structure determination. The combination of fixed-target arrays and a fast, accurate translation system allows high-throughput serial data collection at high hit rates and with low sample consumption. PMID:28375148

  5. Low-dose fixed-target serial synchrotron crystallography.

    PubMed

    Owen, Robin L; Axford, Danny; Sherrell, Darren A; Kuo, Anling; Ernst, Oliver P; Schulz, Eike C; Miller, R J Dwayne; Mueller-Werkmeister, Henrike M

    2017-04-01

    The development of serial crystallography has been driven by the sample requirements imposed by X-ray free-electron lasers. Serial techniques are now being exploited at synchrotrons. Using a fixed-target approach to high-throughput serial sampling, it is demonstrated that high-quality data can be collected from myoglobin crystals, allowing room-temperature, low-dose structure determination. The combination of fixed-target arrays and a fast, accurate translation system allows high-throughput serial data collection at high hit rates and with low sample consumption.

  6. Membrane-Protein Crystallography and Potentiality for Drug Design

    NASA Astrophysics Data System (ADS)

    Yamashita, Atsuko

    Structure-based drug design for membrane proteins is far behind that for soluble proteins due to difficulty in crystallographic structure determination, despite the fact that about 60% of FDA-approved drugs target membrane proteins located at the cell surface. Stable homologs for a membrane protein of interest, such as prokaryotic neurotransmitter transporter homolog LeuT, might enable cooperative analyses by crystallography and functional assays, provide useful information for functional mechanisms, and thus serve as important probes for drug design based on mechanisms as well as structures.

  7. Observation Station

    ERIC Educational Resources Information Center

    Rutherford, Heather

    2011-01-01

    This article describes how a teacher integrates science observations into the writing center. At the observation station, students explore new items with a science theme and use their notes and questions for class writings every day. Students are exposed to a variety of different topics and motivated to write in different styles all while…

  8. Space Station

    NASA Image and Video Library

    1989-08-01

    In response to President Reagan's directive to NASA to develop a permanent marned Space Station within a decade, part of the State of the Union message to Congress on January 25, 1984, NASA and the Administration adopted a phased approach to Station development. This approach provided an initial capability at reduced costs, to be followed by an enhanced Space Station capability in the future. This illustration depicts the baseline configuration, which features a 110-meter-long horizontal boom with four pressurized modules attached in the middle. Located at each end are four photovoltaic arrays generating a total of 75-kW of power. Two attachment points for external payloads are provided along this boom. The four pressurized modules include the following: A laboratory and habitation module provided by the United States; two additional laboratories, one each provided by the European Space Agency (ESA) and Japan; and an ESA-provided Man-Tended Free Flyer, a pressurized module capable of operations both attached to and separate from the Space Station core. Canada was expected to provide the first increment of a Mobile Serving System.

  9. Space Station

    NASA Image and Video Library

    1985-12-01

    Skylab's success proved that scientific experimentation in a low gravity environment was essential to scientific progress. A more permanent structure was needed to provide this space laboratory. President Ronald Reagan, on January 25, 1984, during his State of the Union address, claimed that the United States should exploit the new frontier of space, and directed NASA to build a permanent marned space station within a decade. The idea was that the space station would not only be used as a laboratory for the advancement of science and medicine, but would also provide a staging area for building a lunar base and manned expeditions to Mars and elsewhere in the solar system. President Reagan invited the international community to join with the United States in this endeavour. NASA and several countries moved forward with this concept. By December 1985, the first phase of the space station was well underway with the design concept for the crew compartments and laboratories. Pictured are two NASA astronauts, at Marshall Space Flight Center's (MSFC) Neutral Buoyancy Simulator (NBS), practicing construction techniques they later used to construct the space station after it was deployed.

  10. Antiproton Flux, Antiproton-to-Proton Flux Ratio, and Properties of Elementary Particle Fluxes in Primary Cosmic Rays Measured with the Alpha Magnetic Spectrometer on the International Space Station

    NASA Astrophysics Data System (ADS)

    Aguilar, M.; Ali Cavasonza, L.; Alpat, B.; Ambrosi, G.; Arruda, L.; Attig, N.; Aupetit, S.; Azzarello, P.; Bachlechner, A.; Barao, F.; Barrau, A.; Barrin, L.; Bartoloni, A.; Basara, L.; Başeǧmez-du Pree, S.; Battarbee, M.; Battiston, R.; Bazo, J.; Becker, U.; Behlmann, M.; Beischer, B.; Berdugo, J.; Bertucci, B.; Bindi, V.; Boella, G.; de Boer, W.; Bollweg, K.; Bonnivard, V.; Borgia, B.; Boschini, M. J.; Bourquin, M.; Bueno, E. F.; Burger, J.; Cadoux, F.; Cai, X. D.; Capell, M.; Caroff, S.; Casaus, J.; Castellini, G.; Cernuda, I.; Cervelli, F.; Chae, M. J.; Chang, Y. H.; Chen, A. I.; Chen, G. M.; Chen, H. S.; Cheng, L.; Chou, H. Y.; Choumilov, E.; Choutko, V.; Chung, C. H.; Clark, C.; Clavero, R.; Coignet, G.; Consolandi, C.; Contin, A.; Corti, C.; Coste, B.; Creus, W.; Crispoltoni, M.; Cui, Z.; Dai, Y. M.; Delgado, C.; Della Torre, S.; Demirköz, M. B.; Derome, L.; Di Falco, S.; Dimiccoli, F.; Díaz, C.; von Doetinchem, P.; Dong, F.; Donnini, F.; Duranti, M.; D'Urso, D.; Egorov, A.; Eline, A.; Eronen, T.; Feng, J.; Fiandrini, E.; Finch, E.; Fisher, P.; Formato, V.; Galaktionov, Y.; Gallucci, G.; García, B.; García-López, R. J.; Gargiulo, C.; Gast, H.; Gebauer, I.; Gervasi, M.; Ghelfi, A.; Giovacchini, F.; Goglov, P.; Gómez-Coral, D. M.; Gong, J.; Goy, C.; Grabski, V.; Grandi, D.; Graziani, M.; Guerri, I.; Guo, K. H.; Habiby, M.; Haino, S.; Han, K. C.; He, Z. H.; Heil, M.; Hoffman, J.; Hsieh, T. H.; Huang, H.; Huang, Z. C.; Huh, C.; Incagli, M.; Ionica, M.; Jang, W. Y.; Jinchi, H.; Kang, S. C.; Kanishev, K.; Kim, G. N.; Kim, K. S.; Kirn, Th.; Konak, C.; Kounina, O.; Kounine, A.; Koutsenko, V.; Krafczyk, M. S.; La Vacca, G.; Laudi, E.; Laurenti, G.; Lazzizzera, I.; Lebedev, A.; Lee, H. T.; Lee, S. C.; Leluc, C.; Li, H. S.; Li, J. Q.; Li, J. Q.; Li, Q.; Li, T. X.; Li, W.; Li, Z. H.; Li, Z. Y.; Lim, S.; Lin, C. H.; Lipari, P.; Lippert, T.; Liu, D.; Liu, Hu; Lu, S. Q.; Lu, Y. S.; Luebelsmeyer, K.; Luo, F.; Luo, J. Z.; Lv, S. S.; Majka, R.; Mañá, C.; Marín, J.; Martin, T.; Martínez, G.; Masi, N.; Maurin, D.; Menchaca-Rocha, A.; Meng, Q.; Mo, D. C.; Morescalchi, L.; Mott, P.; Nelson, T.; Ni, J. Q.; Nikonov, N.; Nozzoli, F.; Nunes, P.; Oliva, A.; Orcinha, M.; Palmonari, F.; Palomares, C.; Paniccia, M.; Pauluzzi, M.; Pensotti, S.; Pereira, R.; Picot-Clemente, N.; Pilo, F.; Pizzolotto, C.; Plyaskin, V.; Pohl, M.; Poireau, V.; Putze, A.; Quadrani, L.; Qi, X. M.; Qin, X.; Qu, Z. Y.; Räihä, T.; Rancoita, P. G.; Rapin, D.; Ricol, J. S.; Rodríguez, I.; Rosier-Lees, S.; Rozhkov, A.; Rozza, D.; Sagdeev, R.; Sandweiss, J.; Saouter, P.; Schael, S.; Schmidt, S. M.; Schulz von Dratzig, A.; Schwering, G.; Seo, E. S.; Shan, B. S.; Shi, J. Y.; Siedenburg, T.; Son, D.; Song, J. W.; Sun, W. H.; Tacconi, M.; Tang, X. W.; Tang, Z. C.; Tao, L.; Tescaro, D.; Ting, Samuel C. C.; Ting, S. M.; Tomassetti, N.; Torsti, J.; Türkoǧlu, C.; Urban, T.; Vagelli, V.; Valente, E.; Vannini, C.; Valtonen, E.; Vázquez Acosta, M.; Vecchi, M.; Velasco, M.; Vialle, J. P.; Vitale, V.; Vitillo, S.; Wang, L. Q.; Wang, N. H.; Wang, Q. L.; Wang, X.; Wang, X. Q.; Wang, Z. X.; Wei, C. C.; Weng, Z. L.; Whitman, K.; Wienkenhöver, J.; Willenbrock, M.; Wu, H.; Wu, X.; Xia, X.; Xiong, R. Q.; Xu, W.; Yan, Q.; Yang, J.; Yang, M.; Yang, Y.; Yi, H.; Yu, Y. J.; Yu, Z. Q.; Zeissler, S.; Zhang, C.; Zhang, J.; Zhang, J. H.; Zhang, S. D.; Zhang, S. W.; Zhang, Z.; Zheng, Z. M.; Zhu, Z. Q.; Zhuang, H. L.; Zhukov, V.; Zichichi, A.; Zimmermann, N.; Zuccon, P.; AMS Collaboration

    2016-08-01

    A precision measurement by AMS of the antiproton flux and the antiproton-to-proton flux ratio in primary cosmic rays in the absolute rigidity range from 1 to 450 GV is presented based on 3.49 ×1 05 antiproton events and 2.42 ×1 09 proton events. The fluxes and flux ratios of charged elementary particles in cosmic rays are also presented. In the absolute rigidity range ˜60 to ˜500 GV , the antiproton p ¯, proton p , and positron e+ fluxes are found to have nearly identical rigidity dependence and the electron e- flux exhibits a different rigidity dependence. Below 60 GV, the (p ¯/p ), (p ¯/e+), and (p /e+) flux ratios each reaches a maximum. From ˜60 to ˜500 GV , the (p ¯/p ), (p ¯/e+), and (p /e+) flux ratios show no rigidity dependence. These are new observations of the properties of elementary particles in the cosmos.

  11. Antiproton Flux, Antiproton-to-Proton Flux Ratio, and Properties of Elementary Particle Fluxes in Primary Cosmic Rays Measured with the Alpha Magnetic Spectrometer on the International Space Station.

    PubMed

    Aguilar, M; Ali Cavasonza, L; Alpat, B; Ambrosi, G; Arruda, L; Attig, N; Aupetit, S; Azzarello, P; Bachlechner, A; Barao, F; Barrau, A; Barrin, L; Bartoloni, A; Basara, L; Başeǧmez-du Pree, S; Battarbee, M; Battiston, R; Bazo, J; Becker, U; Behlmann, M; Beischer, B; Berdugo, J; Bertucci, B; Bindi, V; Boella, G; de Boer, W; Bollweg, K; Bonnivard, V; Borgia, B; Boschini, M J; Bourquin, M; Bueno, E F; Burger, J; Cadoux, F; Cai, X D; Capell, M; Caroff, S; Casaus, J; Castellini, G; Cernuda, I; Cervelli, F; Chae, M J; Chang, Y H; Chen, A I; Chen, G M; Chen, H S; Cheng, L; Chou, H Y; Choumilov, E; Choutko, V; Chung, C H; Clark, C; Clavero, R; Coignet, G; Consolandi, C; Contin, A; Corti, C; Coste, B; Creus, W; Crispoltoni, M; Cui, Z; Dai, Y M; Delgado, C; Della Torre, S; Demirköz, M B; Derome, L; Di Falco, S; Dimiccoli, F; Díaz, C; von Doetinchem, P; Dong, F; Donnini, F; Duranti, M; D'Urso, D; Egorov, A; Eline, A; Eronen, T; Feng, J; Fiandrini, E; Finch, E; Fisher, P; Formato, V; Galaktionov, Y; Gallucci, G; García, B; García-López, R J; Gargiulo, C; Gast, H; Gebauer, I; Gervasi, M; Ghelfi, A; Giovacchini, F; Goglov, P; Gómez-Coral, D M; Gong, J; Goy, C; Grabski, V; Grandi, D; Graziani, M; Guerri, I; Guo, K H; Habiby, M; Haino, S; Han, K C; He, Z H; Heil, M; Hoffman, J; Hsieh, T H; Huang, H; Huang, Z C; Huh, C; Incagli, M; Ionica, M; Jang, W Y; Jinchi, H; Kang, S C; Kanishev, K; Kim, G N; Kim, K S; Kirn, Th; Konak, C; Kounina, O; Kounine, A; Koutsenko, V; Krafczyk, M S; La Vacca, G; Laudi, E; Laurenti, G; Lazzizzera, I; Lebedev, A; Lee, H T; Lee, S C; Leluc, C; Li, H S; Li, J Q; Li, J Q; Li, Q; Li, T X; Li, W; Li, Z H; Li, Z Y; Lim, S; Lin, C H; Lipari, P; Lippert, T; Liu, D; Liu, Hu; Lu, S Q; Lu, Y S; Luebelsmeyer, K; Luo, F; Luo, J Z; Lv, S S; Majka, R; Mañá, C; Marín, J; Martin, T; Martínez, G; Masi, N; Maurin, D; Menchaca-Rocha, A; Meng, Q; Mo, D C; Morescalchi, L; Mott, P; Nelson, T; Ni, J Q; Nikonov, N; Nozzoli, F; Nunes, P; Oliva, A; Orcinha, M; Palmonari, F; Palomares, C; Paniccia, M; Pauluzzi, M; Pensotti, S; Pereira, R; Picot-Clemente, N; Pilo, F; Pizzolotto, C; Plyaskin, V; Pohl, M; Poireau, V; Putze, A; Quadrani, L; Qi, X M; Qin, X; Qu, Z Y; Räihä, T; Rancoita, P G; Rapin, D; Ricol, J S; Rodríguez, I; Rosier-Lees, S; Rozhkov, A; Rozza, D; Sagdeev, R; Sandweiss, J; Saouter, P; Schael, S; Schmidt, S M; Schulz von Dratzig, A; Schwering, G; Seo, E S; Shan, B S; Shi, J Y; Siedenburg, T; Son, D; Song, J W; Sun, W H; Tacconi, M; Tang, X W; Tang, Z C; Tao, L; Tescaro, D; Ting, Samuel C C; Ting, S M; Tomassetti, N; Torsti, J; Türkoğlu, C; Urban, T; Vagelli, V; Valente, E; Vannini, C; Valtonen, E; Vázquez Acosta, M; Vecchi, M; Velasco, M; Vialle, J P; Vitale, V; Vitillo, S; Wang, L Q; Wang, N H; Wang, Q L; Wang, X; Wang, X Q; Wang, Z X; Wei, C C; Weng, Z L; Whitman, K; Wienkenhöver, J; Willenbrock, M; Wu, H; Wu, X; Xia, X; Xiong, R Q; Xu, W; Yan, Q; Yang, J; Yang, M; Yang, Y; Yi, H; Yu, Y J; Yu, Z Q; Zeissler, S; Zhang, C; Zhang, J; Zhang, J H; Zhang, S D; Zhang, S W; Zhang, Z; Zheng, Z M; Zhu, Z Q; Zhuang, H L; Zhukov, V; Zichichi, A; Zimmermann, N; Zuccon, P

    2016-08-26

    A precision measurement by AMS of the antiproton flux and the antiproton-to-proton flux ratio in primary cosmic rays in the absolute rigidity range from 1 to 450 GV is presented based on 3.49×10^{5} antiproton events and 2.42×10^{9} proton events. The fluxes and flux ratios of charged elementary particles in cosmic rays are also presented. In the absolute rigidity range ∼60 to ∼500  GV, the antiproton p[over ¯], proton p, and positron e^{+} fluxes are found to have nearly identical rigidity dependence and the electron e^{-} flux exhibits a different rigidity dependence. Below 60 GV, the (p[over ¯]/p), (p[over ¯]/e^{+}), and (p/e^{+}) flux ratios each reaches a maximum. From ∼60 to ∼500  GV, the (p[over ¯]/p), (p[over ¯]/e^{+}), and (p/e^{+}) flux ratios show no rigidity dependence. These are new observations of the properties of elementary particles in the cosmos.

  12. A novel inert crystal delivery medium for serial femtosecond crystallography

    DOE PAGES

    Conrad, Chelsie E.; Basu, Shibom; James, Daniel; ...

    2015-06-30

    Serial femtosecond crystallography (SFX) has opened a new era in crystallography by permitting nearly damage-free, room-temperature structure determination of challenging proteins such as membrane proteins. In SFX, femtosecond X-ray free-electron laser pulses produce diffraction snapshots from nanocrystals and microcrystals delivered in a liquid jet, which leads to high protein consumption. A slow-moving stream of agarose has been developed as a new crystal delivery medium for SFX. It has low background scattering, is compatible with both soluble and membrane proteins, and can deliver the protein crystals at a wide range of temperatures down to 4°C. Using this crystal-laden agarose stream, themore » structure of a multi-subunit complex, phycocyanin, was solved to 2.5 Å resolution using 300 µg of microcrystals embedded into the agarose medium post-crystallization. The agarose delivery method reduces protein consumption by at least 100-fold and has the potential to be used for a diverse population of proteins, including membrane protein complexes.« less

  13. Protein energy landscapes determined by five-dimensional crystallography

    SciTech Connect

    Schmidt, Marius; Srajer, Vukica; Henning, Robert; Ihee, Hyotcherl; Purwar, Namrta; Tenboer, Jason; Tripathi, Shailesh

    2013-12-01

    Barriers of activation within the photocycle of a photoactive protein were extracted from comprehensive time courses of time resolved crystallographic data collected at multiple temperature settings. Free-energy landscapes decisively determine the progress of enzymatically catalyzed reactions [Cornish-Bowden (2012 ▶), Fundamentals of Enzyme Kinetics, 4th ed.]. Time-resolved macromolecular crystallography unifies transient-state kinetics with structure determination [Moffat (2001 ▶), Chem. Rev.101, 1569–1581; Schmidt et al. (2005 ▶), Methods Mol. Biol.305, 115–154; Schmidt (2008 ▶), Ultrashort Laser Pulses in Medicine and Biology] because both can be determined from the same set of X-ray data. Here, it is demonstrated how barriers of activation can be determined solely from five-dimensional crystallography, where in addition to space and time, temperature is a variable as well [Schmidt et al. (2010 ▶), Acta Cryst. A66, 198–206]. Directly linking molecular structures with barriers of activation between them allows insight into the structural nature of the barrier to be gained. Comprehensive time series of crystallographic data at 14 different temperature settings were analyzed and the entropy and enthalpy contributions to the barriers of activation were determined. One hundred years after the discovery of X-ray scattering, these results advance X-ray structure determination to a new frontier: the determination of energy landscapes.

  14. JBluIce-EPICS control system for macromolecular crystallography.

    PubMed

    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

    2011-03-01

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

  15. Smarter Drugs: How Protein Crystallography Revolutionizes Drug Design

    SciTech Connect

    Smith, Clyde

    2005-04-26

    According to Smith, protein crystallography allows scientists to design drugs in a much more efficient way than the standard methods traditionally used by large drug companies, which can cost close to a billion dollars and take 10 to 15 years. 'A lot of the work can be compressed down,' Smith said. Protein crystallography enables researchers to learn the structure of molecules involved in disease and health. Seeing the loops, folds and placement of atoms in anything from a virus to a healthy cell membrane gives important information about how these things work - and how to encourage, sidestep or stop their functions. Drug design can be much faster when the relationship between structure and function tells you what area of a molecule to target. Smith will use a timeline to illustrate the traditional methods of drug development and the new ways it can be done now. 'It is very exciting work. There have been some failures, but many successes too.' A new drug to combat the flu was developed in a year or so. Smith will tell us how. He will also highlight drugs developed to combat HIV, Tuberculosis, hypertension and Anthrax.

  16. Combining X-ray and neutron crystallography with spectroscopy

    PubMed Central

    Smith, Oliver

    2017-01-01

    X-ray protein crystallography has, through the determination of the three-dimensional structures of enzymes and their complexes, been essential to the understanding of biological chemistry. However, as X-rays are scattered by electrons, the technique has difficulty locating the presence and position of H atoms (and cannot locate H+ ions), knowledge of which is often crucially important for the understanding of enzyme mechanism. Furthermore, X-ray irradiation, through photoelectronic effects, will perturb the redox state in the crystal. By using single-crystal spectrophotometry, reactions taking place in the crystal can be monitored, either to trap intermediates or follow photoreduction during X-ray data collection. By using neutron crystallography, the positions of H atoms can be located, as it is the nuclei rather than the electrons that scatter neutrons, and the scattering length is not determined by the atomic number. Combining the two techniques allows much greater insight into both reaction mechanism and X-ray-induced photoreduction. PMID:28177310

  17. Proline: Mother Nature;s cryoprotectant applied to protein crystallography

    SciTech Connect

    Pemberton, Travis A.; Still, Brady R.; Christensen, Emily M.; Singh, Harkewal; Srivastava, Dhiraj; Tanner, John J.

    2012-09-05

    L-Proline is one of Mother Nature's cryoprotectants. Plants and yeast accumulate proline under freeze-induced stress and the use of proline in the cryopreservation of biological samples is well established. Here, it is shown that L-proline is also a useful cryoprotectant for protein crystallography. Proline was used to prepare crystals of lysozyme, xylose isomerase, histidine acid phosphatase and 1-pyrroline-5-carboxylate dehydrogenase for low-temperature data collection. The crystallization solutions in these test cases included the commonly used precipitants ammonium sulfate, sodium chloride and polyethylene glycol and spanned the pH range 4.6-8.5. Thus, proline is compatible with typical protein-crystallization formulations. The proline concentration needed for cryoprotection of these crystals is in the range 2.0-3.0 M. Complete data sets were collected from the proline-protected crystals. Proline performed as well as traditional cryoprotectants based on the diffraction resolution and data-quality statistics. The structures were refined to assess the binding of proline to these proteins. As observed with traditional cryoprotectants such as glycerol and ethylene glycol, the electron-density maps clearly showed the presence of proline molecules bound to the protein. In two cases, histidine acid phosphatase and 1-pyrroline-5-carboxylate dehydrogenase, proline binds in the active site. It is concluded that L-proline is an effective cryoprotectant for protein crystallography.

  18. High-pressure crystallography of periodic and aperiodic crystals

    PubMed Central

    Hejny, Clivia; Minkov, Vasily S.

    2015-01-01

    More than five decades have passed since the first single-crystal X-ray diffraction experiments at high pressure were performed. These studies were applied historically to geochemical processes occurring in the Earth and other planets, but high-pressure crystallography has spread across different fields of science including chemistry, physics, biology, materials science and pharmacy. With each passing year, high-pressure studies have become more precise and comprehensive because of the development of instrumentation and software, and the systems investigated have also become more complicated. Starting with crystals of simple minerals and inorganic compounds, the interests of researchers have shifted to complicated metal–organic frameworks, aperiodic crystals and quasicrystals, molecular crystals, and even proteins and viruses. Inspired by contributions to the microsymposium ‘High-Pressure Crystallography of Periodic and Aperiodic Crystals’ presented at the 23rd IUCr Congress and General Assembly, the authors have tried to summarize certain recent results of single-crystal studies of molecular and aperiodic structures under high pressure. While the selected contributions do not cover the whole spectrum of high-pressure research, they demonstrate the broad diversity of novel and fascinating results and may awaken the reader’s interest in this topic. PMID:25866659

  19. JBluIce-EPICS control system for macromolecular crystallography.

    SciTech Connect

    Stepanov, S.; Makarov, O.; Hilgart, M.; Pothineni, S.; Urakhchin, A.; Devarapalli, S.; Yoder, D.; Becker, M.; Ogata, C.; Sanishvili, R.; Nagarajan, V.; Smith, J. L.; Fischetti, R. F.

    2011-01-01

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

  20. Review: Serial Femtosecond Crystallography: A Revolution in Structural Biology

    PubMed Central

    Martin-Garcia, Jose M.; Conrad, Chelsie E.; Coe, Jesse; Roy-Chowdhury, Shatabdi; Fromme, Petra

    2016-01-01

    Macromolecular crystallography at synchrotron sources has proven to be the most influential method within structural biology, producing thousands of structures since its inception. While its utility has been instrumental in progressing our knowledge of structures of molecules, it suffers from limitations such as the need for large, well-diffracting crystals, and radiation damage that can hamper native structural determination. The recent advent of X-ray free electron lasers (XFELs) and their implementation in the emerging field of serial femtosecond crystallography (SFX) has given rise to a remarkable expansion upon existing crystallographic constraints, allowing structural biologists access to previously restricted scientific territory. SFX relies on exceptionally brilliant, micro-focused X-ray pulses, which are femtoseconds in duration, to probe nano/micrometer sized crystals in a serial fashion. This results in data sets comprised of individual snapshots, each capturing Bragg diffraction of single crystals in random orientations prior to their subsequent destruction. Thus structural elucidation while avoiding radiation damage, even at room temperature, can now be achieved. This emerging field has cultivated new methods for nanocrystallogenesis, sample delivery, and data processing. Opportunities and challenges within SFX are reviewed herein. PMID:27143509

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

    PubMed Central

    Helliwell, John R.; Mitchell, Edward P.

    2015-01-01

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

  2. A novel inert crystal delivery medium for serial femtosecond crystallography

    SciTech Connect

    Conrad, Chelsie E.; Basu, Shibom; James, Daniel; Wang, Dingjie; Schaffer, Alexander; Roy-Chowdhury, Shatabdi; Zatsepin, Nadia A.; Aquila, Andrew; Coe, Jesse; Gati, Cornelius; Hunter, Mark S.; Koglin, Jason E.; Kupitz, Christopher; Nelson, Garrett; Subramanian, Ganesh; White, Thomas A.; Zhao, Yun; Zook, James; Boutet, Sébastien; Cherezov, Vadim; Spence, John C. H.; Fromme, Raimund; Weierstall, Uwe; Fromme, Petra

    2015-06-30

    Serial femtosecond crystallography (SFX) has opened a new era in crystallography by permitting nearly damage-free, room-temperature structure determination of challenging proteins such as membrane proteins. In SFX, femtosecond X-ray free-electron laser pulses produce diffraction snapshots from nanocrystals and microcrystals delivered in a liquid jet, which leads to high protein consumption. A slow-moving stream of agarose has been developed as a new crystal delivery medium for SFX. It has low background scattering, is compatible with both soluble and membrane proteins, and can deliver the protein crystals at a wide range of temperatures down to 4°C. Using this crystal-laden agarose stream, the structure of a multi-subunit complex, phycocyanin, was solved to 2.5Å resolution using 300µg of microcrystals embedded into the agarose medium post-crystallization. The agarose delivery method reduces protein consumption by at least 100-fold and has the potential to be used for a diverse population of proteins, including membrane protein complexes.

  3. A novel inert crystal delivery medium for serial femtosecond crystallography

    SciTech Connect

    Conrad, Chelsie E.; Basu, Shibom; James, Daniel; Wang, Dingjie; Schaffer, Alexander; Roy-Chowdhury, Shatabdi; Zatsepin, Nadia A.; Aquila, Andrew; Coe, Jesse; Gati, Cornelius; Hunter, Mark S.; Koglin, Jason E.; Kupitz, Christopher; Nelson, Garrett; Subramanian, Ganesh; White, Thomas A.; Zhao, Yun; Zook, James; Boutet, Sébastien; Cherezov, Vadim; Spence, John C. H.; Fromme, Raimund; Weierstall, Uwe; Fromme, Petra

    2015-06-30

    Serial femtosecond crystallography (SFX) has opened a new era in crystallography by permitting nearly damage-free, room-temperature structure determination of challenging proteins such as membrane proteins. In SFX, femtosecond X-ray free-electron laser pulses produce diffraction snapshots from nanocrystals and microcrystals delivered in a liquid jet, which leads to high protein consumption. A slow-moving stream of agarose has been developed as a new crystal delivery medium for SFX. It has low background scattering, is compatible with both soluble and membrane proteins, and can deliver the protein crystals at a wide range of temperatures down to 4°C. Using this crystal-laden agarose stream, the structure of a multi-subunit complex, phycocyanin, was solved to 2.5 Å resolution using 300 µg of microcrystals embedded into the agarose medium post-crystallization. The agarose delivery method reduces protein consumption by at least 100-fold and has the potential to be used for a diverse population of proteins, including membrane protein complexes.

  4. Proline: Mother Nature’s cryoprotectant applied to protein crystallography

    PubMed Central

    Pemberton, Travis A.; Still, Brady R.; Christensen, Emily M.; Singh, Harkewal; Srivastava, Dhiraj; Tanner, John J.

    2012-01-01

    l-Proline is one of Mother Nature’s cryoprotectants. Plants and yeast accumulate proline under freeze-induced stress and the use of proline in the cryopreservation of biological samples is well established. Here, it is shown that l-proline is also a useful cryoprotectant for protein crystallography. Proline was used to prepare crystals of lysozyme, xylose isomerase, histidine acid phosphatase and 1-pyrroline-5-carboxylate dehydrogenase for low-temperature data collection. The crystallization solutions in these test cases included the commonly used precipitants ammonium sulfate, sodium chloride and polyethylene glycol and spanned the pH range 4.6–8.5. Thus, proline is compatible with typical protein-crystallization formulations. The proline concentration needed for cryoprotection of these crystals is in the range 2.0–3.0 M. Complete data sets were collected from the proline-protected crystals. Proline performed as well as traditional cryoprotectants based on the diffraction resolution and data-quality statistics. The structures were refined to assess the binding of proline to these proteins. As observed with traditional cryoprotectants such as glycerol and ethylene glycol, the electron-density maps clearly showed the presence of proline molecules bound to the protein. In two cases, histidine acid phosphatase and 1-pyrroline-5-carboxylate dehydrogenase, proline binds in the active site. It is concluded that l-proline is an effective cryoprotectant for protein crystallography. PMID:22868767

  5. Proline: Mother Nature's cryoprotectant applied to protein crystallography.

    PubMed

    Pemberton, Travis A; Still, Brady R; Christensen, Emily M; Singh, Harkewal; Srivastava, Dhiraj; Tanner, John J

    2012-08-01

    L-Proline is one of Mother Nature's cryoprotectants. Plants and yeast accumulate proline under freeze-induced stress and the use of proline in the cryopreservation of biological samples is well established. Here, it is shown that L-proline is also a useful cryoprotectant for protein crystallography. Proline was used to prepare crystals of lysozyme, xylose isomerase, histidine acid phosphatase and 1-pyrroline-5-carboxylate dehydrogenase for low-temperature data collection. The crystallization solutions in these test cases included the commonly used precipitants ammonium sulfate, sodium chloride and polyethylene glycol and spanned the pH range 4.6-8.5. Thus, proline is compatible with typical protein-crystallization formulations. The proline concentration needed for cryoprotection of these crystals is in the range 2.0-3.0 M. Complete data sets were collected from the proline-protected crystals. Proline performed as well as traditional cryoprotectants based on the diffraction resolution and data-quality statistics. The structures were refined to assess the binding of proline to these proteins. As observed with traditional cryoprotectants such as glycerol and ethylene glycol, the electron-density maps clearly showed the presence of proline molecules bound to the protein. In two cases, histidine acid phosphatase and 1-pyrroline-5-carboxylate dehydrogenase, proline binds in the active site. It is concluded that L-proline is an effective cryoprotectant for protein crystallography.

  6. SIBYLS - A SAXS and protein crystallography beamline at the ALS

    SciTech Connect

    Trame, Christine; MacDowell, Alastair A.; Celestre, Richard S.; Padmore, Howard A.; Cambie, Daniella; Domning, Edward E.; Duarte, Robert M.; Kelez, Nicholas; Plate, David W.; Holton, James M.; Frankel, Kenneth; Tsutakawa, Susan; Tsuruta, Hiro; Tainer, John A.; Cooper, Priscilla K.

    2003-08-22

    The new Structurally Integrated BiologY for Life Sciences (SIBYLS) beamline at the Advanced Light Source will be dedicated to Macromolecular Crystallography (PX) and Small Angle X-ray Scattering (SAXS). SAXS will provide structural information of macromolecules in solutions and will complement high resolution PX studies on the same systems but in a crystalline state. The x-ray source is one of the 5 Tesla superbend dipoles recently installed at the ALS that allows for a hard x-ray program to be developed on the relatively low energy Advanced Light Source (ALS) ring (1.9 GeV). The beamline is equipped with fast interchangeable monochromator elements, consisting of either a pair of single Si(111) crystals for crystallography, or a pair of multilayers for the SAXS mode data collection (E/{Delta}E {approx} 1/110). Flux rates with Si(111) crystals for PX are measured as 2 x 10{sup 11} hv/sec/400 mA through a 100 {micro}m pinhole at 12.4 KeV. For SAXS the flux is up to 3 x 10{sup 13} photons/sec at 10 KeV with all apertures open when using the multilayer monochromator elements. The performance characteristics of this unique beamline will be described.

  7. Polycapillary X-ray optics for macromolecular crystallography

    NASA Astrophysics Data System (ADS)

    Hofmann, Frank Alexander

    Macromolecules, such as proteins, nucleic acids, and carbohydrates can be found in every living cell. Nearly every chemical reaction in a cell requires the presence of enzymes, which belong to the class of proteins. In order to understand these processes, it is vital to know the three-dimensional structure of enzymes and other macromolecules. One way to find the structure is X-ray crystallography. Macromolecules are very large compared to most inorganic molecules and they have a very weak diffracting power. Structure determination with X-ray crystallography requires single crystals. Single crystals of macromolecules are difficult to grow except to very small size. Thus, intense X-ray beams are required. In order to generate intense X-ray beams, many crystallographers use synchrotrons. Intense beams can also be generated using X-ray optics. The work described includes a systematic study of the application of both collimating and slightly focusing polycapillary optics to X-ray crystallographic structure determination of egg-white lysozyme using a standard rotating anode source and a low power tabletop microfocusing source. The results summarize a series of measurements comparing duplicate data sets obtained from an individual crystal on a rotating anode source. Intensity and data quality are discussed for measurements with a pinhole collimator, a collimating polycapillary optic, and a focusing polycapillary optic. The collected data were analyzed using conventional analysis software.

  8. Proton maser

    NASA Astrophysics Data System (ADS)

    Ensley, D. L.

    1988-01-01

    New calculations are reported which confirm the ability of an a priori random, initial-phase proton beam to drive a simple, single-stage microwave cavity maser or transit-time oscillator (TTO) to saturation conversion efficiencies of about 11 percent. The required initial TE(011) mode field can be provided from beam ramp-up bandwidth of excitation to a low level from an external source. A saturation field of 45 tesla and output power of 0.2 TW are calculated using an electron insulation field of 10 tesla and a 3 MeV, 400 Ka/sq cm beam. Results are compared to those for an electron beam of the same energy and geometry, and it is shown that proton beams potentially can provide a three order of magnitude increase in overall microwave power production density over that obtainable from electron beam TTOs.

  9. Proton scaling

    SciTech Connect

    Canavan, Gregory H

    2009-01-01

    This note presents analytic estimates of the performance of proton beams in remote surveillance for nuclear materials. The analysis partitions the analysis into the eight steps used by a companion note: (1) Air scattering, (2) Neutron production in the ship and cargo, (3) Target detection probability, (4) Signal produced by target, (5) Attenuation of signal by ship and cargo, (6) Attenuation of signal by air, (7) Geometric dilution, and (8) Detector Efficiency. The above analyses indicate that the dominant air scattering and loss mechanisms for particle remote sensing are calculable with reliable and accepted tools. They make it clear that the conversion of proton beams into neutron sources rapidly goes to completion in all but thinnest targets, which means that proton interrogation is for all purposes executed by neutrons. Diffusion models and limiting approximations to them are simple and credible - apart from uncertainty over the cross sections to be used in them - and uncertainty over the structure of the vessels investigated. Multiplication is essentially unknown, in part because it depends on the details of the target and its shielding, which are unlikely to be known in advance. Attenuation of neutron fluxes on the way out are more complicated due to geometry, the spectrum of fission neutrons, and the details of their slowing down during egress. The attenuation by air is large but less uncertain. Detectors and technology are better known. The overall convolution of these effects lead to large but arguably tolerable levels of attenuation of input beams and output signals. That is particularly the case for small, mobile sensors, which can more than compensate for size with proximity to operate reliably while remaining below flux limits. Overall, the estimates used here appear to be of adequate accuracy for decisions. That assessment is strengthened by their agreement with companion calculations.

  10. Outrunning free radicals in room-temperature macromolecular crystallography

    PubMed Central

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

    2012-01-01

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

  11. A history of experimental phasing in macromolecular crystallography.

    PubMed

    Isaacs, Neil

    2016-03-01

    It was just over a century ago that W. L. Bragg published a paper describing the first crystal structures to be determined using X-ray diffraction data. These structures were obtained from considerations of X-ray diffraction (Bragg equation), crystallography (crystal lattices and symmetry) and the scattering power of different atoms. Although W. H. Bragg proposed soon afterwards, in 1915, that the periodic electron density in crystals could be analysed using Fourier transforms, it took some decades before experimental phasing methods were developed. Many scientists contributed to this development and this paper presents the author's own perspective on this history. There will be other perspectives, so what follows is a history, rather than the history, of experimental phasing.

  12. Crystallography of Co/Pt multilayers and nanostructures

    SciTech Connect

    Zhang, Bing; Krishnan, K.M.; Farrow, R.F.C.

    1992-04-01

    Atomically engineered nanostructures and multilayers of Co/Pt exhibit strong perpendicular anisotropy. This unique property, that determines their potential as a magneto-optic recording media, is dependent on a variety of microstructural parameters that include the overall crystallography, thickness of the layers, orientation, defect formation, interface reactions etc. A series of Co/Pt multilayer samples with different thickness of the Co layer were studied by electron diffraction. It has been determined that the Co layers persists in the fcc structure up to a thickness of 50 {Angstrom}. As the thickness is varied fmm 3{Angstrom} to 50{Angstrom} in the multilayers, the Co film gradually relaxed to its bulk lattice parameter. (111) twinning and lattice strain at the interfaces between Pt and Co layers are also observed. The symmetry forbidden reflections observed at 1/3 (224) positions in (111) zone diffraction patterns of the multilayer are due to (111) twinning and compositional modulations along the multilayer growth direction.

  13. Cryogenic Neutron Protein Crystallography: routine methods and potential benefits

    SciTech Connect

    Weiss, Kevin L; Tomanicek, Stephen J; NG, Joseph D

    2014-01-01

    The use of cryocooling in neutron diffraction has been hampered by several technical challenges such as the need for specialized equipment and techniques. Recently we have developed and deployed equipment and strategies that allow for routine neutron data collection on cryocooled crystals using off the shelf components. This system has several advantages, compared to a closed displex cooling system such as fast cooling coupled with easier crystal mounting and centering. The ability to routinely collect cryogenic neutron data for analysis will significantly broaden the range of scientific questions that can be examined by neutron protein crystallography. Cryogenic neutron data collection for macromolecules has recently become available at the new Biological Diffractometer BIODIFF at FRM II and the Macromolecular Diffractometer (MaNDi) at the Spallation Neutron Source, Oak Ridge National Laboratory. To evaluate the benefits of a cryocooled neutron structure we collected a full neutron data set on the BIODIFF instrument on a Toho-1 lactamase structure at 100K.

  14. Protein-ligand interactions probed by time-resolved crystallography

    SciTech Connect

    Schmidt, M.; Ihee, H.; Pahl, R.; Srajer, V.

    2005-03-09

    Time-resolved (TR) crystallography is a unique method for determining the structures of intermediates in biomolecular reactions. The technique reached its mature stage with the development of the powerful third-generation synchrotron X-ray sources, and the advances in data processing and analysis of time-resolved Laue crystallographic data. A time resolution of 100 ps has been achieved and relatively small structural changes can be detected even from only partial reaction initiation. The remaining challenge facing the application of this technique to a broad range of biological systems is to find an efficient and rapid, system-specific method for the reaction initiation in the crystal. Other frontiers for the technique involve the continued improvement in time resolution and further advances in methods for determining intermediate structures and reaction mechanisms. The time-resolved technique, combined with trapping methods and computational approaches, holds the promise for a complete structure-based description of biomolecular reactions.

  15. A history of experimental phasing in macromolecular crystallography

    PubMed Central

    Isaacs, Neil

    2016-01-01

    It was just over a century ago that W. L. Bragg published a paper describing the first crystal structures to be determined using X-ray diffraction data. These structures were obtained from considerations of X-ray diffraction (Bragg equation), crystallography (crystal lattices and symmetry) and the scattering power of different atoms. Although W. H. Bragg proposed soon afterwards, in 1915, that the periodic electron density in crystals could be analysed using Fourier transforms, it took some decades before experimental phasing methods were developed. Many scientists contributed to this development and this paper presents the author’s own perspective on this history. There will be other perspectives, so what follows is a history, rather than the history, of experimental phasing. PMID:26960116

  16. Lens-Coupled CCD Detector for X-ray Crystallography

    PubMed Central

    Madden, Timothy J.; McGuigan, William; Molitsky, Michael J.; Naday, Istvan; McArthur, Alan; Westbrook, Edwin M.

    2007-01-01

    An x-ray crystallography detector (Blue-1) has been built based upon a Fairchild 486 back-illuminated CCD and a custom lens system designed by Optics One Inc. The advantages of our Blue-1 lens system over more conventional fiber-optic tapers are: lower noise and higher efficiency; improved point spread function; negligible spatial distortion; and lack of “chicken-wire” patterns. Also, the engineering is simpler because the CCD is not bonded to the fiber-optic taper. A unique mechanical design has been employed to accurately focus the image on the CCD. The detector software is based on MATLAB and takes advantage of its powerful imaging and signal processing libraries. The CCD timing can be updated on the fly by using a “CCD controller language” to specify timing. PMID:18185837

  17. Crystallography and elasticity of individual GaN nanotubes

    NASA Astrophysics Data System (ADS)

    Liu, Baodan; Bando, Yoshio; Wang, Mingsheng; Tang, Chengchun; Mitome, Masanori; Golberg, Dmitri

    2009-05-01

    High-purity, crystalline [001]-oriented GaN nanotubes with outer diameters of 200 nm or more, rough surfaces and irregular internal channels were synthesized under epitaxial growth on [001]-oriented sapphire substrates. Elastic property measurements on free-standing individual GaN nanotubes, using the in situ transmission electron microscopy (TEM) electromechanical resonance technique, pointed at an average Young's modulus E of 37 GPa and minimum quality factor of 320. These numbers are notably lower than those for previously reported GaN nanowires. The crystallography and chemistry of the GaN nanotubes were analyzed using TEM and energy dispersion x-ray spectroscopy (EDS). It is suggested that the lowered Young's modulus and quality factor of the nanotubes are mainly due to the surface roughness and defectiveness.

  18. Towards time-resolved serial crystallography in a microfluidic device

    PubMed Central

    Pawate, Ashtamurthy S.; Šrajer, Vukica; Schieferstein, Jeremy; Guha, Sudipto; Henning, Robert; Kosheleva, Irina; Schmidt, Marius; Ren, Zhong; Kenis, Paul J. A.; Perry, Sarah L.

    2015-01-01

    Serial methods for crystallography have the potential to enable dynamic structural studies of protein targets that have been resistant to single-crystal strategies. The use of serial data-collection strategies can circumvent challenges associated with radiation damage and repeated reaction initiation. This work utilizes a microfluidic crystallization platform for the serial time-resolved Laue diffraction analysis of macroscopic crystals of photoactive yellow protein (PYP). Reaction initiation was achieved via pulsed laser illumination, and the resultant electron-density difference maps clearly depict the expected pR1/pRE46Q and pR2/pRCW states at 10 µs and the pB1 intermediate at 1 ms. The strategies presented here have tremendous potential for extension to chemical triggering methods for reaction initiation and for extension to dynamic, multivariable analyses. PMID:26144226

  19. Serial femtosecond crystallography of soluble proteins in lipidic cubic phase

    DOE PAGES

    Fromme, Raimund; Ishchenko, Andrii; Metz, Markus; ...

    2015-08-04

    Serial femtosecond crystallography (SFX) at X-ray free-electron lasers (XFELs) enables high-resolution protein structure determination using micrometre-sized crystals at room temperature with minimal effects from radiation damage. SFX requires a steady supply of microcrystals intersecting the XFEL beam at random orientations. An LCP–SFX method has recently been introduced in which microcrystals of membrane proteins are grown and delivered for SFX data collection inside a gel-like membrane-mimetic matrix, known as lipidic cubic phase (LCP), using a special LCP microextrusion injector. Here, it is shown enabling a dramatic reduction in the amount of crystallized protein required for data collection compared with crystals deliveredmore » by liquid injectors. High-quality LCP–SFX data sets were collected for two soluble proteins, lysozyme and phycocyanin, using less than 0.1 mg of each protein.« less

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

    DOE PAGES

    Ng, Joseph D.; Baird, James K.; Coates, Leighton; ...

    2015-03-30

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

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

    SciTech Connect

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

    2015-03-30

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

  2. Seeing the chemistry in biology with neutron crystallography.

    PubMed

    Langan, Paul; Chen, Julian C-H

    2013-09-07

    New developments in macromolecular neutron crystallography have led to an increasing number of structures published over the last decade. Hydrogen atoms, normally invisible in most X-ray crystal structures, become visible with neutrons. Using X-rays allows one to see structure, while neutrons allow one to reveal the chemistry inherent in these macromolecular structures. A number of surprising and sometimes controversial results have emerged; because it is difficult to see or predict hydrogen atoms in X-ray structures, when they are seen by neutrons they can be in unexpected locations with important chemical and biological consequences. Here we describe examples of chemistry seen with neutrons for the first time in biological macromolecules over the past few years.

  3. Status of the crystallography beamlines at synchrotron SOLEIL⋆

    NASA Astrophysics Data System (ADS)

    Coati, A.; Chavas, L. M. G.; Fontaine, P.; Foos, N.; Guimaraes, B.; Gourhant, P.; Legrand, P.; Itie, J.-P.; Fertey, P.; Shepard, W.; Isabet, T.; Sirigu, S.; Solari, P.-L.; Thiaudiere, D.; Thompson, A.

    2017-04-01

    Synchrotron SOLEIL (www.synchrotron-soleil.fr) is the French national centre for synchrotron radiation research, and has been open, for user applications, since 2008. Operating at an energy of 2.75GeV, injected current of 500mA, with an excellent beam stability of < 1 micron at the source position and beam "top up", and with a high proportion of straight sections for the ring circumference, SOLEIL offers a wide range of possibilities for diffraction experiments. The beamlines serving crystallographic communities are listed, along with their area of expertise and available equipment. A detailed description of the design of the PROXIMA 1 beamline for macromolecular crystallography is given, and an example of an (unsuccessful but significant) experiment is given.

  4. Seeing the chemistry in biology with neutron crystallography

    PubMed Central

    Langan, Paul; Chen, Julian C.-H.

    2017-01-01

    New developments in macromolecular neutron crystallography have led to an increasing number of structures published over the last decade. Hydrogen atoms, normally invisible in most X-ray crystal structures, become visible in neutron structures. Using X-rays allows one to see structure, while neutrons allow one to reveal the chemistry inherent in these macromolecular structures. A number of surprising and sometimes controversial results have emerged from recent neutron structures; because it is difficult to see or predict hydrogen atoms in X-ray structures, when they are seen by neutrons they can be in unexpected locations with important chemical and biological consequences. Here we describe examples of chemistry seen with neutrons for the first time in biological macromolecules over the past few years. PMID:23852376

  5. In-vacuum long-wavelength macromolecular crystallography.

    PubMed

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

    2016-03-01

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

  6. Towards time-resolved serial crystallography in a microfluidic device.

    PubMed

    Pawate, Ashtamurthy S; Šrajer, Vukica; Schieferstein, Jeremy; Guha, Sudipto; Henning, Robert; Kosheleva, Irina; Schmidt, Marius; Ren, Zhong; Kenis, Paul J A; Perry, Sarah L

    2015-07-01

    Serial methods for crystallography have the potential to enable dynamic structural studies of protein targets that have been resistant to single-crystal strategies. The use of serial data-collection strategies can circumvent challenges associated with radiation damage and repeated reaction initiation. This work utilizes a microfluidic crystallization platform for the serial time-resolved Laue diffraction analysis of macroscopic crystals of photoactive yellow protein (PYP). Reaction initiation was achieved via pulsed laser illumination, and the resultant electron-density difference maps clearly depict the expected pR(1)/pR(E46Q) and pR(2)/pR(CW) states at 10 µs and the pB1 intermediate at 1 ms. The strategies presented here have tremendous potential for extension to chemical triggering methods for reaction initiation and for extension to dynamic, multivariable analyses.

  7. In-vacuum long-wavelength macromolecular crystallography

    PubMed Central

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

    2016-01-01

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

  8. Nonequilibrium phase transitions in cuprates observed by ultrafast electron crystallography.

    PubMed

    Gedik, Nuh; Yang, Ding-Shyue; Logvenov, Gennady; Bozovic, Ivan; Zewail, Ahmed H

    2007-04-20

    Nonequilibrium phase transitions, which are defined by the formation of macroscopic transient domains, are optically dark and cannot be observed through conventional temperature- or pressure-change studies. We have directly determined the structural dynamics of such a nonequilibrium phase transition in a cuprate superconductor. Ultrafast electron crystallography with the use of a tilted optical geometry technique afforded the necessary atomic-scale spatial and temporal resolutions. The observed transient behavior displays a notable "structural isosbestic" point and a threshold effect for the dependence of c-axis expansion (Deltac) on fluence (F), with Deltac/F = 0.02 angstrom/(millijoule per square centimeter). This threshold for photon doping occurs at approximately 0.12 photons per copper site, which is unexpectedly close to the density (per site) of chemically doped carriers needed to induce superconductivity.

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

    PubMed Central

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

    2015-01-01

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

  10. Serial femtosecond crystallography of soluble proteins in lipidic cubic phase

    SciTech Connect

    Fromme, Raimund; Ishchenko, Andrii; Metz, Markus; Chowdhury, Shatabdi Roy; Basu, Shibom; Boutet, Sébastien; Fromme, Petra; White, Thomas A.; Barty, Anton; Spence, John C. H.; Weierstall, Uwe; Liu, Wei; Cherezov, Vadim

    2015-08-04

    Serial femtosecond crystallography (SFX) at X-ray free-electron lasers (XFELs) enables high-resolution protein structure determination using micrometre-sized crystals at room temperature with minimal effects from radiation damage. SFX requires a steady supply of microcrystals intersecting the XFEL beam at random orientations. An LCP–SFX method has recently been introduced in which microcrystals of membrane proteins are grown and delivered for SFX data collection inside a gel-like membrane-mimetic matrix, known as lipidic cubic phase (LCP), using a special LCP microextrusion injector. Here, it is shown enabling a dramatic reduction in the amount of crystallized protein required for data collection compared with crystals delivered by liquid injectors. High-quality LCP–SFX data sets were collected for two soluble proteins, lysozyme and phycocyanin, using less than 0.1 mg of each protein.

  11. Proline: Mother Nature’s cryoprotectant applied to protein crystallography

    SciTech Connect

    Pemberton, Travis A.; Still, Brady R.; Christensen, Emily M.; Singh, Harkewal; Srivastava, Dhiraj; Tanner, John J.

    2012-08-01

    The amino acid l-proline is shown to be a good cryoprotectant for protein crystals. Four examples are provided; the range of proline used for cryoprotection is 2.0–3.0 M. l-Proline is one of Mother Nature’s cryoprotectants. Plants and yeast accumulate proline under freeze-induced stress and the use of proline in the cryopreservation of biological samples is well established. Here, it is shown that l-proline is also a useful cryoprotectant for protein crystallography. Proline was used to prepare crystals of lysozyme, xylose isomerase, histidine acid phosphatase and 1-pyrroline-5-carboxylate dehydrogenase for low-temperature data collection. The crystallization solutions in these test cases included the commonly used precipitants ammonium sulfate, sodium chloride and polyethylene glycol and spanned the pH range 4.6–8.5. Thus, proline is compatible with typical protein-crystallization formulations. The proline concentration needed for cryoprotection of these crystals is in the range 2.0–3.0 M. Complete data sets were collected from the proline-protected crystals. Proline performed as well as traditional cryoprotectants based on the diffraction resolution and data-quality statistics. The structures were refined to assess the binding of proline to these proteins. As observed with traditional cryoprotectants such as glycerol and ethylene glycol, the electron-density maps clearly showed the presence of proline molecules bound to the protein. In two cases, histidine acid phosphatase and 1-pyrroline-5-carboxylate dehydrogenase, proline binds in the active site. It is concluded that l-proline is an effective cryoprotectant for protein crystallography.

  12. Application of multigrain crystallography to mineralogy of the deep Earth

    NASA Astrophysics Data System (ADS)

    Zhang, L.; Meng, Y.; Popov, D.; Wang, J.; Mao, H. K.

    2014-12-01

    Laser-heated diamond anvil cell (DAC) technology coupled with x-ray diffraction (XRD) probe has become a powerful tool to explore the mineralogy of the deep Earth. However, powder diffraction alone has the intrinsic limitations when the sample consists of multiple different phases; only a couple of low angle diffraction rings are unique to each of the phases; most overlapping diffraction rings cannot be used for unique identification or accurate determination of crystallographic parameters. Such powder refinements at extreme P-T conditions also suffer from unreliable intensity measurements caused by texturing of the sample and spottiness due to crystal growth under high T. In addition, new structures and minor phases are often overshadowed by the diffraction peaks of major phases. The crystal structure and unit-cell parameters of Fe-bearing minerals change with pressure/temperature, spin transition, and Fe redistribution. Precise structure analysis is required to understand the role of Fe in the geophysical and geochemical processes in the deep Earth. To overcome the difficulties, we introduced a multigrain crystallography method to determine crystallographic orientations of individual crystallites within a polycrystalline sample in-situ in a DAC. Using this method, we are able to separate individual crystallites and treat them as individual single crystals. The high-brilliance x-ray beam available at the 3rd generation synchrotron facilities has made it possible to collect diffraction spots in a powder sample comprised of hundreds of submicron-sized crystallites. Once separated, the data set for each crystallite can be treated with the standard single-crystal refinement program, resulting in excellent statistics in refinement and maximal coverage of the reciprocal space. The combination of powder diffraction and multigrain crystallography is very powerful in unequivocal determination of symmetry and unit cells, solving new structures, and picking out minor phases

  13. JBluIce–EPICS control system for macromolecular crystallography

    PubMed Central

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

    2011-01-01

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

  14. Fermilab Tevatron I project target station for antiproton production

    SciTech Connect

    Hojvat, C.; Biallas, G.; Hanson, R.; Heim, J.; Lange, F.

    1983-03-01

    Production of 8-GeV antiprotons in the Fermilab Tevatron I project will utilize 120-GeV protons from the Main Ring. The Target Station consists of an entrance collimator, the target itself, a pulsed lithium lens for anti proton collection, a pulsed magnet for the separation of the 8-GeV secondaries, and a beam dump. These components are mounted on vertical modules within the Target Service Building. Allowance has been made for future improvements to increase the collected anti proton flux. The design of the Target Station and its components is discussed.

  15. Crystal structure of CO-bound cytochrome c oxidase determined by serial femtosecond X-ray crystallography at room temperature

    DOE PAGES

    Ishigami, Izumi; Zatsepin, Nadia A.; Hikita, Masahide; ...

    2017-07-11

    Here, cytochrome c oxidase (CcO), the terminal enzyme in the electron transfer chain, translocates protons across the inner mitochondrial membrane by harnessing the free energy generated by the reduction of oxygen to water. Several redox-coupled proton translocation mechanisms have been proposed, but they lack confirmation, in part from the absence of reliable structural information due to radiation damage artifacts caused by the intense synchrotron radiation. Here we report the room temperature, neutral pH (6.8), damage-free structure of bovine CcO (bCcO) in the carbon monoxide (CO)-bound state at a resolution of 2.3 Å, obtained by serial femtosecond X-ray crystallography (SFX) withmore » an X-ray free electron laser. As a comparison, an equivalent structure was obtained at a resolution of 1.95 Å, from data collected at a synchrotron light source. In the SFX structure, the CO is coordinated to the heme a3 iron atom, with a bent Fe–C–O angle of ~142°. In contrast, in the synchrotron structure, the Fe–CO bond is cleaved; CO relocates to a new site near CuB, which, in turn, moves closer to the heme a3 iron by ~0.38 Å. Structural comparison reveals that ligand binding to the heme a3 iron in the SFX structure is associated with an allosteric structural transition, involving partial unwinding of the helix-X between heme a and a3, thereby establishing a communication linkage between the two heme groups, setting the stage for proton translocation during the ensuing redox chemistry.« less

  16. Space Station

    NASA Image and Video Library

    1977-01-01

    The Marshall Space Flight Center (MSFC) and the Johnson Space Center (JSC) were each awarded 16-month contracts in April 1976 for the Space Station Systems Analysis Study (SSSAS). Grumman Aerospace Corporation was MSFC's contractor and McDornell Douglas Aerospace Company was JSC's contractor. The goal of this study was to formulate plans for a permanent operational base and laboratory facility in Earth orbit in addition to developing a space construction base design for implementing the program. An expended Space Shuttle external tank was to be the central core platform of the base, and additional pressurized modules could be added to provide laboratory facilities. This artist's concept depicts a space construction base design for implementing the SSSAS.

  17. Spallation neutron source target station issues

    SciTech Connect

    Gabriel, T.A.; Barnes, J.N.; Charlton, L.A.

    1996-10-01

    In many areas of physics, materials and nuclear engineering, it is extremely valuable to have a very intense source of neutrons so that the structure and function of materials can be studied. One facility proposed for this purpose is the National Spallation Neutron Source (NSNS). This facility will consist of two parts: (1) a high-energy ({approximately}1 GeV) and high powered ({approximately} 1 MW) proton accelerator, and (2) a target station which converts the protons to low-energy ({le} 2 eV) neutrons and delivers them to the neutron scattering instruments. This paper deals with the second part, i.e., the design and development of the NSNS target station and the scientifically challenging issues. Many scientific and technical disciplines are required to produce a successful target station. These include engineering, remote handling, neutronics, materials, thermal hydraulics, and instrumentation. Some of these areas will be discussed.

  18. Molecular mechanism of vectorial proton translocation by bacteriorhodopsin

    NASA Astrophysics Data System (ADS)

    Subramaniam, Sriram; Henderson, Richard

    2000-08-01

    Bacteriorhodopsin, a membrane protein with a relative molecular mass of 27,000, is a light driven pump which transports protons across the cell membrane of the halophilic organism Halobacterium salinarum. The chromophore retinal is covalently attached to the protein via a protonated Schiff base. Upon illumination, retinal is isomerized. The Schiff base then releases a proton to the extracellular medium, and is subsequently reprotonated from the cytoplasm. An atomic model for bacteriorhodopsin was first determined by Henderson et al, and has been confirmed and extended by work in a number of laboratories in the last few years. Here we present an atomic model for structural changes involved in the vectorial, light-driven transport of protons by bacteriorhodopsin. A `switch' mechanism ensures the vectorial nature of pumping. First, retinal unbends, triggered by loss of the Schiff base proton, and second, a protein conformational change occurs. This conformational change, which we have determined by electron crystallography at atomic (3.2 Å in-plane and 3.6 Å vertical) resolution, is largely localized to helices F and G, and provides an `opening' of the protein to protons on the cytoplasmic side of the membrane.

  19. Proton radiography to improve proton therapy treatment

    NASA Astrophysics Data System (ADS)

    Takatsu, J.; van der Graaf, E. R.; Van Goethem, M.-J.; van Beuzekom, M.; Klaver, T.; Visser, J.; Brandenburg, S.; Biegun, A. K.

    2016-01-01

    The quality of cancer treatment with protons critically depends on an accurate prediction of the proton stopping powers for the tissues traversed by the protons. Today, treatment planning in proton radiotherapy is based on stopping power calculations from densities of X-ray Computed Tomography (CT) images. This causes systematic uncertainties in the calculated proton range in a patient of typically 3-4%, but can become even 10% in bone regions [1,2,3,4,5,6,7,8]. This may lead to no dose in parts of the tumor and too high dose in healthy tissues [1]. A direct measurement of proton stopping powers with high-energy protons will allow reducing these uncertainties and will improve the quality of the treatment. Several studies have shown that a sufficiently accurate radiograph can be obtained by tracking individual protons traversing a phantom (patient) [4,6,10]. Our studies benefit from the gas-filled time projection chambers based on GridPix technology [2], developed at Nikhef, capable of tracking a single proton. A BaF2 crystal measuring the residual energy of protons was used. Proton radiographs of phantom consisting of different tissue-like materials were measured with a 30×30 mm2 150 MeV proton beam. Measurements were simulated with the Geant4 toolkit.First experimental and simulated energy radiographs are in very good agreement [3]. In this paper we focus on simulation studies of the proton scattering angle as it affects the position resolution of the proton energy loss radiograph. By selecting protons with a small scattering angle, the image quality can be improved significantly.

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

    PubMed

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

    2012-05-01

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

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

    PubMed Central

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

    2012-01-01

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

  2. Fixed target matrix for femtosecond time-resolved and in situ serial micro-crystallography

    PubMed Central

    Mueller, C.; Marx, A.; Epp, S. W.; Zhong, Y.; Kuo, A.; Balo, A. R.; Soman, J.; Schotte, F.; Lemke, H. T.; Owen, R. L.; Pai, E. F.; Pearson, A. R.; Olson, J. S.; Anfinrud, P. A.; Ernst, O. P.; Dwayne Miller, R. J.

    2015-01-01

    We present a crystallography chip enabling in situ room temperature crystallography at microfocus synchrotron beamlines and X-ray free-electron laser (X-FEL) sources. Compared to other in situ approaches, we observe extremely low background and high diffraction data quality. The chip design is robust and allows fast and efficient loading of thousands of small crystals. The ability to load a large number of protein crystals, at room temperature and with high efficiency, into prescribed positions enables high throughput automated serial crystallography with microfocus synchrotron beamlines. In addition, we demonstrate the application of this chip for femtosecond time-resolved serial crystallography at the Linac Coherent Light Source (LCLS, Menlo Park, California, USA). The chip concept enables multiple images to be acquired from each crystal, allowing differential detection of changes in diffraction intensities in order to obtain high signal-to-noise and fully exploit the time resolution capabilities of XFELs. PMID:26798825

  3. Macromolecular crystallography with a large format CMOS detector

    SciTech Connect

    Nix, Jay C.

    2016-07-27

    Recent advances in CMOS technology have allowed the production of large surface area detectors suitable for macromolecular crystallography experiments [1]. The Molecular Biology Consortium (MBC) Beamline 4.2.2 at the Advanced Light Source in Berkeley, CA, has installed a 2952 x 2820 mm RDI CMOS-8M detector with funds from NIH grant S10OD012073. The detector has a 20nsec dead pixel time and performs well with shutterless data collection strategies. The sensor obtains sharp point response and minimal optical distortion by use of a thin fiber-optic plate between the phosphor and sensor module. Shutterless data collections produce high-quality redundant datasets that can be obtained in minutes. The fine-sliced data are suitable for processing in standard crystallographic software packages (XDS, HKL2000, D*TREK, MOSFLM). Faster collection times relative to the previous CCD detector have resulted in a record number of datasets collected in a calendar year and de novo phasing experiments have resulted in publications in both Science and Nature [2,3]. The faster collections are due to a combination of the decreased overhead requirements of shutterless collections combined with exposure times that have decreased by over a factor of 2 for images with comparable signal to noise of the NOIR-1 detector. The overall increased productivity has allowed the development of new beamline capabilities and data collection strategies.

  4. The collection of MicroED data for macromolecular crystallography

    PubMed Central

    Shi, Dan; Nannenga, Brent L; de la Cruz, M Jason; Liu, Jinyang; Sawtelle, Steven; Calero, Guillermo; Reyes, Francis E; Hattne, Johan; Gonen, Tamir

    2017-01-01

    The formation of large, well-ordered crystals for crystallographic experiments remains a crucial bottleneck to the structural understanding of many important biological systems. To help alleviate this problem in crystallography, we have developed the MicroED method for the collection of electron diffraction data from 3D microcrystals and nanocrystals of radiation-sensitive biological material. In this approach, liquid solutions containing protein microcrystals are deposited on carbon-coated electron microscopy grids and are vitrified by plunging them into liquid ethane. MicroED data are collected for each selected crystal using cryo-electron microscopy, in which the crystal is diffracted using very few electrons as the stage is continuously rotated. This protocol gives advice on how to identify microcrystals by light microscopy or by negative-stain electron microscopy in samples obtained from standard protein crystallization experiments. The protocol also includes information about custom-designed equipment for controlling crystal rotation and software for recording experimental parameters in diffraction image metadata. Identifying microcrystals, preparing samples and setting up the microscope for diffraction data collection take approximately half an hour for each step. Screening microcrystals for quality diffraction takes roughly an hour, and the collection of a single data set is ~10 min in duration. Complete data sets and resulting high-resolution structures can be obtained from a single crystal or by merging data from multiple crystals. PMID:27077331

  5. Holographic LEED: A direct method for surface crystallography

    NASA Astrophysics Data System (ADS)

    Vamvakas, John Athanasios

    Since 1960's Low Energy Electron Diffraction (LEED) has been one of the most reliable methods for surface crystallography. It has solved hundreds of structures over the past 20-25 years and continues to be a powerful tool in the hands of crystallographers. Yet, the main disadvantage of the method is the fact that it is very time consuming. The programs that do the multiple scattering calculations can run literally for days! The key part of the method is the initial "guess" of a structure that will be close the one being seeked. A wrong guess would lead to huge amounts of wasted time and effort. We suggest a direct method that can give us a pretty good idea of the structure under determination. We call this method of ours: Holographic LEED (h-LEED) because it is based on the ideas of Dennis Gabor, the inventor of holography. The 3D images h-LEED reconstructs from LEED diffraction patterns can be reliably used to initialize LEED thus reducing the annoying computation time as well as the effort required by the crystallographer. We show that h-LEED produces good images for p(2× 2) reconstruction of adsorbed atoms by testing it on two adsorption systems: O/Ni(001) and K/Ni(001). The images were reconstructed from both diffuse LEED patterns from disordered adsorbates and superstructure Bragg spots from ordered adsorbates.

  6. Macromolecular Crystallography and Structural Biology Databases at NIST.

    PubMed

    Gilliland, G L

    2001-01-01

    In the late 1970s, macromolecular crystallography at NIST began with collaboration between NIST and NIH to establish a single-crystal neutron diffractometer. This instrument was constructed and employed to solve a number of crystal structures: bovine ribonuclease A, bovine-ribonuclease-uridine vanadate complex, and porcine insulin. In the mid 1980s a Biomolecular Structure Group was created establishing NIST capabilities in biomolecular singe-crystal x-ray diffraction. The group worked on a variety of structural problems until joining the NIST/UMBI Center for Advanced Research in Biotechnology (CARB) in 1987. Crystallographic studies at CARB were then focused on protein engineering efforts that included among others chymosin, subtilisin BPN', interleukin 1β, and glutathione S-transferase. Recently, the structural biology efforts have centered on enzymes in the chorismate metabolic pathways involved in amino acid biosynthesis and in structural genomics that involves determining the structures of "hypothetical" proteins to aid in assigning function. In addition to crystallographic studies, structural biology database activities began with the formal establishment of the Biological Macro-molecule Crystallization Database in 1989. Later, in 1997, NIST in partnership with Rutgers and UCSD formed the Research Collaboratory for Structural Bioinformatics that successfully acquired the Protein Data Bank. The NIST efforts in these activities have focused on data uniformity, establishing and maintaining the physical archive, and working with the NMR community.

  7. Translation calibration of inverse-kappa goniometers in macromolecular crystallography.

    PubMed

    Brockhauser, Sandor; White, Kristopher I; McCarthy, Andrew A; Ravelli, Raimond B G

    2011-05-01

    Precise and convenient crystal reorientation is of experimental importance in macromolecular crystallography (MX). The development of multi-axis goniometers, such as the ESRF/EMBL mini-κ, necessitates the corresponding development of calibration procedures that can be used for the setup, maintenance and troubleshooting of such devices. While traditional multi-axis goniometers require all rotation axes to intersect the unique point of the sample position, recently developed miniaturized instruments for sample reorientation in MX are not as restricted. However, the samples must always be re-centred following a change in orientation. To overcome this inconvenience and allow the use of multi-axis goniometers without the fundamental restriction of having all axes intersecting in the same point, an automatic translation correction protocol has been developed for such instruments. It requires precise information about the direction and location of the rotation axes. To measure and supply this information, a general, easy-to-perform translation calibration (TC) procedure has also been developed. The TC procedure is routinely performed on most MX beamlines at the ESRF and some results are presented for reference.

  8. Structure of the Angiotensin Receptor Revealed by Serial Femtosecond Crystallography

    SciTech Connect

    Zhang, Haitao; Unal, Hamiyet; Gati, Cornelius; Han, Gye Won; Liu, Wei; Zatsepin, Nadia A.; James, Daniel; Wang, Dingjie; Nelson, Garrett; Weierstall, Uwe; Sawaya, Michael R.; Xu, Qingping; Messerschmidt, Marc; Williams, Garth J.; Boutet, Sébastien; Yefanov, Oleksandr M.; White, Thomas A.; Wang, Chong; Ishchenko, Andrii; Tirupula, Kalyan C.; Desnoyer, Russell; Coe, Jesse; Conrad, Chelsie E.; Fromme, Petra; Stevens, Raymond C.; Katritch, Vsevolod; Karnik, Sadashiva S.; Cherezov, Vadim

    2015-05-07

    We report that angiotensin II type 1 receptor (AT1R) is a G protein-coupled receptor that serves as a primary regulator for blood pressure maintenance. Although several anti-hypertensive drugs have been developed as AT1R blockers (ARBs), the structural basis for AT1R ligand-binding and regulation has remained elusive, mostly due to the difficulties of growing high quality crystals for structure determination using synchrotron radiation. By applying the recently developed method of serial femtosecond crystallography at an X-ray free-electron laser, we successfully determined the room-temperature crystal structure of the human AT1R in complex with its selective antagonist ZD7155 at 2.9 Å resolution. The AT1R-ZD7155 complex structure revealed key structural features ofAT1R and critical interactions for ZD7155 binding. Finally, docking simulations of the clinically used ARBs into the AT1R structure further elucidated both the common and distinct binding modes for these anti-hypertensive drugs. Our results thereby provide fundamental insights into AT1R structure-function relationship and structure-based drug design.

  9. Acoustic Injectors for Drop-On-Demand Serial Femtosecond Crystallography

    SciTech Connect

    Roessler, Christian G.; Agarwal, Rakhi; Allaire, Marc; Alonso-Mori, Roberto; Andi, Babak; Bachega, José F. R.; Bommer, Martin; Brewster, Aaron S.; Browne, Michael C.; Chatterjee, Ruchira; Cho, Eunsun; Cohen, Aina E.; Cowan, Matthew; Datwani, Sammy; Davidson, Victor L.; Defever, Jim; Eaton, Brent; Ellson, Richard; Feng, Yiping; Ghislain, Lucien P.; Glownia, James M.; Han, Guangye; Hattne, Johan; Hellmich, Julia; Héroux, Annie; Ibrahim, Mohamed; Kern, Jan; Kuczewski, Anthony; Lemke, Henrik T.; Liu, Pinghua; Majlof, Lars; McClintock, William M.; Myers, Stuart; Nelsen, Silke; Olechno, Joe; Orville, Allen M.; Sauter, Nicholas K.; Soares, Alexei S.; Soltis, S.  Michael; Song, Heng; Stearns, Richard G.; Tran, Rosalie; Tsai, Yingssu; Uervirojnangkoorn, Monarin; Wilmot, Carrie M.; Yachandra, Vittal; Yano, Junko; Yukl, Erik T.; Zhu, Diling; Zouni, Athina

    2016-04-01

    X-ray free-electron lasers (XFELs) provide very intense X-ray pulses suitable for macromolecular crystallography. Each X-ray pulse typically lasts for tens of femtoseconds and the interval between pulses is many orders of magnitude longer. Here we describe two novel acoustic injection systems that use focused sound waves to eject picoliter to nanoliter crystal-containing droplets out of microplates and into the X-ray pulse from which diffraction data are collected. The on-demand droplet delivery is synchronized to the XFEL pulse scheme, resulting in X-ray pulses intersecting up to 88% of the droplets. We tested several types of samples in a range of crystallization conditions, wherein the overall crystal hit ratio (e.g., fraction of images with observable diffraction patterns) is a function of the microcrystal slurry concentration. We report crystal structures from lysozyme, thermolysin, and stachydrine demethylase (Stc2). Additional samples were screened to demonstrate that these methods can be applied to rare samples.

  10. Structure Determination Algorithms in Computational X-Ray Crystallography.

    NASA Astrophysics Data System (ADS)

    Chang, Chun-Shi

    This dissertation focuses on the development and implementation of practical algorithms for solving the phase problem of X-ray crystallography. We based our strategies on the Shake-and-Bake method of structure determination which alternates phase refinement in reciprocal space with density modification in real space. The strategies we consider include variants of Shake-and-Bake which incorporate optimization techniques based on parameter shift, genetic algorithms, tangent formula, and one based on special properties of space group P1. These four approaches have been implemented on a variety of parallel and sequential machines, including a Thinking Machine Corporation CM-5, an Intel iPSC/860, and a network of SGI Indigo workstations. Experimental results show that the tangent formula approach is the most cost-effective means for solving structures of small size, while the parameter shift variant is better for medium -size or larger structures. The P1 approach appears to be promising for structures in certain space groups. We show that the tangent formula approach can be successfully applied to the CRAMBIN structure, which contains approximately 400 atoms in the asymmetric unit cell. This represents the first successful application of a tangent formula-based approach to solve the CRAMBIN structure.

  11. Present status of SPring-8 macromolecular crystallography beamlines

    SciTech Connect

    Kawano, Yoshiaki; Hirata, Kunio; Ueno, Go; Hikima, Takaaki; Murakami, Hironori; Maeda, Daisuke; Nisawa, Atsushi; Yamamoto, Masaki; Shimizu, Nobutaka; Baba, Seiki; Hasegawa, Kazuya; Makino, Masatomo; Mizuno, Nobuhiro; Hoshino, Takeshi; Ito, Ren; Wada, Izumi; Kumasaka, Takashi

    2010-06-23

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

  12. Choice and maintenance of equipment for electron crystallography.

    PubMed

    Mills, Deryck J; Vonck, Janet

    2013-01-01

    The choice of equipment for an electron crystallography laboratory will ultimately be determined by the available budget; nevertheless, the ideal lab will have two electron microscopes: a dedicated 300 kV cryo-EM with a field emission gun and a smaller LaB(6) machine for screening. The high-end machine should be equipped with photographic film or a very large CCD or CMOS camera for 2D crystal data collection; the screening microscope needs a mid-size CCD for rapid evaluation of crystal samples. The microscope room installations should provide adequate space and a special environment that puts no restrictions on the collection of high-resolution data. Equipment for specimen preparation includes a carbon coater, glow discharge unit, light microscope, plunge freezer, and liquid nitrogen containers and storage dewars. When photographic film is to be used, additional requirements are a film desiccator, dark room, optical diffractometer, and a film scanner. Having the electron microscopes and ancillary equipment well maintained and always in optimum condition facilitates the production of high-quality data.

  13. Macromolecular Crystallography and Structural Biology Databases at NIST

    PubMed Central

    Gilliland, Gary L.

    2001-01-01

    In the late 1970s, macromolecular crystallography at NIST began with collaboration between NIST and NIH to establish a single-crystal neutron diffractometer. This instrument was constructed and employed to solve a number of crystal structures: bovine ribonuclease A, bovine-ribonuclease-uridine vanadate complex, and porcine insulin. In the mid 1980s a Biomolecular Structure Group was created establishing NIST capabilities in biomolecular singe-crystal x-ray diffraction. The group worked on a variety of structural problems until joining the NIST/UMBI Center for Advanced Research in Biotechnology (CARB) in 1987. Crystallographic studies at CARB were then focused on protein engineering efforts that included among others chymosin, subtilisin BPN', interleukin 1β, and glutathione S-transferase. Recently, the structural biology efforts have centered on enzymes in the chorismate metabolic pathways involved in amino acid biosynthesis and in structural genomics that involves determining the structures of “hypothetical” proteins to aid in assigning function. In addition to crystallographic studies, structural biology database activities began with the formal establishment of the Biological Macro-molecule Crystallization Database in 1989. Later, in 1997, NIST in partnership with Rutgers and UCSD formed the Research Collaboratory for Structural Bioinformatics that successfully acquired the Protein Data Bank. The NIST efforts in these activities have focused on data uniformity, establishing and maintaining the physical archive, and working with the NMR community. PMID:27500071

  14. Serial femtosecond crystallography of soluble proteins in lipidic cubic phase

    SciTech Connect

    Fromme, Raimund; Ishchenko, Andrii; Metz, Markus; Chowdhury, Shatabdi Roy; Basu, Shibom; Boutet, Sébastien; Fromme, Petra; White, Thomas A.; Barty, Anton; Spence, John C. H.; Weierstall, Uwe; Liu, Wei; Cherezov, Vadim

    2015-08-04

    Serial femtosecond crystallography (SFX) at X-ray free-electron lasers (XFELs) enables high-resolution protein structure determination using micrometre-sized crystals at room temperature with minimal effects from radiation damage. SFX requires a steady supply of microcrystals intersecting the XFEL beam at random orientations. An LCP–SFX method has recently been introduced in which microcrystals of membrane proteins are grown and delivered for SFX data collection inside a gel-like membrane-mimetic matrix, known as lipidic cubic phase (LCP), using a special LCP microextrusion injector. Here, it is demonstrated that LCP can also be used as a suitable carrier medium for microcrystals of soluble proteins, enabling a dramatic reduction in the amount of crystallized protein required for data collection compared with crystals delivered by liquid injectors. High-quality LCP–SFX data sets were collected for two soluble proteins, lysozyme and phycocyanin, using less than 0.1 mg of each protein.

  15. Present status of SPring-8 macromolecular crystallography beamlines

    NASA Astrophysics Data System (ADS)

    Kawano, Yoshiaki; Shimizu, Nobutaka; Baba, Seiki; Hasegawa, Kazuya; Makino, Masatomo; Mizuno, Nobuhiro; Hoshino, Takeshi; Ito, Ren; Wada, Izumi; Hirata, Kunio; Ueno, Go; Hikima, Takaaki; Murakami, Hironori; Maeda, Daisuke; Nisawa, Atsushi; Kumasaka, Takashi; Yamamoto, Masaki

    2010-06-01

    Seven beamlines are operated for macromolecular crystallography (MX) at SPring-8. The three undulator beamlines are developed for cutting edge target and four bending-magnet beamlines are developed for high throughput MX. The undulator beamline, BL41XU that provides the most brilliant beam, is dedicated to obtain high quality data even from small-size and weakly-diffracting crystals. The minimum beam size at sample position is achieved to 10 μm diameter using a pin-hole collimator. Its photon flux at wavelength λ = 1.0 Å is 2.8×1011 photons/sec. This small beam coupled with irradiation point scanning method is quite useful to take diffraction dataset from small crystals by suppressing the radiation damage. These advanced technologies made a number of difficult protein structure analysis possible, (i.e. Sodium-potassium ATPase). The bending-magnet beamlines BL26B1/B2 and BL38B1 provide automatic data collection exploiting the high mobility of the beam. The beamline operation software "BSS," sample auto-changer "SPACE" and web-based data management software "D-Cha" have made the automatic data collection possible. The "Mail-in data collection system" that accepts distant users samples via courier service have made users possible to collect diffraction data without visiting SPring-8. The structural genomics research is promoted by these beamlines.

  16. Identification of rogue datasets in serial crystallography1

    PubMed Central

    Assmann, Greta; Brehm, Wolfgang; Diederichs, Kay

    2016-01-01

    Advances in beamline optics, detectors and X-ray sources allow new techniques of crystallographic data collection. In serial crystallography, a large number of partial datasets from crystals of small volume are measured. Merging of datasets from different crystals in order to enhance data completeness and accuracy is only valid if the crystals are isomorphous, i.e. sufficiently similar in cell parameters, unit-cell contents and molecular structure. Identification and exclusion of non-isomorphous datasets is therefore indispensable and must be done by means of suitable indicators. To identify rogue datasets, the influence of each dataset on CC1/2 [Karplus & Diederichs (2012 ▸). Science, 336, 1030–1033], the correlation coefficient between pairs of intensities averaged in two randomly assigned subsets of observations, is evaluated. The presented method employs a precise calculation of CC1/2 that avoids the random assignment, and instead of using an overall CC1/2, an average over resolution shells is employed to obtain sensible results. The selection procedure was verified by measuring the correlation of observed (merged) intensities and intensities calculated from a model. It is found that inclusion and merging of non-isomorphous datasets may bias the refined model towards those datasets, and measures to reduce this effect are suggested. PMID:27275144

  17. Structure of the Angiotensin Receptor Revealed by Serial Femtosecond Crystallography

    DOE PAGES

    Zhang, Haitao; Unal, Hamiyet; Gati, Cornelius; ...

    2015-05-07

    We report that angiotensin II type 1 receptor (AT1R) is a G protein-coupled receptor that serves as a primary regulator for blood pressure maintenance. Although several anti-hypertensive drugs have been developed as AT1R blockers (ARBs), the structural basis for AT1R ligand-binding and regulation has remained elusive, mostly due to the difficulties of growing high quality crystals for structure determination using synchrotron radiation. By applying the recently developed method of serial femtosecond crystallography at an X-ray free-electron laser, we successfully determined the room-temperature crystal structure of the human AT1R in complex with its selective antagonist ZD7155 at 2.9 Å resolution. Themore » AT1R-ZD7155 complex structure revealed key structural features ofAT1R and critical interactions for ZD7155 binding. Finally, docking simulations of the clinically used ARBs into the AT1R structure further elucidated both the common and distinct binding modes for these anti-hypertensive drugs. Our results thereby provide fundamental insights into AT1R structure-function relationship and structure-based drug design.« less

  18. Protein energy landscapes determined by five-dimensional crystallography

    PubMed Central

    Schmidt, Marius; Srajer, Vukica; Henning, Robert; Ihee, Hyotcherl; Purwar, Namrta; Tenboer, Jason; Tripathi, Shailesh

    2013-01-01

    Free-energy landscapes decisively determine the progress of enzymatically catalyzed reactions [Cornish-Bowden (2012 ▶), Fundamentals of Enzyme Kinetics, 4th ed.]. Time-resolved macromolecular crystallography unifies transient-state kinetics with structure determination [Moffat (2001 ▶), Chem. Rev. 101, 1569–1581; Schmidt et al. (2005 ▶), Methods Mol. Biol. 305, 115–154; Schmidt (2008 ▶), Ultrashort Laser Pulses in Medicine and Biology] because both can be determined from the same set of X-ray data. Here, it is demonstrated how barriers of activation can be determined solely from five-dimensional crystallo­graphy, where in addition to space and time, temperature is a variable as well [Schmidt et al. (2010 ▶), Acta Cryst. A66, 198–206]. Directly linking molecular structures with barriers of activation between them allows insight into the structural nature of the barrier to be gained. Comprehensive time series of crystallo­graphic data at 14 different temperature settings were analyzed and the entropy and enthalpy contributions to the barriers of activation were determined. One hundred years after the discovery of X-ray scattering, these results advance X-ray structure determination to a new frontier: the determination of energy landscapes. PMID:24311594

  19. Femtosecond crystallography of membrane proteins in the lipidic cubic phase

    PubMed Central

    Liu, Wei; Wacker, Daniel; Wang, Chong; Abola, Enrique; Cherezov, Vadim

    2014-01-01

    Despite recent technological advances in heterologous expression, stabilization and crystallization of membrane proteins (MPs), their structural studies remain difficult and require new transformative approaches. During the past two years, crystallization in lipidic cubic phase (LCP) has started gaining a widespread acceptance, owing to the spectacular success in high-resolution structure determination of G protein-coupled receptors (GPCRs) and to the introduction of commercial instrumentation, tools and protocols. The recent appearance of X-ray free-electron lasers (XFELs) has enabled structure determination from substantially smaller crystals than previously possible with minimal effects of radiation damage, offering new exciting opportunities in structural biology. The unique properties of LCP material have been exploited to develop special protocols and devices that have established a new method of serial femtosecond crystallography of MPs in LCP (LCP-SFX). In this method, microcrystals are generated in LCP and streamed continuously inside the same media across the intersection with a pulsed XFEL beam at a flow rate that can be adjusted to minimize sample consumption. Pioneering studies that yielded the first room temperature GPCR structures, using a few hundred micrograms of purified protein, validate the LCP-SFX approach and make it attractive for structure determination of difficult-to-crystallize MPs and their complexes with interacting partners. Together with the potential of femtosecond data acquisition to interrogate unstable intermediate functional states of MPs, LCP-SFX holds promise to advance our understanding of this biomedically important class of proteins. PMID:24914147

  20. The collection of MicroED data for macromolecular crystallography.

    PubMed

    Shi, Dan; Nannenga, Brent L; de la Cruz, M Jason; Liu, Jinyang; Sawtelle, Steven; Calero, Guillermo; Reyes, Francis E; Hattne, Johan; Gonen, Tamir

    2016-05-01

    The formation of large, well-ordered crystals for crystallographic experiments remains a crucial bottleneck to the structural understanding of many important biological systems. To help alleviate this problem in crystallography, we have developed the MicroED method for the collection of electron diffraction data from 3D microcrystals and nanocrystals of radiation-sensitive biological material. In this approach, liquid solutions containing protein microcrystals are deposited on carbon-coated electron microscopy grids and are vitrified by plunging them into liquid ethane. MicroED data are collected for each selected crystal using cryo-electron microscopy, in which the crystal is diffracted using very few electrons as the stage is continuously rotated. This protocol gives advice on how to identify microcrystals by light microscopy or by negative-stain electron microscopy in samples obtained from standard protein crystallization experiments. The protocol also includes information about custom-designed equipment for controlling crystal rotation and software for recording experimental parameters in diffraction image metadata. Identifying microcrystals, preparing samples and setting up the microscope for diffraction data collection take approximately half an hour for each step. Screening microcrystals for quality diffraction takes roughly an hour, and the collection of a single data set is ∼10 min in duration. Complete data sets and resulting high-resolution structures can be obtained from a single crystal or by merging data from multiple crystals.

  1. Serial femtosecond crystallography of soluble proteins in lipidic cubic phase

    PubMed Central

    Fromme, Raimund; Ishchenko, Andrii; Metz, Markus; Chowdhury, Shatabdi Roy; Basu, Shibom; Boutet, Sébastien; Fromme, Petra; White, Thomas A.; Barty, Anton; Spence, John C. H.; Weierstall, Uwe; Liu, Wei; Cherezov, Vadim

    2015-01-01

    Serial femtosecond crystallography (SFX) at X-ray free-electron lasers (XFELs) enables high-resolution protein structure determination using micrometre-sized crystals at room temperature with minimal effects from radiation damage. SFX requires a steady supply of microcrystals intersecting the XFEL beam at random orientations. An LCP–SFX method has recently been introduced in which microcrystals of membrane proteins are grown and delivered for SFX data collection inside a gel-like membrane-mimetic matrix, known as lipidic cubic phase (LCP), using a special LCP microextrusion injector. Here, it is demonstrated that LCP can also be used as a suitable carrier medium for microcrystals of soluble proteins, enabling a dramatic reduction in the amount of crystallized protein required for data collection compared with crystals delivered by liquid injectors. High-quality LCP–SFX data sets were collected for two soluble proteins, lysozyme and phycocyanin, using less than 0.1 mg of each protein. PMID:26306196

  2. Grain-boundary plane crystallography and energy in austenitic steel

    SciTech Connect

    Caul, M.; Randle, V.; Fiedler, J.

    1996-10-01

    The presence of grain boundaries in polycrystalline materials affects the materials properties and performance. Recently it has been realized that boundaries can be manipulated to give better properties, and the design and control of grain boundaries is now an area of strong research interest in the search for high performance engineering materials. Grain boundaries can be classified using the Coincident Site Lattice Model (CSL), which defines the periodicity, i.e., the degree of fit between the two lattices which constitute the boundary. Using this model it is possible to divide boundaries into categories: low angle (up to 15{degree} misorientation), CSL and random i.e., high angle non-CSL. Some CSL boundaries have been shown to have special properties: an example from recent research in the same program as that currently reported has shown that twin boundaries ({Sigma} = 3 in CSL notation) in High Nitrogen Austenitic Stainless Steels do not favor the formation of Cr{sub 2}N precipitates. The research presented here examines grain boundary inclinations of surface grains in austenitic steel specimens which have been isothermally aged at higher 700 C or 800 C. Grain boundary plane crystallography has also been obtained for the 800 C aged sample.

  3. Serial Femtosecond Crystallography Opens New Avenues for Structural Biology

    PubMed Central

    Coe, Jesse; Fromme, Petra

    2016-01-01

    Free electron lasers (FELs) provide X-ray pulses in the femtosecond time domain with up to 1012 higher photon flux than synchrotrons and open new avenues for the determination of difficult to crystallize proteins, like large complexes and human membrane proteins. While the X-ray pulses are so strong that they destroy any solid material, the crystals diffract before they are destroyed. The most successful application of FELs for biology has been the method of serial femtosecond crystallography (SFX) where nano or microcrystals are delivered to the FEL beam in a stream of their mother liquid at room temperature, which ensures the replenishment of the sample before the next X-ray pulse arrives. New injector technology allows also for the delivery of crystal in lipidic cubic phases or agarose, which reduces the sample amounts for an SFX data set by two orders of magnitude. Time-resolved SFX also allows for analysis of the dynamics of biomolecules, the proof of principle being recently shown for light-induced reactions in photosystem II and photoactive yellow protein. An SFX data sets consist of thousands of single crystal snapshots in random orientations, which can be analyzed now “on the fly” by data analysis programs specifically developed for SFX, but de-novo phasing is still a challenge, that might be overcome by two-color experiments or phasing by shape transforms. PMID:26786767

  4. Outrunning free radicals in room-temperature macromolecular crystallography

    SciTech Connect

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

    2012-06-15

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

  5. Microbeam MAD Beamline for Challenging Protein Crystallography in TPS

    NASA Astrophysics Data System (ADS)

    Liu, D. G.; Chao, C. H.; Chang, C. H.; Juang, J. M.; Liu, C. Y.; Chang, S. H.; Chang, C. F.; Chou, C. K.; Tseng, C. C.; Chiang, C. H.; Jean, Y. C.; Tang, M. T.; Chung, S. C.; Chang, S. L.

    2013-03-01

    The TPS-05A beamline is the first X-ray beamline at NSRRC built for micro protein crystallography experiment as well as one of the seven ID beamlines in phase I at the TPS synchrotron facility. A 2-meter in-vacuum undulator (IU22) serves as the photon source from which the harmonics #3 to #9 will provide brilliance of 1018-1020 photons s-1 mrad-2 mm-2 (0.1% bandwidth)-1 and photon flux of 1013-1014 photons s-1 (0.1% bandwidth)-1 in the required energy range of 5.7-20 keV (2.175-0.620 Å) to cover MAD phasing experiments at 1 Å and SAD phasing experiments at 2 Å. The beamline optics consists of a cryo-cooled double crystal monochromator (DCM) and a pair of focusing K-B mirrors. Requirements from the user group include a target focus size of 50 μm × 50 μm (H × V) at the sample position, photon flux greater than 2 × 1012 photons s-1 at Se K-edge (0.9795 Å), pinholes for adjusting the beam size down to 5 μm. Calculation of heat load for the first optical element, i.e. the first crystal of DCM, is included in this paper.

  6. Proton decay theory

    SciTech Connect

    Marciano, W.J.

    1983-01-01

    Topics include minimal SU(5) predictions, gauge boson mediated proton decay, uncertainties in tau/sub p/, Higgs scalar effects, proton decay via Higgs scalars, supersymmetric SU(5), dimension 5 operators and proton decay, and Higgs scalars and proton decay. (WHK)

  7. SNS Proton Beam Window Disposal

    NASA Astrophysics Data System (ADS)

    Popova, Irina; Gallmeier, Franz X.; Trotter, Steven

    2017-09-01

    In order to support the disposal of the proton beam window assembly of the Spallation Neutron Source beamline to the target station, waste classification analyses are performed. The window has a limited life-time due to radiation-induced material damage. Analyses include calculation of the radionuclide inventory and shielding analyses for the transport package/container to ensure that the container is compliant with the transportation and waste management regulations. In order to automate this procedure and minimize manual work a script in Perl language was written.

  8. Synchrotron based proton drivers

    SciTech Connect

    Weiren Chou

    2002-09-19

    Proton drivers are the proton sources that produce intense short proton bunches. They have a wide range of applications. This paper discusses the proton drivers based on high-intensity proton synchrotrons. It gives a review of the high-intensity proton sources over the world and a brief report on recent developments in this field in the U.S. high-energy physics (HEP) community. The Fermilab Proton Driver is used as a case study for a number of challenging technical design issues.

  9. Hydrogen bonding in proton-transfer complexes of cytosine with trimesic and pyromellitic acids

    NASA Astrophysics Data System (ADS)

    Thomas, Reji; Kulkarni, G. U.

    2008-02-01

    Protons-transfer complexes (1:1) of cytosine with trimesic and pyromellitic acids have been crystallized and single crystal structures have been solved by X-ray crystallography. Both cocrystals exhibit layered structures, each layer containing a plethora of N-H⋯O and O-H⋯O hydrogen bonds between the proton-transfer duplets. The cytosine-trimesic acid complex exhibits a bilayered structure (2.87 Å) in contrast to the commonly observed layered structure seen in the cytosine-pyromellitic acid complex (3.98 Å). Another layered system, an adduct of pyromellitic acid and 1,4-dihydroxy benzene, has also been studied.

  10. Reactive N-protonated isocyanate species stabilized by bis(μ-hydroxo)divanadium(IV)-substituted polyoxometalate.

    PubMed

    Uehara, Kazuhiro; Fukaya, Keisuke; Mizuno, Noritaka

    2012-07-27

    O- or N-protonated? The bis(μ-hydroxo)divanadium(IV)-substituted γ-Keggin-type polyoxometalate (see picture, left) (TBA)(4)[γ-SiV(IV)(2)W(10)O(36)(μ-OH)(4)] (TBA = tetra(n-butyl)ammonium) was synthesized and characterized by X-ray crystallography. Its reaction with phenyl isocyanate gave (TBA)(4)[γ-SiV(IV)(2)W(10)O(38)(μ-OH)(2)(PhNHCO)(2)], which contains two N-protonated phenyl isocyanate species and catalyzes the cyclotrimerization of phenyl isocyanate.

  11. Proton Therapy - Accelerating Protons to Save Lives

    SciTech Connect

    Keppel, Cynthia

    2011-10-25

    In 1946, physicist Robert Wilson first suggested that protons could be used as a form of radiation therapy in the treatment of cancer because of the sharp drop-off that occurs on the distal edge of the radiation dose. Research soon confirmed that high-energy protons were particularly suitable for treating tumors near critical structures, such as the heart and spinal column. The precision with which protons can be delivered means that more radiation can be deposited into the tumor while the surrounding healthy tissue receives substantially less or, in some cases, no radiation. Since these times, particle accelerators have continuously been used in cancer therapy and today new facilities specifically designed for proton therapy are being built in many countries. Proton therapy has been hailed as a revolutionary cancer treatment, with higher cure rates and fewer side effects than traditional X-ray photon radiation therapy. Proton therapy is the modality of choice for treating certain small tumors of the eye, head or neck. Because it exposes less of the tissue surrounding a tumor to the dosage, proton therapy lowers the risk of secondary cancers later in life - especially important for young children. To date, over 80,000 patients worldwide have been treated with protons. Currently, there are nine proton radiation therapy facilities operating in the United States, one at the Hampton University Proton Therapy Institute. An overview of the treatment technology and this new center will be presented.

  12. Aerospace crew station design

    NASA Technical Reports Server (NTRS)

    Carr, Gerald P. (Editor); Montemerlo, Melvin D. (Editor)

    1984-01-01

    Consideration is given to spacecraft cockpits and work stations, commercial aircraft cockpits and crew stations, high performance aircraft cockpits and crew stations, and space stations and habitat crew stations. Particular attention is given to an historical review of NASA manned spacecraft crew stations, ESA spacelab crew stations, the evolution of commercial aircraft flight station design, Boeing 757/767 flight deck, a historical review of Concorde flight deck design, trends in the cockpit design of new European fighters, and state-of-the-art applications for Space Station crew interface design.

  13. Energy Production Demonstrator for Megawatt Proton Beams

    SciTech Connect

    Pronskikh, Vitaly S.; Mokhov, Nikolai V.; Novitski, Igor; Tyutyunnikov, Sergey I.

    2014-07-16

    A preliminary study of the Energy Production Demonstrator (EPD) concept - a solid heavy metal target irradiated by GeV-range intense proton beams and producing more energy than consuming - is carried out. Neutron production, fission, energy deposition, energy gain, testing volume and helium production are simulated with the MARS15 code for tungsten, thorium, and natural uranium targets in the proton energy range 0.5 to 120 GeV. This study shows that the proton energy range of 2 to 4 GeV is optimal for both a natU EPD and the tungsten-based testing station that would be the most suitable for proton accelerator facilities. Conservative estimates, not including breeding and fission of plutonium, based on the simulations suggest that the proton beam current of 1 mA will be sufficient to produce 1 GW of thermal output power with the natU EPD while supplying < 8% of that power to operate the accelerator. The thermal analysis shows that the concept considered has a problem due to a possible core meltdown; however, a number of approaches (a beam rastering, in first place) are suggested to mitigate the issue. The efficiency of the considered EPD as a Materials Test Station (MTS) is also evaluated in this study.

  14. Radiation damage to nucleoprotein complexes in macromolecular crystallography

    DOE PAGES

    Bury, Charles; Garman, Elspeth F.; Ginn, Helen Mary; ...

    2015-01-30

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

  15. Exploring ribozyme conformational changes with X-ray crystallography.

    PubMed

    Spitale, Robert C; Wedekind, Joseph E

    2009-10-01

    Relating three-dimensional fold to function is a central challenge in RNA structural biology. Toward this goal, X-ray crystallography has long been considered the "gold standard" for structure determinations at atomic resolution, although NMR spectroscopy has become a powerhouse in this arena as well. In the area of dynamics, NMR remains the dominant technique to probe the magnitude and timescales of molecular motion. Although the latter area remains largely unassailable by conventional crystallographic methods, inroads have been made on proteins using Laue radiation on timescales of ms to ns. Proposed 'fourth generation' radiation sources, such as free-electron X-ray lasers, promise ps- to fs-timescale resolution, and credible evidence is emerging that supports the feasibility of single molecule imaging. At present however, the preponderance of RNA structural information has been derived from timescale and motion insensitive crystallographic techniques. Importantly, developments in computing, automation and high-flux synchrotron sources have propelled the rapidity of 'conventional' RNA crystal structure determinations to timeframes of hours once a suitable set of phases is obtained. With a sufficient number of crystal structures, it is possible to create a structural ensemble that can provide insight into global and local molecular motion characteristics that are relevant to biological function. Here we describe techniques to explore conformational changes in the hairpin ribozyme, a representative non-protein-coding RNA catalyst. The approaches discussed include: (i) construct choice and design using prior knowledge to improve X-ray diffraction; (ii) recognition of long-range conformational changes and (iii) use of single-base or single-atom changes to create ensembles. The methods are broadly applicable to other RNA systems.

  16. Radiation damage to nucleoprotein complexes in macromolecular crystallography

    PubMed Central

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

    2015-01-01

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

  17. Femtosecond crystallography of membrane proteins in the lipidic cubic phase.

    PubMed

    Liu, Wei; Wacker, Daniel; Wang, Chong; Abola, Enrique; Cherezov, Vadim

    2014-07-17

    Despite recent technological advances in heterologous expression, stabilization and crystallization of membrane proteins (MPs), their structural studies remain difficult and require new transformative approaches. During the past two years, crystallization in lipidic cubic phase (LCP) has started gaining a widespread acceptance, owing to the spectacular success in high-resolution structure determination of G protein-coupled receptors (GPCRs) and to the introduction of commercial instrumentation, tools and protocols. The recent appearance of X-ray free-electron lasers (XFELs) has enabled structure determination from substantially smaller crystals than previously possible with minimal effects of radiation damage, offering new exciting opportunities in structural biology. The unique properties of LCP material have been exploited to develop special protocols and devices that have established a new method of serial femtosecond crystallography of MPs in LCP (LCP-SFX). In this method, microcrystals are generated in LCP and streamed continuously inside the same media across the intersection with a pulsed XFEL beam at a flow rate that can be adjusted to minimize sample consumption. Pioneering studies that yielded the first room temperature GPCR structures, using a few hundred micrograms of purified protein, validate the LCP-SFX approach and make it attractive for structure determination of difficult-to-crystallize MPs and their complexes with interacting partners. Together with the potential of femtosecond data acquisition to interrogate unstable intermediate functional states of MPs, LCP-SFX holds promise to advance our understanding of this biomedically important class of proteins. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

  18. Radiation damage to nucleoprotein complexes in macromolecular crystallography

    SciTech Connect

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

    2015-01-30

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

  19. International Space Station Overview

    NASA Technical Reports Server (NTRS)

    Bates, William V., Jr.

    1999-01-01

    The overview of the International Space Station (ISS) is comprised of the program vision and mission; Space Station uses; definition of program phases; as well as descriptions and status of several scheduled International Space Station Overview assembly flights.

  20. Intelligent Virtual Station (IVS)

    NASA Technical Reports Server (NTRS)

    2002-01-01

    The Intelligent Virtual Station (IVS) is enabling the integration of design, training, and operations capabilities into an intelligent virtual station for the International Space Station (ISS). A viewgraph of the IVS Remote Server is presented.

  1. Space Station Freedom

    NASA Technical Reports Server (NTRS)

    1991-01-01

    In 1982, the Space Station Task Force was formed, signaling the initiation of the Space Station Freedom Program, and eventually resulting in the Marshall Space Flight Center's responsibilities for Space Station Work Package 1.

  2. Intelligent Virtual Station (IVS)

    NASA Technical Reports Server (NTRS)

    2002-01-01

    The Intelligent Virtual Station (IVS) is enabling the integration of design, training, and operations capabilities into an intelligent virtual station for the International Space Station (ISS). A viewgraph of the IVS Remote Server is presented.

  3. A novel salt of antidiabetic drug metformin resulting from a proton transfer reaction: Synthesis, characterization, crystal structure and solution studies

    NASA Astrophysics Data System (ADS)

    Ghasemi, Fatemeh; Ghasemi, Khaled; Rezvani, Ali Reza; Shokrollahi, Ardeshir; Refahi, Masoud; García-Granda, Santiago; Mendoza-Meroño, Rafael

    2017-03-01

    Reaction between N,N-dimethylebiguanidine, Met = Metformin, and 4-hydroxy-2,6-pyridinedicarboxylic acid, HO-dipicH2, results in the formation of a novel proton transfer compound, [MetH2][HO-dipicH]2·H2O, 1. The characterization was performed using FTIR, UV-Vis, 1H and 13C NMR spectroscopy and X-ray crystallography. The crystal system is triclinic with space group P 1 bar and two molecules per unit cell. The protonation constants of O-dipic and Met, in all of probability protonated forms, and the equilibrium constants for the O-dipic-Met proton transfer system were investigated by the potentiometric pH titration method using the Hyperquad2008 program. The stoichiometry of the proton transfer species in solution were in agreement with the solid state result.

  4. Elastic proton-proton scattering at RHIC

    SciTech Connect

    Yip, K.

    2011-09-03

    Here we describe elastic proton+proton (p+p) scattering measurements at RHIC in p+p collisions with a special optics run of {beta}* {approx} 21 m at STAR, at the center-of-mass energy {radical}s = 200 GeV during the last week of the RHIC 2009 run. We present preliminary results of single and double spin asymmetries.

  5. Development of a dose-limiting data collection strategy for serial synchrotron rotation crystallography

    PubMed Central

    Hasegawa, Kazuya; Yamashita, Keitaro; Murai, Tomohiro; Nuemket, Nipawan; Hirata, Kunio; Ueno, Go; Ago, Hideo; Nakatsu, Toru; Kumasaka, Takashi; Yamamoto, Masaki

    2017-01-01

    Serial crystallography, in which single-shot diffraction images are collected, has great potential for protein microcrystallography. Although serial femtosecond crystallography (SFX) has been successfully demonstrated, limited beam time prevents its routine use. Inspired by SFX, serial synchrotron crystallography (SSX) has been investigated at synchrotron macromolecular crystallography beamlines. Unlike SFX, the longer exposure time of milliseconds to seconds commonly used in SSX causes radiation damage. However, in SSX, crystals can be rotated during the exposure, which can achieve efficient coverage of the reciprocal space. In this study, mercury single-wavelength anomalous diffraction (Hg-SAD) phasing of the luciferin regenerating enzyme (LRE) was performed using serial synchrotron rotation crystallography. The advantages of rotation and influence of dose on the data collected were evaluated. The results showed that sample rotation was effective for accurate data collection, and the optimum helical rotation step depended on multiple factors such as multiplicity and partiality of reflections, exposure time per rotation angle and the contribution from background scattering. For the LRE microcrystals, 0.25° was the best rotation step for the achievable resolution limit, whereas a rotation step larger than or equal to 1° was favorable for Hg-SAD phasing. Although an accumulated dose beyond 1.1 MGy caused specific damage at the Hg site, increases in resolution and anomalous signal were observed up to 3.4 MGy because of a higher signal-to-noise ratio. PMID:28009544

  6. Non-contact luminescence lifetime cryothermometry for macromolecular crystallography

    PubMed Central

    Mykhaylyk, V. B.; Kraus, H.

    2017-01-01

    Temperature is a very important parameter when aiming to minimize radiation damage to biological samples during experiments that utilize intense ionizing radiation. A novel technique for remote, non-contact, in situ monitoring of the protein crystal temperature has been developed for the new I23 beamline at the Diamond Light Source, a facility dedicated to macromolecular crystallography (MX) with long-wavelength X-rays. The temperature is derived from the temperature-dependent decay time constant of luminescence from a minuscule scintillation sensor (<0.05 mm3) located in very close proximity to the sample under test. In this work the underlying principle of cryogenic luminescence lifetime thermometry is presented, the features of the detection method and the choice of temperature sensor are discussed, and it is demonstrated how the temperature monitoring system was integrated within the viewing system of the endstation used for the visualization of protein crystals. The thermometry system was characterized using a Bi4Ge3O12 crystal scintillator that exhibits good responsivity of the decay time constant as a function of temperature over a wide range (8–270 K). The scintillation sensor was calibrated and the uncertainty of the temperature measurements over the primary operation temperature range of the beamline (30–150 K) was assessed to be ±1.6 K. It has been shown that the temperature of the sample holder, measured using the luminescence sensor, agrees well with the expected value. The technique was applied to characterize the thermal performance of different sample mounts that have been used in MX experiments at the I23 beamline. The thickness of the mount is shown to have the greatest impact upon the temperature distribution across the sample mount. Altogether, these tests and findings demonstrate the usefulness of the thermometry system in highlighting the challenges that remain to be addressed for the in-vacuum MX experiment to become a reliable

  7. Non-contact luminescence lifetime cryothermometry for macromolecular crystallography.

    PubMed

    Mykhaylyk, V B; Wagner, A; Kraus, H

    2017-05-01

    Temperature is a very important parameter when aiming to minimize radiation damage to biological samples during experiments that utilize intense ionizing radiation. A novel technique for remote, non-contact, in situ monitoring of the protein crystal temperature has been developed for the new I23 beamline at the Diamond Light Source, a facility dedicated to macromolecular crystallography (MX) with long-wavelength X-rays. The temperature is derived from the temperature-dependent decay time constant of luminescence from a minuscule scintillation sensor (<0.05 mm(3)) located in very close proximity to the sample under test. In this work the underlying principle of cryogenic luminescence lifetime thermometry is presented, the features of the detection method and the choice of temperature sensor are discussed, and it is demonstrated how the temperature monitoring system was integrated within the viewing system of the endstation used for the visualization of protein crystals. The thermometry system was characterized using a Bi4Ge3O12 crystal scintillator that exhibits good responsivity of the decay time constant as a function of temperature over a wide range (8-270 K). The scintillation sensor was calibrated and the uncertainty of the temperature measurements over the primary operation temperature range of the beamline (30-150 K) was assessed to be ±1.6 K. It has been shown that the temperature of the sample holder, measured using the luminescence sensor, agrees well with the expected value. The technique was applied to characterize the thermal performance of different sample mounts that have been used in MX experiments at the I23 beamline. The thickness of the mount is shown to have the greatest impact upon the temperature distribution across the sample mount. Altogether, these tests and findings demonstrate the usefulness of the thermometry system in highlighting the challenges that remain to be addressed for the in-vacuum MX experiment to become a reliable and

  8. Towards a compact and precise sample holder for macromolecular crystallography.

    PubMed

    Papp, Gergely; Rossi, Christopher; Janocha, Robert; Sorez, Clement; Lopez-Marrero, Marcos; Astruc, Anthony; McCarthy, Andrew; Belrhali, Hassan; Bowler, Matthew W; Cipriani, Florent

    2017-10-01

    Most of the sample holders currently used in macromolecular crystallography offer limited storage density and poor initial crystal-positioning precision upon mounting on a goniometer. This has now become a limiting factor at high-throughput beamlines, where data collection can be performed in a matter of seconds. Furthermore, this lack of precision limits the potential benefits emerging from automated harvesting systems that could provide crystal-position information which would further enhance alignment at beamlines. This situation provided the motivation for the development of a compact and precise sample holder with corresponding pucks, handling tools and robotic transfer protocols. The development process included four main phases: design, prototype manufacture, testing with a robotic sample changer and validation under real conditions on a beamline. Two sample-holder designs are proposed: NewPin and miniSPINE. They share the same robot gripper and allow the storage of 36 sample holders in uni-puck footprint-style pucks, which represents 252 samples in a dry-shipping dewar commonly used in the field. The pucks are identified with human- and machine-readable codes, as well as with radio-frequency identification (RFID) tags. NewPin offers a crystal-repositioning precision of up to 10 µm but requires a specific goniometer socket. The storage density could reach 64 samples using a special puck designed for fully robotic handling. miniSPINE is less precise but uses a goniometer mount compatible with the current SPINE standard. miniSPINE is proposed for the first implementation of the new standard, since it is easier to integrate at beamlines. An upgraded version of the SPINE sample holder with a corresponding puck named SPINEplus is also proposed in order to offer a homogenous and interoperable system. The project involved several European synchrotrons and industrial companies in the fields of consumables and sample-changer robotics. Manual handling of mini

  9. Proton pump inhibitors

    MedlinePlus

    Proton pump inhibitors (PPIs) are medicines that work by reducing the amount of stomach acid made by ... Proton pump inhibitors are used to: Relieve symptoms of acid reflux, or gastroesophageal reflux disease (GERD). This ...

  10. What's In a Proton?

    ScienceCinema

    Brookhaven Lab

    2016-07-12

    Physicist Peter Steinberg explains that fundamental particles like protons are themselves made up of still smaller particles called quarks. He discusses how new particles are produced when quarks are liberated from protons...a process that can be observed

  11. What's In a Proton?

    SciTech Connect

    Brookhaven Lab

    2009-07-08

    Physicist Peter Steinberg explains that fundamental particles like protons are themselves made up of still smaller particles called quarks. He discusses how new particles are produced when quarks are liberated from protons...a process that can be observed

  12. Proton: the particle.

    PubMed

    Suit, Herman

    2013-11-01

    The purpose of this article is to review briefly the nature of protons: creation at the Big Bang, abundance, physical characteristics, internal components, and life span. Several particle discoveries by proton as the experimental tool are considered. Protons play important roles in science, medicine, and industry. This article was prompted by my experience in the curative treatment of cancer patients by protons and my interest in the nature of protons as particles. The latter has been stimulated by many discussions with particle physicists and reading related books and journals. Protons in our universe number ≈10(80). Protons were created at 10(-6) -1 second after the Big Bang at ≈1.37 × 10(10) years beforethe present. Proton life span has been experimentally determined to be ≥10(34) years; that is, the age of the universe is 10(-24)th of the minimum life span of a proton. The abundance of the elements is hydrogen, ≈74%; helium, ≈24%; and heavier atoms, ≈2%. Accordingly, protons are the dominant baryonic subatomic particle in the universe because ≈87% are protons. They are in each atom in our universe and thus involved in virtually every activity of matter in the visible universe, including life on our planet. Protons were discovered in 1919. In 1968, they were determined to be composed of even smaller particles, principally quarks and gluons. Protons have been the experimental tool in the discoveries of quarks (charm, bottom, and top), bosons (W(+), W(-), Z(0), and Higgs), antiprotons, and antineutrons. Industrial applications of protons are numerous and important. Additionally, protons are well appreciated in medicine for their role in radiation oncology and in magnetic resonance imaging. Protons are the dominant baryonic subatomic particle in the visible universe, comprising ≈87% of the particle mass. They are present in each atom of our universe and thus a participant in every activity involving matter.

  13. Proton: The Particle

    SciTech Connect

    Suit, Herman

    2013-11-01

    The purpose of this article is to review briefly the nature of protons: creation at the Big Bang, abundance, physical characteristics, internal components, and life span. Several particle discoveries by proton as the experimental tool are considered. Protons play important roles in science, medicine, and industry. This article was prompted by my experience in the curative treatment of cancer patients by protons and my interest in the nature of protons as particles. The latter has been stimulated by many discussions with particle physicists and reading related books and journals. Protons in our universe number ≈10{sup 80}. Protons were created at 10{sup −6} –1 second after the Big Bang at ≈1.37 × 10{sup 10} years beforethe present. Proton life span has been experimentally determined to be ≥10{sup 34} years; that is, the age of the universe is 10{sup −24}th of the minimum life span of a proton. The abundance of the elements is hydrogen, ≈74%; helium, ≈24%; and heavier atoms, ≈2%. Accordingly, protons are the dominant baryonic subatomic particle in the universe because ≈87% are protons. They are in each atom in our universe and thus involved in virtually every activity of matter in the visible universe, including life on our planet. Protons were discovered in 1919. In 1968, they were determined to be composed of even smaller particles, principally quarks and gluons. Protons have been the experimental tool in the discoveries of quarks (charm, bottom, and top), bosons (W{sup +}, W{sup −}, Z{sup 0}, and Higgs), antiprotons, and antineutrons. Industrial applications of protons are numerous and important. Additionally, protons are well appreciated in medicine for their role in radiation oncology and in magnetic resonance imaging. Protons are the dominant baryonic subatomic particle in the visible universe, comprising ≈87% of the particle mass. They are present in each atom of our universe and thus a participant in every activity involving matter.

  14. Interstellar protonated molecular species

    NASA Astrophysics Data System (ADS)

    Etim, Emmanuel E.; Gorai, Prasanta; Das, Ankan; Arunan, Elangannan

    2017-08-01

    Majority of the known interstellar cations are protonated species believed to be the natural precursors for their corresponding neutral analogues formed via the dissociative recombination process. The protonation of a neutral species can occur in more than one position on the molecular structure thus resulting in more than one proton binding energy value and different protonated species for the same neutral species. In the present work, ab initio quantum calculations are employed to calculate accurate proton binding energies for over 100 neutral interstellar molecules of which majority of the neutral molecules are protonated in more than one position. From the results, protonated species resulting from a high proton binding energy prefers to remain protonated rather than transferring a proton and returning to its neutral form as compared to its analogue that gives rise to a lower proton binding energy (PBE) from the same neutral species. For two protonated species resulting from the same neutral molecule, the one that results in a higher PBE is more stable as compared to its counterpart that is responsible for the lower PBE for the same neutral species. Here, the most stable species are highlighted for all the systems considered.

  15. Space station user's handbook

    NASA Technical Reports Server (NTRS)

    1972-01-01

    A user's handbook for the modular space station concept is presented. The document is designed to acquaint science personnel with the overall modular space station program, the general nature and capabilities of the station itself, some of the scientific opportunities presented by the station, the general policy governing its operation, and the relationship between the program and participants from the scientific community.

  16. Space Station Spartan study

    NASA Technical Reports Server (NTRS)

    Lane, J. H.; Schulman, J. R.; Neupert, W. M.

    1985-01-01

    The required extension, enhancement, and upgrading of the present Spartan concept are described to conduct operations from the space station using the station's unique facilities and operational features. The space station Spartan (3S), the free flyer will be deployed from and returned to the space station and will conduct scientific missions of much longer duration than possible with the current Spartan. The potential benefits of a space station Spartan are enumerated. The objectives of the study are: (1) to develop a credible concept for a space station Spartan; and (2) to determine the associated requirements and interfaces with the space station to help ensure that the 3S can be properly accommodated.

  17. Merging Structural Information from X-ray Crystallography, Quantum Chemistry, and EXAFS Spectra: The Oxygen-Evolving Complex in PSII.

    PubMed

    Chernev, Petko; Zaharieva, Ivelina; Rossini, Emanuele; Galstyan, Artur; Dau, Holger; Knapp, Ernst-Walter

    2016-10-12

    Structural data of the oxygen-evolving complex (OEC) in photosystem II (PSII) determined by X-ray crystallography, quantum chemistry (QC), and extended X-ray absorption fine structure (EXAFS) analyses are presently inconsistent. Therefore, a detailed study of what information can be gained about the OEC through a comparison of QC and crystallographic structure information combined with the information from range-extended EXAFS spectra was undertaken. An analysis for determining the precision of the atomic coordinates of the OEC by QC is carried out. OEC model structures based on crystallographic data that are obtained by QC from different research groups are compared with one another and with structures obtained by high-resolution crystallography. The theory of EXAFS spectra is summarized, and the application of EXAFS spectra to the experimental determination of the structure of the OEC is detailed. We discriminate three types of parameters entering the formula for the EXAFS spectrum: (1) model-independent, predefined, and fixed; (2) model-dependent that can be computed or adjusted; and (3) model-dependent that must be adjusted. The information content of EXAFS spectra is estimated and is related to the precision of atomic coordinates and resolution power to discriminate different atom-pair distances of the OEC. It is demonstrated how a precise adjustment of atomic coordinates can yield a nearly perfect representation of the experimental OEC EXAFS spectrum, but at the expense of overfitting and losing the knowledge of the initial OEC model structure. Introducing a novel type of penalty function, it is shown that moderate adjustment of atomic coordinates to the EXAFS spectrum limited by constraints avoids overfitting and can be used to validate different OEC model structures. This technique is used to identify the OEC model structures whose computed OEC EXAFS spectra agree best with the measured spectrum. In this way, the most likely S-state and protonation pattern

  18. The Protein Micro-Crystallography Beamlines for Targeted Protein Research Program

    NASA Astrophysics Data System (ADS)

    Hirata, Kunio; Yamamoto, Masaki; Matsugaki, Naohiro; Wakatsuki, Soichi

    In order to collect proper diffraction data from outstanding micro-crystals, a brand-new data collection system should be designed to provide high signal-to noise ratio in diffraction images. SPring-8 and KEK-PF are currently developing two micro-beam beamlines for Targeted Proteins Research Program by MEXT of Japan. The program aims to reveal the structure and function of proteins that are difficult to solve but have great importance in both academic research and industrial application. At SPring-8, a new 1-micron beam beamline for protein micro-crystallography, RIKEN Targeted Proteins Beamline (BL32XU), is developed. At KEK-PF a new low energy micro-beam beamline, BL-1A, is dedicated for SAD micro-crystallography. The two beamlines will start operation in the end of 2010. The present status of the research and development for protein micro-crystallography will be presented.

  19. New paradigm for macromolecular crystallography experiments at SSRL: automated crystal screening and remote data collection

    PubMed Central

    Soltis, S. Michael; Cohen, Aina E.; Deacon, Ashley; Eriksson, Thomas; González, Ana; McPhillips, Scott; Chui, Hsui; Dunten, Pete; Hollenbeck, Michael; Mathews, Irimpan; Miller, Mitch; Moorhead, Penjit; Phizackerley, R. Paul; Smith, Clyde; Song, Jinhu; van dem Bedem, Henry; Ellis, Paul; Kuhn, Peter; McPhillips, Timothy; Sauter, Nicholas; Sharp, Kenneth; Tsyba, Irina; Wolf, Guenter

    2008-01-01

    Complete automation of the macromolecular crystallography experiment has been achieved at SSRL through the combination of robust mechanized experimental hardware and a flexible control system with an intuitive user interface. These highly reliable systems have enabled crystallography experiments to be carried out from the researchers’ home institutions and other remote locations while retaining complete control over even the most challenging systems. A breakthrough component of the system, the Stanford Auto-Mounter (SAM), has enabled the efficient mounting of cryocooled samples without human intervention. Taking advantage of this automation, researchers have successfully screened more than 200 000 samples to select the crystals with the best diffraction quality for data collection as well as to determine optimal crystallization and cryocooling conditions. These systems, which have been deployed on all SSRL macromolecular crystallography beamlines and several beamlines worldwide, are used by more than 80 research groups in remote locations, establishing a new paradigm for macromolecular crystallo­graphy experimentation. PMID:19018097

  20. X-ray crystallography and the elucidation of the structure of DNA.

    PubMed

    McGregor, Hugh C J; Gunderman, Richard B

    2011-06-01

    Since their discovery by Roentgen in 1895, x-rays have contributed to some of the most important advances in science. X-ray crystallography is an imaging technique that uses x-ray diffraction to evaluate the molecular structure of a crystalline solid. This article discusses the critical role played by x-ray crystallography in the elucidation of the structure of DNA. The story of DNA includes insights on molecular structure provided by x-rays and also lessons on scientific collaboration and innovation that can be applied to radiology today.

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

    SciTech Connect

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

    2008-09-01

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

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

    SciTech Connect

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

    2011-12-31

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

  3. Optimized multi-step NMR-crystallography approach for structural characterization of a stable quercetin solvate.

    PubMed

    Filip, Xenia; Miclaus, Maria; Martin, Flavia; Filip, Claudiu; Grosu, Ioana Georgeta

    2017-01-31

    Herein we report the preparation and solid state structural investigation of the 1,4-dioxane-quercetin solvate. NMR crystallography methods were employed for crystal structure determination of the solvate from microcrystalline powder. The stability of the compound relative to other reported quercetin solvates is discussed and found to be in perfect agreement with the hydrogen bonding networks/supra-molecular architectures formed in each case. It is also clearly shown that NMR crystallography represents an ideal analytical tool in such cases when hydrogen-bonding networks are required to be constrained at a high accuracy level.

  4. A Maltose-Binding Protein Fusion Construct Yields a Robust Crystallography Platform for MCL1.

    PubMed

    Clifton, Matthew C; Dranow, David M; Leed, Alison; Fulroth, Ben; Fairman, James W; Abendroth, Jan; Atkins, Kateri A; Wallace, Ellen; Fan, Dazhong; Xu, Guoping; Ni, Z J; Daniels, Doug; Van Drie, John; Wei, Guo; Burgin, Alex B; Golub, Todd R; Hubbard, Brian K; Serrano-Wu, Michael H

    2015-01-01

    Crystallization of a maltose-binding protein MCL1 fusion has yielded a robust crystallography platform that generated the first apo MCL1 crystal structure, as well as five ligand-bound structures. The ability to obtain fragment-bound structures advances structure-based drug design efforts that, despite considerable effort, had previously been intractable by crystallography. In the ligand-independent crystal form we identify inhibitor binding modes not observed in earlier crystallographic systems. This MBP-MCL1 construct dramatically improves the structural understanding of well-validated MCL1 ligands, and will likely catalyze the structure-based optimization of high affinity MCL1 inhibitors.

  5. A Maltose-Binding Protein Fusion Construct Yields a Robust Crystallography Platform for MCL1

    PubMed Central

    Clifton, Matthew C.; Dranow, David M.; Leed, Alison; Fulroth, Ben; Fairman, James W.; Abendroth, Jan; Atkins, Kateri A.; Wallace, Ellen; Fan, Dazhong; Xu, Guoping; Ni, Z. J.; Daniels, Doug; Van Drie, John; Wei, Guo; Burgin, Alex B.; Golub, Todd R.; Hubbard, Brian K.; Serrano-Wu, Michael H.

    2015-01-01

    Crystallization of a maltose-binding protein MCL1 fusion has yielded a robust crystallography platform that generated the first apo MCL1 crystal structure, as well as five ligand-bound structures. The ability to obtain fragment-bound structures advances structure-based drug design efforts that, despite considerable effort, had previously been intractable by crystallography. In the ligand-independent crystal form we identify inhibitor binding modes not observed in earlier crystallographic systems. This MBP-MCL1 construct dramatically improves the structural understanding of well-validated MCL1 ligands, and will likely catalyze the structure-based optimization of high affinity MCL1 inhibitors. PMID:25909780

  6. Study of proton radioactivities

    SciTech Connect

    Davids, C.N.; Back, B.B.; Henderson, D.J.

    1995-08-01

    About a dozen nuclei are currently known to accomplish their radioactive decay by emitting a proton. These nuclei are situated far from the valley of stability, and mark the very limits of existence for proton-rich nuclei: the proton drip line. A new 39-ms proton radioactivity was observed following the bombardment of a {sup 96}Ru target by a beam of 420-MeV {sup 78}Kr. Using the double-sided Si strip detector implantation system at the FMA, a proton group having an energy of 1.05 MeV was observed, correlated with the implantation of ions having mass 167. The subsequent daughter decay was identified as {sup 166}Os by its characteristic alpha decay, and therefore the proton emitter is assigned to the {sup 167}Ir nucleus. Further analysis showed that a second weak proton group from the same nucleus is present, indicating an isomeric state. Two other proton emitters were discovered recently at the FMA: {sup 171}Au and {sup 185}Bi, which is the heaviest known proton radioactivity. The measured decay energies and half-lives will enable the angular momentum of the emitted protons to be determined, thus providing spectroscopic information on nuclei that are beyond the proton drip line. In addition, the decay energy yields the mass of the nucleus, providing a sensitive test of mass models in this extremely proton-rich region of the chart of the nuclides. Additional searches for proton emitters will be conducted in the future, in order to extend our knowledge of the location of the proton drip line.

  7. Proton Exchange in a Paramagnetic Chemical Exchange Saturation Transfer Agent from Experimental Studies and ab Initio Metadynamics Simulation.

    PubMed

    Pollet, Rodolphe; Bonnet, Célia S; Retailleau, Pascal; Durand, Philippe; Tóth, Éva

    2017-03-27

    The proton-exchange process between water and a carbamate has been studied experimentally and theoretically in a lanthanide-based paramagnetic chemical exchange saturation transfer agent endowed with potential multimodality detection capabilities (optical imaging, or T1 MRI for the Gd(III) analogue). In addition to an in-depth structural analysis by a combined approach (using X-ray crystallography, NMR, and molecular dynamics), our ab initio simulation in aqueous solution sheds light on the reaction mechanism for this proton exchange, which involves structural Grotthuss diffusion.

  8. Variations of the radiation dose onboard Mir station.

    PubMed

    Panasyuk, M I; Teltsov, M V; Shumshurov, V I; Tsetlin, V V

    1998-01-01

    Dose variations, associated with the 11-year solar activity cycle, seasonal variations of particle fluxes in the Earth's radiation belts at the station orbit, and solar proton events are studied, using prolonged measurements of radiation doses inside orbital station Mir. Daily averages of radiation doses during the declining phase of the 22nd solar cycle and during transition to the 23rd solar activity cycle reached very large values for astronauts and significantly exceed the values calculated according to existing models.

  9. The crystallography beamline I711 at MAX II.

    PubMed

    Cerenius, Y; Ståhl, K; Svensson, L A; Ursby, T; Oskarsson, A; Albertsson, J; Liljas, A

    2000-07-01

    A new X-ray crystallographic beamline is operational at the MAX II synchrotron in Lund. The beamline has been in regular use since August 1998 and is used both for macro- and small molecule diffraction as well as powder diffraction experiments. The radiation source is a 1.8 T multipole wiggler. The beam is focused vertically by a bendable mirror and horizontally by an asymmetrically cut Si(111) monochromator. The wavelength range is 0.8-1.55 A with a measured flux at 1 A of more than 10(11) photons s(-1) in 0.3 mm x 0.3 mm at the sample position. The station is currently equipped with a Mar345 imaging plate, a Bruker Smart 1000 area CCD detector and a Huber imaging-plate Guinier camera. An ADSC 210 area CCD detector is planned to be installed during 2000.

  10. 47 CFR 73.877 - Station logs for LPFM stations.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 47 Telecommunication 4 2012-10-01 2012-10-01 false Station logs for LPFM stations. 73.877 Section... BROADCAST SERVICES Low Power FM Broadcast Stations (LPFM) § 73.877 Station logs for LPFM stations. The licensee of each LPFM station must maintain a station log. Each log entry must include the time and date...

  11. 47 CFR 73.877 - Station logs for LPFM stations.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 47 Telecommunication 4 2014-10-01 2014-10-01 false Station logs for LPFM stations. 73.877 Section... BROADCAST SERVICES Low Power FM Broadcast Stations (LPFM) § 73.877 Station logs for LPFM stations. The licensee of each LPFM station must maintain a station log. Each log entry must include the time and date...

  12. 47 CFR 73.877 - Station logs for LPFM stations.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 47 Telecommunication 4 2011-10-01 2011-10-01 false Station logs for LPFM stations. 73.877 Section... BROADCAST SERVICES Low Power FM Broadcast Stations (LPFM) § 73.877 Station logs for LPFM stations. The licensee of each LPFM station must maintain a station log. Each log entry must include the time and date...

  13. 47 CFR 73.877 - Station logs for LPFM stations.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 47 Telecommunication 4 2013-10-01 2013-10-01 false Station logs for LPFM stations. 73.877 Section... BROADCAST SERVICES Low Power FM Broadcast Stations (LPFM) § 73.877 Station logs for LPFM stations. The licensee of each LPFM station must maintain a station log. Each log entry must include the time and date...

  14. 47 CFR 73.877 - Station logs for LPFM stations.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 47 Telecommunication 4 2010-10-01 2010-10-01 false Station logs for LPFM stations. 73.877 Section... BROADCAST SERVICES Low Power FM Broadcast Stations (LPFM) § 73.877 Station logs for LPFM stations. The licensee of each LPFM station must maintain a station log. Each log entry must include the time and date...

  15. 100 Years Later: Celebrating the Contributions of X-ray Crystallography to Allergy and Clinical Immunology

    PubMed Central

    Pomés, Anna; Chruszcz, Maksymilian; Gustchina, Alla; Minor, Wladek; Mueller, Geoffrey A.; Pedersen, Lars C.; Wlodawer, Alexander; Chapman, Martin D.

    2015-01-01

    Current knowledge of molecules involved in immunology and allergic disease results from significant contributions of X-ray crystallography, a discipline that just celebrated its 100th anniversary. The histories of allergens and X-ray crystallography are intimately intertwined. The first enzyme structure to be determined was lysozyme, also known as the chicken food allergen Gal d 4. Crystallography determines the exact three-dimensional positions of atoms in molecules. Structures of molecular complexes in the disciplines of immunology and allergy have revealed the atoms involved in molecular interactions and in mechanisms of disease. These complexes include peptides presented by MHC class II molecules, cytokines bound to their receptors, allergen-antibody complexes, and innate immune receptors with their ligands. The information derived from crystallographic studies provides insights into the function of molecules. Allergen function is one of the determinants of environmental exposure, which is essential for IgE sensitization. Proteolytic activity of allergens or their capacity to bind lipopolysaccharides may also contribute to allergenicity. The atomic positions define the molecular surface that is accessible to antibodies. This surface in turn determines antibody specificity and cross-reactivity that are important factors for the selection of allergen panels used for molecular diagnosis and for the interpretation of clinical symptoms. This review celebrates the contributions of X-ray crystallography to clinical immunology and allergy, focusing on new molecular perspectives that influence the diagnosis and treatment of allergic diseases. PMID:26145985

  16. The status of beam lines for macromolecular crystallography at the Siberia-2 storage ring

    SciTech Connect

    Kusev, S.V.; Raiko, V.I.; Skuratovskii, I.Y. )

    1992-01-01

    An overview is presented of the x-ray optics of the four macromolecular crystallography beam lines under construction at the storage ring SIBERIA-2, Moscow. The four workstations are to utilize isomorphous replacement, anomalous dispersion, reflections energy profile, and the Laue technique. The instrumentation details, the results of ray-tracing analysis, and the use of an area detector are discussed.

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

    PubMed

    Jaskolski, Mariusz; Dauter, Zbigniew; Wlodawer, Alexander

    2014-09-01

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

  18. Present and future of membrane protein structure determination by electron crystallography

    PubMed Central

    Ubarretxena-Belandia, Iban; Stokes, David L.

    2011-01-01

    Membrane proteins are critical to cell physiology, playing roles in signaling, trafficking, transport, adhesion, and recognition. Despite their relative abundance in the proteome and their prevalence as targets of therapeutic drugs, structural information about membrane proteins is in short supply. This review describes the use of electron crystallography as a tool for determining membrane protein structures. Electron crystallography offers distinct advantages relative to the alternatives of X-ray crystallography and NMR spectroscopy. Namely, membrane proteins are placed in their native membranous environment, which is likely to favor a native conformation and allow changes in conformation in response to physiological ligands. Nevertheless, there are significant logistical challenges in finding appropriate conditions for inducing membrane proteins to form two-dimensional arrays within the membrane and in using electron cryo-microscopy to collect the data required for structure determination. A number of developments are described for high-throughput screening of crystallization trials and for automated imaging of crystals with the electron microscope. These tools are critical for exploring the necessary range of factors governing the crystallization process. There have also been recent software developments to facilitate the process of structure determination. However, further innovations in the algorithms used for processing images and electron diffraction are necessary to improve throughput and to make electron crystallography truly viable as a method for determining atomic structures of membrane proteins. PMID:21115172

  19. Using the Plan View to Teach Basic Crystallography in General Chemistry

    ERIC Educational Resources Information Center

    Cushman, Cody V.; Linford, Matthew R.

    2015-01-01

    The plan view is used in crystallography and materials science to show the positions of atoms in crystal structures. However, it is not widely used in teaching general chemistry. In this contribution, we introduce the plan view, and show these views for the simple cubic, body-centered cubic, face-centered cubic, hexagonal close packed, CsCl, NaCl,…

  20. Frontiers of Crystallography: A Project-Based Research-Led Learning Exercise

    ERIC Educational Resources Information Center

    Wilson, Chick C.; Parkin, Andrew; Thomas, Lynne H.

    2012-01-01

    A highly interactive research-led learning session for chemistry undergraduates is described, which aims to lead students to an awareness of the applications of crystallography technique through a mentored hands-on crystal structure solution and refinement session. The research-based environment is inherent throughout the 4.5 h program and is…

  1. Celebrating the International Year of Crystallography with a Wisconsin High School Crystal Growing Competition

    ERIC Educational Resources Information Center

    Guzei, Ilia A.

    2014-01-01

    In honor of the 2014 International Year of Crystallography, the first Wisconsin Crystal Growing Competition was successfully organized and conducted. High school students from 26 schools across the state competed for prizes by growing large crystals of CuSO[subscript4]·5(H[subscript2]O). This paper describes how the event was planned and carried…

  2. Design and feasibility of active matrix flat panel detector using avalanche amorphous selenium for protein crystallography.

    PubMed

    Sultana, Afrin; Reznik, Alla; Karim, Karim S; Rowlands, J A

    2008-10-01

    Protein crystallography is the most important technique for resolving the three-dimensional atomic structure of protein by measuring the intensity of its x-ray diffraction pattern. This work proposes a large area flat panel detector for protein crystallography based on direct conversion x-ray detection technique using avalanche amorphous selenium (a-Se) as the high gain photoconductor, and active matrix readout using amorphous silicon (a-Si:H) thin film transistors. The detector employs avalanche multiplication phenomenon of a-Se to make the detector sensitive to each incident x ray. The advantages of the proposed detector over the existing imaging plate and charge coupled device detectors are large area, high dynamic range coupled to single x-ray detection capability, fast readout, high spatial resolution, and inexpensive manufacturing process. The optimal detector design parameters (such as detector size, pixel size, and thickness of a-Se layer), and operating parameters (such as electric field across the a-Se layer) are determined based on the requirements for protein crystallography application. The performance of the detector is evaluated in terms of readout time (<1 s), dynamic range (approximately 10(5)), and sensitivity (approximately 1 x-ray photon), thus validating the detector's efficacy for protein crystallography.

  3. Using the Plan View to Teach Basic Crystallography in General Chemistry

    ERIC Educational Resources Information Center

    Cushman, Cody V.; Linford, Matthew R.

    2015-01-01

    The plan view is used in crystallography and materials science to show the positions of atoms in crystal structures. However, it is not widely used in teaching general chemistry. In this contribution, we introduce the plan view, and show these views for the simple cubic, body-centered cubic, face-centered cubic, hexagonal close packed, CsCl, NaCl,…

  4. Fixed target matrix for femtosecond time-resolved and in situ serial micro-crystallography

    DOE PAGES

    Mueller, C.; Marx, A.; Epp, S. W.; ...

    2015-08-18

    We present a crystallography chip enabling in situ room temperature crystallography at microfocus synchrotron beamlines and X-ray free-electron laser (X-FEL) sources. Compared to other in situ approaches, we observe extremely low background and high diffraction data quality. The chip design is robust and allows fast and efficient loading of thousands of small crystals. The ability to load a large number of protein crystals, at room temperature and with high efficiency, into prescribed positions enables high throughput automated serial crystallography with microfocus synchrotron beamlines. In addition, we demonstrate the application of this chip for femtosecond time-resolved serial crystallography at the Linacmore » Coherent Light Source (LCLS, Menlo Park, California, USA). As a result, the chip concept enables multiple images to be acquired from each crystal, allowing differential detection of changes in diffraction intensities in order to obtain high signal-to-noise and fully exploit the time resolution capabilities of XFELs.« less

  5. 100 Years later: Celebrating the contributions of x-ray crystallography to allergy and clinical immunology.

    PubMed

    Pomés, Anna; Chruszcz, Maksymilian; Gustchina, Alla; Minor, Wladek; Mueller, Geoffrey A; Pedersen, Lars C; Wlodawer, Alexander; Chapman, Martin D

    2015-07-01

    Current knowledge of molecules involved in immunology and allergic disease results from the significant contributions of x-ray crystallography, a discipline that just celebrated its 100th anniversary. The histories of allergens and x-ray crystallography are intimately intertwined. The first enzyme structure to be determined was lysozyme, also known as the chicken food allergen Gal d 4. Crystallography determines the exact 3-dimensional positions of atoms in molecules. Structures of molecular complexes in the disciplines of immunology and allergy have revealed the atoms involved in molecular interactions and mechanisms of disease. These complexes include peptides presented by MHC class II molecules, cytokines bound to their receptors, allergen-antibody complexes, and innate immune receptors with their ligands. The information derived from crystallographic studies provides insights into the function of molecules. Allergen function is one of the determinants of environmental exposure, which is essential for IgE sensitization. Proteolytic activity of allergens or their capacity to bind LPSs can also contribute to allergenicity. The atomic positions define the molecular surface that is accessible to antibodies. In turn, this surface determines antibody specificity and cross-reactivity, which are important factors for the selection of allergen panels used for molecular diagnosis and the interpretation of clinical symptoms. This review celebrates the contributions of x-ray crystallography to clinical immunology and allergy, focusing on new molecular perspectives that influence the diagnosis and treatment of allergic diseases. Copyright © 2015 American Academy of Allergy, Asthma & Immunology. All rights reserved.

  6. Celebrating the International Year of Crystallography with a Wisconsin High School Crystal Growing Competition

    ERIC Educational Resources Information Center

    Guzei, Ilia A.

    2014-01-01

    In honor of the 2014 International Year of Crystallography, the first Wisconsin Crystal Growing Competition was successfully organized and conducted. High school students from 26 schools across the state competed for prizes by growing large crystals of CuSO[subscript4]·5(H[subscript2]O). This paper describes how the event was planned and carried…

  7. Frontiers of Crystallography: A Project-Based Research-Led Learning Exercise

    ERIC Educational Resources Information Center

    Wilson, Chick C.; Parkin, Andrew; Thomas, Lynne H.

    2012-01-01

    A highly interactive research-led learning session for chemistry undergraduates is described, which aims to lead students to an awareness of the applications of crystallography technique through a mentored hands-on crystal structure solution and refinement session. The research-based environment is inherent throughout the 4.5 h program and is…

  8. Apparatus and method for nanoflow liquid jet and serial femtosecond x-ray protein crystallography

    DOEpatents

    Bogan, Michael J.; Laksmono, Hartawan; Sierra, Raymond G.

    2016-03-01

    Techniques for nanoflow serial femtosecond x-ray protein crystallography include providing a sample fluid by mixing a plurality of a first target of interest with a carrier fluid and injecting the sample fluid into a vacuum chamber at a rate less than about 4 microliters per minute. In some embodiments, the carrier fluid has a viscosity greater than about 3 centipoise.

  9. Station Tour: Russian Segment

    NASA Image and Video Library

    Expedition 33 Commander Suni Williams concludes her tour of the International Space Station with a visit to the Russian segment, which includes Zarya, the first segment of the station launched in 1...

  10. Proton Remains Puzzling

    SciTech Connect

    Gao, Haiyan; Liu, Tianbo; Peng, Chao; Ye, Zhihong; Zhao, Zhiwen

    2015-01-01

    Nucleons are building blocks of visible matter, and are responsible for more than 99% of the visible mass in the universe despite the fact that the discovery of the Higgs boson is almost irrelevant to the origin of the proton mass. While major progress has been made in the last two decades in understanding the proton spin puzzle discovered in the late 1980s by the European Muon Collaboration, a new proton puzzle emerged in the last several years concerning the proton charge radius, which is the charge weighted size of the proton. In this paper we will review the latest situation concerning the proton charge radius, mass and spin, and discuss upcoming new experiments addressing these puzzles, as well as implications for new physics.

  11. Radio spectrum surveillance station

    NASA Technical Reports Server (NTRS)

    Hersey, D. R.

    1979-01-01

    The paper presents a general and functional description of a low-cost surveillance station designed as the first phase of NASA's program to develop a radio spectrum surveillance capability for deep space stations for identifying radio frequency interference sources. The station described has identified several particular interferences and is yielding spectral signature data which, after cataloging, will serve as a library for rapid identification of frequently observed interference. Findings from the use of the station are discussed.

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

    PubMed Central

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

    2014-01-01

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

  13. Serial crystallography captures enzyme catalysis in copper nitrite reductase at atomic resolution from one crystal

    PubMed Central

    Horrell, Sam; Antonyuk, Svetlana V.; Eady, Robert R.; Hasnain, S. Samar; Hough, Michael A.; Strange, Richard W.

    2016-01-01

    Relating individual protein crystal structures to an enzyme mechanism remains a major and challenging goal for structural biology. Serial crystallography using multiple crystals has recently been reported in both synchrotron-radiation and X-ray free-electron laser experiments. In this work, serial crystallography was used to obtain multiple structures serially from one crystal (MSOX) to study in crystallo enzyme catalysis. Rapid, shutterless X-ray detector technology on a synchrotron MX beamline was exploited to perform low-dose serial crystallography on a single copper nitrite reductase crystal, which survived long enough for 45 consecutive 100 K X-ray structures to be collected at 1.07–1.62 Å resolution, all sampled from the same crystal volume. This serial crystallography approach revealed the gradual conversion of the substrate bound at the catalytic type 2 Cu centre from nitrite to nitric oxide, following reduction of the type 1 Cu electron-transfer centre by X-ray-generated solvated electrons. Significant, well defined structural rearrangements in the active site are evident in the series as the enzyme moves through its catalytic cycle, namely nitrite reduction, which is a vital step in the global denitrification process. It is proposed that such a serial crystallography approach is widely applicable for studying any redox or electron-driven enzyme reactions from a single protein crystal. It can provide a ‘catalytic reaction movie’ highlighting the structural changes that occur during enzyme catalysis. The anticipated developments in the automation of data analysis and modelling are likely to allow seamless and near-real-time analysis of such data on-site at some of the powerful synchrotron crystallographic beamlines. PMID:27437114

  14. International Space Station (ISS)

    NASA Image and Video Library

    1997-07-20

    Photograph shows the International Space Station Laboratory Module under fabrication at Marshall Space Flight Center (MSFC), Building 4708 West High Bay. Although management of the U.S. elements for the Station were consolidated in 1994, module and node development continued at MSFC by Boeing Company, the prime contractor for the Space Station.

  15. Kinetic effects of increased proton transfer distance on proton-coupled oxidations of phenol-amines.

    PubMed

    Markle, Todd F; Rhile, Ian J; Mayer, James M

    2011-11-02

    To test the effect of varying the proton donor-acceptor distance in proton-coupled electron transfer (PCET) reactions, the oxidation of a bicyclic amino-indanol (2) is compared with that of a closely related phenol with an ortho CPh(2)NH(2) substituent (1). Spectroscopic, structural, thermochemical, and computational studies show that the two amino-phenols are very similar, except that the O···N distance (d(ON)) is >0.1 Å longer in 2 than in 1. The difference in d(ON) is 0.13 ± 0.03 Å from X-ray crystallography and 0.165 Å from DFT calculations. Oxidations of these phenols by outer-sphere oxidants yield distonic radical cations (•)OAr-NH(3)(+) by concerted proton-electron transfer (CPET). Simple tunneling and classical kinetic models both predict that the longer donor-acceptor distance in 2 should lead to slower reactions, by ca. 2 orders of magnitude, as well as larger H/D kinetic isotope effects (KIEs). However, kinetic studies show that the compound with the longer proton-transfer distance, 2, exhibits smaller KIEs and has rate constants that are quite close to those of 1. For example, the oxidation of 2 by the triarylamminium radical cation N(C(6)H(4)OMe)(3)(•+) (3a(+)) occurs at (1.4 ± 0.1) × 10(4) M(-1) s(-1), only a factor of 2 slower than the closely related reaction of 1 with N(C(6)H(4)OMe)(2)(C(6)H(4)Br)(•+) (3b(+)). This difference in rate constants is well accounted for by the slightly different free energies of reaction: ΔG° (2 + 3a(+)) = +0.078 V versus ΔG° (1 + 3b(+)) = +0.04 V. The two phenol-amines do display some subtle kinetic differences: for instance, compound 2 has a shallower dependence of CPET rate constants on driving force (Brønsted α, Δ ln(k)/Δ ln(K(eq))). These results show that the simple tunneling model is not a good predictor of the effect of proton donor-acceptor distance on concerted-electron transfer reactions involving strongly hydrogen-bonded systems. Computational analysis of the observed similarity of the

  16. Space Station Live: Station Communications Upgrade

    NASA Image and Video Library

    NASA Public Affairs Officer Nicole Cloutier-Lemasters recently spoke with Penny Roberts, one of the leads for the International Space Station Avionics and Software group, about the upgrade of the K...

  17. Space Station attached payloads

    NASA Technical Reports Server (NTRS)

    Clark, Lenwood G.

    1990-01-01

    The Space Station Freedom is being designed and developed with user requirements being used to shape the configuration. Plans include accommodation provisions for a wide variety of attached payloads including the Earth sciences research activities which are the focus of this conference. The station program is even beginning some preliminary payload manifesting which involves planning for accommodation of payload during the station's assembly flights. Potential payload organizations should be aware of the station's plans for payload accommodations so as to guide their own payload activities for future space station use.

  18. Neuroradiology viewing station

    NASA Astrophysics Data System (ADS)

    Lou, Shyhliang A.; Lufkin, Robert B.; Valentino, Daniel J.; Huang, H. K.; Hanafee, William; Jabour, Bradly; Bentsen, John R.; Duckwiler, Gary R.; Dion, Jacques E.

    1990-07-01

    A distributed CT/MR digital viewing station for the neuroradiology section has been developed and is being evaluated in our department. The major components of the station consist of a SUN host computer, a PIXAR II image processor, and four 1K x 1K progressive video monitors. The software modules operating in the station include an image acquisition process, a local database process, and an user image display and processing process. Functions provided by the station are described. Preliminary results obtained from clinical evaluation are reported. Future plans to refine the station are presented.

  19. The Schwarzschild Proton

    SciTech Connect

    Haramein, Nassim

    2010-11-24

    We review our model of a proton that obeys the Schwarzschild condition. We find that only a very small percentage ({approx}10{sup -39}%) of the vacuum fluctuations available within a proton volume need be cohered and converted to mass-energy in order for the proton to meet the Schwarzschild condition. This proportion is equivalent to that between gravitation and the strong force where gravitation is thought to be {approx}10{sup -38} to 10{sup -40} weaker than the strong force. Gravitational attraction between two contiguous Schwarzschild protons can accommodate both nucleon and quark confinement. We calculate that two contiguous Schwarzschild protons would rotate at c and have a period of 10{sup -23} s and a frequency of 10{sup 22} Hz which is characteristic of the strong force interaction time and a close approximation of the gamma emission typically associated with nuclear decay. We include a scaling law and find that the Schwarzschild proton data point lies near the least squares trend line for organized matter. Using a semi-classical model, we find that a proton charge orbiting at a proton radius at c generates a good approximation to the measured anomalous magnetic moment.

  20. Method and apparatus for laser-controlled proton beam radiology

    DOEpatents

    Johnstone, C.J.

    1998-06-02

    A proton beam radiology system provides cancer treatment and proton radiography. The system includes an accelerator for producing an H{sup {minus}} beam and a laser source for generating a laser beam. A photodetachment module is located proximate the periphery of the accelerator. The photodetachment module combines the H{sup {minus}} beam and laser beam to produce a neutral beam therefrom within a subsection of the H{sup {minus}} beam. The photodetachment module emits the neutral beam along a trajectory defined by the laser beam. The photodetachment module includes a stripping foil which forms a proton beam from the neutral beam. The proton beam is delivered to a conveyance segment which transports the proton beam to a patient treatment station. The photodetachment module further includes a laser scanner which moves the laser beam along a path transverse to the cross-section of the H{sup {minus}} beam in order to form the neutral beam in subsections of the H{sup {minus}} beam. As the scanning laser moves across the H{sup {minus}} beam, it similarly varies the trajectory of the proton beam emitted from the photodetachment module and in turn varies the target location of the proton beam upon the patient. Intensity modulation of the proton beam can also be achieved by controlling the output of the laser. 9 figs.

  1. Method and apparatus for laser-controlled proton beam radiology

    DOEpatents

    Johnstone, Carol J.

    1998-01-01

    A proton beam radiology system provides cancer treatment and proton radiography. The system includes an accelerator for producing an H.sup.- beam and a laser source for generating a laser beam. A photodetachment module is located proximate the periphery of the accelerator. The photodetachment module combines the H.sup.- beam and laser beam to produce a neutral beam therefrom within a subsection of the H.sup.- beam. The photodetachment module emits the neutral beam along a trajectory defined by the laser beam. The photodetachment module includes a stripping foil which forms a proton beam from the neutral beam. The proton beam is delivered to a conveyance segment which transports the proton beam to a patient treatment station. The photodetachment module further includes a laser scanner which moves the laser beam along a path transverse to the cross-section of the H.sup.- beam in order to form the neutral beam in subsections of the H.sup.- beam. As the scanning laser moves across the H.sup.- beam, it similarly varies the trajectory of the proton beam emitted from the photodetachment module and in turn varies the target location of the proton beam upon the patient. Intensity modulation of the proton beam can also be achieved by controlling the output of the laser.

  2. Surface Protonics Promotes Catalysis

    NASA Astrophysics Data System (ADS)

    Manabe, R.; Okada, S.; Inagaki, R.; Oshima, K.; Ogo, S.; Sekine, Y.

    2016-12-01

    Catalytic steam reforming of methane for hydrogen production proceeds even at 473 K over 1 wt% Pd/CeO2 catalyst in an electric field, thanks to the surface protonics. Kinetic analyses demonstrated the synergetic effect between catalytic reaction and electric field, revealing strengthened water pressure dependence of the reaction rate when applying an electric field, with one-third the apparent activation energy at the lower reaction temperature range. Operando–IR measurements revealed that proton conduction via adsorbed water on the catalyst surface occurred during electric field application. Methane was activated by proton collision at the Pd–CeO2 interface, based on the inverse kinetic isotope effect. Proton conduction on the catalyst surface plays an important role in methane activation at low temperature. This report is the first describing promotion of the catalytic reaction by surface protonics.

  3. Electron-proton spectrometer

    NASA Technical Reports Server (NTRS)

    Winckler, J. R.

    1973-01-01

    An electron-proton spectrometer was designed to measure the geomagnetically trapped radiation in a geostationary orbit at 6.6 earth radii in the outer radiation belt. This instrument is to be flown on the Applications Technology Satellite-F (ATS-F). The electron-proton spectrometer consists of two permanent magnet surface barrier detector arrays and associated electronics capable of selecting and detecting electrons in three energy ranges: (1) 30-50 keV, (2) 150-200 keV, and (3) 500 keV and protons in three energy ranges. The electron-proton spectrometer has the capability of measuring the fluxes of electrons and protons in various directions with respect to the magnetic field lines running through the satellite. One magnet detector array system is implemented to scan between EME north and south through west, sampling the directional flux in 15 steps. The other magnet-detector array system is fixed looking toward EME east.

  4. Surface Protonics Promotes Catalysis

    PubMed Central

    Manabe, R.; Okada, S.; Inagaki, R.; Oshima, K.; Ogo, S.; Sekine, Y.

    2016-01-01

    Catalytic steam reforming of methane for hydrogen production proceeds even at 473 K over 1 wt% Pd/CeO2 catalyst in an electric field, thanks to the surface protonics. Kinetic analyses demonstrated the synergetic effect between catalytic reaction and electric field, revealing strengthened water pressure dependence of the reaction rate when applying an electric field, with one-third the apparent activation energy at the lower reaction temperature range. Operando–IR measurements revealed that proton conduction via adsorbed water on the catalyst surface occurred during electric field application. Methane was activated by proton collision at the Pd–CeO2 interface, based on the inverse kinetic isotope effect. Proton conduction on the catalyst surface plays an important role in methane activation at low temperature. This report is the first describing promotion of the catalytic reaction by surface protonics. PMID:27905505

  5. Gating Topology of the Proton-Coupled Oligopeptide Symporters

    PubMed Central

    Fowler, Philip W.; Orwick-Rydmark, Marcella; Radestock, Sebastian; Solcan, Nicolae; Dijkman, Patricia M.; Lyons, Joseph A.; Kwok, Jane; Caffrey, Martin; Watts, Anthony; Forrest, Lucy R.; Newstead, Simon

    2015-01-01

    Summary Proton-coupled oligopeptide transporters belong to the major facilitator superfamily (MFS) of membrane transporters. Recent crystal structures suggest the MFS fold facilitates transport through rearrangement of their two six-helix bundles around a central ligand binding site; how this is achieved, however, is poorly understood. Using modeling, molecular dynamics, crystallography, functional assays, and site-directed spin labeling combined with double electron-electron resonance (DEER) spectroscopy, we present a detailed study of the transport dynamics of two bacterial oligopeptide transporters, PepTSo and PepTSt. Our results identify several salt bridges that stabilize outward-facing conformations and we show that, for all the current structures of MFS transporters, the first two helices of each of the four inverted-topology repeat units form half of either the periplasmic or cytoplasmic gate and that these function cooperatively in a scissor-like motion to control access to the peptide binding site during transport. PMID:25651061

  6. Automating existing stations

    SciTech Connect

    Little, J.E.

    1986-09-01

    The task was to automate 20 major compressor stations along ANR Pipeline Co.'s Southeastern and Southwestern pipelines in as many months. Meeting this schedule required standardized hardware and software design. Working with Bristol Babcock Co., ANR came up with an off-the-shelf station automation package suitable for a variety of compressor stations. The project involved 148 engines with 488,880-hp in the 20 stations. ANR Pipeline developed software for these engines and compressors, including horsepower prediction and efficiency. The system places processors ''intelligence'' at each station and engine to monitor and control operations. The station processor receives commands from the company's gas dispatch center at Detroit and informs dispatchers of alarms, conditions, and decision it makes. The automation system is controlled by the Detroit center through a central communications network. Operating orders from the center are sent to the station processor, which obeys orders using the most efficient means of operation at the station's disposal. In a malfunction, a control and communications backup system takes over. Commands and information are directly transmitted between the center and the individual compressor stations. Stations receive their orders based on throughput, with suction and discharge pressure overrides. Additionally, a discharge temperature override protects pipeline coatings.

  7. Proton-proton colliding beam facility ISABELLE

    SciTech Connect

    Hahn, H

    1980-01-01

    This paper attempts to present the status of the ISABELLE construction project, which has the objective of building a 400 + 400 GeV proton colliding beam facility. The major technical features of the superconducting accelerators with their projected performance are described. Progress made so far, difficulties encountered, and the program until completion in 1986 is briefly reviewed.

  8. Proton tracking for medical imaging and dosimetry

    NASA Astrophysics Data System (ADS)

    Taylor, J. T.; Allport, P. P.; Casse, G. L.; Smith, N. A.; Tsurin, I.; Allinson, N. M.; Esposito, M.; Kacperek, A.; Nieto-Camero, J.; Price, T.; Waltham, C.

    2015-02-01

    For many years, silicon micro-strip detectors have been successfully used as tracking detectors for particle and nuclear physics experiments. A new application of this technology is to the field of particle therapy, where radiotherapy is carried out by use of charged particles such as protons or carbon ions. Such a treatment has been shown to have advantages over standard x-ray radiotherapy and as a result of this, many new centres offering particle therapy are currently under construction—including two in the U.K.. The characteristics of a new silicon micro-strip detector based system for this application will be presented. The array uses specifically designed large area sensors in several stations in an x-u-v co-ordinate configuration suitable for very fast proton tracking with minimal ambiguities. The sensors will form a tracker capable of giving information on the path of high energy protons entering and exiting a patient. This will allow proton computed tomography (pCT) to aid the accurate delivery of treatment dose with tuned beam profile and energy. The tracker will also be capable of proton counting and position measurement at the higher fluences and full range of energies used during treatment allowing monitoring of the beam profile and total dose. Results and initial characterisation of sensors will be presented along with details of the proposed readout electronics. Radiation tests and studies with different electronics at the Clatterbridge Cancer Centre and the higher energy proton therapy facility of iThemba LABS in South Africa will also be shown.

  9. Radiation studies for the MOMENT target station

    NASA Astrophysics Data System (ADS)

    Xu, Qing-Nian; Tong, Jian-Fei; Vassilopoulos, Nikolaos; Cao, Jun; He, Miao; Hou, Zhi-Long; Jing, Han-Tao; Liu, Huai-Min; Lü, Xiao-Rui; Tang, Jing-Yu; Yuan, Ye; Zhao, Guang; Zheng, Yang-Heng

    2016-12-01

    The discovery of the neutrino mixing angle θ13 opens new opportunities for the discovery of leptonic CP violation at high intensity neutrino beams. MOMENT, a future neutrino facility with a high-power proton beam of 15 MW from a continuous-wave linac, is focused on that discovery. The high power of the proton beam causes extreme radiation conditions for the facility and especially for the target station, where the pion capture system of five superconducting solenoids is located. In this paper initial studies are performed for the effects of the radiation on the solenoid structure and the area surrounding it. A concept cooling system is also proposed. Supported by National Natural Science Foundation of China (11425524, 11527811, 11575226) and Strategic Priority Research Program of the Chinese Academy of Sciences (XDA10010100)

  10. Mechanism of pH-dependent activation of the sodium-proton antiporter NhaA

    NASA Astrophysics Data System (ADS)

    Huang, Yandong; Chen, Wei; Dotson, David L.; Beckstein, Oliver; Shen, Jana

    2016-10-01

    Escherichia coli NhaA is a prototype sodium-proton antiporter, which has been extensively characterized by X-ray crystallography, biochemical and biophysical experiments. However, the identities of proton carriers and details of pH-regulated mechanism remain controversial. Here we report constant pH molecular dynamics data, which reveal that NhaA activation involves a net charge switch of a pH sensor at the entrance of the cytoplasmic funnel and opening of a hydrophobic gate at the end of the funnel. The latter is triggered by charging of Asp164, the first proton carrier. The second proton carrier Lys300 forms a salt bridge with Asp163 in the inactive state, and releases a proton when a sodium ion binds Asp163. These data reconcile current models and illustrate the power of state-of-the-art molecular dynamics simulations in providing atomic details of proton-coupled transport across membrane which is challenging to elucidate by experimental techniques.

  11. Mechanism of pH-dependent activation of the sodium-proton antiporter NhaA

    PubMed Central

    Huang, Yandong; Chen, Wei; Dotson, David L.; Beckstein, Oliver; Shen, Jana

    2016-01-01

    Escherichia coli NhaA is a prototype sodium-proton antiporter, which has been extensively characterized by X-ray crystallography, biochemical and biophysical experiments. However, the identities of proton carriers and details of pH-regulated mechanism remain controversial. Here we report constant pH molecular dynamics data, which reveal that NhaA activation involves a net charge switch of a pH sensor at the entrance of the cytoplasmic funnel and opening of a hydrophobic gate at the end of the funnel. The latter is triggered by charging of Asp164, the first proton carrier. The second proton carrier Lys300 forms a salt bridge with Asp163 in the inactive state, and releases a proton when a sodium ion binds Asp163. These data reconcile current models and illustrate the power of state-of-the-art molecular dynamics simulations in providing atomic details of proton-coupled transport across membrane which is challenging to elucidate by experimental techniques. PMID:27708266

  12. Space station, 1959 to . .

    NASA Astrophysics Data System (ADS)

    Butler, G. V.

    1981-04-01

    Early space station designs are considered, taking into account Herman Oberth's first space station, the London Daily Mail Study, the first major space station design developed during the moon mission, and the Manned Orbiting Laboratory Program of DOD. Attention is given to Skylab, new space station studies, the Shuttle and Spacelab, communication satellites, solar power satellites, a 30 meter diameter radiometer for geological measurements and agricultural assessments, the mining of the moons, and questions of international cooperation. It is thought to be very probable that there will be very large space stations at some time in the future. However, for the more immediate future a step-by-step development that will start with Spacelab stations of 3-4 men is envisaged.

  13. Space Station Freedom Utilization Conference

    NASA Technical Reports Server (NTRS)

    1992-01-01

    The topics addressed in Space Station Freedom Utilization Conference are: (1) space station freedom overview and research capabilities; (2) space station freedom research plans and opportunities; (3) life sciences research on space station freedom; (4) technology research on space station freedom; (5) microgravity research and biotechnology on space station freedom; and (6) closing plenary.

  14. Reverse pH-dependence of chromophore protonation explains the large Stokes shift of the red fluorescent protein mKeima.

    PubMed

    Violot, Sebastien; Carpentier, Philippe; Blanchoin, Laurent; Bourgeois, Dominique

    2009-08-05

    The recently developed red fluorescent protein Keima exhibits the largest Stokes shift (180 nm) observed to date. Combining X-ray crystallography with (in crystallo) UV-visible absorption, fluorescence, and Raman spectroscopy, we have investigated molecular determinants of this peculiar property. The results demonstrate a pH-dependent "reverse chromophore protonation" triggered by the key residue Asp157 and which couples to cis/trans isomerization of the chromophore. These data provided guidelines to rationally design a useful Keima variant.

  15. Developments in optics and performance at BL13-XALOC, the macromolecular crystallography beamline at the Alba Synchrotron

    PubMed Central

    Juanhuix, Jordi; Gil-Ortiz, Fernando; Cuní, Guifré; Colldelram, Carles; Nicolás, Josep; Lidón, Julio; Boter, Eva; Ruget, Claude; Ferrer, Salvador; Benach, Jordi

    2014-01-01

    BL13-XALOC is currently the only macromolecular crystallography beamline at the 3 GeV ALBA synchrotron near Barcelona, Spain. The optics design is based on an in-vacuum undulator, a Si(111) channel-cut crystal monochromator and a pair of KB mirrors. It allows three main operation modes: a focused configuration, where both mirrors can focus the beam at the sample position to 52 µm × 5.5 µm FWHM (H × V); a defocused configuration that can match the size of the beam to the dimensions of the crystals or to focus the beam at the detector; and an unfocused configuration, where one or both mirrors are removed from the photon beam path. To achieve a uniform defocused beam, the slope errors of the mirrors were reduced down to 55 nrad RMS by employing a novel method that has been developed at the ALBA high-accuracy metrology laboratory. Thorough commissioning with X-ray beam and user operation has demonstrated an excellent energy and spatial stability of the beamline. The end-station includes a high-accuracy single-axis diffractometer, a removable mini-kappa stage, an automated sample-mounting robot and a photon-counting detector that allows shutterless operation. The positioning tables of the diffractometer and the detector are based on a novel and highly stable design. This equipment, together with the operation flexibility of the beamline, allows a large variety of types of crystals to be tackled, from medium-sized crystals with large unit-cell parameters to microcrystals. Several examples of data collections measured during beamline commissioning are described. The beamline started user operation on 18 July 2012. PMID:24971961

  16. Space station power system

    NASA Technical Reports Server (NTRS)

    Baraona, Cosmo R.

    1987-01-01

    The major requirements and guidelines that affect the space station configuration and power system are explained. The evolution of the space station power system from the NASA program development-feasibility phase through the current preliminary design phase is described. Several early station concepts are described and linked to the present concept. Trade study selections of photovoltaic system technologies are described in detail. A summary of present solar dynamic and power management and distribution systems is also given.

  17. Technology for space station

    NASA Astrophysics Data System (ADS)

    Colladay, R. S.; Carlisle, R. F.

    1984-10-01

    Some of the most significant advances made in the space station discipline technology program are examined. Technological tasks and advances in the areas of systems/operations, environmental control and life support systems, data management, power, thermal considerations, attitude control and stabilization, auxiliary propulsion, human capabilities, communications, and structures, materials, and mechanisms are discussed. An overview of NASA technology planning to support the initial space station and the evolutionary growth of the space station is given.

  18. X-ray crystallography, an essential tool for the determination of thermodynamic relationships between crystalline polymorphs.

    PubMed

    Céolin, R; Rietveld, I-B

    2016-01-01

    After a short review of the controversies surrounding the discovery of crystalline polymorphism in relation to our present day understanding, the methods of how to solve the stability hierarchy of different polymorphs will be briefly discussed. They involve either theoretical calculations, or, more commonly, experimental methods based on classical thermodynamics. The experimental approach is mainly carried out using heat-exchange data associated to the transition of one form into another. It will be demonstrated that work-related data associated to the phase transition should be taken into account and the role of X-ray crystallography therein will be discussed. X-ray crystallography has become increasingly precise and can nowadays provide specific volumes and their differences as a function of temperature, and also as a function of pressure, humidity, and time. Copyright © 2015 Académie Nationale de Pharmacie. Published by Elsevier Masson SAS. All rights reserved.

  19. Mapping the continuous reciprocal space intensity distribution of X-ray serial crystallography.

    PubMed

    Yefanov, Oleksandr; Gati, Cornelius; Bourenkov, Gleb; Kirian, Richard A; White, Thomas A; Spence, John C H; Chapman, Henry N; Barty, Anton

    2014-07-17

    Serial crystallography using X-ray free-electron lasers enables the collection of tens of thousands of measurements from an equal number of individual crystals, each of which can be smaller than 1 µm in size. This manuscript describes an alternative way of handling diffraction data recorded by serial femtosecond crystallography, by mapping the diffracted intensities into three-dimensional reciprocal space rather than integrating each image in two dimensions as in the classical approach. We call this procedure 'three-dimensional merging'. This procedure retains information about asymmetry in Bragg peaks and diffracted intensities between Bragg spots. This intensity distribution can be used to extract reflection intensities for structure determination and opens up novel avenues for post-refinement, while observed intensity between Bragg peaks and peak asymmetry are of potential use in novel direct phasing strategies.

  20. Operational experience of a large area x-ray camera for protein crystallography.

    SciTech Connect

    Joachimiak, A.; Jorden, A. R.; Loeffen, P. W.; Naday, I.; Sanishvili, R.; Westbrook, E. M.

    1999-07-13

    After 3 years experience of operating very large area (210mm x 210mm) CCD-based detectors at the Advanced Photon Source, operational experience is reported. Four such detectors have been built, two for Structural Biology Center (APS-1 and SBC-2), one for Basic Energy Sciences Synchrotrons Radiation Center (Gold-2) at Argonne National Laboratory's Advanced Photon Source and one for Osaka University by Oxford Instruments, for use at Spring 8 (PX-21O). The detector is specifically designed as a high resolution and fast readout camera for macromolecular crystallography. Design trade-offs for speed and size are reviewed in light of operational experience and future requirements are considered. Operational data and examples of crystallography data are presented, together with plans for more development.

  1. Beyond crystallography: diffractive imaging using coherent x-ray light sources.

    PubMed

    Miao, Jianwei; Ishikawa, Tetsuya; Robinson, Ian K; Murnane, Margaret M

    2015-05-01

    X-ray crystallography has been central to the development of many fields of science over the past century. It has now matured to a point that as long as good-quality crystals are available, their atomic structure can be routinely determined in three dimensions. However, many samples in physics, chemistry, materials science, nanoscience, geology, and biology are noncrystalline, and thus their three-dimensional structures are not accessible by traditional x-ray crystallography. Overcoming this hurdle has required the development of new coherent imaging methods to harness new coherent x-ray light sources. Here we review the revolutionary advances that are transforming x-ray sources and imaging in the 21st century. Copyright © 2015, American Association for the Advancement of Science.

  2. Towards an integrative structural biology approach: combining Cryo-TEM, X-ray crystallography, and NMR.

    PubMed

    Lengyel, Jeffrey; Hnath, Eric; Storms, Marc; Wohlfarth, Thomas

    2014-09-01

    Cryo-transmission electron microscopy (Cryo-TEM) and particularly single particle analysis is rapidly becoming the premier method for determining the three-dimensional structure of protein complexes, and viruses. In the last several years there have been dramatic technological improvements in Cryo-TEM, such as advancements in automation and use of improved detectors, as well as improved image processing techniques. While Cryo-TEM was once thought of as a low resolution structural technique, the method is currently capable of generating nearly atomic resolution structures on a routine basis. Moreover, the combination of Cryo-TEM and other methods such as X-ray crystallography, nuclear magnetic resonance spectroscopy, and molecular dynamics modeling are allowing researchers to address scientific questions previously thought intractable. Future technological developments are widely believed to further enhance the method and it is not inconceivable that Cryo-TEM could become as routine as X-ray crystallography for protein structure determination.

  3. Personal remarks on the future of protein crystallography and structural biology.

    PubMed

    Jaskolski, Mariusz

    2010-01-01

    Protein crystallography, the main experimental method of structural biology, has undergone in the recent past three revolutionary changes leading to its unexpected renaissance. They were connected with (i) the introduction of synchrotron radiation sources for X-ray diffraction experiments, (ii) implementation of Se-Met multiwavelength anomalous diffraction (MAD) for phasing, and (iii) initiation of structural genomics (SG) programs. It can be foreseen that in the next 10-15 years protein crystallography will continue to be in this revolutionary phase. We can expect not only an avalanche of protein crystal structures from SG centers, but also attacking of more demanding projects, such as the structure of membrane proteins and of very large macromolecular complexes. On the technological front, the introduction of X-ray radiation from free-electron lasers will revolutionize the experimental possibilities, making feasible even the imaging of single molecules and of intact biological cells.

  4. Long-Wavelength X-Ray Diffraction and Its Applications in Macromolecular Crystallography.

    PubMed

    Weiss, Manfred S

    2017-01-01

    For many years, diffraction experiments in macromolecular crystallography at X-ray wavelengths longer than that of Cu-K α (1.54 Å) have been largely underappreciated. Effects caused by increased X-ray absorption result in the fact that these experiments are more difficult than the standard diffraction experiments at short wavelengths. However, due to the also increased anomalous scattering of many biologically relevant atoms, important additional structural information can be obtained. This information, in turn, can be used for phase determination, for substructure identification, in molecular replacement approaches, as well as in structure refinement. This chapter reviews the possibilities and the difficulties associated with such experiments, and it provides a short description of two macromolecular crystallography synchrotron beam lines dedicated to long-wavelength X-ray diffraction experiments.

  5. Structural isomserism in gold nanoparticles revealed by X-ray crystallography

    PubMed Central

    Tian, Shubo; Li, Yi-Zhi; Li, Man-Bo; Yuan, Jinyun; Yang, Jinlong; Wu, Zhikun; Jin, Rongchao

    2015-01-01

    Revealing structural isomerism in nanoparticles using single-crystal X-ray crystallography remains a largely unresolved task, although it has been theoretically predicted with some experimental clues. Here we report a pair of structural isomers, Au38T and Au38Q, as evidenced using electrospray ionization mass spectrometry, X-ray photoelectron spectroscopy, thermogravimetric analysis and indisputable single-crystal X-ray crystallography. The two isomers show different optical and catalytic properties, and differences in stability. In addition, the less stable Au38T can be irreversibly transformed to the more stable Au38Q at 50 °C in toluene. This work may represent an important advance in revealing structural isomerism at the nanoscale. PMID:26482704

  6. Beyond crystallography: Diffractive imaging using coherent x-ray light sources

    SciTech Connect

    Miao, J.; Ishikawa, T.; Robinson, I. K.; Murnane, M. M.

    2015-04-30

    X-ray crystallography has been central to the development of many fields of science over the past century. It has now matured to a point that as long as good-quality crystals are available, their atomic structure can be routinely determined in three dimensions. However, many samples in physics, chemistry, materials science, nanoscience, geology, and biology are noncrystalline, and thus their three-dimensional structures are not accessible by traditional x-ray crystallography. Overcoming this hurdle has required the development of new coherent imaging methods to harness new coherent x-ray light sources. Here we review the revolutionary advances that are transforming x-ray sources and imaging in the 21st century.

  7. Protein crystal growth and the International Space Station

    NASA Technical Reports Server (NTRS)

    DeLucas, L. J.; Moore, K. M.; Long, M. M.

    1999-01-01

    Protein structural information plays a key role in understanding biological structure-function relationships and in the development of new pharmaceuticals for both chronic and infectious diseases. The Center for Macromolecular Crystallography (CMC) has devoted considerable effort studying the fundamental processes involved in macromolecular crystal growth both in a 1-g and microgravity environment. Results from experiments performed on more than 35 U.S. space shuttle flights have clearly indicated that microgravity can provide a beneficial environment for macromolecular crystal growth. This research has led to the development of a new generation of pharmaceuticals that are currently in preclinical or clinical trials for diseases such as cutaneous T-cell lymphoma, psoriasis, rheumatoid arthritis, AIDS, influenza, stroke and other cardiovascular complications. The International Space Station (ISS) provides an opportunity to have complete crystallographic capability on orbit, which was previously not possible with the space shuttle orbiter. As envisioned, the x-ray Crystallography Facility (XCF) will be a complete facility for growing protein crystals; selecting, harvesting, and mounting sample crystals for x-ray diffraction; cryo-freezing mounted crystals if necessary; performing x-ray diffraction studies; and downlinking the data for use by crystallographers on the ground. Other advantages of such a facility include crystal characterization so that iterations in the crystal growth conditions can be made, thereby optimizing the final crystals produced in a three month interval on the ISS.

  8. Protein crystal growth and the International Space Station

    NASA Technical Reports Server (NTRS)

    DeLucas, L. J.; Moore, K. M.; Long, M. M.

    1999-01-01

    Protein structural information plays a key role in understanding biological structure-function relationships and in the development of new pharmaceuticals for both chronic and infectious diseases. The Center for Macromolecular Crystallography (CMC) has devoted considerable effort studying the fundamental processes involved in macromolecular crystal growth both in a 1-g and microgravity environment. Results from experiments performed on more than 35 U.S. space shuttle flights have clearly indicated that microgravity can provide a beneficial environment for macromolecular crystal growth. This research has led to the development of a new generation of pharmaceuticals that are currently in preclinical or clinical trials for diseases such as cutaneous T-cell lymphoma, psoriasis, rheumatoid arthritis, AIDS, influenza, stroke and other cardiovascular complications. The International Space Station (ISS) provides an opportunity to have complete crystallographic capability on orbit, which was previously not possible with the space shuttle orbiter. As envisioned, the x-ray Crystallography Facility (XCF) will be a complete facility for growing protein crystals; selecting, harvesting, and mounting sample crystals for x-ray diffraction; cryo-freezing mounted crystals if necessary; performing x-ray diffraction studies; and downlinking the data for use by crystallographers on the ground. Other advantages of such a facility include crystal characterization so that iterations in the crystal growth conditions can be made, thereby optimizing the final crystals produced in a three month interval on the ISS.

  9. Crystallography from Haüy to Laue: controversies on the molecular and atomistic nature of solids.

    PubMed

    Kubbinga, Henk

    2012-01-01

    The history of crystallography has been assessed in the context of the emergence and spread of the molecular theory. The present paper focuses on the 19th century, which saw the emancipation of crystallography as a science sui generis. Around 1800, Laplace's molecularism called the tune in the various sciences (physics, chemistry, biology, crystallography). In crystallography, two schools opposed each other: that of Weiss, in Berlin, and that of Haüy, in Paris. Symmetry proved essential. It will be shown how the lattice theory arose in an essentially molecular framework and how group theory imposed itself. The salt hydrates suggested the idea of (two or more) superimposed molecular lattices. Gradually it became clear that an ultimate lattice theory ought to be atomic. The experiments of Laue, Friedrich and Knipping confirmed that atomic basis.

  10. Space Station operations

    NASA Technical Reports Server (NTRS)

    Gray, R. H.

    1985-01-01

    An evaluation of the success of the Space Station will be based on the service provided to the customers by the Station crew, the productivity of the crew, and the costs of operation. Attention is given to details regarding Space Station operations, a summary of operational philosophies and requirements, logistics and resupply operations, prelaunch processing and launch operations, on-orbit operations, aspects of maintainability and maintenance, habitability, and questions of medical care. A logistics module concept is considered along with a logistics module processing timeline, a habitability module concept, and a Space Station rescue mission.

  11. Control of space stations

    NASA Technical Reports Server (NTRS)

    Lee, K. Y.

    1983-01-01

    A study is made to develop controllers for the NASA-JSC Triangular Space Station and evaluate their performances to make recommendations for structural design and/or control alternatives. The control system design assumes the rigid body of the Space Station and developes the lumped parameter control system by using the Inverse Optimal Control Theory. In order to evaluate the performance of the control system, a Parameter Estimation algorithm is being developed which will be used in modeling an equivalent but simpler Space Station model. Finally, a scaled version of the Space Station is being built for the purpose of physical experiments to evaluate the control system performance.

  12. Space Station fluid resupply

    NASA Astrophysics Data System (ADS)

    Winters, Al

    Viewgraphs on space station fluid resupply are presented. Space Station Freedom is resupplied with supercritical O2 and N2 for the ECLSS and USL on a 180 day resupply cycle. Resupply fluids are stored in the subcarriers on station between resupply cycles and transferred to the users as required. ECLSS contingency fluids (O2 and N2) are supplied and stored on station in a gaseous state. Efficiency and flexibility are major design considerations. Subcarrier approach allows multiple manifest combinations. Growth is achieved by adding modular subcarriers.

  13. Station Crew Celebrates Christmas

    NASA Image and Video Library

    Aboard the orbiting International Space Station, Expedition 34 Commander Kevin Ford, Russian Flight Engineers Oleg Novitskiy, Evgeny Tarelkin and Roman Romanenko, NASA Flight Engineer Tom Marshburn...

  14. Proton therapy in Japan

    SciTech Connect

    Tsunemoto, H.; Morita, S.; Ishikawa, T.; Furukawa, S.; Kawachi, K.; Kanai, T.; Ohara, H.; Kitagawa, T.; Inada, T.

    1985-01-01

    There are two facilities for clinical trials with protons in Japan: the National Institute of Radiological Sciences (NIRS), Chiba, and the Particle Radiation Medical Science Center (PARMS), University of Tsukuba. At the National Institute of Radiological Sciences, patient treatment with the 70 MeV proton beam began in November 1979, and 29 patients were treated through December 1984. Of 11 patients who received protons only, 9 have had local control of the tumor. Two of the 9 patients, suffering from recurrent tumor after radical photon beam irradiation, developed complications after proton treatment. In the patients treated with photons or neutrons followed by proton boost, tumors were controlled in 12 of 18 patients (66.6%), and no complications were observed in this series. Malignant melanoma could not be controlled with the proton beam. A spot-beam-scanning system for protons has been effectively used in the clinical trials to minimize the dose to the normal tissues and to concentrate the dose in the target volume. At the Particle Radiation Medical Science Center, University of Tsukuba, treatment with a vertical 250 MeV proton beam was begun in April 1983, and 22 patients were treated through February 1984. Local control of the tumor was observed in 14 of 22 patients (63.6%), whereas there was no local control in the treatment of glioblastoma multiforme. There have been no severe complications in patients treated at PARMS. The results suggest that local control of tumors will be better with proton beams than with photon beams, whereas additional modalities are required to manage radioresistant tumors.

  15. Concentric-flow electrokinetic injector enables serial crystallography of ribosome and photosystem II.

    PubMed

    Sierra, Raymond G; Gati, Cornelius; Laksmono, Hartawan; Dao, E Han; Gul, Sheraz; Fuller, Franklin; Kern, Jan; Chatterjee, Ruchira; Ibrahim, Mohamed; Brewster, Aaron S; Young, Iris D; Michels-Clark, Tara; Aquila, Andrew; Liang, Mengning; Hunter, Mark S; Koglin, Jason E; Boutet, Sébastien; Junco, Elia A; Hayes, Brandon; Bogan, Michael J; Hampton, Christina Y; Puglisi, Elisabetta V; Sauter, Nicholas K; Stan, Claudiu A; Zouni, Athina; Yano, Junko; Yachandra, Vittal K; Soltis, S Michael; Puglisi, Joseph D; DeMirci, Hasan

    2016-01-01

    We describe a concentric-flow electrokinetic injector for efficiently delivering microcrystals for serial femtosecond X-ray crystallography analysis that enables studies of challenging biological systems in their unadulterated mother liquor. We used the injector to analyze microcrystals of Geobacillus stearothermophilus thermolysin (2.2-Å structure), Thermosynechococcus elongatus photosystem II (<3-Å diffraction) and Thermus thermophilus small ribosomal subunit bound to the antibiotic paromomycin at ambient temperature (3.4-Å structure).

  16. Preparation and Delivery of Protein Microcrystals in Lipidic Cubic Phase for Serial Femtosecond Crystallography

    PubMed Central

    Ishchenko, Andrii; Cherezov, Vadim; Liu, Wei

    2016-01-01

    Membrane proteins (MPs) are essential components of cellular membranes and primary drug targets. Rational drug design relies on precise structural information, typically obtained by crystallography; however MPs are difficult to crystallize. Recent progress in MP structural determination has benefited greatly from the development of lipidic cubic phase (LCP) crystallization methods, which typically yield well-diffracting, but often small crystals that suffer from radiation damage during traditional crystallographic data collection at synchrotron sources. The development of new-generation X-ray free-electron laser (XFEL) sources that produce extremely bright femtosecond pulses has enabled room temperature data collection from microcrystals with no or negligible radiation damage. Our recent efforts in combining LCP technology with serial femtosecond crystallography (LCP-SFX) have resulted in high-resolution structures of several human G protein-coupled receptors, which represent a notoriously difficult target for structure determination. In the LCP-SFX technique, LCP is recruited as a matrix for both growth and delivery of MP microcrystals to the intersection of the injector stream with an XFEL beam for crystallographic data collection. It has been demonstrated that LCP-SFX can substantially improve the diffraction resolution when only sub-10 µm crystals are available, or when the use of smaller crystals at room temperature can overcome various problems associated with larger cryocooled crystals, such as accumulation of defects, high mosaicity and cryocooling artifacts. Future advancements in X-ray sources and detector technologies should make serial crystallography highly attractive and practicable for implementation not only at XFELs, but also at more accessible synchrotron beamlines. Here we present detailed visual protocols for the preparation, characterization and delivery of microcrystals in LCP for serial crystallography experiments. These protocols include

  17. Concentric-flow electrokinetic injector enables serial crystallography of ribosome and photosystem II

    DOE PAGES

    Sierra, Raymond G.; Gati, Cornelius; Laksmono, Hartawan; ...

    2015-11-30

    In this paper, we describe a concentric-flow electrokinetic injector for efficiently delivering microcrystals for serial femtosecond X-ray crystallography analysis that enables studies of challenging biological systems in their unadulterated mother liquor. Finally, we used the injector to analyze microcrystals of Geobacillus stearothermophilus thermolysin (2.2-Å structure), Thermosynechococcus elongatus photosystem II (<3-Å diffraction) and Thermus thermophilus small ribosomal subunit bound to the antibiotic paromomycin at ambient temperature (3.4-Å structure).

  18. Stress Corrosion Cracking Facet Crystallography of Ti-8Al-1Mo-1V (Preprint)

    DTIC Science & Technology

    2011-05-01

    both specimens, the regions not characterized by faceted fracture generally consisted of features like flutes [33;34] and dimples consistent with...received specimen studied here switches from ductile dimple / fluted growth [34] to faceted growth with increasing crack length. Since crack formation...Crystallography of fluted fracture in near-α titanium alloys, Metall. Mater. Trans. A. 41 (2010) 22-25. [35] J.C. Chesnutt, J.C. Williams, Comments on the

  19. Concentric-flow electrokinetic injector enables serial crystallography of ribosome and photosystem II

    SciTech Connect

    Sierra, Raymond G.; Gati, Cornelius; Laksmono, Hartawan; Dao, E. Han; Gul, Sheraz; Fuller, Franklin; Kern, Jan; Chatterjee, Ruchira; Ibrahim, Mohamed; Brewster, Aaron S.; Young, Iris D.; Michels-Clark, Tara; Aquila, Andrew; Liang, Mengning; Hunter, Mark S.; Koglin, Jason E.; Boutet, Sébastien; Junco, Elia A.; Hayes, Brandon; Bogan, Michael J.; Hampton, Christina Y.; Puglisi, Elisabetta V.; Sauter, Nicholas K.; Stan, Claudiu A.; Zouni, Athina; Yano, Junko; Yachandra, Vittal K.; Soltis, S. Michael; Puglisi, Joseph D.; DeMirci, Hasan

    2015-11-30

    We describe a concentric-flow electrokinetic injector for efficiently delivering microcrystals for serial femtosecond X-ray crystallography analysis that enables studies of challenging biological systems in their unadulterated mother liquor. We used the injector to analyze microcrystals of Geobacillus stearothermophilus thermolysin (2.2-Å structure), Thermosynechococcus elongatus photosystem II (<3-Å diffraction) and Thermus thermophilus small ribosomal subunit bound to the antibiotic paromomycin at ambient temperature (3.4-Å structure).

  20. Distributed control of protein crystallography beamline 5.0 using CORBA

    SciTech Connect

    Timossi, Chris

    1999-09-24

    The Protein Crystallography Beamline at Berkeley Lab's Advanced Light Source is a facility that is being used to solve the structure of proteins. The software that is being used to control this beamline uses Java for user interface applications which communicate via CORBA with workstations that control the beamline hardware. We describe the software architecture for the beamline and our experiences after two years of operation.

  1. An exponential modeling algorithm for protein structure completion by X-ray crystallography.

    PubMed

    Shneerson, V L; Wild, D L; Saldin, D K

    2001-03-01

    An exponential modeling algorithm is developed for protein structure completion by X-ray crystallography and tested on experimental data from a 59-residue protein. An initial noisy difference Fourier map of missing residues of up to half of the protein is transformed by the algorithm into one that allows easy identification of the continuous tube of electron density associated with that polypeptide chain. The method incorporates the paradigm of phase hypothesis generation and cross validation within an automated scheme.

  2. Two-Dimensional Crystallization of the Ca(2+)-ATPase for Electron Crystallography.

    PubMed

    Glaves, John Paul; Primeau, Joseph O; Young, Howard S

    2016-01-01

    Electron crystallography of two-dimensional crystalline arrays is a powerful alternative for the structure determination of membrane proteins. The advantages offered by this technique include a native membrane environment and the ability to closely correlate function and dynamics with crystalline preparations and structural data. Herein, we provide a detailed protocol for the reconstitution and two-dimensional crystallization of the sarcoplasmic reticulum calcium pump (also known as Ca(2+)-ATPase or SERCA) and its regulatory subunits phospholamban and sarcolipin.

  3. NMR crystallography: structure and properties of materials from solid-state nuclear magnetic resonance observables.

    PubMed

    Bryce, David L

    2017-07-01

    This topical review provides a brief overview of recent developments in NMR crystallography and related NMR approaches to studying the properties of molecular and ionic solids. Areas of complementarity with diffraction-based methods are underscored. These include the study of disordered systems, of dynamic systems, and other selected examples where NMR can provide unique insights. Highlights from the literature as well as recent work from my own group are discussed.

  4. System and method for forming synthetic protein crystals to determine the conformational structure by crystallography

    DOEpatents

    Craig, George D.; Glass, Robert; Rupp, Bernhard

    1997-01-01

    A method for forming synthetic crystals of proteins in a carrier fluid by use of the dipole moments of protein macromolecules that self-align in the Helmholtz layer adjacent to an electrode. The voltage gradients of such layers easily exceed 10.sup.6 V/m. The synthetic protein crystals are subjected to x-ray crystallography to determine the conformational structure of the protein involved.

  5. System and method for forming synthetic protein crystals to determine the conformational structure by crystallography

    DOEpatents

    Craig, G.D.; Glass, R.; Rupp, B.

    1997-01-28

    A method is disclosed for forming synthetic crystals of proteins in a carrier fluid by use of the dipole moments of protein macromolecules that self-align in the Helmholtz layer adjacent to an electrode. The voltage gradients of such layers easily exceed 10{sup 6}V/m. The synthetic protein crystals are subjected to x-ray crystallography to determine the conformational structure of the protein involved. 2 figs.

  6. The Proton launcher

    NASA Astrophysics Data System (ADS)

    Bond, A.; Parfitt, J.

    1985-08-01

    The capabilities, design features and missions for the Soviet Proton booster are described. The Proton, outfitted with six strap-on boosters, launched the Vega 1 and 2 Venus/Halley dual mission spacecraft. RD-253 engines burn N2O4 and UDMH fuels, possibly through a preburner before the combustion chamber. A vacuum thrust of 450,000 lb is projected for the engine. Analyses are presented to set the launch weight at 1,600,000 lb, implying that the vehicle is based on an ICBM design. It is suggested that the Proton has sufficiently high noise and vibration levels to prohibit it from being man-rated.

  7. Are protons nonidentical fermions?

    SciTech Connect

    Mart, T.

    2014-09-25

    We briefly review the progress of our investigation on the electric (charge) radius of the proton. In order to explain the recently measured proton radius, which is significantly smaller than the standard CODATA value, we assume that the real protons radii are not identical, they are randomly distributed in a certain range. To obtain the measured radius we average the radii and fit both the mean radius and the range. By using an averaged dipole form factor we obtain the charge radius r{sub E} = 0.8333 fm, in accordance with the recent measurement of the Lamb shift in muonic hydrogen.

  8. SPINE-compatible ‘carboloops’: a new microshaped vitreous carbon sample mount for X-ray and neutron crystallography

    PubMed Central

    Romoli, Filippo; Mossou, Estelle; Cuypers, Maxime; van der Linden, Peter; Carpentier, Philippe; Mason, Sax A.; Forsyth, V. Trevor; McSweeney, Sean

    2014-01-01

    A novel vitreous carbon mount for macromolecular crystallography, suitable for neutron and X-ray crystallographic studies, has been developed. The technology described here is compatible both with X-ray and neutron cryo-crystallography. The mounts have low density and low background scattering for both neutrons and X-rays. They are prepared by laser cutting, allowing high standards of production quality, the ability to custom-design the mount to specific crystal sizes and large-scale production. PMID:24817737

  9. Electron crystallography of ultrathin 3D protein crystals: atomic model with charges.

    PubMed

    Yonekura, Koji; Kato, Kazuyuki; Ogasawara, Mitsuo; Tomita, Masahiro; Toyoshima, Chikashi

    2015-03-17

    Membrane proteins and macromolecular complexes often yield crystals too small or too thin for even the modern synchrotron X-ray beam. Electron crystallography could provide a powerful means for structure determination with such undersized crystals, as protein atoms diffract electrons four to five orders of magnitude more strongly than they do X-rays. Furthermore, as electron crystallography yields Coulomb potential maps rather than electron density maps, it could provide a unique method to visualize the charged states of amino acid residues and metals. Here we describe an attempt to develop a methodology for electron crystallography of ultrathin (only a few layers thick) 3D protein crystals and present the Coulomb potential maps at 3.4-Å and 3.2-Å resolution, respectively, obtained from Ca(2+)-ATPase and catalase crystals. These maps demonstrate that it is indeed possible to build atomic models from such crystals and even to determine the charged states of amino acid residues in the Ca(2+)-binding sites of Ca(2+)-ATPase and that of the iron atom in the heme in catalase.

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

    PubMed Central

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

    2014-01-01

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

  11. The room temperature crystal structure of a bacterial phytochrome determined by serial femtosecond crystallography

    DOE PAGES

    Edlund, Petra; Takala, Heikki; Claesson, Elin; ...

    2016-10-19

    Phytochromes are a family of photoreceptors that control light responses of plants, fungi and bacteria. A sequence of structural changes, which is not yet fully understood, leads to activation of an output domain. Time-resolved serial femtosecond crystallography (SFX) can potentially shine light on these conformational changes. Here we report the room temperature crystal structure of the chromophore-binding domains of the Deinococcus radiodurans phytochrome at 2.1 Å resolution. The structure was obtained by serial femtosecond X-ray crystallography from microcrystals at an X-ray free electron laser. We find overall good agreement compared to a crystal structure at 1.35 Å resolution derived frommore » conventional crystallography at cryogenic temperatures, which we also report here. The thioether linkage between chromophore and protein is subject to positional ambiguity at the synchrotron, but is fully resolved with SFX. As a result, the study paves the way for time-resolved structural investigations of the phytochrome photocycle with time-resolved SFX.« less

  12. The room temperature crystal structure of a bacterial phytochrome determined by serial femtosecond crystallography

    SciTech Connect

    Edlund, Petra; Takala, Heikki; Claesson, Elin; Henry, Léocadie; Dods, Robert; Lehtivuori, Heli; Panman, Matthijs; Pande, Kanupriya; White, Thomas; Nakane, Takanori; Berntsson, Oskar; Gustavsson, Emil; Båth, Petra; Modi, Vaibhav; Roy-Chowdhury, Shatabdi; Zook, James; Berntsen, Peter; Pandey, Suraj; Poudyal, Ishwor; Tenboer, Jason; Kupitz, Christopher; Barty, Anton; Fromme, Petra; Koralek, Jake D.; Tanaka, Tomoyuki; Spence, John; Liang, Mengning; Hunter, Mark S.; Boutet, Sebastien; Nango, Eriko; Moffat, Keith; Groenhof, Gerrit; Ihalainen, Janne; Stojković, Emina A.; Schmidt, Marius; Westenhoff, Sebastian

    2016-10-19

    Phytochromes are a family of photoreceptors that control light responses of plants, fungi and bacteria. A sequence of structural changes, which is not yet fully understood, leads to activation of an output domain. Time-resolved serial femtosecond crystallography (SFX) can potentially shine light on these conformational changes. Here we report the room temperature crystal structure of the chromophore-binding domains of the Deinococcus radiodurans phytochrome at 2.1 Å resolution. The structure was obtained by serial femtosecond X-ray crystallography from microcrystals at an X-ray free electron laser. We find overall good agreement compared to a crystal structure at 1.35 Å resolution derived from conventional crystallography at cryogenic temperatures, which we also report here. The thioether linkage between chromophore and protein is subject to positional ambiguity at the synchrotron, but is fully resolved with SFX. As a result, the study paves the way for time-resolved structural investigations of the phytochrome photocycle with time-resolved SFX.

  13. The room temperature crystal structure of a bacterial phytochrome determined by serial femtosecond crystallography

    PubMed Central

    Edlund, Petra; Takala, Heikki; Claesson, Elin; Henry, Léocadie; Dods, Robert; Lehtivuori, Heli; Panman, Matthijs; Pande, Kanupriya; White, Thomas; Nakane, Takanori; Berntsson, Oskar; Gustavsson, Emil; Båth, Petra; Modi, Vaibhav; Roy-Chowdhury, Shatabdi; Zook, James; Berntsen, Peter; Pandey, Suraj; Poudyal, Ishwor; Tenboer, Jason; Kupitz, Christopher; Barty, Anton; Fromme, Petra; Koralek, Jake D.; Tanaka, Tomoyuki; Spence, John; Liang, Mengning; Hunter, Mark S.; Boutet, Sebastien; Nango, Eriko; Moffat, Keith; Groenhof, Gerrit; Ihalainen, Janne; Stojković, Emina A.; Schmidt, Marius; Westenhoff, Sebastian

    2016-01-01

    Phytochromes are a family of photoreceptors that control light responses of plants, fungi and bacteria. A sequence of structural changes, which is not yet fully understood, leads to activation of an output domain. Time-resolved serial femtosecond crystallography (SFX) can potentially shine light on these conformational changes. Here we report the room temperature crystal structure of the chromophore-binding domains of the Deinococcus radiodurans phytochrome at 2.1 Å resolution. The structure was obtained by serial femtosecond X-ray crystallography from microcrystals at an X-ray free electron laser. We find overall good agreement compared to a crystal structure at 1.35 Å resolution derived from conventional crystallography at cryogenic temperatures, which we also report here. The thioether linkage between chromophore and protein is subject to positional ambiguity at the synchrotron, but is fully resolved with SFX. The study paves the way for time-resolved structural investigations of the phytochrome photocycle with time-resolved SFX. PMID:27756898

  14. Integrated Controlling System and Unified Database for High Throughput Protein Crystallography Experiments

    NASA Astrophysics Data System (ADS)

    Gaponov, Yu. A.; Igarashi, N.; Hiraki, M.; Sasajima, K.; Matsugaki, N.; Suzuki, M.; Kosuge, T.; Wakatsuki, S.

    2004-05-01

    An integrated controlling system and a unified database for high throughput protein crystallography experiments have been developed. Main features of protein crystallography experiments (purification, crystallization, crystal harvesting, data collection, data processing) were integrated into the software under development. All information necessary to perform protein crystallography experiments is stored (except raw X-ray data that are stored in a central data server) in a MySQL relational database. The database contains four mutually linked hierarchical trees describing protein crystals, data collection of protein crystal and experimental data processing. A database editor was designed and developed. The editor supports basic database functions to view, create, modify and delete user records in the database. Two search engines were realized: direct search of necessary information in the database and object oriented search. The system is based on TCP/IP secure UNIX sockets with four predefined sending and receiving behaviors, which support communications between all connected servers and clients with remote control functions (creating and modifying data for experimental conditions, data acquisition, viewing experimental data, and performing data processing). Two secure login schemes were designed and developed: a direct method (using the developed Linux clients with secure connection) and an indirect method (using the secure SSL connection using secure X11 support from any operating system with X-terminal and SSH support). A part of the system has been implemented on a new MAD beam line, NW12, at the Photon Factory Advanced Ring for general user experiments.

  15. The room temperature crystal structure of a bacterial phytochrome determined by serial femtosecond crystallography

    NASA Astrophysics Data System (ADS)

    Edlund, Petra; Takala, Heikki; Claesson, Elin; Henry, Léocadie; Dods, Robert; Lehtivuori, Heli; Panman, Matthijs; Pande, Kanupriya; White, Thomas; Nakane, Takanori; Berntsson, Oskar; Gustavsson, Emil; Båth, Petra; Modi, Vaibhav; Roy-Chowdhury, Shatabdi; Zook, James; Berntsen, Peter; Pandey, Suraj; Poudyal, Ishwor; Tenboer, Jason; Kupitz, Christopher; Barty, Anton; Fromme, Petra; Koralek, Jake D.; Tanaka, Tomoyuki; Spence, John; Liang, Mengning; Hunter, Mark S.; Boutet, Sebastien; Nango, Eriko; Moffat, Keith; Groenhof, Gerrit; Ihalainen, Janne; Stojković, Emina A.; Schmidt, Marius; Westenhoff, Sebastian

    2016-10-01

    Phytochromes are a family of photoreceptors that control light responses of plants, fungi and bacteria. A sequence of structural changes, which is not yet fully understood, leads to activation of an output domain. Time-resolved serial femtosecond crystallography (SFX) can potentially shine light on these conformational changes. Here we report the room temperature crystal structure of the chromophore-binding domains of the Deinococcus radiodurans phytochrome at 2.1 Å resolution. The structure was obtained by serial femtosecond X-ray crystallography from microcrystals at an X-ray free electron laser. We find overall good agreement compared to a crystal structure at 1.35 Å resolution derived from conventional crystallography at cryogenic temperatures, which we also report here. The thioether linkage between chromophore and protein is subject to positional ambiguity at the synchrotron, but is fully resolved with SFX. The study paves the way for time-resolved structural investigations of the phytochrome photocycle with time-resolved SFX.

  16. Raster-scanning serial protein crystallography using micro- and nano-focused synchrotron beams

    SciTech Connect

    Coquelle, Nicolas; Brewster, Aaron S.; Kapp, Ulrike; Shilova, Anastasya; Weinhausen, Britta; Burghammer, Manfred; Colletier, Jacques-Philippe

    2015-05-01

    A raster scanning serial protein crystallography approach is presented, that consumes as low ∼200–700 nl of sedimented crystals. New serial data pre-analysis software, NanoPeakCell, is introduced. High-resolution structural information was obtained from lysozyme microcrystals (20 µm in the largest dimension) using raster-scanning serial protein crystallography on micro- and nano-focused beamlines at the ESRF. Data were collected at room temperature (RT) from crystals sandwiched between two silicon nitride wafers, thereby preventing their drying, while limiting background scattering and sample consumption. In order to identify crystal hits, new multi-processing and GUI-driven Python-based pre-analysis software was developed, named NanoPeakCell, that was able to read data from a variety of crystallographic image formats. Further data processing was carried out using CrystFEL, and the resultant structures were refined to 1.7 Å resolution. The data demonstrate the feasibility of RT raster-scanning serial micro- and nano-protein crystallography at synchrotrons and validate it as an alternative approach for the collection of high-resolution structural data from micro-sized crystals. Advantages of the proposed approach are its thriftiness, its handling-free nature, the reduced amount of sample required, the adjustable hit rate, the high indexing rate and the minimization of background scattering.

  17. Implementation of remote monitoring and diffraction evaluation systems at the Photon Factory macromolecular crystallography beamlines

    PubMed Central

    Yamada, Yusuke; pHonda, Nobuo; Matsugaki, Naohiro; Igarashi, Noriyuki; Hiraki, Masahiko; Wakatsuki, Soichi

    2008-01-01

    Owing to recent advances in high-throughput technology in macromolecular crystallography beamlines, such as high-brilliant X-ray sources, high-speed readout detectors and robotics, the number of samples that can be examined in a single visit to the beamline has increased dramatically. In order to make these experiments more efficient, two functions, remote monitoring and diffraction image evaluation, have been implemented in the macromolecular crystallography beamlines at the Photon Factory (PF). Remote monitoring allows scientists to participate in the experiment by watching from their laboratories, without having to come to the beamline. Diffraction image evaluation makes experiments easier, especially when using the sample exchange robot. To implement these two functions, two independent clients have been developed that work specifically for remote monitoring and diffraction image evaluation. In the macromolecular crystallography beamlines at PF, beamline control is performed using STARS (simple transmission and retrieval system). The system adopts a client–server style in which client programs communicate with each other through a server process using the STARS protocol. This is an advantage of the extension of the system; implementation of these new functions required few modifications of the existing system. PMID:18421163

  18. Affinity Crystallography: A New Approach to Extracting High-Affinity Enzyme Inhibitors from Natural Extracts.

    PubMed

    Aguda, Adeleke H; Lavallee, Vincent; Cheng, Ping; Bott, Tina M; Meimetis, Labros G; Law, Simon; Nguyen, Nham T; Williams, David E; Kaleta, Jadwiga; Villanueva, Ivan; Davies, Julian; Andersen, Raymond J; Brayer, Gary D; Brömme, Dieter

    2016-08-26

    Natural products are an important source of novel drug scaffolds. The highly variable and unpredictable timelines associated with isolating novel compounds and elucidating their structures have led to the demise of exploring natural product extract libraries in drug discovery programs. Here we introduce affinity crystallography as a new methodology that significantly shortens the time of the hit to active structure cycle in bioactive natural product discovery research. This affinity crystallography approach is illustrated by using semipure fractions of an actinomycetes culture extract to isolate and identify a cathepsin K inhibitor and to compare the outcome with the traditional assay-guided purification/structural analysis approach. The traditional approach resulted in the identification of the known inhibitor antipain (1) and its new but lower potency dehydration product 2, while the affinity crystallography approach led to the identification of a new high-affinity inhibitor named lichostatinal (3). The structure and potency of lichostatinal (3) was verified by total synthesis and kinetic characterization. To the best of our knowledge, this is the first example of isolating and characterizing a potent enzyme inhibitor from a partially purified crude natural product extract using a protein crystallographic approach.

  19. Beta-delayed proton emission from 20Mg

    NASA Astrophysics Data System (ADS)

    Lund, M. V.; Andreyev, A.; Borge, M. J. G.; Cederkäll, J.; De Witte, H.; Fraile, L. M.; Fynbo, H. O. U.; Greenlees, P. T.; Harkness-Brennan, L. J.; Howard, A. M.; Huyse, M.; Jonson, B.; Judson, D. S.; Kirsebom, O. S.; Konki, J.; Kurcewicz, J.; Lazarus, I.; Lica, R.; Lindberg, S.; Madurga, M.; Marginean, N.; Marginean, R.; Marroquin, I.; Mihai, C.; Munch, M.; Nacher, E.; Negret, A.; Nilsson, T.; Page, R. D.; Pascu, S.; Perea, A.; Pucknell, V.; Rahkila, P.; Rapisarda, E.; Riisager, K.; Rotaru, F.; Sotty, C.; Stanoiu, M.; Tengblad, O.; Turturica, A.; Van Duppen, P.; Vedia, V.; Wadsworth, R.; Warr, N.

    2016-10-01

    Beta-delayed proton emission from 20 Mg has been measured at ISOLDE, CERN, with the ISOLDE Decay Station (IDS) setup including both charged-particle and gamma-ray detection capabilities. A total of 27 delayed proton branches were measured including seven so far unobserved. An updated decay scheme, including three new resonances above the proton separation energy in 20 Na and more precise resonance energies, is presented. Beta-decay feeding to two resonances above the Isobaric Analogue State (IAS) in 20 Na is observed. This may allow studies of the 4032.9(2.4)keV resonance in 19 Ne through the beta decay of 20 Mg, which is important for the astrophysically relevant reaction 15O( α, γ)19Ne . Beta-delayed protons were used to obtain a more precise value for the half-life of 20 Mg, 91.4(1.0)ms.

  20. In vivo crystallography at X-ray free-electron lasers: the next generation of structural biology?

    PubMed

    Gallat, François-Xavier; Matsugaki, Naohiro; Coussens, Nathan P; Yagi, Koichiro J; Boudes, Marion; Higashi, Tetsuya; Tsuji, Daisuke; Tatano, Yutaka; Suzuki, Mamoru; Mizohata, Eiichi; Tono, Kensuke; Joti, Yasumasa; Kameshima, Takashi; Park, Jaehyun; Song, Changyong; Hatsui, Takaki; Yabashi, Makina; Nango, Eriko; Itoh, Kohji; Coulibaly, Fasséli; Tobe, Stephen; Ramaswamy, S; Stay, Barbara; Iwata, So; Chavas, Leonard M G

    2014-07-17

    The serendipitous discovery of the spontaneous growth of protein crystals inside cells has opened the field of crystallography to chemically unmodified samples directly available from their natural environment. On the one hand, through in vivo crystallography, protocols for protein crystal preparation can be highly simplified, although the technique suffers from difficulties in sampling, particularly in the extraction of the crystals from the cells partly due to their small sizes. On the other hand, the extremely intense X-ray pulses emerging from X-ray free-electron laser (XFEL) sources, along with the appearance of serial femtosecond crystallography (SFX) is a milestone for radiation damage-free protein structural studies but requires micrometre-size crystals. The combination of SFX with in vivo crystallography has the potential to boost the applicability of these techniques, eventually bringing the field to the point where in vitro sample manipulations will no longer be required, and direct imaging of the crystals from within the cells will be achievable. To fully appreciate the diverse aspects of sample characterization, handling and analysis, SFX experiments at the Japanese SPring-8 angstrom compact free-electron laser were scheduled on various types of in vivo grown crystals. The first experiments have demonstrated the feasibility of the approach and suggest that future in vivo crystallography applications at XFELs will be another alternative to nano-crystallography. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

  1. THEORY OF PROTON EMITTERS

    SciTech Connect

    P. TALOU

    2000-08-01

    Modern theoretical methods used to interpret recent experimental data on ground-state proton emission near the proton drip line are reviewed. Most of them are stationary and are aimed to compute proton decay widths {Gamma}{sub p} only. Comparison is made between these approaches before being compared to experimental data. Our time-dependent approach based on the numerical solution of the time-dependent Schroedinger equation (TDSE) for initial quasi-stationary single-proton states is then introduced. It is shown that much deeper insights into the physics of this clean multidimensional quantum tunneling effect can be accessed, and that in addition to {Gamma}{sub p}, other physical quantities could be tested experimentally, offering new stringent tests on nuclear physics models away from the valley of {beta}-stability. Finally, the necessity of using the TDSE approach in more complex, dynamical, problems is demonstrated.

  2. The Proton Radius Puzzle

    NASA Astrophysics Data System (ADS)

    Downie, E. J.

    2016-03-01

    The proton radius puzzle is the difference between the proton radius as measured with electron scattering and in the excitation spectrum of atomic hydrogen, and that measured with muonic hydrogen spectroscopy. Since the inception of the proton radius puzzle in 2010 by the measurement of Pohl et al.[1], many possible resolutions to the puzzle have been postulated, but, to date, none has been generally accepted. New data are therefore necessary to resolve the issue. We briefly review the puzzle, the proposed solutions, and the new electron scattering and spectroscopy experiments planned and underway. We then introduce the MUSE experiment, which seeks to resolve the puzzle by simultaneously measuring elastic electron and muon scattering on the proton, in both charge states, thereby providing new information to the puzzle. MUSE addresses issues of two-photon effects, lepton universality and, possibly, new physics, while providing simultaneous form factor, and therefore radius, measurements with both muons and electrons.

  3. Proton channel models

    PubMed Central

    Pupo, Amaury; Baez-Nieto, David; Martínez, Agustín; Latorre, Ramón; González, Carlos

    2014-01-01

    Voltage-gated proton channels are integral membrane proteins with the capacity to permeate elementary particles in a voltage and pH dependent manner. These proteins have been found in several species and are involved in various physiological processes. Although their primary topology is known, lack of details regarding their structures in the open conformation has limited analyses toward a deeper understanding of the molecular determinants of their function and regulation. Consequently, the function-structure relationships have been inferred based on homology models. In the present work, we review the existing proton channel models, their assumptions, predictions and the experimental facts that support them. Modeling proton channels is not a trivial task due to the lack of a close homolog template. Hence, there are important differences between published models. This work attempts to critically review existing proton channel models toward the aim of contributing to a better understanding of the structural features of these proteins. PMID:24755912

  4. Lorentz contracted proton

    NASA Astrophysics Data System (ADS)

    Bedoya Fierro, D.; Kelkar, N. G.; Nowakowski, M.

    2015-09-01

    The proton charge and magnetization density distributions can be related to the well known Sachs electromagnetic form factors G E, M ( q 2) through Fourier transforms, only in the Breit frame. The Breit frame however moves with relativistic velocities in the Lab and a Lorentz boost must be applied before extracting the static properties of the proton from the corresponding densities. Apart from this, the Fourier transform relating the densities and form factors is inherently a non-relativistic expression. We show that the relativistic corrections to it can be obtained by extending the standard Breit equation to higher orders in its 1 /c 2 expansion. We find that the inclusion of the above corrections reduces the size of the proton as determined from electron proton scattering data by about 4%.

  5. Uncertainty estimates for proton-proton fusion

    NASA Astrophysics Data System (ADS)

    Acharya, Bijaya

    2017-01-01

    We calculate the proton-proton fusion cross section using chiral effective field theory (χEFT) and perform a rigorous analysis of the associated uncertainties. The statistical errors in the low-energy constants, which are fitted too scattering and bound-state observables in the pion-nucleon, nucleon-nucleon, and few-nucleon sectors, are propagated to the calculated cross section. We also investigate the sensitivity of the fusion cross section to the high-momentum cutoff of the χEFT. We extract a value for the zero-energy S-factor using a polynomial extrapolant and analyze the errors associated with this procedure. Our result is compared to that of another χEFT calculation in which the wave functions were represented in a truncated Hilbert space with discrete basis states. Supported by the NSF under Grant Nos. PHY-1516077 and PHY- 1555030.

  6. "Inventive" Learning Stations

    ERIC Educational Resources Information Center

    Jarrett, Olga

    2010-01-01

    Learning stations can be used for myriad purposes--to teach concepts, integrate subject matter, build interest, and allow for inquiry--the possibilities are limited only by the imagination of the teacher and the supplies available. In this article, the author shares suggestions and a checklist for setting up successful learning stations. In…

  7. International Space Station (ISS)

    NASA Image and Video Library

    2006-07-06

    Though very close to the International Space Station, the majority of Discovery's underside is visible in this frame. The image was captured by one of the Expedition 13 crew members onboard the International Space Station (ISS) during the STS-121 Rotating Pitch Maneuver (RPM) survey prior to docking of the two spacecraft.

  8. Summit Station Skiway Review

    DTIC Science & Technology

    2013-03-01

    delivery of personnel and materials, is by skied airplanes (currently Twin Otters and LC-130s) or by annual traverse. To support aircraft, the station...Station during the first sea - son (2009) of skiway construction at Pegasus Airfield (Haehnel et al. 2013) but consistently lower than densities of

  9. International Space Station (ISS)

    NASA Image and Video Library

    2007-08-13

    Back dropped by the blue and white Earth is a Materials International Space Station Experiment (MISSE) on the exterior of the Station. The photograph was taken during the second bout of STS-118 Extra Vehicular Activity (EVA). MISSE collects information on how different materials weather in the environment of space.

  10. International Space Station (ISS)

    NASA Image and Video Library

    2000-12-01

    This image of the International Space Station in orbit was taken from the Space Shuttle Endeavour prior to docking. Most of the Station's components are clearly visible in this photograph. They are the Node 1 or Unity Module docked with the Functional Cargo Block or Zarya (top) that is linked to the Zvezda Service Module. The Soyuz spacecraft is at the bottom.

  11. "Inventive" Learning Stations

    ERIC Educational Resources Information Center

    Jarrett, Olga

    2010-01-01

    Learning stations can be used for myriad purposes--to teach concepts, integrate subject matter, build interest, and allow for inquiry--the possibilities are limited only by the imagination of the teacher and the supplies available. In this article, the author shares suggestions and a checklist for setting up successful learning stations. In…

  12. Space station dynamics

    NASA Technical Reports Server (NTRS)

    Berka, Reg

    1990-01-01

    Structural dynamic characteristics and responses of the Space Station due to the natural and induced environment are discussed. Problems that are peculiar to the Space Station are also discussed. These factors lead to an overall acceleration environment that users may expect. This acceleration environment can be considered as a loading, as well as a disturbance environment.

  13. Proton irradiation on materials

    NASA Technical Reports Server (NTRS)

    Chang, C. Ken

    1993-01-01

    A computer code is developed by utilizing a radiation transport code developed at NASA Langley Research Center to study the proton radiation effects on materials which have potential application in NASA's future space missions. The code covers the proton energy from 0.01 Mev to 100 Gev and is sufficient for energetic protons encountered in both low earth and geosynchronous orbits. With some modification, the code can be extended for particles heavier than proton as the radiation source. The code is capable of calculating the range, stopping power, exit energy, energy deposition coefficients, dose, and cumulative dose along the path of the proton in a target material. The target material can be any combination of the elements with atomic number ranging from 1 to 92, or any compound with known chemical composition. The generated cross section for a material is stored and is reused in future to save computer time. This information can be utilized to calculate the proton dose a material would receive in an orbit when the radiation environment is known. It can also be used to determine, in the laboratory, the parameters such as beam current of proton and irradiation time to attain the desired dosage for accelerated ground testing of any material. It is hoped that the present work be extended to include polymeric and composite materials which are prime candidates for use as coating, electronic components, and structure building. It is also desirable to determine, for ground testing these materials, the laboratory parameters in order to simulate the dose they would receive in space environments. A sample print-out for water subject to 1.5 Mev proton is included as a reference.

  14. Proton beam therapy facility

    SciTech Connect

    Not Available

    1984-10-09

    It is proposed to build a regional outpatient medical clinic at the Fermi National Accelerator Laboratory (Fermilab), Batavia, Illinois, to exploit the unique therapeutic characteristics of high energy proton beams. The Fermilab location for a proton therapy facility (PTF) is being chosen for reasons ranging from lower total construction and operating costs and the availability of sophisticated technical support to a location with good access to patients from the Chicago area and from the entire nation. 9 refs., 4 figs., 26 tabs.

  15. Proton irradiation on materials

    NASA Astrophysics Data System (ADS)

    Chang, C. Ken

    1993-12-01

    A computer code is developed by utilizing a radiation transport code developed at NASA Langley Research Center to study the proton radiation effects on materials which have potential application in NASA's future space missions. The code covers the proton energy from 0.01 Mev to 100 Gev and is sufficient for energetic protons encountered in both low earth and geosynchronous orbits. With some modification, the code can be extended for particles heavier than proton as the radiation source. The code is capable of calculating the range, stopping power, exit energy, energy deposition coefficients, dose, and cumulative dose along the path of the proton in a target material. The target material can be any combination of the elements with atomic number ranging from 1 to 92, or any compound with known chemical composition. The generated cross section for a material is stored and is reused in future to save computer time. This information can be utilized to calculate the proton dose a material would receive in an orbit when the radiation environment is known. It can also be used to determine, in the laboratory, the parameters such as beam current of proton and irradiation time to attain the desired dosage for accelerated ground testing of any material. It is hoped that the present work be extended to include polymeric and composite materials which are prime candidates for use as coating, electronic components, and structure building. It is also desirable to determine, for ground testing these materials, the laboratory parameters in order to simulate the dose they would receive in space environments. A sample print-out for water subject to 1.5 Mev proton is included as a reference.

  16. [STEM on Station Education

    NASA Technical Reports Server (NTRS)

    Lundebjerg, Kristen

    2016-01-01

    The STEM on Station team is part of Education which is part of the External Relations organization (ERO). ERO has traditional goals based around BHAG (Big Hairy Audacious Goal). The BHAG model is simplified to a saying: Everything we do stimulates actions by others to advance human space exploration. The STEM on Station education initiate is a project focused on bringing off the earth research and learning into classrooms. Educational resources such as lesson plans, activities to connect with the space station and STEM related contests are available and hosted by the STEM on Station team along with their partners such as Texas Instruments. These educational activities engage teachers and students in the current happenings aboard the international space station, inspiring the next generation of space explorers.

  17. Proton transport by halorhodopsin

    SciTech Connect

    Varo, G.; Brown, L.S.; Needleman, R.

    1996-05-28

    In halorhodopsin from Natronobacterium pharaonis, a light-driven chloride pump, the chloride binding site also binds azide. When azide is bound at this location the retinal Schiff base transiently deprotonates after photoexcitation with light >530 nm, like in the light-driven proton pump bacteriorhodopsin. As in the photocycle of bacteriorhodopsin, pyranine detects the release of protons to the bulk. The subsequent reprotonation of the Schiff base is also dependent on azide, but with different kinetics that suggest a shuttling of protons from the surface as described earlier for halorhodopsin from Halobacterium salinarium. The azide-dependent, bacteriorhodopsin-like photocycle results in active electrogenic proton transport in the cytoplasmic to extracellular direction, detected in cell envelope vesicle suspensions both with a potential-sensitive electrode and by measuring light-dependent pH change. We conclude that in halorhodopsin an azide bound to the extracellular side of the Schiff base, and another azide shuttling between the Schiff base and the cytoplasmic surface, fulfill the functions of Asp-85 and Asp-96, respectively, in bacteriorhodopsin. Thus, although halorhodopsin is normally a chloride ion pump, it evidently contains all structural requirements, except an internal proton acceptor and a donor, of a proton pump. This observation complements our earlier finding that when a chloride binding site was created in bacteriorhodopsin through replacement of Asp-85 with a threonine, that protein became a chloride ion pump. 52 refs., 9 figs.

  18. PROTON MICROSCOPY AT FAIR

    SciTech Connect

    Merrill, F. E.; Mariam, F. G.; Golubev, A. A.; Turtikov, V. I.; Varentsov, D.

    2009-12-28

    Proton radiography was invented in the 1990's at Los Alamos National Laboratory (LANL) as a diagnostic to study dynamic material properties under extreme pressures, strain and strain rate. Since this time hundreds of dynamic proton radiography experiments have been performed at LANL and a facility has been commissioned at the Institute for Theoretical and Experimental Physics (ITEP) in Russia for similar applications in dynamic material studies. Recently an international effort has investigated a new proton radiography capability for the study of dynamic material properties at the Facility for Anti-proton and Ion Research (FAIR) located in Darmstadt, Germany. This new Proton microscope for FAIR(PRIOR) will provide radiographic imaging of dynamic systems with unprecedented spatial, temporal and density resolution, resulting in a window for understanding dynamic material properties at new length scales. It is also proposed to install the PRIOR system at the GSI Helmholtzzentrum fuer Schwerionenforschung before installation at FAIR for dynamic experiments with different drivers including high explosives, pulsed power and lasers. The design of the proton microscope and expected radiographic performance is presented.

  19. Combining Electron Crystallography and X-ray Crystallography to Study the MlotiK1 Cyclic Nucleotide-Regulated Potassium Channel

    SciTech Connect

    Clayton, G.; Aller, S; Wang, J; Unger, V; Morais-Cabral, J

    2009-01-01

    We have recently reported the X-ray structure of the cyclic nucleotide-regulated potassium channel, MlotiK1. Here we describe the application of both electron and X-ray crystallography to obtain high quality crystals. We suggest that the combined application of these techniques provides a useful strategy for membrane protein structure determination. We also present negative stain projection and cryo-data projection maps. These maps provide new insights about the properties of the MlotiK1 channel. In particular, a comparison of a 9 {angstrom} cryo-data projection with calculated model maps strongly suggests that there is a very weak interaction between the pore and the S1-S4 domains of this 6 TM tetrameric cation channel and that the S1-S4 domains can adopt multiple orientations relative to the pore.

  20. International Space Station (ISS)

    NASA Image and Video Library

    2002-04-16

    Docked to the International Space Station (ISS), a Soyuz vehicle (foreground) and the Space Shuttle Atlantis were photographed by a crew member in the Pirs docking compartment on the orbital outpost. Atlantis launched on April 8, 2002, carrying the the STS-110 mission which prepared the ISS for future space walks by installing and outfitting the 43-foot-long Starboard side S0 (S-zero) truss and preparing the first railroad in space, the Mobile Transporter. The 27,000 pound S0 truss was the first of 9 segments that will make up the Station's external framework that will eventually stretch 356 feet (109 meters), or approximately the length of a football field. This central truss segment also includes a flatcar called the Mobile Transporter and rails that will become the first "space railroad," which will allow the Station's robotic arm to travel up and down the finished truss for future assembly and maintenance. The completed truss structure will hold solar arrays and radiators to provide power and cooling for additional international research laboratories from Japan and Europe that will be attached to the Station. STS-110 Extravehicular Activity (EVA) marked the first use of the Station's robotic arm to maneuver space walkers around the Station and was the first time all of a shuttle crew's scapulas were based out of the Station's Quest Airlock.

  1. International Space Station (ISS)

    NASA Image and Video Library

    2001-03-13

    Astronaut Paul W. Richards, STS-102 mission specialist, works in the cargo bay of the Space Shuttle Discovery during the second of two scheduled space walks. Richards, along with astronaut Andy Thomas, spent 6.5 hours outside the International Space Station (ISS), continuing work to outfit the station and prepare for delivery of its robotic arm. STS-102 delivered the first Multipurpose Logistics Modules (MPLM) named Leonardo, which was filled with equipment and supplies to outfit the U.S. Destiny Laboratory Module. The Leonardo MPLM is the first of three such pressurized modules that will serve as the ISS' moving vans, carrying laboratory racks filled with equipment, experiments, and supplies to and from the Station aboard the Space Shuttle. The cylindrical module is approximately 21-feet long and 15- feet in diameter, weighing almost 4.5 tons. It can carry up to 10 tons of cargo in 16 standard Space Station equipment racks. Of the 16 racks the module can carry, 5 can be furnished with power, data, and fluid to support refrigerators or freezers. In order to function as an attached station module as well as a cargo transport, the logistics module also includes components that provide life support, fire detection and suppression, electrical distribution, and computer functions. NASA's 103rd overall mission and the 8th Space Station Assembly Flight, STS-102 mission also served as a crew rotation flight. It delivered the Expedition Two crew to the Station and returned the Expedition One crew back to Earth.

  2. Overview of guideway, Pratt Street Station, Bridge Street Station and ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Overview of guideway, Pratt Street Station, Bridge Street Station and train yard, looking east. Dyre street in foreground. - Frankford Elevated, 52100-5400 Frankford Avenue (guideway & stations), Philadelphia, Philadelphia County, PA

  3. 4. EASTBOUND VIEW. NORTH TRACK WAITING STATION ON LEFT. STATION ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    4. EASTBOUND VIEW. NORTH TRACK WAITING STATION ON LEFT. STATION ON RIGHT. NOTE TUNNEL IN BACKGROUND. - Baltimore & Ohio Railroad, Harpers Ferry Station, Potomac Street, Harpers Ferry, Jefferson County, WV

  4. The O2-Evolving Complex of Photosystem II: Recent Insights from Quantum Mechanics/Molecular Mechanics (QM/MM), Extended X-ray Absorption Fine Structure (EXAFS), and Femtosecond X-ray Crystallography Data.

    PubMed

    Askerka, Mikhail; Brudvig, Gary W; Batista, Victor S

    2017-01-17

    Efficient photoelectrochemical water oxidation may open a way to produce energy from renewable solar power. In biology, generation of fuel due to water oxidation happens efficiently on an immense scale during the light reactions of photosynthesis. To oxidize water, photosynthetic organisms have evolved a highly conserved protein complex, Photosystem II. Within that complex, water oxidation happens at the CaMn4O5 inorganic catalytic cluster, the so-called oxygen-evolving complex (OEC), which cycles through storage "S" states as it accumulates oxidizing equivalents and produces molecular oxygen. In recent years, there has been significant progress in understanding the OEC as it evolves through the catalytic cycle. Studies have combined conventional and femtosecond X-ray crystallography with extended X-ray absorption fine structure (EXAFS) and quantum mechanics/molecular mechanics (QM/MM) methods and have addressed changes in protonation states of μ-oxo bridges and the coordination of substrate water through the analysis of ammonia binding as a chemical analog of water. These advances are thought to be critical to understanding the catalytic cycle since protonation states regulate the relative stability of different redox states and the geometry of the OEC. Therefore, establishing the mechanism for substrate water binding and the nature of protonation/redox state transitions in the OEC is essential for understanding the catalytic cycle of O2 evolution. The structure of the dark-stable S1 state has been a target for X-ray crystallography for the past 15 years. However, traditional X-ray crystallography has been hampered by radiation-induced reduction of the OEC. Very recently, a revolutionary X-ray free electron laser (XFEL) technique was applied to PSII to reveal atomic positions at 1.95 Å without radiation damage, which brought us closer than ever to establishing the ultimate structure of the OEC in the S1 state. However, the atom positions in this crystal

  5. Station Climatic Summaries, Asia

    DTIC Science & Technology

    1989-07-01

    MANDALAY 480420 8809 (OCDS) .................................................. .022 MYITKYINA 480080 8809 (OCDS...0 1 0 0 0 2 0 5 2 1 06-20 LST 8 3 # 1 # 1 1 2 4 10 11 13 4 ECR-KRW-7a OZi OPERATIONAL CLIMATIC DATA SUMMARY STATION: MANDALAY , BM STATION #: 480420...18-20 LST # 0 # 0 # 1 0 2 1 # 1 1 1 06-20 LST 1 2 2 1 1 1 2 1 1 1 2 5 1 ECR-KRW-6 oZ3 OPERATIONAL CLIMATIC DATA SUPPLEMENT STATION: MANDALAY , BM

  6. International Space Station (ISS)

    NASA Image and Video Library

    1997-06-01

    Artist's digital concept of the International Space Station (ISS), a gateway to permanent human presence in space, after all assembly is completed in Year 2003. The Station will be powered by almost an acre of solar panels and have a mass of almost one million pounds. Station modules are being provided by the United States, Russia, Japan, and Europe. Canada is providing a mechanical arm and Canada Hand. Sixteen countries are cooperating to provide a multidisciplinary laboratory, technology test bed, and observatory that will provide an unprecedented undertaking in scientific, technological, and international experimentation.

  7. Madrid space station

    NASA Technical Reports Server (NTRS)

    Fahnestock, R. J.; Renzetti, N. A.

    1975-01-01

    The Madrid space station, operated under bilateral agreements between the governments of the United States and Spain, is described in both Spanish and English. The space station utilizes two tracking and data acquisition networks: the Deep Space Network (DSN) of the National Aeronautics and Space Administration and the Spaceflight Tracking and Data Network (STDN) operated under the direction of the Goddard Space Flight Center. The station, which is staffed by Spanish employees, comprises four facilities: Robledo 1, Cebreros, and Fresnedillas-Navalagamella, all with 26-meter-diameter antennas, and Robledo 2, with a 64-meter antenna.

  8. The space station

    NASA Technical Reports Server (NTRS)

    Munoz, Abraham

    1988-01-01

    Conceived since the beginning of time, living in space is no longer a dream but rather a very near reality. The concept of a Space Station is not a new one, but a redefined one. Many investigations on the kinds of experiments and work assignments the Space Station will need to accommodate have been completed, but NASA specialists are constantly talking with potential users of the Station to learn more about the work they, the users, want to do in space. Present configurations are examined along with possible new ones.

  9. Space Station Induced Monitoring

    NASA Technical Reports Server (NTRS)

    Spann, James F. (Editor); Torr, Marsha R. (Editor)

    1988-01-01

    This report contains the results of a conference convened May 10-11, 1988, to review plans for monitoring the Space Station induced environment, to recommend primary components of an induced environment monitoring package, and to make recommendations pertaining to suggested modifications of the Space Station External Contamination Control Requirements Document JSC 30426. The contents of this report are divided as Follows: Monitoring Induced Environment - Space Station Work Packages Requirements, Neutral Environment, Photon Emission Environment, Particulate Environment, Surface Deposition/Contamination; and Contamination Control Requirements.

  10. Space station operations management

    NASA Technical Reports Server (NTRS)

    Cannon, Kathleen V.

    1989-01-01

    Space Station Freedom operations management concepts must be responsive to the unique challenges presented by the permanently manned international laboratory. Space Station Freedom will be assembled over a three year period where the operational environment will change as significant capability plateaus are reached. First Element Launch, Man-Tended Capability, and Permanent Manned Capability, represent milestones in operational capability that is increasing toward mature operations capability. Operations management concepts are being developed to accomodate the varying operational capabilities during assembly, as well as the mature operational environment. This paper describes operations management concepts designed to accomodate the uniqueness of Space Station Freedoom, utilizing tools and processes that seek to control operations costs.

  11. A functional [NiFe]-hydrogenase model compound that undergoes biologically relevant reversible thiolate protonation.

    PubMed

    Weber, Katharina; Krämer, Tobias; Shafaat, Hannah S; Weyhermüller, Thomas; Bill, Eckhard; van Gastel, Maurice; Neese, Frank; Lubitz, Wolfgang

    2012-12-26

    Two model compounds of the active site of [NiFe]-hydrogenases with an unusual {S(2)Ni(μ-S)(μ-CO)Fe(CO)(2)S}-coordination environment around the metals are reported. The neutral compound [Ni(xbsms)(μ-CO)(μ-S)Fe(CO)(2)('S')], (1) (H(2)xbsms = 1,2-bis(4-mercapto-3,3-dimethyl-2-thiabutyl)benzene) is converted to [1H][BF(4)] by reversible protonation using HBF(4)·Et(2)O. The protonation takes place at the terminal thiolate sulfur atom that is coordinated to nickel. Catalytic intermediates with a protonated terminal cysteinate were suggested for the native protein but have not yet been confirmed experimentally. [1H][BF(4)] is the first dinuclear [NiFe] model compound for such a species. Both complexes have been synthesized and characterized by X-ray crystallography, NMR-, FTIR-, and (57)Fe-Mössbauer spectroscopy as well as by electronic absorption and resonance Raman spectroscopy. The experimental results clearly show that the protonation has a significant impact on the electronic structure of the iron center, although it takes place at the nickel site. DFT calculations support the interpretation of the spectroscopic data and indicate the presence of a bonding interaction between the metal ions, which is relevant for the enzyme as well. Electrochemical experiments show that both 1 and [1H][BF(4)] are active for electrocatalytic proton reduction in aprotic solvents.

  12. The differences in binding 12-carbon aliphatic ligands by bovine β-lactoglobulin isoform A and B studied by isothermal titration calorimetry and X-ray crystallography.

    PubMed

    Loch, Joanna I; Bonarek, Piotr; Polit, Agnieszka; Swiątek, Śylwia; Dziedzicka-Wasylewska, Marta; Lewiński, Krzysztof

    2013-08-01

    Isoforms A (LGB-A) and B (LGB-B) of bovine lactoglobulin, the milk protein, differ in positions 64 (D↔G) and 118 (V↔A). Interactions of LGB-A and LGB-B with sodium dodecyl sulfate (SDS), dodecyltrimethylammonium chloride (DTAC) and lauric acid (LA), 12-carbon ligands possessing differently charged polar groups, were investigated using isothermal titration calorimetry and X-ray crystallography, to study the proton linkage phenomenon and to distinguish between effects related to different isoforms and different ligand properties. The determined values of ΔS and ΔH revealed that for all ligands, binding is entropically driven. The contribution from enthalpy change is lower and shows strong dependence on type of buffer that indicates proton release from the protein varying with protein isoform and ligand type and involvement of LA and Asp64 (in isoform A) in this process. The ligand affinities for both isoforms were arranged in the same order, DTAC < LA < SDS, and were systematically lower for variant B. The entropy change of the complexation process was always higher for isoform A, but these values were compensated by changes in enthalpy, resulting in almost identical ΔG for complexes of both isoforms. The determined crystal structures showed that substitution in positions 64 and 118 did not influence the overall structure of LGB complexes. The chemical character of the ligand polar group did not affect the position of its aliphatic chain in protein β-barrel, indicating a major role of hydrophobic interactions in ligand binding that prevailed even with the repulsion between positively charged DTAC and lysine residues located at binding site entrance.

  13. High Temperature Protonic Conductors

    NASA Technical Reports Server (NTRS)

    Dynys, Fred; Berger, Marie-Helen; Sayir, Ali

    2007-01-01

    High Temperature Protonic Conductors (HTPC) with the perovskite structure are envisioned for electrochemical membrane applications such as H2 separation, H2 sensors and fuel cells. Successive membrane commercialization is dependent upon addressing issues with H2 permeation rate and environmental stability with CO2 and H2O. HTPC membranes are conventionally fabricated by solid-state sintering. Grain boundaries and the presence of intergranular second phases reduce the proton mobility by orders of magnitude than the bulk crystalline grain. To enhanced protonic mobility, alternative processing routes were evaluated. A laser melt modulation (LMM) process was utilized to fabricate bulk samples, while pulsed laser deposition (PLD) was utilized to fabricate thin film membranes . Sr3Ca(1+x)Nb(2-x)O9 and SrCe(1-x)Y(x)O3 bulk samples were fabricated by LMM. Thin film BaCe(0.85)Y(0.15)O3 membranes were fabricated by PLD on porous substrates. Electron microscopy with chemical mapping was done to characterize the resultant microstructures. High temperature protonic conduction was measured by impedance spectroscopy in wet air or H2 environments. The results demonstrate the advantage of thin film membranes to thick membranes but also reveal the negative impact of defects or nanoscale domains on protonic conductivity.

  14. Proton dynamics in cancer

    PubMed Central

    2010-01-01

    Cancer remains a leading cause of death in the world today. Despite decades of research to identify novel therapeutic approaches, durable regressions of metastatic disease are still scanty and survival benefits often negligible. While the current strategy is mostly converging on target-therapies aimed at selectively affecting altered molecular pathways in tumor cells, evidences are in parallel pointing to cell metabolism as a potential Achilles' heel of cancer, to be disrupted for achieving therapeutic benefit. Critical differences in the metabolism of tumor versus normal cells, which include abnormal glycolysis, high lactic acid production, protons accumulation and reversed intra-extracellular pH gradients, make tumor site a hostile microenvironment where only cancer cells can proliferate and survive. Inhibiting these pathways by blocking proton pumps and transporters may deprive cancer cells of a key mechanism of detoxification and thus represent a novel strategy for a pleiotropic and multifaceted suppression of cancer cell growth. Research groups scattered all over the world have recently started to investigate various aspects of proton dynamics in cancer cells with quite encouraging preliminary results. The intent of unifying investigators involved in this research line led to the formation of the "International Society for Proton Dynamics in Cancer" (ISPDC) in January 2010. This is the manifesto of the newly formed society where both basic and clinical investigators are called to foster translational research and stimulate interdisciplinary collaboration for the development of more specific and less toxic therapeutic strategies based on proton dynamics in tumor cell biology. PMID:20550689

  15. Proton charge extensions

    NASA Astrophysics Data System (ADS)

    Stryker, Jesse R.; Miller, Gerald A.

    2016-01-01

    We examine how corrections to S -state energy levels En S in hydrogenic atoms due to the finite proton size are affected by moments of the proton charge distribution. The corrections to En S are computed moment by moment. The results demonstrate that the next-to-leading order term in the expansion is of order rp/aB times the size of the leading order term. Our analysis thus dispels any concern that the larger relative size of this term for muonic hydrogen versus electronic hydrogen might account for the current discrepancy of proton radius measurements extracted from the two systems. Furthermore, the next-to-leading order term in powers of rp/aB that we derive from a dipole proton form factor is proportional to , rather than , as would be expected from the scalar nature of the form factor. The dependence of the finite-size correction on and higher odd-power moments is shown to be a general result for any spherically symmetric proton charge distribution. A method for computing the moment expansion of the finite-size correction to arbitrary order is introduced and the results are tabulated for principal quantum numbers up to n =7 .

  16. Enabler operator station

    NASA Technical Reports Server (NTRS)

    Bailey, Andrea; Kietzman, John; King, Shirlyn; Stover, Rae; Wegner, Torsten

    1992-01-01

    The objective of this project was to design an onboard operator station for the conceptual Lunar Work Vehicle (LWV). The LWV would be used in the colonization of a lunar outpost. The details that follow, however, are for an Earth-bound model. The operator station is designed to be dimensionally correct for an astronaut wearing the current space shuttle EVA suit (which include life support). The proposed operator station will support and restrain an astronaut as well as to provide protection from the hazards of vehicle rollover. The threat of suit puncture is eliminated by rounding all corners and edges. A step-plate, located at the front of the vehicle, provides excellent ease of entry and exit. The operator station weight requirements are met by making efficient use of rigid members, semi-rigid members, and woven fabrics.

  17. Space Station Software Recommendations

    NASA Technical Reports Server (NTRS)

    Voigt, S. (Editor)

    1985-01-01

    Four panels of invited experts and NASA representatives focused on the following topics: software management, software development environment, languages, and software standards. Each panel deliberated in private, held two open sessions with audience participation, and developed recommendations for the NASA Space Station Program. The major thrusts of the recommendations were as follows: (1) The software management plan should establish policies, responsibilities, and decision points for software acquisition; (2) NASA should furnish a uniform modular software support environment and require its use for all space station software acquired (or developed); (3) The language Ada should be selected for space station software, and NASA should begin to address issues related to the effective use of Ada; and (4) The space station software standards should be selected (based upon existing standards where possible), and an organization should be identified to promulgate and enforce them. These and related recommendations are described in detail in the conference proceedings.

  18. Space station data flow

    NASA Technical Reports Server (NTRS)

    1972-01-01

    The results of the space station data flow study are reported. Conceived is a low cost interactive data dissemination system for space station experiment data that includes facility and personnel requirements and locations, phasing requirements and implementation costs. Each of the experiments identified by the operating schedule is analyzed and the support characteristics identified in order to determine data characteristics. Qualitative and quantitative comparison of candidate concepts resulted in a proposed data system configuration baseline concept that includes a data center which combines the responsibility of reprocessing, archiving, and user services according to the various agencies and their responsibility assignments. The primary source of data is the space station complex which provides through the Tracking Data Relay Satellite System (TDRS) and by space shuttle delivery data from experiments in free flying modules and orbiting shuttles as well as from the experiments in the modular space station itself.

  19. The Space Station Chronicles

    NASA Image and Video Library

    As early as the nineteenth century, writers and artists and scientists around the world began to publish their visions of a crewed outpost in space. Learn about the history of space stations, from ...

  20. Station Assembly Animation

    NASA Image and Video Library

    This animation depicts the assembly of the International Space Station since Nov. 20, 1998, with the delivery of the Zarya module, through May 16, 2011, with the delivery of the EXPRESS Logistics C...

  1. Space station propulsion technology

    NASA Technical Reports Server (NTRS)

    Briley, G. L.

    1986-01-01

    The progress on the Space Station Propulsion Technology Program is described. The objectives are to provide a demonstration of hydrogen/oxygen propulsion technology readiness for the Initial Operating Capability (IOC) space station application, specifically gaseous hydrogen/oxygen and warm hydrogen thruster concepts, and to establish a means for evolving from the IOC space station propulsion to that required to support and interface with advanced station functions. The evaluation of concepts was completed. The accumulator module of the test bed was completed and, with the microprocessor controller, delivered to NASA-MSFC. An oxygen/hydrogen thruster was modified for use with the test bed and successfully tested at mixture ratios from 4:1 to 8:1.

  2. Station Commander Praises AMS

    NASA Image and Video Library

    When asked what's the most important International Space Station experiment, Commander Chris Hadfield names the Alpha Magnetic Spectrometer-2, a state-of-the-art particle physics detector that coul...

  3. Multiple Craft Stations.

    ERIC Educational Resources Information Center

    Johns, Mary Sue

    1980-01-01

    Described are three craft stations (claywork, papermaking, and stamp designing) for intermediate grade students, to correlate with their classroom study which focused on Ohio: its history, geography, cities, industries, products and famous natives. (KC)

  4. Space Station Food System

    NASA Technical Reports Server (NTRS)

    Thurmond, Beverly A.; Gillan, Douglas J.; Perchonok, Michele G.; Marcus, Beth A.; Bourland, Charles T.

    1986-01-01

    A team of engineers and food scientists from NASA, the aerospace industry, food companies, and academia are defining the Space Station Food System. The team identified the system requirements based on an analysis of past and current space food systems, food systems from isolated environment communities that resemble Space Station, and the projected Space Station parameters. The team is resolving conflicts among requirements through the use of trade-off analyses. The requirements will give rise to a set of specifications which, in turn, will be used to produce concepts. Concept verification will include testing of prototypes, both in 1-g and microgravity. The end-item specification provides an overall guide for assembling a functional food system for Space Station.

  5. Enabler operator station

    NASA Astrophysics Data System (ADS)

    Bailey, Andrea; Keitzman, John; King, Shirlyn; Stover, Rae; Wegner, Torsten

    The objective of this project was to design an onboard operator station for the conceptual Lunar Work Vehicle (LWV). This LWV would be used in the colonization of a lunar outpost. The details that follow, however, are for an earth-bound model. Several recommendations are made in the appendix as to the changes needed in material selection for the lunar environment. The operator station is designed dimensionally correct for an astronaut wearing the current space shuttle EVA suit (which includes life support). The proposed operator station will support and restrain an astronaut as well as provide protection from the hazards of vehicle rollover. The threat of suit puncture is eliminated by rounding all corners and edges. A step-plate, located at the front of the vehicle, provides excellent ease of entry and exit. The operator station weight requirements are met by making efficient use of grid members, semi-rigid members and woven fabrics.

  6. International Space Station (ISS)

    NASA Image and Video Library

    1995-04-17

    This computer generated scene of the International Space Station (ISS) represents the first addition of hardware following the completion of Phase II. The 8-A Phase shows the addition of the S-9 truss.

  7. International Space Station (ISS)

    NASA Image and Video Library

    1994-04-20

    An artist's concept of a fully deployed International Space Station (ISS) Alpha. The ISS-A is a multidisciplinary laboratory, technology test bed, and observatory that will provide an unprecedented undertaking in scientific, technological, and international experiments.

  8. International Space Station (ISS)

    NASA Image and Video Library

    2000-02-01

    A section of the International Space Station truss assembly arrived at the Marshall Space Flight Center on NASA's Super Guppy cargo plane for structural and design testing as well as installation of critical flight hardware.

  9. International Space Station (ISS)

    NASA Image and Video Library

    2000-12-01

    This image of the International Space Station (ISS) in orbit was taken during a fly-around inspection by the Space Shuttle Endeavour after successfull attachment of the 240-foot-long, 38-foot-wide solar array.

  10. International Space Station (ISS)

    NASA Image and Video Library

    1994-09-21

    Artist's concept of the final configuration of the International Space Station (ISS) Alpha. The ISS is a multidisciplinary laboratory, technology test bed, and observatory that will provide an unprecedented undertaking in scientific, technological, and international experimentation.

  11. Space Station Live! Tour

    NASA Image and Video Library

    NASA is using the Internet and smartphones to provide the public with a new inside look at what happens aboard the International Space Station and in the Mission Control Center. NASA Public Affairs...

  12. Space Station Software Issues

    NASA Technical Reports Server (NTRS)

    Voigt, S. (Editor); Beskenis, S. (Editor)

    1985-01-01

    Issues in the development of software for the Space Station are discussed. Software acquisition and management, software development environment, standards, information system support for software developers, and a future software advisory board are addressed.

  13. Destination Station Atlanta

    NASA Image and Video Library

    Destination Station was recently in Atlanta from April 15 through April 21. During the week, NASA visited schools, hospitals, museums, and the city’s well known Atlanta Science Tavern Meet Up gro...

  14. Low Earth orbit assessment of proton anisotropy using AP8 and AP9 trapped proton models.

    PubMed

    Badavi, Francis F; Walker, Steven A; Santos Koos, Lindsey M

    2015-04-01

    The completion of the International Space Station (ISS) in 2011 has provided the space research community with an ideal evaluation and testing facility for future long duration human activities in space. Ionized and secondary neutral particles radiation measurements inside ISS form the ideal tool for validation of radiation environmental models, nuclear reaction cross sections and transport codes. Studies using thermo-luminescent detectors (TLD), tissue equivalent proportional counter (TPEC), and computer aided design (CAD) models of early ISS configurations confirmed that, as input, computational dosimetry at low Earth orbit (LEO) requires an environmental model with directional (anisotropic) capability to properly describe the exposure of trapped protons within ISS. At LEO, ISS encounters exposure from trapped electrons, protons and geomagnetically attenuated galactic cosmic rays (GCR). For short duration studies at LEO, one can ignore trapped electrons and ever present GCR exposure contributions during quiet times. However, within the trapped proton field, a challenge arises from properly estimating the amount of proton exposure acquired. There exist a number of models to define the intensity of trapped particles. Among the established trapped models are the historic AE8/AP8, dating back to the 1980s and the recently released AE9/AP9/SPM. Since at LEO electrons have minimal exposure contribution to ISS, this work ignores the AE8 and AE9 components of the models and couples a measurement derived anisotropic trapped proton formalism to omnidirectional output from the AP8 and AP9 models, allowing the assessment of the differences between the two proton models. The assessment is done at a target point within the ISS-11A configuration (circa 2003) crew quarter (CQ) of Russian Zvezda service module (SM), during its ascending and descending nodes passes through the south Atlantic anomaly (SAA). The anisotropic formalism incorporates the contributions of proton narrow

  15. Low Earth orbit assessment of proton anisotropy using AP8 and AP9 trapped proton models

    NASA Astrophysics Data System (ADS)

    Badavi, Francis F.; Walker, Steven A.; Santos Koos, Lindsey M.

    2015-04-01

    The completion of the International Space Station (ISS) in 2011 has provided the space research community with an ideal evaluation and testing facility for future long duration human activities in space. Ionized and secondary neutral particles radiation measurements inside ISS form the ideal tool for validation of radiation environmental models, nuclear reaction cross sections and transport codes. Studies using thermo-luminescent detectors (TLD), tissue equivalent proportional counter (TPEC), and computer aided design (CAD) models of early ISS configurations confirmed that, as input, computational dosimetry at low Earth orbit (LEO) requires an environmental model with directional (anisotropic) capability to properly describe the exposure of trapped protons within ISS. At LEO, ISS encounters exposure from trapped electrons, protons and geomagnetically attenuated galactic cosmic rays (GCR). For short duration studies at LEO, one can ignore trapped electrons and ever present GCR exposure contributions during quiet times. However, within the trapped proton field, a challenge arises from properly estimating the amount of proton exposure acquired. There exist a number of models to define the intensity of trapped particles. Among the established trapped models are the historic AE8/AP8, dating back to the 1980s and the recently released AE9/AP9/SPM. Since at LEO electrons have minimal exposure contribution to ISS, this work ignores the AE8 and AE9 components of the models and couples a measurement derived anisotropic trapped proton formalism to omnidirectional output from the AP8 and AP9 models, allowing the assessment of the differences between the two proton models. The assessment is done at a target point within the ISS-11A configuration (circa 2003) crew quarter (CQ) of Russian Zvezda service module (SM), during its ascending and descending nodes passes through the south Atlantic anomaly (SAA). The anisotropic formalism incorporates the contributions of proton narrow

  16. Protons and how they are transported by proton pumps.

    PubMed

    Buch-Pedersen, M J; Pedersen, B P; Veierskov, B; Nissen, P; Palmgren, M G

    2009-01-01

    The very high mobility of protons in aqueous solutions demands special features of membrane proton transporters to sustain efficient yet regulated proton transport across biological membranes. By the use of the chemical energy of ATP, plasma-membrane-embedded ATPases extrude protons from cells of plants and fungi to generate electrochemical proton gradients. The recently published crystal structure of a plasma membrane H(+)-ATPase contributes to our knowledge about the mechanism of these essential enzymes. Taking the biochemical and structural data together, we are now able to describe the basic molecular components that allow the plasma membrane proton H(+)-ATPase to carry out proton transport against large membrane potentials. When divergent proton pumps such as the plasma membrane H(+)-ATPase, bacteriorhodopsin, and F(O)F(1) ATP synthase are compared, unifying mechanistic premises for biological proton pumps emerge. Most notably, the minimal pumping apparatus of all pumps consists of a central proton acceptor/donor, a positively charged residue to control pK(a) changes of the proton acceptor/donor, and bound water molecules to facilitate rapid proton transport along proton wires.

  17. Recent Major Improvements to the ALS Sector 5 MacromolecularCrystallography Beamlines

    SciTech Connect

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

    2007-07-01

    Although the Advanced Light Source (ALS) was initially conceived primarily as a low energy (1.9GeV) 3rd generation source of VUV and soft x-ray radiation it was realized very early in the development of the facility that a multipole wiggler source coupled with high quality, (brightness preserving), optics would result in a beamline whose performance across the optimal energy range (5-15keV) for macromolecular crystallography (MX) would be comparable to, or even exceed, that of many existing crystallography beamlines at higher energy facilities. Hence, starting in 1996, a suite of three beamlines, branching off a single wiggler source, was constructed, which together formed the ALS Macromolecular Crystallography Facility. From the outset this facility was designed to cater equally to the needs of both academic and industrial users with a heavy emphasis placed on the development and introduction of high throughput crystallographic tools, techniques, and facilities--such as large area CCD detectors, robotic sample handling and automounting facilities, a service crystallography program, and a tightly integrated, centralized, and highly automated beamline control environment for users. This facility was immediately successful, with the primary Multiwavelength Anomalous Diffraction beamline (5.0.2) in particular rapidly becoming one of the foremost crystallographic facilities in the US--responsible for structures such as the 70S ribosome. This success in-turn triggered enormous growth of the ALS macromolecular crystallography community and spurred the development of five additional ALS MX beamlines all utilizing the newly developed superconducting bending magnets ('superbends') as sources. However in the years since the original Sector 5.0 beamlines were built the performance demands of macromolecular crystallography users have become ever more exacting; with growing emphasis placed on studying larger complexes, more difficult structures, weakly diffracting or smaller

  18. International Space Station (ISS)

    NASA Image and Video Library

    2000-10-01

    Not long after separation of the Space Shuttle Discovery from the International Space Station (ISS), a crew member was able to use a 70mm handheld camera to grab this image of the station, featuring its newest additions. Backdropped against the blackness of space, the Z1 truss structure and its anterna, as well as the new Pressurized Mating Adapter (PMA-3), are visible in the foreground.

  19. International Space Station (ISS)

    NASA Image and Video Library

    2001-04-28

    A Canadian "handshake" in space occurred on April 28, 2001, as the Canadian-built space station robotic arm (Canadarm-2) transferred its launch cradle over to Endeavor's robotic arm. Marning the controls from the shuttle's aft flight deck, Canadian Mission Specialist Chris A. Hadfield of the Canadian Space Agency (CSA) was instrumental in the activity. The Spacelab pallet that carried the Canadarm2 robotic arm to the station was developed at the Marshall Space Flight Center (MSFC) in Huntsville, Alabama.

  20. International Space Station (ISS)

    NASA Image and Video Library

    2002-04-17

    This close-up view of the International Space Station (ISS), newly equipped with its new 27,000-pound S0 (S-zero) truss, was photographed by an astronaut aboard the Space Shuttle Atlantis STS-110 upon its ISS flyaround mission while pulling away from the ISS. The STS-110 mission prepared the Station for future spacewalks by installing and outfitting the 43-foot-long S0 truss and preparing the first railroad in space, the Mobile Transporter. The 27,000 pound S0 truss was the first of 9 segments that will make up the Station's external framework that will eventually stretch 356 feet (109 meters), or approximately the length of a football field. This central truss segment also includes a flatcar called the Mobile Transporter and rails that will become the first "space railroad," which will allow the Station's robotic arm to travel up and down the finished truss for future assembly and maintenance. The completed truss structure will hold solar arrays and radiators to provide power and cooling for additional international research laboratories from Japan and Europe that will be attached to the Station. STS-110 Extravehicular Activity (EVA) marked the first use of the Station's robotic arm to maneuver spacewalkers around the station and was the first time all of a Shuttle crew's spacewalks were based out of the Station's Quest Airlock. It was also the first Shuttle to use three Block II Main Engines. The Space Shuttle Orbiter Atlantis STS-110 mission, was launched April 8, 2002 and returned to Earth April 19, 2002.