Faculty Opinions recommendation of Automated pipeline for purification, biophysical and x-ray analysis of biomacromolecular solutions.

AbstractAlthough experimental protein structure determination usually targets known proteins, chains of unknown sequence are often encountered. They can be purified from natural sources, appear as an unexpected fragment of a well characterized protein or as a contaminant. Regardless of the source of the problem, the unknown protein always requires tedious characterization. Here we present an automated pipeline for the identification of protein sequences from cryo-EM reconstructions and crystallographic data. We present the method’s application to characterize the crystal structure of an unknown protein purified from a snake venom. We also show that the approach can be successfully applied to the identification of protein sequences and validation of sequence assignments in cryo-EM protein structures.

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findMySequence: a neural-network-based approach for identification of unknown proteins in X-ray crystallography and cryo-EM

IUCrJ ◽

10.1107/s2052252521011088 ◽

2021 ◽

Vol 9 (1) ◽

Author(s):

Grzegorz Chojnowski ◽

Adam J. Simpkin ◽

Diego A. Leonardo ◽

Wolfram Seifert-Davila ◽

Dan E. Vivas-Ruiz ◽

...

Keyword(s):

Neural Network ◽

Protein Structures ◽

Protein Sequences ◽

Protein Structure Determination ◽

Natural Sources ◽

X Ray ◽

X Ray Crystallography ◽

Unknown Protein ◽

Automated Pipeline ◽

Unknown Sequence

Although experimental protein-structure determination usually targets known proteins, chains of unknown sequence are often encountered. They can be purified from natural sources, appear as an unexpected fragment of a well characterized protein or appear as a contaminant. Regardless of the source of the problem, the unknown protein always requires characterization. Here, an automated pipeline is presented for the identification of protein sequences from cryo-EM reconstructions and crystallographic data. The method's application to characterize the crystal structure of an unknown protein purified from a snake venom is presented. It is also shown that the approach can be successfully applied to the identification of protein sequences and validation of sequence assignments in cryo-EM protein structures.

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Automated Pipeline for Purification, Biophysical and X-Ray Analysis of Biomacromolecular Solutions

Scientific Reports ◽

10.1038/srep10734 ◽

2015 ◽

Vol 5 (1) ◽

Cited By ~ 65

Author(s):

Melissa A. Graewert ◽

Daniel Franke ◽

Cy M. Jeffries ◽

Clement E. Blanchet ◽

Darja Ruskule ◽

...

Keyword(s):

Biological Macromolecules ◽

Analysis Pipeline ◽

X Ray ◽

X Ray Scattering ◽

Automated Pipeline ◽

Automated Data Analysis ◽

Sample Component ◽

Data Analysis Pipeline ◽

Line Sample

Abstract Small angle X-ray scattering (SAXS), an increasingly popular method for structural analysis of biological macromolecules in solution, is often hampered by inherent sample polydispersity. We developed an all-in-one system combining in-line sample component separation with parallel biophysical and SAXS characterization of the separated components. The system coupled to an automated data analysis pipeline provides a novel tool to study difficult samples at the P12 synchrotron beamline (PETRA-3, EMBL/DESY, Hamburg).

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Space and Time Distribution of Hard X-Ray Emission in a Loop at the Beginning of a Flare

International Astronomical Union Colloquium ◽

10.1017/s0252921100025446 ◽

1994 ◽

Vol 144 ◽

pp. 275-277

Author(s):

M. Karlický ◽

J. C. Hénoux

Keyword(s):

Time Distribution ◽

Electron Bombardment ◽

Spatial Evolution ◽

Superthermal Electrons ◽

Flare Loop ◽

X Ray ◽

Superthermal Electron ◽

Flare Loops ◽

Chromospheric Evaporation ◽

Temporal And Spatial

AbstractUsing a new ID hybrid model of the electron bombardment in flare loops, we study not only the evolution of densities, plasma velocities and temperatures in the loop, but also the temporal and spatial evolution of hard X-ray emission. In the present paper a continuous bombardment by electrons isotropically accelerated at the top of flare loop with a power-law injection distribution function is considered. The computations include the effects of the return-current that reduces significantly the depth of the chromospheric layer which is evaporated. The present modelling is made with superthermal electron parameters corresponding to the classical resistivity regime for an input energy flux of superthermal electrons of 109erg cm−2s−1. It was found that due to the electron bombardment the two chromospheric evaporation waves are generated at both feet of the loop and they propagate up to the top, where they collide and cause temporary density and hard X-ray enhancements.

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Some Problems in Understanding the Solar Corona

International Astronomical Union Colloquium ◽

10.1017/s025292110002491x ◽

1994 ◽

Vol 144 ◽

pp. 1-9

Author(s):

A. H. Gabriel

Keyword(s):

Solar Corona ◽

Solar Atmosphere ◽

Theoretical Modelling ◽

Total System ◽

Major Advance ◽

X Ray ◽

Proper Perspective ◽

Space Observations

The development of the physics of the solar atmosphere during the last 50 years has been greatly influenced by the increasing capability of observations made from space. Access to images and spectra of the hotter plasma in the UV, XUV and X-ray regions provided a major advance over the few coronal forbidden lines seen in the visible and enabled the cooler chromospheric and photospheric plasma to be seen in its proper perspective, as part of a total system. In this way space observations have stimulated new and important advances, not only in space but also in ground-based observations and theoretical modelling, so that today we find a well-balanced harmony between the three techniques.

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White-Light Coronal Structures: Streamers and CMEs

International Astronomical Union Colloquium ◽

10.1017/s0252921100025045 ◽

1994 ◽

Vol 144 ◽

pp. 82

Author(s):

E. Hildner

Keyword(s):

Emission Line ◽

Electron Density ◽

White Light ◽

Coronal Mass Ejections ◽

X Rays ◽

Solar Cycles ◽

Temperature Function ◽

X Ray ◽

Eclipse Observations ◽

Coronal Structures

AbstractOver the last twenty years, orbiting coronagraphs have vastly increased the amount of observational material for the whitelight corona. Spanning almost two solar cycles, and augmented by ground-based K-coronameter, emission-line, and eclipse observations, these data allow us to assess,inter alia: the typical and atypical behavior of the corona; how the corona evolves on time scales from minutes to a decade; and (in some respects) the relation between photospheric, coronal, and interplanetary features. This talk will review recent results on these three topics. A remark or two will attempt to relate the whitelight corona between 1.5 and 6 R⊙to the corona seen at lower altitudes in soft X-rays (e.g., with Yohkoh). The whitelight emission depends only on integrated electron density independent of temperature, whereas the soft X-ray emission depends upon the integral of electron density squared times a temperature function. The properties of coronal mass ejections (CMEs) will be reviewed briefly and their relationships to other solar and interplanetary phenomena will be noted.

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Iron K-Line Emission from X-Ray Binaries

International Astronomical Union Colloquium ◽

10.1017/s0252921100107389 ◽

1988 ◽

Vol 102 ◽

pp. 47-50

Author(s):

K. Masai ◽

S. Hayakawa ◽

F. Nagase

Keyword(s):

Accretion Disk ◽

Radiative Recombination ◽

Characteristic Temperature ◽

Line Emission ◽

Ionization Front ◽

Continuum Radiation ◽

X Ray ◽

Low Mass ◽

X Ray Binaries

AbstractEmission mechanisms of the iron Kα-lines in X-ray binaries are discussed in relation with the characteristic temperature Txof continuum radiation thereof. The 6.7 keV line is ascribed to radiative recombination followed by cascades in a corona of ∼ 100 eV formed above the accretion disk. This mechanism is attained for Tx≲ 10 keV as observed for low mass X-ray binaries. The 6.4 keV line observed for binary X-ray pulsars with Tx> 10 keV is likely due to fluorescence outside the He II ionization front.

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Diagnostics of Gold Laser Plasmas

International Astronomical Union Colloquium ◽

10.1017/s0252921100108085 ◽

1988 ◽

Vol 102 ◽

pp. 357-360

Author(s):

J.C. Gauthier ◽

J.P. Geindre ◽

P. Monier ◽

C. Chenais-Popovics ◽

N. Tragin ◽

...

Keyword(s):

Experimental Results ◽

Pure Gold ◽

Electronic Temperature ◽

X Ray ◽

Laser Plasmas ◽

Collisional Radiative Model ◽

Radiative Model

AbstractIn order to achieve a nickel-like X ray laser scheme we need a tool to determine the parameters which characterise the high-Z plasma. The aim of this work is to study gold laser plasmas and to compare experimental results to a collisional-radiative model which describes nickel-like ions. The electronic temperature and density are measured by the emission of an aluminium tracer. They are compared to the predictions of the nickel-like model for pure gold. The results show that the density and temperature can be estimated in a pure gold plasma.

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Axial Observation of X-Ray Spectra from a Beam-Foil Source

International Astronomical Union Colloquium ◽

10.1017/s0252921100108048 ◽

1988 ◽

Vol 102 ◽

pp. 339-342

Author(s):

J.M. Laming ◽

J.D. Silver ◽

R. Barnsley ◽

J. Dunn ◽

K.D. Evans ◽

...

Keyword(s):

Spectral Resolution ◽

Heavy Ion ◽

Ion Beams ◽

Beam Axis ◽

Doppler Broadening ◽

X Ray ◽

Beam Foil

AbstractNew observations of x-ray spectra from foil-excited heavy ion beams are reported. By observing the target in a direction along the beam axis, an improvement in spectral resolution, δλ/λ, by about a factor of two is achieved, due to the reduced Doppler broadening in this geometry.

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