scholarly journals Graphene as a protein crystal mounting material to reduce background scatter

2013 ◽  
Vol 46 (5) ◽  
pp. 1501-1507 ◽  
Author(s):  
Jennifer L. Wierman ◽  
Jonathan S. Alden ◽  
Chae Un Kim ◽  
Paul L. McEuen ◽  
Sol M. Gruner
Keyword(s):  
Signal To Noise Ratio ◽  
Protein Crystal ◽  
Protein Crystals ◽  
Graphene Sheets ◽  
X Ray Diffraction ◽  
Signal To Noise ◽  
X Ray ◽  
Background Reduction ◽  
Diffraction Imaging ◽  
Unit Dose

The overall signal-to-noise ratio per unit dose for X-ray diffraction data from protein crystals can be improved by reducing the mass and density of all material surrounding the crystals. This article demonstrates a path towards the practical ultimate in background reduction by use of atomically thin graphene sheets as a crystal mounting platform for protein crystals. The results show the potential for graphene in protein crystallography and other cases where X-ray scatter from the mounting material must be reduced and specimen dehydration prevented, such as in coherent X-ray diffraction imaging of microscopic objects.

Enhancing the Signal-to-Noise Ratio of X-ray Diffraction Profiles by Smoothed Principal Component Analysis

2005 ◽  
Vol 77 (20) ◽  
pp. 6563-6570 ◽  
Author(s):  
Zeng Ping Chen ◽  
Julian Morris ◽  
Elaine Martin ◽  
Robert B. Hammond ◽  
Xiaojun Lai ◽  
...  
Keyword(s):  
Principal Component Analysis ◽  
Signal To Noise Ratio ◽  
Principal Component ◽  
Component Analysis ◽  
X Ray Diffraction ◽  
Signal To Noise ◽  
X Ray ◽  
Noise Ratio

Waveguide-enhanced scattering from thin biomolecular films

2002 ◽  
Vol 35 (2) ◽  
pp. 163-167 ◽  
Author(s):  
F. Pfeiffer ◽  
U. Mennicke ◽  
T. Salditt
Keyword(s):  
Lipid Bilayers ◽  
Signal To Noise Ratio ◽  
Acyl Chain ◽  
Grazing Incidence ◽  
Waveguide Structure ◽  
X Ray Diffraction ◽  
Signal To Noise ◽  
X Ray ◽  
Grazing Incidence Diffraction ◽  
Chain Ordering

An X-ray diffraction experiment on multilamellar membranes incorporated into an X-ray waveguide structure is reported. In the device, the lipid bilayers are confined to one side by the silicon substrate and to the other side by an evaporated thin metal cap layer. Shining a highly brilliant X-ray beam onto the system, resonantly enhanced, precisely defined and clearly distinguishable standing-wavefield distributions (modes) are excited. The in-plane structure of the acyl chain ordering is then studied by grazing incidence diffraction under simultaneously excited modes. A significant gain in signal-to-noise ratio as well as enhanced spatial resolution can be obtained with such a setup.

scholarly journals Comparison of the Quality of Protein Crystals Grown by CLPC Seeds Method

Crystals ◽  
2019 ◽  
Vol 9 (10) ◽  
pp. 501 ◽  
Author(s):  
Li ◽  
Yan ◽  
Liu ◽  
Wu ◽  
Liu ◽  
...  
Keyword(s):  
Diffraction Data ◽  
Protein Crystal ◽  
Protein Crystals ◽  
X Ray Diffraction ◽  
High Quality ◽  
X Ray ◽  
High Quality Protein

We present a systematic quality comparison of protein crystals obtained with and without cross-linked protein crystal (CLPC) seeds. Four proteins were used to conduct the experiments, and the results showed that crystals obtained in the presence of CLPC seeds exhibited a better morphology. In addition, the X-ray diffraction data showed that the CLPC seeds method is a powerful tool to obtain high-quality protein crystals. Therefore, we recommend the use of CLPC seeds in preparing high-quality diffracting protein crystals.

scholarly journals FELIX: an algorithm for indexing multiple crystallites in X-ray free-electron laser snapshot diffraction images

2017 ◽  
Vol 50 (4) ◽  
pp. 1075-1083 ◽  
Author(s):  
Kenneth R. Beyerlein ◽  
Thomas A. White ◽  
Oleksandr Yefanov ◽  
Cornelius Gati ◽  
Ivan G. Kazantsev ◽  
...  
Keyword(s):  
Free Electron Laser ◽  
Signal To Noise Ratio ◽  
X Ray Diffraction ◽  
Signal To Noise ◽  
Monoclinic Crystal ◽  
Slight Tendency ◽  
X Ray ◽  
Serial Crystallography ◽  
Diffraction Patterns ◽  
Novel Algorithm

A novel algorithm for indexing multiple crystals in snapshot X-ray diffraction images, especially suited for serial crystallography data, is presented. The algorithm, FELIX, utilizes a generalized parametrization of the Rodrigues–Frank space, in which all crystal systems can be represented without singularities. The new algorithm is shown to be capable of indexing more than ten crystals per image in simulations of cubic, tetragonal and monoclinic crystal diffraction patterns. It is also used to index an experimental serial crystallography dataset from lysozyme microcrystals. The increased number of indexed crystals is shown to result in a better signal-to-noise ratio, and fewer images are needed to achieve the same data quality as when indexing one crystal per image. The relative orientations between the multiple crystals indexed in an image show a slight tendency of the lysozme microcrystals to adhere on (\overline 110) facets.

scholarly journals Femtosecond X-ray diffraction from two-dimensional protein crystals

IUCrJ ◽  
2014 ◽  
Vol 1 (2) ◽  
pp. 95-100 ◽  
Author(s):  
Matthias Frank ◽  
David B. Carlson ◽  
Mark S. Hunter ◽  
Garth J. Williams ◽  
Marc Messerschmidt ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Bragg Diffraction ◽  
Protein Crystal ◽  
Protein Crystals ◽  
Two Dimensional ◽  
X Ray Diffraction ◽  
X Ray ◽  
Linac Coherent Light Source ◽  
Diffraction Patterns ◽  
Better Than

X-ray diffraction patterns from two-dimensional (2-D) protein crystals obtained using femtosecond X-ray pulses from an X-ray free-electron laser (XFEL) are presented. To date, it has not been possible to acquire transmission X-ray diffraction patterns from individual 2-D protein crystals due to radiation damage. However, the intense and ultrafast pulses generated by an XFEL permit a new method of collecting diffraction data before the sample is destroyed. Utilizing a diffract-before-destroy approach at the Linac Coherent Light Source, Bragg diffraction was acquired to better than 8.5 Å resolution for two different 2-D protein crystal samples each less than 10 nm thick and maintained at room temperature. These proof-of-principle results show promise for structural analysis of both soluble and membrane proteins arranged as 2-D crystals without requiring cryogenic conditions or the formation of three-dimensional crystals.

scholarly journals Why Do Protein Crystals Grown With the Aid of Porous Materials Show Better Diffraction Quality?

2021 ◽  
Author(s):  
Christo N. Nanev ◽  
Emmanuel Saridakis ◽  
Lata Govada ◽  
Naomi E. Chayen
Keyword(s):  
Exceptional Case ◽  
Crystal Nucleation ◽  
Protein Crystal ◽  
Protein Crystals ◽  
X Ray Diffraction ◽  
Subsequent Growth ◽  
X Ray ◽  
Porous Gold ◽  
Nucleation Stage ◽  
Mechanism Of Growth

Abstract Well-diffracting protein crystals are indispensable for X-ray diffraction analysis, which is still the most powerful method for structure-function studies of biomolecules. A promising approach to growing such crystals is by using porous nucleation-inducing materials. However, while protein crystal nucleation in pores has been thoroughly considered, little attention has been paid to the subsequent growth of the crystals. Although the nucleation stage is decisive, it is the subsequent growth of the crystals outside the pore that determines their diffraction quality. The molecular-scale mechanism of growth of protein crystals in and outside pores is here considered theoretically. Due to the metastable conditions, the crystals that emerge from the pores grow slowly, which is a prerequisite for better diffraction. This expectation has been corroborated by experiments carried out with several types of porous material, such as Bioglass (“Naomi’s Nucleant”), Buckypaper, porous gold and porous silicon. Protein crystals grown with the aid of Bioglass and Buckypaper yielded significantly better diffraction quality compared with crystals grown conventionally. In all cases, visually superior crystals are usually obtained. We furthermore conclude that heterogeneous nucleation of a crystal outside the pore is an exceptional case. Rather, the protein crystals nucleating inside the pores continue growing outside them.

scholarly journals Investigation into the binding of dyes within protein crystals

2018 ◽  
Vol 74 (9) ◽  
pp. 593-602 ◽  
Author(s):  
Alexander McPherson ◽  
Steven B. Larson
Keyword(s):  
Strong Association ◽  
Protein Crystal ◽  
Protein Crystals ◽  
Dye Molecules ◽  
X Ray Diffraction ◽  
X Ray ◽  
Satellite Tobacco Mosaic Virus ◽  
Hydrophobic Cores ◽  
Difference Fourier ◽  
Intense Color

It was found that the crystals of at least a dozen different proteins could be thoroughly stained to an intense color with a panel of dyes. Many, if not most, of the stained protein crystals retained the dyes almost indefinitely when placed in large volumes of dye-free mother liquor. Dialysis experiments showed that most of the dyes that were retained in crystals also bound to the protein when free in solution; less frequently, some dyes bound only in the crystal. The experiments indicated a strong association of the dyes with the proteins. Four protein crystals were investigated by X-ray diffraction to ascertain the mode of binding. These were crystals of lysozyme, thaumatin, trypsin inhibited with benzamidine and satellite tobacco mosaic virus. In 30 X-ray analyses of protein crystal–dye complexes, in only three difference Fourier maps was any difference electron density present that was consistent with the binding of dye molecules, and even in these three cases (thaumatin plus thioflavin T, xylene cyanol and m-cresol purple) the amount of dye observed was inadequate to explain the intense color of the crystals. It was concluded that the dye molecules, which are clearly inside the crystals, are disordered but are paradoxically tightly bound to the protein. It is speculated that the dyes, which exhibit large hydrophobic cores and peripheral charged groups, may interact with the crystalline proteins in the manner of conventional detergents.

scholarly journals Radiation damage in protein crystals examined under various conditions by different methods

2009 ◽  
Vol 16 (2) ◽  
pp. 129-132 ◽  
Author(s):  
Elspeth F. Garman ◽  
Colin Nave
Keyword(s):  
Radiation Damage ◽  
Electronic State ◽  
Room Temperature ◽  
Protein Crystal ◽  
Protein Crystals ◽  
X Rays ◽  
X Ray Diffraction ◽  
Radiation Physics ◽  
X Ray ◽  
The Past

Investigation of radiation damage in protein crystals has progressed in several directions over the past couple of years. There have been improvements in the basic procedures such as calibration of the incident X-ray intensity and calculation of the dose likely to be deposited in a crystal of known size and composition with this intensity. There has been increased emphasis on using additional techniques such as optical, Raman or X-ray spectroscopy to complement X-ray diffraction. Apparent discrepancies between the results of different techniques can be explained by the fact that they are sensitive to different length scales or to changes in the electronic state rather than to movement of atoms. Investigations have been carried out at room temperature as well as cryo-temperatures and, in both cases, with the introduction of potential scavenger molecules. These and other studies are leading to an overall description of the changes which can occur when a protein crystal is irradiated with X-rays at both cryo- and room temperatures. Results from crystallographic and spectroscopic radiation-damage experiments can be reconciled with other studies in the field of radiation physics and chemistry.

Development of a novel apparatus for experiments in soft X-ray diffraction imaging and diffraction tomography

2003 ◽  
Vol 104 ◽  
pp. 27-30 ◽  
Author(s):  
T. Beetz ◽  
C. Jacobsen ◽  
C.-C. Kao ◽  
J. Kirz ◽  
O. Mentes ◽  
...  
Keyword(s):  
Diffraction Tomography ◽  
X Ray Diffraction ◽  
X Ray ◽  
Diffraction Imaging
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