scholarly journals New light on protein structure: Macromolecular crystallography

2007 ◽  
Vol 29 (4) ◽  
pp. 32-35
Author(s):  
Armin Wagner
Keyword(s):  
Light Source ◽  
Structural Information ◽  
Considerable Change ◽  
Imperial College ◽  
Atomic Resolution ◽  
Biological Macromolecules ◽  
Macromolecular Crystallography ◽  
X Ray Diffraction ◽  
X Ray ◽  
Structure Solution

X-ray diffraction is the method of choice to determine structural information from biological mac romolecules to atomic resolution. This technique depends on the availability of single crystals of protein, which are notoriously difficult to produce. It can take months or even years to find crystal lization conditions capable of producing crystals with sufficient diffraction quality. During the last few years the field of MX (macromolecular crystallography) has undergone considerable change and most of the steps from protein expression to structure solution have been automated, speeding up the process significantly. Facilities such as Diamond Light Source, the new UK synchrotron radia tion source in Oxfordshire, have been developed to incorporate new automation technologies and Diamond will provide an important user resource for XRD (X-ray diffraction) experiments on crystals of biological macromolecules. Furthermore, in collaboration with Professor So Iwata (Imperial College and Diamond Light Source) and funded by the Wellcome Trust, Diamond Light Source is developing a laboratory dedicated specifically to solving the structure of membrane proteins, the crystallization of which poses a particular problem to the crystallographer.

scholarly journals 7 Å resolution in protein two-dimensional-crystal X-ray diffraction at Linac Coherent Light Source

2014 ◽  
Vol 369 (1647) ◽  
pp. 20130500 ◽  
Author(s):  
Bill Pedrini ◽  
Ching-Ju Tsai ◽  
Guido Capitani ◽  
Celestino Padeste ◽  
Mark S. Hunter ◽  
...  
Keyword(s):  
Light Source ◽  
Molecular Mechanisms ◽  
Structural Information ◽  
Ultrashort Pulses ◽  
Two Dimensional ◽  
Coherent Light ◽  
X Ray Diffraction ◽  
X Ray ◽  
Linac Coherent Light Source ◽  
Coherent Light Source

Membrane proteins arranged as two-dimensional crystals in the lipid environment provide close-to-physiological structural information, which is essential for understanding the molecular mechanisms of protein function. Previously, X-ray diffraction from individual two-dimensional crystals did not represent a suitable investigational tool because of radiation damage. The recent availability of ultrashort pulses from X-ray free-electron lasers (XFELs) has now provided a means to outrun the damage. Here, we report on measurements performed at the Linac Coherent Light Source XFEL on bacteriorhodopsin two-dimensional crystals mounted on a solid support and kept at room temperature. By merging data from about a dozen single crystal diffraction images, we unambiguously identified the diffraction peaks to a resolution of 7 Å, thus improving the observable resolution with respect to that achievable from a single pattern alone. This indicates that a larger dataset will allow for reliable quantification of peak intensities, and in turn a corresponding increase in the resolution. The presented results pave the way for further XFEL studies on two-dimensional crystals, which may include pump–probe experiments at subpicosecond time resolution.

scholarly journals Comparing serial X-ray crystallography and microcrystal electron diffraction (MicroED) as methods for routine structure determination from small macromolecular crystals

IUCrJ ◽  
2020 ◽  
Vol 7 (2) ◽  
pp. 306-323 ◽  
Author(s):  
Alexander M. Wolff ◽  
Iris D. Young ◽  
Raymond G. Sierra ◽  
Aaron S. Brewster ◽  
Michael W. Martynowycz ◽  
...  
Keyword(s):  
Electron Diffraction ◽  
Structural Information ◽  
Biological Macromolecules ◽  
Structural Studies ◽  
Macromolecular Crystallography ◽  
Delivery Methods ◽  
X Ray ◽  
X Ray Crystallography ◽  
Physical Conditions ◽  
Serial Crystallography

Innovative new crystallographic methods are facilitating structural studies from ever smaller crystals of biological macromolecules. In particular, serial X-ray crystallography and microcrystal electron diffraction (MicroED) have emerged as useful methods for obtaining structural information from crystals on the nanometre to micrometre scale. Despite the utility of these methods, their implementation can often be difficult, as they present many challenges that are not encountered in traditional macromolecular crystallography experiments. Here, XFEL serial crystallography experiments and MicroED experiments using batch-grown microcrystals of the enzyme cyclophilin A are described. The results provide a roadmap for researchers hoping to design macromolecular microcrystallography experiments, and they highlight the strengths and weaknesses of the two methods. Specifically, we focus on how the different physical conditions imposed by the sample-preparation and delivery methods required for each type of experiment affect the crystal structure of the enzyme.

scholarly journals Macromolecular crystallography using neutrons

2014 ◽  
Vol 36 (3) ◽  
pp. 40-42
Author(s):  
Matthew Blakeley
Keyword(s):  
Nucleic Acids ◽  
Biological Systems ◽  
Biological Macromolecules ◽  
X Rays ◽  
Macromolecular Crystallography ◽  
X Ray Diffraction ◽  
Vast Array ◽  
X Ray ◽  
Macromolecular Assemblies

When you think about macromolecular crystallography, the technique that most often comes to mind is X-ray diffraction and it's no wonder. Over 88000 structures of biological macromolecules – from proteins and nucleic acids to viruses and macromolecular assemblies – have been determined using X-rays, and these have contributed significantly to our understanding of a vast array of biological systems and processes.

scholarly journals Comparing serial X-ray crystallography and microcrystal electron diffraction (MicroED) as methods for routine structure determination from small macromolecular crystals

2019 ◽  
Author(s):  
Alexander M Wolff ◽  
Iris D Young ◽  
Raymond G Sierra ◽  
Aaron S Brewster ◽  
Michael W Martynowycz ◽  
...  
Keyword(s):  
Electron Diffraction ◽  
Structural Information ◽  
Biological Macromolecules ◽  
Structural Studies ◽  
Macromolecular Crystallography ◽  
Delivery Methods ◽  
X Ray ◽  
X Ray Crystallography ◽  
Physical Conditions ◽  
Serial Crystallography

AbstractInnovative new crystallographic methods are facilitating structural studies from ever smaller crystals of biological macromolecules. In particular, serial X-ray crystallography and microcrystal electron diffraction (MicroED) have emerged as useful methods for obtaining structural information from crystals on the nanometer to micron scale. Despite the utility of these methods, their implementation can often be difficult, as they present many challenges not encountered in traditional macromolecular crystallography experiments. Here, we describe XFEL serial crystallography experiments and MicroED experiments using batch-grown microcrystals of the enzyme cyclophilin A (CypA). Our results provide a roadmap for researchers hoping to design macromolecular microcrystallography experiments, and they highlight the strengths and weaknesses of the two methods. Specifically, we focus on how the different physical conditions imposed by the sample preparation and delivery methods required for each type of experiment effect the crystal structure of the enzyme.

scholarly journals The State of the Canadian Macromolecular Crystallography Facility

2014 ◽  
Vol 70 (a1) ◽  
pp. C1735-C1735
Author(s):  
James Gorin ◽  
Shaunivan Labiuk ◽  
Julien Cotelesage ◽  
Kathryn Janzen ◽  
Michel Fodje ◽  
...  
Keyword(s):  
Data Collection ◽  
Light Source ◽  
Structure Determination ◽  
Low Energy ◽  
Air Bearing ◽  
Beam Size ◽  
Macromolecular Crystallography ◽  
X Ray Diffraction ◽  
X Ray ◽  
Data Management Software

The Canadian Macromolecular Crystallography Facility (CMCF) at the Canadian Light Source consists of two macromolecular crystallography beamlines for structure determination using x-ray diffraction. The equipment at the CMCF beamlines have undergone or will undergo changes and improvements to better meet the needs of the most challenging experiments users may present. Among these improvements are: 1) Automounter improvements; 2) Better goniometry on 08ID-1 with the addition of a Huber air-bearing goniometer; 3) Added beam size capabilities on 08ID-1 with the addition of a multiple beam defining aperture holder; 4) XAFS capability on 08B1-1; 5) Improved low energy S-SAD data collection with the addition of a Helium path; 6) Improvements to the data collection and data management software; 7) A vacuum path for scattering experiments with detector distances up to 1 m; 8) A comprehensive beamline upgrade project on the 08ID-1 beamline; and 9) Service crystallography services.

scholarly journals A new on-axis micro-spectrophotometer for combining Raman, fluorescence and UV/Vis absorption spectroscopy with macromolecular crystallography at the Swiss Light Source

2013 ◽  
Vol 20 (5) ◽  
pp. 765-776 ◽  
Author(s):  
Guillaume Pompidor ◽  
Florian S. N. Dworkowski ◽  
Vincent Thominet ◽  
Clemens Schulze-Briese ◽  
Martin R. Fuchs
Keyword(s):  
Light Source ◽  
Detection Efficiency ◽  
Resonance Raman Spectroscopy ◽  
Optical Methods ◽  
Macromolecular Crystallography ◽  
X Ray Diffraction ◽  
X Ray ◽  
Application Range ◽  
Swiss Light Source ◽  
And Control

The combination of X-ray diffraction experiments with optical methods such as Raman, UV/Vis absorption and fluorescence spectroscopy greatly enhances and complements the specificity of the obtained information. The upgraded version of thein situon-axis micro-spectrophotometer, MS2, at the macromolecular crystallography beamline X10SA of the Swiss Light Source is presented. The instrument newly supports Raman and resonance Raman spectroscopy, in addition to the previously available UV/Vis absorption and fluorescence modes. With the recent upgrades of the spectral bandwidth, instrument stability, detection efficiency and control software, the application range of the instrument and its ease of operation were greatly improved. Its on-axis geometry with collinear X-ray and optical axes to ensure optimal control of the overlap of sample volumes probed by each technique is still unique amongst comparable facilities worldwide and the instrument has now been in general user operation for over two years.

Biophysical applications in structural and molecular biology

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Solomon Tsegaye ◽  
Gobena Dedefo ◽  
Mohammed Mehdi
Keyword(s):  
Structural Biology ◽  
Structural Information ◽  
Conformational Dynamics ◽  
Biological Macromolecules ◽  
X Ray Diffraction ◽  
Biological Mechanisms ◽  
X Ray ◽  
X Ray Crystallography ◽  
Cryo Electron Microscopy ◽  
Biophysical Techniques

Abstract The main objective of structural biology is to model proteins and other biological macromolecules and link the structural information to function and dynamics. The biological functions of protein molecules and nucleic acids are inherently dependent on their conformational dynamics. Imaging of individual molecules and their dynamic characteristics is an ample source of knowledge that brings new insights about mechanisms of action. The atomic-resolution structural information on most of the biomolecules has been solved by biophysical techniques; either by X-ray diffraction in single crystals or by nuclear magnetic resonance (NMR) spectroscopy in solution. Cryo-electron microscopy (cryo-EM) is emerging as a new tool for analysis of a larger macromolecule that couldn’t be solved by X-ray crystallography or NMR. Now a day’s low-resolution Cryo-EM is used in combination with either X-ray crystallography or NMR. The present review intends to provide updated information on applications like X-ray crystallography, cryo-EM and NMR which can be used independently and/or together in solving structures of biological macromolecules for our full comprehension of their biological mechanisms.

Direct visualization of phase-separated domains in lipid membranes

1978 ◽  
Vol 36 (2) ◽  
pp. 290-291
Author(s):  
S. W. Hui ◽  
T. P. Stewart
Keyword(s):  
Lipid Membranes ◽  
Structural Information ◽  
Freeze Fracture ◽  
Biological Molecules ◽  
Vacuum Drying ◽  
Direct Visualization ◽  
X Ray Diffraction ◽  
Electron Microscopic ◽  
X Ray ◽  
Hydrocarbon Chains

Direct electron microscopic study of biological molecules has been hampered by such factors as radiation damage, lack of contrast and vacuum drying. In certain cases, however, the difficulties may be overcome by using redundent structural information from repeating units and by various specimen preservation methods. With bilayers of phospholipids in which both the solid and fluid phases co-exist, the ordering of the hydrocarbon chains may be utilized to form diffraction contrast images. Domains of different molecular packings may be recgnizable by placing properly chosen filters in the diffraction plane. These domains would correspond to those observed by freeze fracture, if certain distinctive undulating patterns are associated with certain molecular packing, as suggested by X-ray diffraction studies. By using an environmental stage, we were able to directly observe these domains in bilayers of mixed phospholipids at various temperatures at which their phases change from misible to inmissible states.

Characterizations of Synthetic 8mol% YSZ with Comparison to 3mol %YSZ for HT-SOFC

2020 ◽  
Vol 38 (4A) ◽  
pp. 491-500
Author(s):  
Abeer F. Al-Attar ◽  
Saad B. H. Farid ◽  
Fadhil A. Hashim
Keyword(s):  
Ionic Conductivity ◽  
Electrochemical Impedance ◽  
Structural Information ◽  
Impedance Analysis ◽  
High Energy ◽  
Yttria Stabilized Zirconia ◽  
X Ray Diffraction ◽  
Stabilized Zirconia ◽  
Powder Morphology ◽  
X Ray

In this work, Yttria (Y2O3) was successfully doped into tetragonal 3mol% yttria stabilized Zirconia (3YSZ) by high energy-mechanical milling to synthesize 8mol% yttria stabilized Zirconia (8YSZ) used as an electrolyte for high temperature solid oxide fuel cells (HT-SOFC). This work aims to evaluate the densification and ionic conductivity of the sintered electrolytes at 1650°C. The bulk density was measured according to ASTM C373-17. The powder morphology and the microstructure of the sintered electrolytes were analyzed via Field Emission Scanning Electron Microscopy (FESEM). The chemical analysis was obtained with Energy-dispersive X-ray spectroscopy (EDS). Also, X-ray diffraction (XRD) was used to obtain structural information of the starting materials and the sintered electrolytes. The ionic conductivity was obtained through electrochemical impedance spectroscopy (EIS) in the air as a function of temperatures at a frequency range of 100(mHz)-100(kHz). It is found that the 3YSZ has a higher density than the 8YSZ. The impedance analysis showed that the ionic conductivity of the prepared 8YSZ at 800°C is0.906 (S.cm) and it was 0.214(S.cm) of the 3YSZ. Besides, 8YSZ has a lower activation energy 0.774(eV) than that of the 3YSZ 0.901(eV). Thus, the prepared 8YSZ can be nominated as an electrolyte for the HT-SOFC.

scholarly journals High-pressure synthesis of REB5O8(OH)2 (RE = Ho, Er, Tm)

2020 ◽  
Vol 0 (0) ◽  
Author(s):  
Michael Zoller ◽  
Hubert Huppertz
Keyword(s):  
High Pressure ◽  
Rare Earth ◽  
Ir Spectroscopy ◽  
Earth Metal ◽  
Monoclinic Space Group ◽  
X Ray Diffraction ◽  
X Ray ◽  
Structure Solution ◽  
Pressure Synthesis ◽  
The Rare Earth

AbstractThe rare earth oxoborates REB5O8(OH)2 (RE = Ho, Er, Tm) were synthesized in a Walker-type multianvil apparatus at a pressure of 2.5 GPa and a temperature of 673 K. Single-crystal X-ray diffraction data provided the basis for the structure solution and refinement. The compounds crystallize in the monoclinic space group C2 (no. 5) and are composed of a layer-like structure containing dreier and sechser rings of corner sharing [BO4]5− tetrahedra. The rare earth metal cations are coordinated between two adjacent sechser rings. Further characterization was performed utilizing IR spectroscopy.

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