X-ray Crystallography at High Pressure to Probe Conformational Fluctuations in Biological Macromolecules

2007 ◽  
Author(s):  
Eric Girard ◽  
Richard Kahn ◽  
Anne-Claire Dhaussy ◽  
Isabella Ascone ◽  
Mohamed Mezouar ◽  
...  
Keyword(s):  
High Pressure ◽  
Biological Macromolecules ◽  
X Ray ◽  
X Ray Crystallography

C−H- - -O Hydrogen Bonds in β-Sheetlike Networks:  Combined X-ray Crystallography and High-Pressure Infrared Study

2003 ◽  
Vol 125 (40) ◽  
pp. 12358-12364 ◽  
Author(s):  
Kwang Ming Lee ◽  
Hai-Chou Chang ◽  
Jyh-Chiang Jiang ◽  
Jack C. C. Chen ◽  
Hsiang-En Kao ◽  
...  
Keyword(s):  
High Pressure ◽  
Hydrogen Bonds ◽  
Infrared Study ◽  
X Ray ◽  
X Ray Crystallography

Three-dimensional crystallization of membrane proteins

1988 ◽  
Vol 21 (4) ◽  
pp. 429-477 ◽  
Author(s):  
W. Kühlbrandt
Keyword(s):  
High Resolution ◽  
Membrane Proteins ◽  
Membrane Protein ◽  
Protein Complexes ◽  
Three Dimensional ◽  
Biological Macromolecules ◽  
X Ray ◽  
X Ray Crystallography ◽  
Membrane Protein Complexes ◽  
Essential Prerequisite

As recently as 10 years ago, the prospect of solving the structure of any membrane protein by X-ray crystallography seemed remote. Since then, the threedimensional (3-D) structures of two membrane protein complexes, the bacterial photosynthetic reaction centres of Rhodopseudomonas viridis (Deisenhofer et al. 1984, 1985) and of Rhodobacter sphaeroides (Allen et al. 1986, 1987 a, 6; Chang et al. 1986) have been determined at high resolution. This astonishing progress would not have been possible without the pioneering work of Michel and Garavito who first succeeded in growing 3-D crystals of the membrane proteins bacteriorhodopsin (Michel & Oesterhelt, 1980) and matrix porin (Garavito & Rosenbusch, 1980). X-ray crystallography is still the only routine method for determining the 3-D structures of biological macromolecules at high resolution and well-ordered 3-D crystals of sufficient size are the essential prerequisite.

scholarly journals Compressibility Studies of Zirconium Based Metal-Organic Frameworks

2014 ◽  
Vol 70 (a1) ◽  
pp. C157-C157
Author(s):  
Claire Hobday ◽  
Stephen Moggach ◽  
Carole Morrison ◽  
Tina Duren ◽  
Ross Forgan
Keyword(s):  
High Pressure ◽  
Mechanical Stability ◽  
Metal Organic Frameworks ◽  
External Pressure ◽  
X Ray Diffraction ◽  
X Ray ◽  
X Ray Crystallography ◽  
Pressure Medium ◽  
Metal Organic ◽  
University Of Oslo

Metal-organic frameworks (MOFs) are a well-studied class of porous materials with the potential to be used in many applications such as gas storage and catalysis.[1] UiO-67 (UiO = University of Oslo), a MOF built from zirconium oxide units connected with 4,4-biphenyldicarboxylate (BDC) linkers, forms a face centred cubic structure. Zirconium has a high affinity towards oxygen ligands making these bridges very strong, resulting in UiO-based MOFs having high chemical and thermal stability compared to other MOF structures. Moreover, UiO-67 has become popular in engineering studies due to its high mechanical stability.[2] Using high pressure x-ray crystallography we can exert MOFs to GPa pressures, experimentally exploring the mechanical stability of MOFs to external pressure. By immersing the crystal in a hydrostatic medium, pressure is applied evenly to the crystal. On surrounding a porous MOF with a hydrostatic medium composed of small molecules (e.g. methanol), the medium can penetrate the MOF, resulting in medium-dependant compression. On compressing MOF-5 (Zn4O(BDC)3) using diethylformamide as a penetrating medium, the framework was shown to have an increased resistance to compression, becoming amorphous several orders of magnitude higher in pressure than observed on grinding the sample.[3] Here we present a high-pressure x-ray diffraction study on the UiO-based MOF UiO-67, and several new synthesised derivatives built from same metal node but with altered organic linkers, allowing us to study in a systematic way, the mechanical stability of the MOF, and its pressure dependence on both the linker, and pressure medium.

scholarly journals High-Pressure Protein X-Ray Crystallography

2017 ◽  
Vol 27 (1) ◽  
pp. 18-25
Author(s):  
Nobuhisa WATANABE ◽  
Hiroyuki YAMADA ◽  
Takayuki NAGAE
Keyword(s):  
High Pressure ◽  
X Ray ◽  
X Ray Crystallography ◽  
Protein X

scholarly journals The Resolution in X-ray Crystallography and Single-Particle Cryogenic Electron Microscopy

Crystals ◽  
2020 ◽  
Vol 10 (7) ◽  
pp. 580
Author(s):  
Victor R.A. Dubach ◽  
Albert Guskov
Keyword(s):  
Electron Microscopy ◽  
Single Particle ◽  
Signal To Noise Ratio ◽  
Three Dimensional ◽  
Particle Analysis ◽  
Biological Macromolecules ◽  
Single Particle Analysis ◽  
X Ray ◽  
X Ray Crystallography ◽  
The Fourier Transform

X-ray crystallography and single-particle analysis cryogenic electron microscopy are essential techniques for uncovering the three-dimensional structures of biological macromolecules. Both techniques rely on the Fourier transform to calculate experimental maps. However, one of the crucial parameters, resolution, is rather broadly defined. Here, the methods to determine the resolution in X-ray crystallography and single-particle analysis are summarized. In X-ray crystallography, it is becoming increasingly more common to include reflections discarded previously by traditionally used standards, allowing for the inclusion of incomplete and anisotropic reflections into the refinement process. In general, the resolution is the smallest lattice spacing given by Bragg’s law for a particular set of X-ray diffraction intensities; however, typically the resolution is truncated by the user during the data processing based on certain parameters and later it is used during refinement. However, at which resolution to perform such a truncation is not always clear and this makes it very confusing for the novices entering the structural biology field. Furthermore, it is argued that the effective resolution should be also reported as it is a more descriptive measure accounting for anisotropy and incompleteness of the data. In single particle cryo-EM, the situation is not much better, as multiple ways exist to determine the resolution, such as Fourier shell correlation, spectral signal-to-noise ratio and the Fourier neighbor correlation. The most widely accepted is the Fourier shell correlation using a threshold of 0.143 to define the resolution (so-called “gold-standard”), although it is still debated whether this is the correct threshold. Besides, the resolution obtained from the Fourier shell correlation is an estimate of varying resolution across the density map. In reality, the interpretability of the map is more important than the numerical value of the resolution.

scholarly journals Temperature-dependent macromolecular X-ray crystallography

2010 ◽  
Vol 66 (4) ◽  
pp. 437-446 ◽  
Author(s):  
Martin Weik ◽  
Jacques-Philippe Colletier
Keyword(s):  
Radiation Damage ◽  
Routine Data ◽  
Dynamical Behaviour ◽  
Biological Macromolecules ◽  
X Ray ◽  
X Ray Crystallography ◽  
Structural Details ◽  
Induced Changes ◽  
Structural Insights ◽  
Reaction Initiation

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.

scholarly journals New developments in crystallography: exploring its technology, methods and scope in the molecular biosciences

2017 ◽  
Vol 37 (4) ◽  
Author(s):  
John R. Helliwell
Keyword(s):  
Crystal Structure ◽  
Data Bank ◽  
Crystal Structure Analysis ◽  
Public Understanding ◽  
Biological Macromolecules ◽  
Hydrogen Atoms ◽  
X Ray ◽  
The Public ◽  
X Ray Crystallography ◽  
Chemical Catalysis

Since the Protein Data Bank (PDB) was founded in 1971, there are now over 120,000 depositions, the majority of which are from X-ray crystallography and 90% of those made use of synchrotron beamlines. At the Cambridge Structure Database (CSD), founded in 1965, there are more than 800,000 ‘small molecule’ crystal structure depositions and a very large number of those are relevant in the biosciences as ligands or cofactors. The technology for crystal structure analysis is still developing rapidly both at synchrotrons and in home labs. Determination of the details of the hydrogen atoms in biological macromolecules is well served using neutrons as probe. Large multi-macromolecular complexes cause major challenges to crystallization; electrons as probes offer unique advantages here. Methods developments naturally accompany technology change, mainly incremental but some, such as the tuneability, intensity and collimation of synchrotron radiation, have effected radical changes in capability of biological crystallography. In the past few years, the X-ray laser has taken X-ray crystallography measurement times into the femtosecond range. In terms of applications many new discoveries have been made in the molecular biosciences. The scope of crystallographic techniques is indeed very wide. As examples, new insights into chemical catalysis of enzymes and relating ligand bound structures to thermodynamics have been gained but predictive power is seen as not yet achieved. Metal complexes are also an emerging theme for biomedicine applications. Our studies of coloration of live and cooked lobsters proved to be an unexpected favourite with the public and schoolchildren. More generally, public understanding of the biosciences and crystallography’s role within the field have been greatly enhanced by the United Nations International Year of Crystallography coordinated by the International Union of Crystallography. This topical review describes each of these areas along with illustrative results to document the scope of each methodology.

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 Illuminating the Secrets of Crystals - Microcrystal Electron Diffraction in Structural Biology

2018 ◽  
Author(s):  
Rob Barringer ◽  
Thomas Meier
Keyword(s):  
Electron Diffraction ◽  
Structural Biology ◽  
Biological Macromolecules ◽  
X Ray ◽  
X Ray Crystallography ◽  
Novel Method ◽  
Practical Level ◽  
Crystallographic Theory

An exploration of the crystallographic theory of the relatively novel method of Microcrystal Electron Diffraction (MicroED), via comparison to X-ray crystallography at the theoretical and practical level as it applies to biological macromolecules. We then attempt to outline the limitations and challenges that the technique currently faces in structural biology, and suggest future areas of study that may improve and optimize the technique.

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