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Acta Crystallographica. Section D,... Aug 2018The use of boiled-off liquid nitrogen to maintain protein crystals at 100 K during X-ray data collection has become almost universal. Applying this to neutron protein... (Review)
Review
The use of boiled-off liquid nitrogen to maintain protein crystals at 100 K during X-ray data collection has become almost universal. Applying this to neutron protein crystallography offers the opportunity to significantly broaden the scope of biochemical problems that can be addressed, although care must be taken in assuming that direct extrapolation to room temperature is always valid. Here, the history to date of neutron protein cryo-crystallography and the particular problems and solutions associated with the mounting and cryocooling of the larger crystals needed for neutron crystallography are reviewed. Finally, the outlook for further cryogenic neutron studies using existing and future neutron instrumentation is discussed.
Topics: Cold Temperature; Crystallography; History, 20th Century; History, 21st Century; Neutron Diffraction; Proteins
PubMed: 30082515
DOI: 10.1107/S205979831800640X -
Current Protocols in Nucleic Acid... Jun 2016A detailed understanding of chemical and biological function and the mechanisms underlying the molecular activities ultimately requires atomic-resolution structural... (Review)
Review
A detailed understanding of chemical and biological function and the mechanisms underlying the molecular activities ultimately requires atomic-resolution structural data. Diffraction-based techniques such as single-crystal X-ray crystallography, electron microscopy, and neutron diffraction are well established and they have paved the road to the stunning successes of modern-day structural biology. The major advances achieved in the last twenty years in all aspects of structural research, including sample preparation, crystallization, the construction of synchrotron and spallation sources, phasing approaches, and high-speed computing and visualization, now provide specialists and nonspecialists alike with a steady flow of molecular images of unprecedented detail. The present unit combines a general overview of diffraction methods with a detailed description of the process of a single-crystal X-ray structure determination experiment, from chemical synthesis or expression to phasing and refinement, analysis, and quality control. For novices it may serve as a stepping-stone to more in-depth treatises of the individual topics. Readers relying on structural information for interpreting functional data may find it a useful consumer guide. © 2016 by John Wiley & Sons, Inc.
Topics: Crystallography, X-Ray; Magnetic Resonance Spectroscopy; Microscopy, Electron; Molecular Biology; Neutron Diffraction; X-Ray Diffraction
PubMed: 27248784
DOI: 10.1002/cpnc.4 -
Acta Crystallographica. Section D,... Aug 2018The Protein Data Bank (PDB) contains a growing number of models that have been determined using neutron diffraction or a hybrid method that combines X-ray and neutron... (Review)
Review
The Protein Data Bank (PDB) contains a growing number of models that have been determined using neutron diffraction or a hybrid method that combines X-ray and neutron diffraction. The advantage of neutron diffraction experiments is that the positions of all atoms can be determined, including H atoms, which are hardly detectable by X-ray diffraction. This allows the determination of protonation states and the assignment of H atoms to water molecules. Because neutrons are scattered differently by hydrogen and its isotope deuterium, neutron diffraction in combination with H/D exchange can provide information on accessibility, dynamics and chemical lability. In this study, the deposited data, models and model-to-data fit for all PDB entries that used neutron diffraction as the source of experimental data have been analysed. In many cases, the reported R and R values were not reproducible. In such cases, the model and data files were analysed to identify the reasons for this mismatch. The issues responsible for the discrepancies are summarized and explained. The analysis unveiled limitations to the annotation, deposition and validation of models and data, and a lack of community-wide accepted standards for the description of neutron models and data, as well as deficiencies in current model refinement tools. Most of the issues identified concern the handling of H atoms. Since the primary use of neutron macromolecular crystallography is to locate and directly visualize H atoms, it is important to address these issues, so that the deposited neutron models allow the retrieval of the maximum amount of information with the smallest effort of manual intervention. A path forward to improving the annotation, validation and deposition of neutron models and hybrid X-ray and neutron models is suggested.
Topics: Databases, Protein; Deuterium Exchange Measurement; Macromolecular Substances; Models, Molecular; Neutron Diffraction; Proteins
PubMed: 30082516
DOI: 10.1107/S2059798318004588 -
Acta Crystallographica. Section D,... Oct 2021Metalloproteins catalyze a range of reactions, with enhanced chemical functionality due to their metal cofactor. The reaction mechanisms of metalloproteins have been... (Review)
Review
Metalloproteins catalyze a range of reactions, with enhanced chemical functionality due to their metal cofactor. The reaction mechanisms of metalloproteins have been experimentally characterized by spectroscopy, macromolecular crystallography and cryo-electron microscopy. An important caveat in structural studies of metalloproteins remains the artefacts that can be introduced by radiation damage. Photoreduction, radiolysis and ionization deriving from the electromagnetic beam used to probe the structure complicate structural and mechanistic interpretation. Neutron protein diffraction remains the only structural probe that leaves protein samples devoid of radiation damage, even when data are collected at room temperature. Additionally, neutron protein crystallography provides information on the positions of light atoms such as hydrogen and deuterium, allowing the characterization of protonation states and hydrogen-bonding networks. Neutron protein crystallography has further been used in conjunction with experimental and computational techniques to gain insight into the structures and reaction mechanisms of several transition-state metal oxidoreductases with iron, copper and manganese cofactors. Here, the contribution of neutron protein crystallography towards elucidating the reaction mechanism of metalloproteins is reviewed.
Topics: Animals; Catalysis; Crystallography, X-Ray; Humans; Metalloproteins; Models, Molecular; Neutron Diffraction; Neutrons; Oxidoreductases
PubMed: 34605429
DOI: 10.1107/S2059798321009025 -
Nature Communications Oct 2022Naturally occurring plant cellulose, our most abundant renewable resource, consists of fibers of long polymer chains that are tightly packed in parallel arrays in either...
Naturally occurring plant cellulose, our most abundant renewable resource, consists of fibers of long polymer chains that are tightly packed in parallel arrays in either of two crystal phases collectively referred to as cellulose I. During mercerization, a process that involves treatment with sodium hydroxide, cellulose goes through a conversion to another crystal form called cellulose II, within which every other chain has remarkably changed direction. We designed a neutron diffraction experiment with deuterium labelling in order to understand how this change of cellulose chain direction is possible. Here we show that during mercerization of bacterial cellulose, chains fold back on themselves in a zigzag pattern to form crystalline anti-parallel domains. This result provides a molecular level understanding of one of the most widely used industrial processes for improving cellulosic materials.
Topics: Cellulose; Sodium Hydroxide; Deuterium; Neutron Diffraction
PubMed: 36261428
DOI: 10.1038/s41467-022-33812-w -
Current Opinion in Structural Biology Jun 2022Small-angle neutron scattering (SANS) has been a beneficial tool for studying the structure of biological macromolecules in solution for several decades. Continued... (Review)
Review
Small-angle neutron scattering (SANS) has been a beneficial tool for studying the structure of biological macromolecules in solution for several decades. Continued improvements in sample preparation techniques, including deuterium labeling, neutron instrumentation and complementary techniques such as small-angle x-ray scattering (SAXS), cryo-EM, NMR and x-ray crystallography, along with the availability of more powerful structure prediction algorithms and computational resources has made SANS more important than ever as a means to obtain unique information on the structure of biological complexes in solution. In particular, the contrast variation (CV) technique, which requires a large commitment in both sample preparation and measurement time, has become more practical with the advent of these improved resources. Here, challenges and recent triumphs as well as future prospects are discussed.
Topics: Crystallography, X-Ray; Neutron Diffraction; Neutrons; Scattering, Small Angle; X-Ray Diffraction
PubMed: 35490650
DOI: 10.1016/j.sbi.2022.102375 -
Acta Crystallographica. Section D,... Dec 2023Neutron diffraction is one of the three crystallographic techniques (X-ray, neutron and electron diffraction) used to determine the atomic structures of molecules. Its...
Neutron diffraction is one of the three crystallographic techniques (X-ray, neutron and electron diffraction) used to determine the atomic structures of molecules. Its particular strengths derive from the fact that H (and D) atoms are strong neutron scatterers, meaning that their positions, and thus protonation states, can be derived from crystallographic maps. However, because of technical limitations and experimental obstacles, the quality of neutron diffraction data is typically much poorer (completeness, resolution and signal to noise) than that of X-ray diffraction data for the same sample. Further, refinement is more complex as it usually requires additional parameters to describe the H (and D) atoms. The increase in the number of parameters may be mitigated by using the `riding hydrogen' refinement strategy, in which the positions of H atoms without a rotational degree of freedom are inferred from their neighboring heavy atoms. However, this does not address the issues related to poor data quality. Therefore, neutron structure determination often relies on the presence of an X-ray data set for joint X-ray and neutron (XN) refinement. In this approach, the X-ray data serve to compensate for the deficiencies of the neutron diffraction data by refining one model simultaneously against the X-ray and neutron data sets. To be applicable, it is assumed that both data sets are highly isomorphous, and preferably collected from the same crystals and at the same temperature. However, the approach has a number of limitations that are discussed in this work by comparing four separately re-refined neutron models. To address the limitations, a new method for joint XN refinement is introduced that optimizes two different models against the different data sets. This approach is tested using neutron models and data deposited in the Protein Data Bank. The efficacy of refining models with H atoms as riding or as individual atoms is also investigated.
Topics: X-Rays; X-Ray Diffraction; Crystallography; Neutron Diffraction; Neutrons; Crystallography, X-Ray
PubMed: 37942718
DOI: 10.1107/S2059798323008914 -
Acta Crystallographica. Section D,... Dec 2018This article reviews recent work in applying neutron and X-ray scattering towards the elucidation of the molecular mechanisms of volatile anesthetics. Experimental... (Review)
Review
This article reviews recent work in applying neutron and X-ray scattering towards the elucidation of the molecular mechanisms of volatile anesthetics. Experimental results on domain mixing in ternary lipid mixtures, and the influence of volatile anesthetics and hydrostatic pressure are placed in the contexts of ion-channel function and receptor trafficking at the postsynaptic density.
Topics: Anesthetics; Animals; Humans; Hydrostatic Pressure; Ion Channels; Membrane Lipids; Membrane Microdomains; Membrane Proteins; Neuronal Plasticity; Neutron Diffraction; Post-Synaptic Density; Receptors, Cell Surface; Scattering, Small Angle; Volatile Organic Compounds; X-Ray Diffraction
PubMed: 30605131
DOI: 10.1107/S2059798318004771 -
Biochimica Et Biophysica Acta.... Mar 2023Protomembranes at the origin of life were likely composed of short-chain lipids, readily available on the early Earth. Membranes formed by such lipids are less stable...
Protomembranes at the origin of life were likely composed of short-chain lipids, readily available on the early Earth. Membranes formed by such lipids are less stable and more permeable under extreme conditions, so a novel membrane architecture was suggested to validate the accuracy of this assumption. The model membrane includes the presence of a layer of alkanes in the mid-plane of the protomembrane in between the two monolayer leaflets and lying perpendicular to the lipid acyl chains. Here, we investigated such a possibility experimentally for membranes formed by the short-chain phospholipid 1,2-didecanoyl-sn-glycero-3-phophocholine, including or not the alkanes eicosane, squalane or triacontane by means of neutron membrane diffraction and contrast variation. We found strong indications for incorporation of two of the three alkanes in the membrane mid-plane through the determination of neutron scattering length density profiles with hydrogenated vs deuterated alkanes and membrane swelling at various relative humidities indicating a slightly increased bilayer thickness when the alkanes are incorporated into the bilayers. The selectivity of the incorporation points out the role of the length of the n-alkanes with respect to the capacity of the membrane to incorporate them.
Topics: Lipid Bilayers; Neutron Diffraction; Phospholipids; Alkanes
PubMed: 36638951
DOI: 10.1016/j.bbamem.2023.184119 -
Biochimica Et Biophysica Acta. General... Mar 2020Experiments to characterize intracellular molecular dynamics in vivo are discussed following a description of the incoherent neutron scattering method. Work reviewed... (Review)
Review
Experiments to characterize intracellular molecular dynamics in vivo are discussed following a description of the incoherent neutron scattering method. Work reviewed includes water diffusion in bacteria, archaea, red blood cells, brain cells and cancer cells, and the role of proteome molecular dynamics in adaptation to physiological temperature and pressure, and in response to low salt stress in an extremophile. A brief discussion of the potential links between neutron scattering results and MD simulations on in-cell dynamics concludes the review.
Topics: Diffusion; Molecular Dynamics Simulation; Neutron Diffraction; Neutrons; Proteome; Temperature; Water
PubMed: 31734456
DOI: 10.1016/j.bbagen.2019.129475