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Current Opinion in Structural Biology Jun 2023With the recent advances in serial crystallography methods at both synchrotron and X-ray free electron laser sources, more details of intermediate or transient states... (Review)
Review
With the recent advances in serial crystallography methods at both synchrotron and X-ray free electron laser sources, more details of intermediate or transient states of the catalytic reactions are being revealed structurally. These structural studies of reaction dynamics drive the need for on-line in crystallo spectroscopy methods to complement the crystallography experiment. The recent applications of combined spectroscopy and crystallography methods enable on-line determination of in crystallo reaction kinetics and structures of catalytic intermediates, sample integrity, and radiation-induced sample modifications, if any, as well as heterogeneity of crystals from different preparations or sample batches. This review describes different modes of spectroscopy that are combined with the crystallography experiment at both synchrotron and X-ray free-electron laser facilities, and the complementary information that each method can provide to facilitate the structural study of enzyme catalysis and protein dynamics.
Topics: Synchrotrons; Electrons; Crystallography, X-Ray; Spectrum Analysis; Lasers
PubMed: 37148654
DOI: 10.1016/j.sbi.2023.102604 -
Acta Crystallographica. Section D,... Feb 2018Macromolecular crystallography (MX) has been a motor for biology for over half a century and this continues apace. A series of revolutions, including the production of... (Review)
Review
Macromolecular crystallography (MX) has been a motor for biology for over half a century and this continues apace. A series of revolutions, including the production of recombinant proteins and cryo-crystallography, have meant that MX has repeatedly reinvented itself to dramatically increase its reach. Over the last 30 years synchrotron radiation has nucleated a succession of advances, ranging from detectors to optics and automation. These advances, in turn, open up opportunities. For instance, a further order of magnitude could perhaps be gained in signal to noise for general synchrotron experiments. In addition, X-ray free-electron lasers offer to capture fragments of reciprocal space without radiation damage, and open up the subpicosecond regime of protein dynamics and activity. But electrons have recently stolen the limelight: so is X-ray crystallography in rude health, or will imaging methods, especially single-particle electron microscopy, render it obsolete for the most interesting biology, whilst electron diffraction enables structure determination from even the smallest crystals? We will lay out some information to help you decide.
Topics: Crystallography; Macromolecular Substances; Microscopy, Electron; Microscopy, Electron, Transmission; Synchrotrons
PubMed: 29533241
DOI: 10.1107/S2059798317016709 -
Annual Review of Biophysics May 2022Directly observing enzyme catalysis in real time at the molecular level has been a long-standing goal of structural enzymology. Time-resolved serial crystallography... (Review)
Review
Directly observing enzyme catalysis in real time at the molecular level has been a long-standing goal of structural enzymology. Time-resolved serial crystallography methods at synchrotron and X-ray free electron laser (XFEL) sources have enabled researchers to follow enzyme catalysis and other nonequilibrium events at ambient conditions with unprecedented time resolution. X-ray crystallography provides detailed information about conformational heterogeneity and protein dynamics, which is enhanced when time-resolved approaches are used. This review outlines the ways in which information about the underlying energy landscape of a protein can be extracted from X-ray crystallographic data, with an emphasis on new developments in XFEL and synchrotron time-resolved crystallography. The emerging view of enzyme catalysis afforded by these techniques can be interpreted as enzymes moving on a time-dependent energy landscape. Some consequences of this view are discussed, including the proposal that irreversible enzymes or enzymes that use covalent catalytic mechanisms may commonly exhibit catalysis-activated motions.
Topics: Crystallography, X-Ray; Electrons; Lasers; Synchrotrons; X-Rays
PubMed: 34932909
DOI: 10.1146/annurev-biophys-100421-110959 -
International Journal of Molecular... Aug 2022Stem cells have shown great potential functions for tissue regeneration and repair because of their unlimited self-renewal and differentiation. Stem cells reside in... (Review)
Review
Stem cells have shown great potential functions for tissue regeneration and repair because of their unlimited self-renewal and differentiation. Stem cells reside in their niches, making them a hotspot for the development and diagnosis of diseases. Complex interactions between niches and stem cells create the balance between differentiation, self-renewal, maturation, and proliferation. However, the multi-facet applications of stem cells have been challenged since the complicated responses of stem cells to biological processes were explored along with the limitations of current systems or methods. Emerging evidence highlights that synchrotron infrared microspectroscopy, known as synchrotron radiation-based Fourier transform infrared microspectroscopy, has been investigated as a potentially attractive technology with its non-invasive and non-biological probes in stem cell research. With their unique vibration bands, the quantitative mapping of the content and distribution of biomolecules can be detected and characterized in cells or tissues. In this review, we focus on the potential applications of synchrotron infrared microspectroscopy for investigating the differentiation and fate determination of stem cells.
Topics: Cell Differentiation; Spectroscopy, Fourier Transform Infrared; Stem Cell Research; Synchrotrons
PubMed: 36077277
DOI: 10.3390/ijms23179878 -
Acta Crystallographica. Section D,... Jan 2022With recent developments in X-ray sources, instrumentation and data-analysis tools, time-resolved crystallographic experiments, which were originally the preserve of a... (Review)
Review
With recent developments in X-ray sources, instrumentation and data-analysis tools, time-resolved crystallographic experiments, which were originally the preserve of a few expert groups, are becoming simpler and can be carried out at more radiation sources, and are thus increasingly accessible to a growing user base. However, these experiments are just that: discrete experiments, not just `data collections'. As such, careful planning and consideration of potential pitfalls is required to enable a successful experiment. Here, some of the key factors that should be considered during the planning and execution of a time-resolved structural study are outlined, with a particular focus on synchrotron-based experiments.
Topics: Animals; Crystallography, X-Ray; Data Analysis; Enzymes; Humans; Synchrotrons
PubMed: 34981758
DOI: 10.1107/S2059798321011621 -
Physica Medica : PM : An International... Nov 2020Many lung disease processes are characterized by structural and functional heterogeneity that is not directly appreciable with traditional physiological measurements.... (Review)
Review
Many lung disease processes are characterized by structural and functional heterogeneity that is not directly appreciable with traditional physiological measurements. Experimental methods and lung function modeling to study regional lung function are crucial for better understanding of disease mechanisms and for targeting treatment. Synchrotron radiation offers useful properties to this end: coherence, utilized in phase-contrast imaging, and high flux and a wide energy spectrum which allow the selection of very narrow energy bands of radiation, thus allowing imaging at very specific energies. K-edge subtraction imaging (KES) has thus been developed at synchrotrons for both human and small animal imaging. The unique properties of synchrotron radiation extend X-ray computed tomography (CT) capabilities to quantitatively assess lung morphology, and also to map regional lung ventilation, perfusion, inflammation and biomechanical properties, with microscopic spatial resolution. Four-dimensional imaging, allows the investigation of the dynamics of regional lung functional parameters simultaneously with structural deformation of the lung as a function of time. This review summarizes synchrotron radiation imaging methods and overviews examples of its application in the study of disease mechanisms in preclinical animal models, as well as the potential for clinical translation both through the knowledge gained using these techniques and transfer of imaging technology to laboratory X-ray sources.
Topics: Animals; Humans; Lung; Radiography; Subtraction Technique; Synchrotrons; Tomography, X-Ray Computed
PubMed: 33070047
DOI: 10.1016/j.ejmp.2020.10.001 -
Acta Crystallographica. Section D,... Feb 2019The high peak brilliance and femtosecond pulse duration of X-ray free-electron lasers (XFELs) provide new scientific opportunities for experiments in physics, chemistry... (Review)
Review
The high peak brilliance and femtosecond pulse duration of X-ray free-electron lasers (XFELs) provide new scientific opportunities for experiments in physics, chemistry and biology. In structural biology, one of the major applications is serial femtosecond crystallography. The intense XFEL pulse results in the destruction of any exposed microcrystal, making serial data collection mandatory. This requires a high-throughput serial approach to sample delivery. To this end, a number of such sample-delivery techniques have been developed, some of which have been ported to synchrotron sources, where they allow convenient low-dose data collection at room temperature. Here, the current sample-delivery techniques used at XFEL and synchrotron sources are reviewed, with an emphasis on liquid injection and high-viscosity extrusion, including their application for time-resolved experiments. The challenges associated with sample delivery at megahertz repetition-rate XFELs are also outlined.
Topics: Animals; Crystallography, X-Ray; Electrons; Flow Injection Analysis; Humans; Lasers; Proteins; Synchrotrons; Time Factors; Viscosity
PubMed: 30821706
DOI: 10.1107/S205979831801567X -
Current Opinion in Structural Biology Dec 2021An estimated half of all proteins contain a metal, with these being essential for a tremendous variety of biological functions. X-ray crystallography is the major method... (Review)
Review
An estimated half of all proteins contain a metal, with these being essential for a tremendous variety of biological functions. X-ray crystallography is the major method for obtaining structures at high resolution of these metalloproteins, but there are considerable challenges to obtain intact structures due to the effects of radiation damage. Serial crystallography offers the prospect of determining low-dose synchrotron or effectively damage free XFEL structures at room temperature and enables time-resolved or dose-resolved approaches. Complementary spectroscopic data can validate redox and or ligand states within metalloprotein crystals. In this opinion, we discuss developments in the application of serial crystallographic approaches to metalloproteins and comment on future directions.
Topics: Catalysis; Crystallography, X-Ray; Metalloproteins; Spectrum Analysis; Synchrotrons
PubMed: 34455163
DOI: 10.1016/j.sbi.2021.07.007 -
Trends in Biochemical Sciences Dec 2000The past decade has seen an explosive growth in atomic-level structures determined by X-ray crystallography. Synchrotron radiation and a number of technical advances... (Review)
Review
The past decade has seen an explosive growth in atomic-level structures determined by X-ray crystallography. Synchrotron radiation and a number of technical advances related quite directly to its development have fueled this growth. With the most recent advances coming to be used collectively and new resources being built, the foundation is laid for a dramatic further expansion of synchrotron crystallography in the next decade. Both the high-throughput applications of structural genomics and also the challenging studies of macromolecular machinery are expected to flourish.
Topics: Crystallography, X-Ray; Software; Synchrotrons
PubMed: 11116192
DOI: 10.1016/s0968-0004(00)01721-7 -
Current Opinion in Structural Biology Dec 2020The current state-of-the-art experiments in time-resolved structural biology are undoubtedly the recent extremely impressive results that are emerging from XFEL-based... (Review)
Review
The current state-of-the-art experiments in time-resolved structural biology are undoubtedly the recent extremely impressive results that are emerging from XFEL-based experiments. However, there is a large range of macromolecular systems where the biological interest is predominantly in the slower dynamics (μs-s), that produce well diffracting microcrystals, and for which synchrotron-based experiments are extremely well suited. The combination of microfocus X-ray beams and the development of a range of sample delivery platforms has now made routine millisecond time-resolved experiments at microfocus macromolecular crystallography beamlines a real possibility and is driving development of dedicated endstations for time-resolved serial synchrotron crystallography.
Topics: Crystallography, X-Ray; Macromolecular Substances; Molecular Biology; Synchrotrons
PubMed: 32846363
DOI: 10.1016/j.sbi.2020.06.019