scholarly journals Time-resolved structural studies with serial crystallography: A new light on retinal proteins

2015 ◽  
Vol 2 (4) ◽  
pp. 041718 ◽  
Author(s):  
Valérie Panneels ◽  
Wenting Wu ◽  
Ching-Ju Tsai ◽  
Przemek Nogly ◽  
Jan Rheinberger ◽  
...  
Keyword(s):  
Structural Studies ◽  
Time Resolved ◽  
Serial Crystallography ◽  
Retinal Proteins

scholarly journals Millisecond mix-and-quench crystallography (MMQX) enables time-resolved studies of PEPCK with remote data collection

IUCrJ ◽  
2021 ◽  
Vol 8 (5) ◽  
Author(s):  
Jonathan A. Clinger ◽  
David W. Moreau ◽  
Matthew J. McLeod ◽  
Todd Holyoak ◽  
Robert E. Thorne
Keyword(s):  
Data Collection ◽  
Protein Dynamics ◽  
Time Resolution ◽  
Phosphoenolpyruvate Carboxykinase ◽  
Structural Studies ◽  
Widespread Application ◽  
Entry Barrier ◽  
Time Resolved ◽  
Oxaloacetic Acid ◽  
Serial Crystallography

Time-resolved crystallography of biomolecules in action has advanced rapidly as methods for serial crystallography have improved, but the large number of crystals and the complex experimental infrastructure that are required remain serious obstacles to its widespread application. Here, millisecond mix-and-quench crystallography (MMQX) has been developed, which yields millisecond time-resolved data using far fewer crystals and routine remote synchrotron data collection. To demonstrate the capabilities of MMQX, the conversion of oxaloacetic acid to phosphoenolpyruvate by phosphoenolpyruvate carboxykinase (PEPCK) is observed with a time resolution of 40 ms. By lowering the entry barrier to time-resolved crystallography, MMQX should enable a broad expansion in structural studies of protein dynamics.

scholarly journals Towards time-resolved serial crystallography in a microfluidic device

2015 ◽  
Vol 71 (7) ◽  
pp. 823-830 ◽  
Author(s):  
Ashtamurthy S. Pawate ◽  
Vukica Šrajer ◽  
Jeremy Schieferstein ◽  
Sudipto Guha ◽  
Robert Henning ◽  
...  
Keyword(s):  
Photoactive Yellow Protein ◽  
Structural Studies ◽  
Time Resolved ◽  
Protein Targets ◽  
Laser Illumination ◽  
Serial Data ◽  
Multivariable Analyses ◽  
Serial Crystallography ◽  
Collection Strategies ◽  
Reaction Initiation

Serial methods for crystallography have the potential to enable dynamic structural studies of protein targets that have been resistant to single-crystal strategies. The use of serial data-collection strategies can circumvent challenges associated with radiation damage and repeated reaction initiation. This work utilizes a microfluidic crystallization platform for the serial time-resolved Laue diffraction analysis of macroscopic crystals of photoactive yellow protein (PYP). Reaction initiation was achievedviapulsed laser illumination, and the resultant electron-density difference maps clearly depict the expected pR1/pRE46Qand pR2/pRCWstates at 10 µs and the pB1intermediate at 1 ms. The strategies presented here have tremendous potential for extension to chemical triggering methods for reaction initiation and for extension to dynamic, multivariable analyses.

scholarly journals Millisecond Mix-and-Quench Crystallography (MMQX) Enables Time-Resolved Studies of PEPCK With Remote Data Collection

2021 ◽  
Author(s):  
Jonathan A Clinger ◽  
David W. Moreau ◽  
Matthew J McLeod ◽  
Todd Holyoak ◽  
Robert E Thorne
Keyword(s):  
Data Collection ◽  
Protein Dynamics ◽  
Time Resolution ◽  
Phosphoenolpyruvate Carboxykinase ◽  
Structural Studies ◽  
Widespread Application ◽  
Entry Barrier ◽  
Time Resolved ◽  
Oxaloacetic Acid ◽  
Serial Crystallography

Time-resolved crystallography of biomolecules in action has advanced rapidly as methods for serial crystallography have improved, but the large number of crystals and complex experimental infrastructure required remain serious obstacles to widespread application. We have developed Millisecond Mix-and-Quench crystallography (MMQX), which yields millisecond time-resolved data using far fewer crystals and routine remote synchrotron data collection. To demonstrate the capabilities of MMQX, the conversion of oxaloacetic acid to phosphoenolpyruvate by phosphoenolpyruvate carboxykinase is observed with a time resolution of 40 ms. MMQX, by lowering the entry barrier to time-resolved crystallography, should enable broad expansion in structural studies of protein dynamics.

scholarly journals Synchrotron radiation macromolecular crystallography: our science and spin offs

2014 ◽  
Vol 70 (a1) ◽  
pp. C10-C10
Author(s):  
John Helliwell
Keyword(s):  
Synchrotron Radiation ◽  
Protein Complexes ◽  
Bound Water ◽  
Water Structure ◽  
Public Understanding ◽  
Anomalous Scattering ◽  
Structural Studies ◽  
Macromolecular Crystallography ◽  
Time Resolved ◽  
Chemical Crystallography

I will give an overview of synchrotron radiation (SR) in macromolecular crystallography (MX) instrumentation, methods and applications from the early days to the present, including the evolution of SR sources and on to the `ultimate storage ring'. The build of dedicated beamlines for resonant anomalous scattering, large unit cells, ever smaller crystals and studies up to ultra-high resolution are core benefits. Results include a high output of PDB depositions, the successful use of microcrystals, pushing the frontiers of using high and low photon energies and time-resolved structural studies at even sub-nanosecond resolutions. These intensively physics based developments will be complemented by biological and chemical crystallography research results, encompassing catalysis and marine coloration, as well as the public understanding of our science and its impacts. Spin off benefits include services to the pharmaceutical industry and helping develop chemical crystallography uses of SR. The development of the Laue method with SR has led to pioneering spin off developments in neutron MX, including transfer of the well validated Daresbury Laue software to various neutron facilities worldwide. Neutron MX is gathering pace as new instrumentation and dedicated sample preparation facilities are in place at reactor and spallation neutron sources; smaller samples and much larger molecular weight protein complexes are now feasible for investigation so as to establish their protonation states and bound water structure. With the X-ray lasers, closely linked to the SR developments, we anticipate the use of ever smaller samples such as nanocrystals, nanoclusters and single molecules, as well as opening up femtosecond time-resolved diffraction structural studies. At the SR sources, a very high throughput assessment for the best crystal samples and tackling sub-micron crystals will become widespread.

Time course of chemical and structural events in protein crystals measured by microspectrophotometry

1992 ◽  
Vol 340 (1657) ◽  
pp. 191-207 ◽  
Keyword(s):  
Time Course ◽  
Equilibrium Distribution ◽  
Synergistic Effects ◽  
Conformational Transitions ◽  
Structural Studies ◽  
Time Resolved ◽  
The Past ◽  
Catalytic Intermediates ◽  
Single Form ◽  
Half Site

The functional properties of proteins in the crystalline state have been investigated over the past 30 years by a variety of methods, including single crystal polarized absorption spectroscopy. This technique has provided information on the accumulation and equilibrium distribution of protein-ligand complexes in the crystal and, in a few cases, on the rates of interconversion of catalytic intermediates. It has been possible to detect synergistic effects in the binding of different ligands, cooperativity and half-site reactivity and even formation of active multiprotein complexes, obtained by diffusion of one small protein in the pre-formed crystals of the other. Lattice interactions restrain the conformational transitions of some proteins existing in multiple states in solution. The crystal offers the unique opportunity to analyse not only the structure but also the function of a single form of the protein. The relevance of these data to the planning and interpretation of structural studies, especially in the perspectives of time-resolved crystallography, will be discussed with reference to well-characterized systems.

scholarly journals Approach of Serial Crystallography

Crystals ◽  
2020 ◽  
Vol 10 (10) ◽  
pp. 854
Author(s):  
Ki Hyun Nam
Keyword(s):  
Radiation Damage ◽  
Room Temperature ◽  
Time Resolved ◽  
X Ray ◽  
X Ray Crystallography ◽  
The Past ◽  
Wide Range ◽  
Experimental Limitation ◽  
Serial Crystallography ◽  
Collection Strategies

Radiation damage and cryogenic sample environment are an experimental limitation observed in the traditional X-ray crystallography technique. However, the serial crystallography (SX) technique not only helps to determine structures at room temperature with minimal radiation damage, but it is also a useful tool for profound understanding of macromolecules. Moreover, it is a new tool for time-resolved studies. Over the past 10 years, various sample delivery techniques and data collection strategies have been developed in the SX field. It also has a wide range of applications in instruments ranging from the X-ray free electron laser (XFEL) facility to synchrotrons. The importance of the various approaches in terms of the experimental techniques and a brief review of the research carried out in the field of SX has been highlighted in this editorial.

scholarly journals Towards time-resolved structural studies of ba3-type cytochrome c oxidase

2018 ◽  
Vol 1859 ◽  
pp. e72
Author(s):  
Cecilia Safari ◽  
Swagatha Ghosh ◽  
Rebecka Andersson ◽  
Gisela Brändén
Keyword(s):  
Cytochrome C ◽  
Cytochrome C Oxidase ◽  
Structural Studies ◽  
Time Resolved

Comparative study of primary photochemical events of two retinal proteins, bacteriorhodopsin and halorhodopsin, by use of subpicosecond time-resolved spectroscopy

1993 ◽  
Vol 211 (4-5) ◽  
pp. 385-391 ◽  
Author(s):  
Hideki Kandori ◽  
Keitaro Yoshihara ◽  
Hiroaki Tomioka ◽  
Hiroyuki Sasabe ◽  
Yoshinori Shichida
Keyword(s):  
Comparative Study ◽  
Time Resolved ◽  
Time Resolved Spectroscopy ◽  
Retinal Proteins

X-Ray Absorption Spectroscopy as an in-situ Tool in Materials Science

1997 ◽  
Vol 502 ◽  
Author(s):  
T. Ressler ◽  
Joe Wong ◽  
W. Metz
Keyword(s):  
Absorption Spectroscopy ◽  
Materials Science ◽  
Ex Situ ◽  
Structural Studies ◽  
Time Resolved ◽  
X Ray ◽  
Complementary Techniques ◽  
X Ray Absorption ◽  
Established Technique

ABSTRACTIn addition to being an established technique for ex-situ structural studies, x-ray absorption spectroscopy (XAS) has recently been realized to be a powerful tool for in-situ time-resolved investigations in materials science. This paper describes two complementary techniques: quick-scanning EXAFS (QEXAFS) and energy-dispersive XAS (DXAS) which offer time resolution in the seconds and milliseconds range, respectively. Formation of a heterogeneous catalyst from a solid-state reaction of a precursor is presented as an example of a time-resolved XAS application.

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.

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