scholarly journals Angular-split/temporal-delay approach to ultrafast protein dynamics at XFELs

2016 ◽  
Vol 72 (7) ◽  
pp. 871-882 ◽  
Author(s):  
Zhong Ren ◽  
Xiaojing Yang
Keyword(s):  
Structural Changes ◽  
Ultrashort Pulses ◽  
Atomic Displacement ◽  
Atomic Resolution ◽  
Biological Macromolecules ◽  
X Rays ◽  
Temporal Delay ◽  
X Ray ◽  
X Ray Crystallography ◽  
Before And After

X-ray crystallography promises direct insights into electron-density changes that lead to and arise from structural changes such as electron and proton transfer and the formation, rupture and isomerization of chemical bonds. The ultrashort pulses of hard X-rays produced by free-electron lasers present an exciting opportunity for capturing ultrafast structural events in biological macromolecules within femtoseconds after photoexcitation. However, shot-to-shot fluctuations, which are inherent to the very process of self-amplified spontaneous emission (SASE) that generates the ultrashort X-ray pulses, are a major source of noise that may conceal signals from structural changes. Here, a new approach is proposed to angularly split a single SASE pulse and to produce a temporal delay of picoseconds between the split pulses. These split pulses will allow the probing of two distinct states before and after photoexcitation triggered by a laser pulse between the split X-ray pulses. The split pulses originate from a single SASE pulse and share many common properties; thus, noise arising from shot-to-shot fluctuations is self-canceling. The unambiguous interpretation of ultrafast structural changes would require diffraction data at atomic resolution, as these changes may or may not involve any atomic displacement. This approach, in combination with the strategy of serial crystallography, offers a solution to study ultrafast dynamics of light-initiated biochemical reactions or biological processes at atomic resolution.

scholarly journals Introduction to high-resolution cryo-electron microscopy

2016 ◽  
Vol 62 (3) ◽  
pp. 383-394
Author(s):  
Mariusz Czarnocki-Cieciura ◽  
Marcin Nowotny
Keyword(s):  
Electron Microscopy ◽  
Nmr Spectroscopy ◽  
Structural Biology ◽  
Atomic Resolution ◽  
Biological Macromolecules ◽  
X Ray ◽  
X Ray Crystallography ◽  
Cryo Electron Microscopy ◽  
Transmission Electron ◽  
Electron Microscopes

For many years two techniques have dominated structural biology – X-ray crystallography and NMR spectroscopy. Traditional cryo-electron microscopy of biological macromolecules produced macromolecular reconstructions at resolution limited to 6–10 Å. Recent development of transmission electron microscopes, in particular the development of direct electron detectors, and continuous improvements in the available software, have led to the “resolution revolution” in cryo-EM. It is now possible to routinely obtain near-atomic-resolution 3D maps of intact biological macromolecules as small as ~100 kDa. Thus, cryo-EM is now becoming the method of choice for structural analysis of many complex assemblies that are unsuitable for structure determination by other methods.

In-Situ X-ray Photoemission Spectromicroscopy of Electromigration in Patterned Al-Cu Lines With Maximum

1998 ◽  
Vol 516 ◽  
Author(s):  
H.H. Solak ◽  
G.F. Lorusso ◽  
S. Singh ◽  
F. Cerrina ◽  
J.H. Underwood ◽  
...  
Keyword(s):  
Spectral Region ◽  
Structural Changes ◽  
Region Of Interest ◽  
Sample Surface ◽  
X Rays ◽  
Energy Analyzer ◽  
X Ray ◽  
Before And After ◽  
Chemical States

AbstractWe report the application of a unique photoemission spectromicroscope (MAXIMUM) to the study of electromigration phenomena in Al-Cu interconnects. MAXIMUM is a scanning type photoemission microscope that uses multilayer-coated optics to focus 130 eV x-rays to a sub-0.1 µm spot. An electron energy analyzer collects photoelectrons in a chosen spectral region of interest to form an image of the sample that is sensitive to chemical states of elements on the sample surface. Al-Cu lines were characterized by spectromicroscopy techniques before and after electromigration stressing in the UHV environment of the microscope chamber. We present spectro-micrographs showing the chemical and structural changes on Al-Cu line surfaces as a result of the electromigration process.

scholarly journals Sub-atomic resolution X-ray crystallography and neutron crystallography: promise, challenges and potential

IUCrJ ◽  
2015 ◽  
Vol 2 (4) ◽  
pp. 464-474 ◽  
Author(s):  
Matthew P. Blakeley ◽  
Samar S. Hasnain ◽  
Svetlana V. Antonyuk
Keyword(s):  
Radiation Damage ◽  
Diffraction Data ◽  
Atomic Resolution ◽  
Current Status ◽  
X Rays ◽  
Macromolecular Crystallography ◽  
X Ray ◽  
X Ray Crystallography ◽  
Small Proteins ◽  
Neutron Crystallography

The International Year of Crystallography saw the number of macromolecular structures deposited in the Protein Data Bank cross the 100000 mark, with more than 90000 of these provided by X-ray crystallography. The number of X-ray structures determined to sub-atomic resolution (i.e.≤1 Å) has passed 600 and this is likely to continue to grow rapidly with diffraction-limited synchrotron radiation sources such as MAX-IV (Sweden) and Sirius (Brazil) under construction. A dozen X-ray structures have been deposited to ultra-high resolution (i.e.≤0.7 Å), for which precise electron density can be exploited to obtain charge density and provide information on the bonding character of catalytic or electron transfer sites. Although the development of neutron macromolecular crystallography over the years has been far less pronounced, and its application much less widespread, the availability of new and improved instrumentation, combined with dedicated deuteration facilities, are beginning to transform the field. Of the 83 macromolecular structures deposited with neutron diffraction data, more than half (49/83, 59%) were released since 2010. Sub-mm3crystals are now regularly being used for data collection, structures have been determined to atomic resolution for a few small proteins, and much larger unit-cell systems (cell edges >100 Å) are being successfully studied. While some details relating to H-atom positions are tractable with X-ray crystallography at sub-atomic resolution, the mobility of certain H atoms precludes them from being located. In addition, highly polarized H atoms and protons (H+) remain invisible with X-rays. Moreover, the majority of X-ray structures are determined from cryo-cooled crystals at 100 K, and, although radiation damage can be strongly controlled, especially since the advent of shutterless fast detectors, and by using limited doses and crystal translation at micro-focus beams, radiation damage can still take place. Neutron crystallography therefore remains the only approach where diffraction data can be collected at room temperature without radiation damage issues and the only approach to locate mobile or highly polarized H atoms and protons. Here a review of the current status of sub-atomic X-ray and neutron macromolecular crystallography is given and future prospects for combined approaches are outlined. New results from two metalloproteins, copper nitrite reductase and cytochromec′, are also included, which illustrate the type of information that can be obtained from sub-atomic-resolution (∼0.8 Å) X-ray structures, while also highlighting the need for complementary neutron studies that can provide details of H atoms not provided by 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.

Preliminary Study on the Anti-radiation Effect of Jen-Sheng-Yang-Yung-Tang

1993 ◽  
Vol 21 (02) ◽  
pp. 187-195 ◽  
Author(s):  
Hsue-yin Hsu ◽  
Yau-hui Ho ◽  
Shi-Iong Lian ◽  
Chun-ching Lin
Keyword(s):  
Bone Marrow ◽  
Radiation Effect ◽  
Bone Marrow Cells ◽  
X Rays ◽  
Male Mice ◽  
X Ray ◽  
Colony Forming Units ◽  
Before And After ◽  
Preliminary Study ◽  
Different Doses

Six to seven week old male mice of ICR strain were exposed to different doses of x-rays to determine if Jen-Sheng-Yang-Yung-Tang could be a modifier in the elimination of radiation damage. Colony forming units of bone marrow cells in the spleen (CFUs) were measured before and after x-ray irradiation with intraperitoneal injection of 10 mg/20 g or 20 mg/20 g body weight of Jen-Sheng-Yang-Yung-Tang, once a day for seven consecutive days. The recovery of CFUs and hemocytes counts by 4 Gy irradiation with Jen-Sheng-Yang-Yung-Tang administration was faster for a concentration of 20 mg/20 g than 10 mg/20 g. The measurement of 10-day CFUs showed an increase of radiotolerance in the treatment of 20 mg/20 g administration before x-ray irradiation. The injection of Jen-Sheng-Yang-Yung-Tang accelerated the recovery of hemocyte counts in mice irradiated with 4 Gy x-ray; the effect was especially profound for leukocytes with 20 mg/20 g Jen-Sheng-Yang-Yung-Tang administration after irradiation.

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

XRD investigation of thermal degradation of some gamma-irradiated polyethylene terephthalate samples

2019 ◽  
Vol 33 (12) ◽  
pp. 1950111 ◽  
Author(s):  
Mihai Todica ◽  
Zoltan Kovacs-Krauss ◽  
Carmen Niculaescu ◽  
Marieta Mureşan-Pop
Keyword(s):  
Thermal Treatment ◽  
Polyethylene Terephthalate ◽  
Structural Changes ◽  
Diffraction Method ◽  
Resonance Spectroscopy ◽  
X Ray Diffraction ◽  
X Ray ◽  
Before And After ◽  
Gamma Irradiated ◽  
Different Doses

The modification of local structure of some commercial polyethylene terephthalate (PET) samples, gamma irradiated at different doses, was investigated by X-ray diffraction method before and after thermal treatment. Before the thermal treatment, the samples exposed to different doses of gamma radiations, does not show noticeable structural changes. However, the gamma exposure affects the thermal behavior of samples submitted to melting–cooling process. These modifications have been highlighted by X-ray diffraction, and confirmed also by thermal analysis and electron spin resonance spectroscopy.

scholarly journals Reaction Mechanism Based on X-ray Crystallography at Atomic Resolution of Endopolygalacutronase I from Fungus Stereum purpureum

2004 ◽  
Vol 51 (2) ◽  
pp. 161-167 ◽  
Author(s):  
Tetsuya Shimizu ◽  
Toru Nakatsu ◽  
Kazuo Miyairi ◽  
Toshikatsu Okuno ◽  
Hiroaki Kato
Keyword(s):  
Reaction Mechanism ◽  
Atomic Resolution ◽  
X Ray ◽  
X Ray Crystallography

scholarly journals Optical control, selection and analysis of population dynamics in ultrafast protein X-ray crystallography

2019 ◽  
Vol 377 (2145) ◽  
pp. 20170474 ◽  
Author(s):  
Christopher D. M. Hutchison ◽  
Jasper J. van Thor
Keyword(s):  
Structural Dynamics ◽  
Time Domain ◽  
Optical Pumping ◽  
High Repetition Rate ◽  
X Rays ◽  
X Ray Diffraction ◽  
X Ray ◽  
Vibrational Coherence ◽  
X Ray Crystallography ◽  
Ultrafast Optical

Ultrafast pump-probe X-ray crystallography has now been established at X-ray free electron lasers that operate at hard X-ray energies. We discuss the performance and development of current applications in terms of the available data quality and sensitivity to detect and analyse structural dynamics. A discussion of technical capabilities expected at future high repetition rate applications as well as future non-collinear multi-pulse schemes focuses on the possibility to advance the technique to the practical application of the X-ray crystallographic equivalent of an impulse time-domain Raman measurement of vibrational coherence. Furthermore, we present calculations of the magnitude of population differences and distributions prepared with ultrafast optical pumping of single crystals in the typical serial femtosecond crystallography geometry, which are developed for the general uniaxial and biaxial cases. The results present opportunities for polarization resolved anisotropic X-ray diffraction analysis of photochemical populations for the ultrafast time domain. This article is part of the theme issue ‘Measurement of ultrafast electronic and structural dynamics with X-rays’.

Sign in / Sign up

Export Citation Format

Share Document