scholarly journals Opportunities and challenges in neutron crystallography

2020 ◽  
Vol 236 ◽  
pp. 02001
Author(s):  
Nathan Richard Zaccai ◽  
Nicolas Coquelle

Neutron and X-ray crystallography are complementary to each other. While X-ray scattering is directly proportional to the number of electrons of an atom, neutrons interact with the atomic nuclei themselves. Neutron crystallography therefore provides an excellent alternative in determining the positions of hydrogens in a biological molecule. In particular, since highly polarized hydrogen atoms (H+) do not have electrons, they cannot be observed by X-rays. Neutron crystallography has its own limitations, mainly due to inherent low flux of neutrons sources, and as a consequence, the need for much larger crystals and for different data collection and analysis strategies. These technical challenges can however be overcome to yield crucial structural insights about protonation states in enzyme catalysis, ligand recognition, as well as the presence of unusual hydrogen bonds in proteins.

Author(s):  
Philip Coppens

This chapter starts with a discussion of the classical treatment of X-ray scattering, followed by a brief overview of the quantum-mechanical theory in the first Born approximation. The scattering of a periodic arrangement is derived by considering the crystal as a convolution of the unit cell contents and a periodic lattice. The atomic description of the charge density, which is the basis for structure analysis, is introduced. The origin of resonance anomalous scattering is discussed. While its effect must be accounted for before charge densities can be derived from the X-ray scattering amplitudes, resonance scattering itself can give invaluable information on the electronic states of the resonating atoms. The final section of this chapter deals with the scattering of neutrons by atomic nuclei. Nuclear neutron scattering is independent of the distribution of the electrons, and can provide atomic positions and thermal amplitudes unbiased by the bonding effects which are the subject of this book. In the classical theory of scattering (Cohen-Tannoudji et al. 1977, James 1982), atoms are considered to scatter as dipole oscillators with definite natural frequencies. They undergo harmonic vibrations in the electromagnetic field, and emit radiation as a result of the oscillations.


IUCrJ ◽  
2015 ◽  
Vol 2 (4) ◽  
pp. 464-474 ◽  
Author(s):  
Matthew P. Blakeley ◽  
Samar S. Hasnain ◽  
Svetlana V. Antonyuk

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.


2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Navdeep Kaur ◽  
Amin Sagar ◽  
Pankaj Sharma ◽  
Ashish ◽  
Pratap Kumar Pati

Abstract Salinity is one of the major stresses affecting rice production worldwide, and various strategies are being employed to increase salt tolerance. Recently, there has been resurgence of interest to characterize SalTol QTL harbouring number of critical genes involved in conferring salt stress tolerance in rice. The present study reports the structure of SALT, a SalTol QTL encoded protein by X-ray crystallography (PDB ID: 5GVY; resolution 1.66 Å). Each SALT chain was bound to one mannose via 8 hydrogen bonds. Compared to previous structure reported for similar protein, our structure showed a buried surface area of 900 Å2 compared to only 240 Å2 for previous one. Small-angle X-ray scattering (SAXS) data analysis showed that the predominant solution shape of SALT protein in solution is also dimer characterized by a radius of gyration and maximum linear dimension of 2.1 and 6.5 nm, respectively. The SAXS profiles and modelling confirmed that the dimeric association and relative positioning in solution matched better with our crystal structure instead of previously reported structure. Together, structural/biophysical data analysis uphold a tight dimeric structure for SALT protein with one mannose bound to each protein, which remains novel to date, as previous structures indicated one sugar unit sandwiched loosely between two protein chains.


eLife ◽  
2018 ◽  
Vol 7 ◽  
Author(s):  
Michael D Healy ◽  
Manuela K Hospenthal ◽  
Ryan J Hall ◽  
Mintu Chandra ◽  
Molly Chilton ◽  
...  

The COMMD proteins are a conserved family of proteins with central roles in intracellular membrane trafficking and transcription. They form oligomeric complexes with each other and act as components of a larger assembly called the CCC complex, which is localized to endosomal compartments and mediates the transport of several transmembrane cargos. How these complexes are formed however is completely unknown. Here, we have systematically characterised the interactions between human COMMD proteins, and determined structures of COMMD proteins using X-ray crystallography and X-ray scattering to provide insights into the underlying mechanisms of homo- and heteromeric assembly. All COMMD proteins possess an α-helical N-terminal domain, and a highly conserved C-terminal domain that forms a tightly interlocked dimeric structure responsible for COMMD-COMMD interactions. The COMM domains also bind directly to components of CCC and mediate non-specific membrane association. Overall these studies show that COMMD proteins function as obligatory dimers with conserved domain architectures.


1996 ◽  
Vol 11 (5) ◽  
pp. 1169-1178 ◽  
Author(s):  
Kentaro Suzuya ◽  
Michihiro Furusaka ◽  
Noboru Watanabe ◽  
Makoto Osawa ◽  
Kiyohito Okamura ◽  
...  

Mesoscopic structures of SiC fibers produced from polycarbosilane by different methods were studied by diffraction and small-angle scattering of neutrons and x-rays. Microvoids of a size of 4–10 Å in diameter have been observed for the first time by neutron scattering in a medium momentum transfer range (Q = 0.1–1.0 Å−1). The size and the volume fraction of β–SiC particles were determined for fibers prepared at different heat-treatment temperatures. The results show that wide-angle neutron scattering measurements are especially useful for the study of the mesoscopic structure of multicomponent materials.


2012 ◽  
Vol 25 (4) ◽  
pp. 9-15 ◽  
Author(s):  
L. Braicovich ◽  
N. B. Brookes ◽  
G. Ghiringhelli ◽  
M. Minola ◽  
G. Monaco ◽  
...  
Keyword(s):  
X Rays ◽  
X Ray ◽  

2013 ◽  
Vol 46 (5) ◽  
pp. 1508-1512 ◽  
Author(s):  
Byron Freelon ◽  
Kamlesh Suthar ◽  
Jan Ilavsky

Coupling small-angle X-ray scattering (SAXS) and ultra-small-angle X-ray scattering (USAXS) provides a powerful system of techniques for determining the structural organization of nanostructured materials that exhibit a wide range of characteristic length scales. A new facility that combines high-energy (HE) SAXS and USAXS has been developed at the Advanced Photon Source (APS). The application of X-rays across a range of energies, from 10 to 50 keV, offers opportunities to probe structural behavior at the nano- and microscale. An X-ray setup that can characterize both soft matter or hard matter and high-Zsamples in the solid or solution forms is described. Recent upgrades to the Sector 15ID beamline allow an extension of the X-ray energy range and improved beam intensity. The function and performance of the dedicated USAXS/HE-SAXS ChemMatCARS-APS facility is described.


2011 ◽  
Vol 286 (44) ◽  
pp. 38748-38756 ◽  
Author(s):  
Linda Brunotte ◽  
Romy Kerber ◽  
Weifeng Shang ◽  
Florian Hauer ◽  
Meike Hass ◽  
...  

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