Since its discovery in 1912, X-ray crystallography has become a most useful tool in physics, chemistry, material science, mineralogy, metallurgy, and even in the biological sciences. In 1914, Max von Laue was awarded the Nobel Prize “for the discovery of X-ray diffraction by crystals,” followed by the 1915 Nobel Prize to William Henry Bragg and William Lawrence Bragg “for their services in analysis of crystal structure by means of X-rays.” And these early Nobel prizes marked only the (...) beginning of X-ray crystallography as one of the most fruitful methods in the history of modern science. A 100 years after Laue’s Nobel Prize and 50 years after another Nobel Prize to Dorothy Hodgkin “for her determination by X-ray technique of the structures of important biochemical substances,” the UN proclaimed 2014 the International Year of Crystallography. “In all, 45 scientists have been awarded over the past century for work that is either directly or indirectly related to crystallo .. (shrink)

Sarco/endoplasmic reticulum Ca2+ ATPase 2b (SERCA2b), a member of the SERCA family, is expressed ubiquitously and transports Ca2+ into the sarco/endoplasmic reticulum using the energy provided by ATP binding and hydrolysis. The crystal structure of SERCA2b in its Ca2+‐ and ATP‐bound (E1∙2Ca2+‐ATP) state and cryo‐electron microscopy (cryo‐EM) structures of the protein in its E1∙2Ca2+‐ATP and Ca2+‐unbound phosphorylated (E2P) states have provided essential insights into how the overall conformation and ATPase activity of SERCA2b is regulated by the transmembrane helix (...) 11 and the subsequent luminal extension loop, both of which are specific to this isoform. More recently, our cryo‐EM analysis has revealed that SERCA2b likely adopts open and closed conformations of the cytosolic domains in the Ca2+‐bound but ATP‐free (E1∙2Ca2+) state, and that the closed conformation represents a state immediately prior to ATP binding. This review article summarizes the unique mechanisms underlying the conformational and functional regulation of SERCA2b. (shrink)

Rapidly advancing studies on rhodopsin have focused on new strategies for crystallization of this integral membrane protein for x-ray analysis and on alternative methods for structural determination from nuclear magnetic resonance data. Functional studies of the interactions between the apoprotein and its chromophore have clarified the role of the chromophore in deactivation of opsin and in photoactivation of the pigment.

The preceding five years have brought remarkable advances in our understanding of the primary structure of drug receptors. The roles of certain amino acid residues in binding drugs and effecting receptor function have been proposed. As even more detailed structures become available, the goal of rational design of drug molecules based on predicted fits between the drug and its receptor will be near at hand. Although none of the classical receptors has yet yielded to X‐ray crystallographic analysis, the (...) methods of molecular biology facilitate the production of the large amounts of these rare proteins necessary for crystallization. Receptor proteins share one fundamental characteristic with allosterically regulated enzymes. Both have the structural flexibility that allows information to be transmitted to distant parts of the molecule. We will discuss recent observations about receptor structure and the dynamic nature of drug receptors, and pose questions about the significance of receptor dynamics for drug design. (shrink)

A study of the structural perfection of icosahedral quasicrystalline grains of various alloys and Al-Cu-Fe), grown by different slow solidification techniques was performed using high-resolution diffraction, including recording rocking curves combined with X-ray topography and phase contrast radiography, at a third-generation synchrotron radiation source . For Al-Pd-Mn, additional coherent diffraction and diffuse scattering measurements were also carried out. After evaluating the potentialities of the techniques used, in the light of the criteria defined for crystals, it is shown that the structural (...) perfection of icosahedral quasicrystals is quite comparable with that of metallic crystals but is considerably influenced by either uniform phason strains which can destroy the quasiperiodic long-range order, or by long-wavelength phason fluctuations leading to diffuse scattering. The structural perfection was also found to be extremely variable across the as-grown quasicrystalline grains and to be dependent on the presence and characteristics of inhomogeneities often included in the quasicrystalline matrix. Regarding the grains that we used, it has been impossible to distinguish a clear influence of either the type of alloy or the growth method. It has, however, been noticed that Al-Pd-Mn and Al-Cu-Fe grains appeared less defective than Zn-Mg-RE grains and that the microstructure of these latter grains looks like that of crystals grown by the same technique. Annealing and mechanical polishing effects have also been analysed in the case of Al-Pd-Mn grains. It appeared that annealing improves the quasicrystalline lattice perfection by lowering phason strains insofar as no precipitates are nucleated. Mechanical polishing can introduce defects, located at the external surfaces, having the shape of bands. (shrink)

Strong arguments are presented by Hargrave suggesting that the crystallization of visual rhodopsin for high resolution analysis by X-ray crystallography or electron microscopy is feasible. However, the effort needed to achieve this goal will most likely exceed the resources of a single laboratory and a concerted approach to the research is necessary.

In the present work, the microstructure of the melt-spun Al 90 Ce 10 alloy has been characterized using X-ray diffraction and transmission electron microscopy together with energy-dispersive spectrometry. It has been found that the microstructure of the melt-spun Al 90 Ce 10 alloy is composed of the amorphous phase, f -Al, f -Al 11 Ce 3 , Al 3 Ce and unidentified phases, quite different from that of the ingot-like alloy consisting of coarse primary f -Al- f -Al 11 Ce (...) 3 dendrites embedded in the f -Al- f -Al 11 Ce 3 eutectic matrix. Moreover, the amorphous phase is dominant in the melt-spun Al 90 Ce 10 alloy according to the XRD and TEM results. Al 3 Ce particles, less than 100 nm in size, are dispersed in the partial amorphous phase. Polygonal f -Al 11 Ce 3 crystals embedded in the f -Al matrix are also observed. The presence of the hexagonal, kite-like and petal-like intermetallic particles surrounded by the amorphous phase indicates that there exist micro-inhomogeneous structures in the Al 90 Ce 10 melt. These results demonstrate that the overheating of the melt has a significant effect on the amorphization of the Al 90 Ce 10 alloy. (shrink)

Deamination of adenosine in RNA to form inosine has wide ranging consequences on RNA function including amino acid substitution to give proteins not encoded in the genome. What determines which adenosines in an mRNA are subject to this modification reaction? The answer lies in an understanding of the mechanism and substrate recognition properties of adenosine deaminases that act on RNA (ADARs). Our recent publication of X‐ray crystal structures of the human ADAR2 deaminase domain bound to RNA editing substrates shed (...) considerable light on how the catalytic domains of these enzymes bind RNA and promote adenosine deamination. Here we review in detail the deaminase domain‐RNA contact surfaces and present models of how full length ADARs, bearing double stranded RNA‐binding domains (dsRBDs) and deaminase domains, could process naturally occurring substrate RNAs. (shrink)

One popular recombinant DNA tool is the EcoRI endonuclease, which cleaves DNA at GAATTC sites and serves as a paradigm for sequence specific DNA‐enzyme interactions. The recently revised X‐ray crystal structure of an EcoRI‐DNA complex reveals EcoRI employs novel DNA recognition motifs, a four α‐helix bundle and two extended chains, which project into the major groove to contact substrate purines and pyrimidines. Interestingly, pyrimidine contacts had been predicted based on genetic and biochemical studies. Current work focuses on the (...) EcoRI active site structure, enzyme and substrate conformational changes during catalysis, and host‐restriction system interactions. (shrink)

To understand how the photoreceptor protein rhodopsin performs in its role as a receptor, its structure needs to be determined at the atomic level. Upon receiving a photon of light, rhodopsin undergoes a change in conformation that allows it to bind and activate the C-protein, transducin. An important future goal should be to determine the structure of both the inactive and the photoactivated state of rhodopsin, R*. This should provide the groundwork necessary for experiments on how rhodopsin achieves (...) its signaling state R*, and how R* functions to activate transducin. To do this, the crystal structure of both rhodopsin and R* must be determined. Few membrane proteins have been successfully crystallized, so this is not a trivial undertaking. Two- or three dimensional crystals of rhodopsin must be prepared that are well ordered, to produce a high-resolution structure. Rhodopsin must be purified to homogeneity and the appropriate detergent(s) selected for crystallization experiments. Long-term thermal stability of the rhodopsin-detergent complex must be achieved in the presence of a precipitant. Two-dimensional crystals may offer advantages in investigating the structure of R*, but the structure obtained may be limited in resolution. It is necessary to work with rhodopsin in the dark, unless suitable light-stable retinal derivatives are developed. Protein engineering of rhodopsin offers attractive opportunities to improve its ability to crystallize, but is presently hindered by the absence of a high-yielding expression system. Knowledge of the structure of rhodopsin will have general importance. Because rhodopsin is a member of the family of C-protein-coupled receptors, knowledge of the structure and the mechanism of action of rhodopsin suggests by analogy how other members of the receptor family may function. (shrink)

Structural biology has experienced several transformative technological advances in recent years. These include: development of extremely bright X-ray sources and the use of electrons to extend protein crystallography to ever decreasing crystal sizes; and an increase in the resolution attainable by cryo-electron microscopy. Here we discuss the use of these techniques in general terms and highlight their application for biological filament systems, an area that is severely underrepresented in atomic resolution structures. We assemble a model of a capped tropomyosin-actin (...) minifilament to demonstrate the utility of combining structures determined by different techniques. Finally, we survey the methods that attempt to transform high resolution structural biology into more physiological environments, such as the cell. Together these techniques promise a compelling decade for structural biology and, more importantly, they will provide exciting discoveries in understanding the designs and purposes of biological machines. Structural biology is undergoing technological advancements that now reveal the structures of previously inaccessible biological machines. Microfocus synchrotron beamlines, X-ray free electron lasers, and MicroED cope with vanishingly small crystals, while cryo-electron microscopy targets single molecules at near atomic resolution. These advances promise an exciting decade for structural biology. (shrink)

© Ginn et al. 2016.The indexing methods currently used for serial femtosecond crystallography were originally developed for experiments in which crystals are rotated in the X-ray beam, providing significant three-dimensional information. On the other hand, shots from both X-ray free-electron lasers and serial synchrotron crystallography experiments are still images, in which the few three-dimensional data available arise only from the curvature of the Ewald sphere. Traditional synchrotron crystallography methods are thus less well suited to still image data processing. Here, a (...) new indexing method is presented with the aim of maximizing information use from a still image given the known unit-cell dimensions and space group. Efficacy for cubic, hexagonal and orthorhombic space groups is shown, and for those showing some evidence of diffraction the indexing rate ranged from 90% to 151%. Here, the indexing rate refers to the number of lattices indexed per image. (shrink)

An attempt is made to establish the historical context in which the structure and function of haemoglobin were investigated by X-ray crystallographers in the 1940s and 50s. It is concluded that until the 1960s the interpretations of the data of crystallographic investigations were dependent upon the results of applying traditional techniques of physical and organic chemistry. In the case of haemoglobin, no less than in those of smaller organic molecules, crystallographic studies in the 1940s and early 50s served to (...) validate, and metricize conclusions already suggested or adopted on other grounds, but the subsequent tracing of the actual conformation of the polypeptide chains in the globin portion of the molecule was a unique achievement of the X-ray crystallographers and marked the beginning of the independent establishment of structures by this profession. The impact of this achievement upon the structure-function relationships of haemoglobin is discussed briefly. (shrink)

The crystallization behaviour of Fe 70.8 Nb 3.7 Cu 1 Al 2.7 Mn 0.7 Si 13.5 B 7.6 alloy prepared in the form of amorphous ribbons by melt-spinning technique was studied using differential scanning calorimetry and the temperature variation in resistivity. An X-ray diffaction and transmission electron microscopy study showed the formation of f -Fe and/or Fe 3 nanoparticles after the first stage of crystallization. The activation energy for this nanophase formation was 68 kcal mol m 1 . The brittleness (...) of the alloy increased with the formation of nanoparticles after heat treatment. Superior soft magnetic properties were achieved when the material was heat treated at 790 K for 15 min. The particle size at the optimum heat treatment condition for superior soft magnetic properties was found to be 6.0 - 0.5 nm which was less compared than for the Fe-Nb-Cu-Si-B system. The observed coercivity value at the optimum heat treatment condition was found to be 0.32 A m m 1 . The presence of Al in the alloy reduced the particle size and the magnetic anisotropy energy of the system, which resulted in superior soft magnetic properties of the heat-treated materials. (shrink)

Thomas S. Kuhn’s theory of normal science (NS), aside from being a provocative philosophical reconstruction of the relatively conservative phase of scientific research, contains useful ideas for systematic analysis of specific episodes in the history of science. Therefore, although the theory has been looked at from different angles since the first edition of The Structure of Scientific Revolutions (TSSR) was published in 1962, its detailed exploration of the cumulative phase of research in mature science is of abiding relevance (...) in the philosophy of science. This is because NS provides a compelling account of how and why members of scientific communities succeed, largely, to produce reliable knowledge about an incompletely known phenomenal world. Again, the theory elucidates special features of scientific research that differentiate it from other creative enterprises. In that regard, this paper reconstructs Arthur Compton’s research into x-ray scattering as a good instantiation of NS. Discussion of Compton’s convincing demonstration of the particulate properties of electromagnetic radiation within the framework of NS showcases the elucidatory power of Kuhn’s theory with respect to selected episodes in science, and corroborates the notion that the bulk of scientific work is a conservative puzzle-solving activity with the potential for precipitating scientific revolutions. To the best of my knowledge, this is the first time that Compton’s groundbreaking work on x-ray scattering has been analysed within the framework of Kuhn’s philosophy of science. (shrink)

In this paper, I argue that Plotinus offers us a new and interesting account of self-intellection. It is an account which is informed to some extent by a dilemma that Sextus Empiricus raised about the intellect being to apprehend itself. The significance of Sextus' dilemma is that it sets out the framework within which such a cognitive activity is to be dealt with, namely the intellect must apprehend itself qua part or qua whole, both of which according to him are (...) impossible. Plotinus, I think, successfully gets around this dilemma and is able to explain how the intellect can think itself qua whole. In the process of doing so, he offers an account of self-intellection in which the thinking subject or thinker becomes active in terms of generating its intellectual content, namely itself; a move which is a break from the traditional Platonic/Aristotelian account of the intellect. The paper itself is set up as follows. I start by mentioning the dilemma which Sextus raises about self-intellection. Then I attempt, through an analysis of the noetic intellect's structure, to show how Plotinus is able to offer an account of self-intellection in terms of whole apprehending whole. I conclude with Plotinus' analysis of the light analogy as a means of explaining how this intellectual process works. (shrink)

This monograph introduces the functional characteristics and conceptual significance of a simulation software system called CyberRat (Ray, 1996a, 2003a, 2012a, 2012b). CyberRat expands upon prior illustrations (Ray & Delprato, 1989; Ray, 1992) of how such computer-based simulations can serve to formatively enhance, and eventually validate, the descriptive research methodology upon which their development relies. To illustrate this process I also review highlights of previous publications (cf. Ray & Brown, 1975, 1976; Ray & Delprato, 1989), detailing the unique research methodology used (...) to collect data that guided CyberRat’s development. This methodology integrates interbehavioral psychology (Kantor, 1959) and general systems analysis (von Bertalanffy, 1968), and thus is referred to as interbehavioral systems analysis (IBSA). CyberRat’s validation of IBSA methods involves a process analogous to Turing’s (1950) famous test for simulation authenticity, in that it relies upon “phenomenological equivalence” criteria for observers to compare experiences of real vs. simulated events. And because IBSA stresses three convergent strategies for research, including structural analysis, functional analysis, and operations analysis, my organizing theme addresses how closely CyberRat comes to passing a trilogy of hypothetical Turing tests—one for each of these three analytic strategies. (shrink)

Systematic variation of anisotropic X-ray line broadening in vapour-deposited Pb films of various thicknesses on glass substrates is studied using dislocation model of strain anisotropy incorporated into a modified Williamson-Hall and modified Warren-Averbach procedure. For smaller film thicknesses in the range of about 100-200 nm, the dislocation network is less correlated and contains substantial screw component and twin or growth faults. The films of larger thicknesses , on the other hand, consist mostly of edge dislocations with a more regular and (...) correlated dislocation structure. The present study reveals the inadequacy of applicability of conventional Warren-Averbach analysis in regular and correlated dislocation structures. (shrink)

The composition of nitrogen-doped hydrogenated amorphous carbon films grown in a magnetically confined rf plasma-enhanced chemical vapour deposition system has been determined by X-ray photoelectron spectroscopy and compared with that determined using a combination of elastic recoil detection analysis, Rutherford back-scattering and nuclear reaction analysis. The importance of nitrogen doping or 'incorporation' in hydrogenated amorphous carbon films is discussed in relation to the significant variation in the sp 2 -to-sp 3 ratio that takes place. At 7 at.% N (...) in the a-C : H matrix, a critical change in the microstructure is observed, which governs the resulting mechanical, optical and electronic properties. Finally, the correlation between the sp 2 and sp 3 fractions determined by a non-destructive method of obtaining the bond fractions and by electron-energy-loss spectroscopy is discussed, with a view to evaluating accurately the sp 2 fraction in a-C : H : N films. (shrink)

Cryo‐electron microscopy allows the visualization of macromolecules in their native state. Combined with techniques of three‐dimensional reconstruction, cryo‐EM images of single molecules can be used to study macromolecular interactions. The ribosome, a large RNA–protein complex with multiple binding interactions, is an excellent test case illustrating the power of these new techniques. Conformational changes during the binding of tRNA and protein factors to the ribosome can now be studied without the interference of crystal packing. Now that the first X‐ray structures (...) of ribosomal subunits have become available, conformational changes observed by cryo‐EM in different functional states can be traced back to internal rearrangements of the underlying structural framework. Electron microscopy, X‐ray crystallography, and modeling should be used together in the endeavor to understand the functioning of the translational machinery. BioEssays 23:725–732, 2001. © 2001 John Wiley & Sons, Inc. (shrink)