Structural Biology: A Century-long Journey into an Unseen World.
ABSTRACT: When the first atomic structures of salt crystals were determined by the Braggs in 1912-1913, the analytical power of X-ray crystallography was immediately evident. Within a few decades the technique was being applied to the more complex molecules of chemistry and biology and is rightly regarded as the foundation stone of structural biology, a field that emerged in the 1950s when X-ray diffraction analysis revealed the atomic architecture of DNA and protein molecules. Since then the toolbox of structural biology has been augmented by other physical techniques, including nuclear magnetic resonance spectroscopy, electron microscopy, and solution scattering of X-rays and neutrons. Together these have transformed our understanding of the molecular basis of life. Here I review the major and most recent developments in structural biology that have brought us to the threshold of a landscape of astonishing molecular complexity.
Project description:The types of Scarabaeidae deposited in the collection of the National Museum of Natural History of Luxembourg are reported for the first time along with some historic and taxonomic remarks: <i>Entypophanabiapicata</i> Moser, 1913; <i>Metabolusthibetanus</i> Moser, 1914 (currently, <i>Pseudosymmachia</i>); <i>Autosericaannamensis</i> Moser, 1915 (currently, <i>Maladera</i>); <i>Euphoresiaalboparsa</i> Moser, 1913; <i>Hybocamentaferranti</i> Moser, 1917; <i>Microsericaflaveola</i> Moser, 1911; <i>Triodontalujai</i> Moser, 1917 (currently, <i>Triodontella</i>); <i>Trochalusferranti</i> Moser, 1917; <i>Anomalacondophora</i> Ohaus, 1913 (currently, <i>Mimela</i>); <i>Amaurinaferranti</i> Moser, 1911 (currently, <i>Leucocelis</i>); <i>Amaurinavittipennis</i> Moser, 1909; Cetonia (Eucetonia) kolbei Curti, 1914; <i>Lomapteradichropusviridipes</i> Moser, 1908; <i>Cosmovalgusferranti</i> Moser, 1912.
Project description:Local structures around impurities in solids provide important information for understanding the mechanisms of material functions, because most of them are controlled by dopants. For this purpose, the x-ray absorption fine structure method, which provides radial distribution functions around specific elements, is most widely used. However, a similar method using neutron techniques has not yet been developed. If one can establish a method of local structural analysis with neutrons, then a new frontier of materials science can be explored owing to the specific nature of neutron scattering-that is, its high sensitivity to light elements and magnetic moments. Multiple-wavelength neutron holography using the time-of-flight technique with pulsed neutrons has great potential to realize this. We demonstrated multiple-wavelength neutron holography using a Eu-doped CaF2 single crystal and obtained a clear three-dimensional atomic image around trivalent Eu substituted for divalent Ca, revealing an interesting feature of the local structure that allows it to maintain charge neutrality. The new holography technique is expected to provide new information on local structures using the neutron technique.
Project description:Stephanidae Leach, 1815 (Hymenoptera: Stephanoidea) from China are revised. Five genera are reported from China: Foenatopus Smith, 1861; Megischus Brullé, 1846; Parastephanellus Enderlein, 1906; Schlettererius Ashmead, 1900; and Stephanus Jurine (in Panzer), 1801, and the genera are keyed. All the Chinese species are described and illustrated and new synonyms are established. Keys to species of the five genera occurring in China and adjacent regions are provided.SIX SPECIES ARE NEW TO SCIENCE: Foenatopus brevimaculatussp. n., Foenatopus maculiferussp. n., Foenatopus yangisp. n., Parastephanellus angulatussp. n., Parastephanellus brevicoxalissp. n. and Parastephanellus zhejiangensissp. n. One species, Parastephanellus matsumotoi van Achterberg, 2006, is newly recorded from China.The following 9 new synonyms are proposed: Foenatopus aratifrons Enderlein, 1913 and Foenatopus yunnanensis Chao, 1964, new synonymys for Foenatopus annulitarsus Enderlein, 1913; Foenatopus cerviculatus (Chao, 1964) and Foenatopus chaoi Belokobylskij, 1995 for Foenatopus chinensis (Elliott, 1919); Foenatopus formosanus Enderlein, 1913 for Foenatopus cinctus (Matsumura, 1912); Foenatopus simillimus (Elliott, 1920) and Foenatopus trilineatus (Elliott, 1920) for Foenatopus flavidentatus (Enderlein, 1913); Foenatopus trilobatus (Elliott, 1920) for Foenatopus ruficollis (Enderlein, 1913); Parastephanellus austrochinensis Belokobylskij, 1995 for Parastephanellus brevistigma Enderlein, 1913. A lectotype is designated for Diastephanus trilineatus Elliott, 1920.
Project description:Grating interferometer based imaging with X-rays and neutrons has proven to hold huge potential for applications in key research fields conveying biology and medicine as well as engineering and magnetism, respectively. The thereby amenable dark-field imaging modality implied the promise to access structural information beyond reach of direct spatial resolution. However, only here a yet missing approach is reported that finally allows exploiting this outstanding potential for non-destructive materials characterizations. It enables to obtain quantitative structural small angle scattering information combined with up to 3-dimensional spatial image resolution even at lab based x-ray or at neutron sources. The implied two orders of magnitude efficiency gain as compared to currently available techniques in this regime paves the way for unprecedented structural investigations of complex sample systems of interest for material science in a vast range of fields.
Project description:With the ability to resolve structures of macromolecules at atomic resolution, X-ray crystallography has been the most powerful tool in modern structural biology. At the same time, recent technical improvements have triggered a resolution revolution in the single particle cryo-EM method. While the two methods are different in many respects, from sample preparation to structure determination, they both have the power to solve macromolecular structures at atomic resolution. It is important to understand the unique advantages and caveats of the two methods in solving structures and to appreciate the complementary nature of the two methods in structural biology. In this review we provide some examples, and discuss how X-ray crystallography and cryo-EM can be combined in deciphering structures of macromolecules for our full understanding of their biological mechanisms.
Project description:X-ray protein crystallography has, through the determination of the three-dimensional structures of enzymes and their complexes, been essential to the understanding of biological chemistry. However, as X-rays are scattered by electrons, the technique has difficulty locating the presence and position of H atoms (and cannot locate H+ ions), knowledge of which is often crucially important for the understanding of enzyme mechanism. Furthermore, X-ray irradiation, through photoelectronic effects, will perturb the redox state in the crystal. By using single-crystal spectrophotometry, reactions taking place in the crystal can be monitored, either to trap intermediates or follow photoreduction during X-ray data collection. By using neutron crystallography, the positions of H atoms can be located, as it is the nuclei rather than the electrons that scatter neutrons, and the scattering length is not determined by the atomic number. Combining the two techniques allows much greater insight into both reaction mechanism and X-ray-induced photoreduction.
Project description:The study of virus structures has contributed to methodological advances in structural biology that are generally applicable (molecular replacement and noncrystallographic symmetry are just two of the best known examples). Moreover, structural virology has been instrumental in forging the more general concept of exploiting phase information derived from multiple structural techniques. This hybridization of structural methods, primarily electron microscopy (EM) and X-ray crystallography, but also small-angle X-ray scattering (SAXS) and nuclear magnetic resonance (NMR) spectroscopy, is central to integrative structural biology. Here, the interplay of X-ray crystallography and EM is illustrated through the example of the structural determination of the marine lipid-containing bacteriophage PM2. Molecular replacement starting from an ~13 Å cryo-EM reconstruction, followed by cycling density averaging, phase extension and solvent flattening, gave the X-ray structure of the intact virus at 7 Å resolution This in turn served as a bridge to phase, to 2.5 Å resolution, data from twinned crystals of the major coat protein (P2), ultimately yielding a quasi-atomic model of the particle, which provided significant insights into virus evolution and viral membrane biogenesis.
Project description:Time-of-flight neutron powder diffraction data have been measured from ?90?mol% deuterated isotopologues of Na2MoO4·2H2O and Na2WO4·2H2O at 295?K to a resolution of sin?(?)/? = 0.77?Å(-1). The use of neutrons has allowed refinement of structural parameters with a precision that varies by a factor of two from the heaviest to the lightest atoms; this contrasts with the X-ray based refinements where precision may be > 20× poorer for O atoms in the presence of atoms such as Mo and W. The accuracy and precision of inter-atomic distances and angles are in excellent agreement with recent X-ray single-crystal structure refinements whilst also completing our view of the hydrogen-bond geometry to the same degree of statistical certainty. The two structures are isotypic, space-group Pbca, with all atoms occupying general positions, being comprised of edge- and corner-sharing NaO5 and NaO6 polyhedra that form layers parallel with (010) inter-leaved with planes of XO4 (X = Mo, W) tetra-hedra that are linked by chains of water mol-ecules along  and . The complete structure is identical with the previously described molybdate [Capitelli et al. (2006 ?). Asian J. Chem. 18, 2856-2860] but shows that the purported three-centred inter-action involving one of the water mol-ecules in the tungstate [Farrugia (2007 ?). Acta Cryst. E63, i142] is in fact an ordinary two-centred 'linear' hydrogen bond.
Project description:X-ray crystallography often requires non-native constructs involving mutations or truncations, and is challenged by membrane proteins and large multicomponent complexes. We present here a bottom-up endogenous structural proteomics approach whereby near-atomic-resolution cryo electron microscopy (cryoEM) maps are reconstructed ab initio from unidentified protein complexes enriched directly from the endogenous cellular milieu, followed by identification and atomic modeling of the proteins. The proteins in each complex are identified using cryoID, a program we developed to identify proteins in ab initio cryoEM maps. As a proof of principle, we applied this approach to the malaria-causing parasite Plasmodium falciparum, an organism that has resisted conventional structural-biology approaches, to obtain atomic models of multiple protein complexes implicated in intraerythrocytic survival of the parasite. Our approach is broadly applicable for determining structures of undiscovered protein complexes enriched directly from endogenous sources.