Notes of a protein crystallographer: the legacy of J.-B. J. Fourier - crystallography, time and beyond

The importance of the Fourier transform as a fundamental tool for crystallography is well known in the field. However, the complete legacy of Jean-Baptiste Joseph Fourier (1768-1830) as a pioneer Egyptologist and premier mathematician and physicist of his time, and the implications of his work in other scientific fields, is less well known. Significantly, his theoretical and experimental work on phenomena related to the transmission of heat founded the mathematical study of irreversible phenomena and introduced the flow of time in physico-chemical processes and geology, with its implications for biological evolution. Fourier's insights are discussed in contrast to the prevalent notion of reversible dynamic time in the early 20th century, which was dominated by Albert Einstein's (1875-1953) theory of general relativity versus the philosophical notion of durée proposed by the French philosopher Henri-Louis Bergson (1859-1941). The current status of the mathematical description of irreversible processes by Ilya Romanovich Prigogine (1917-2003) is briefly discussed as part of the enduring legacy of the pioneering work of J.-B. J. Fourier, first established nearly two centuries ago, in numerous scientific endeavors.

50 Years of structural immunology

Fifty years ago, the first landmark structures of antibodies heralded the dawn of structural immunology. Momentum then started to build toward understanding how antibodies could recognize the vast universe of potential antigens and how antibody-combining sites could be tailored to engage antigens with high specificity and affinity through recombination of germline genes (V, D, J) and somatic mutation. Equivalent groundbreaking structures in the cellular immune system appeared some 15 to 20 years later and illustrated how processed protein antigens in the form of peptides are presented by MHC molecules to T cell receptors. Structures of antigen receptors in the innate immune system then explained their inherent specificity for particular microbial antigens including lipids, carbohydrates, nucleic acids, small molecules, and specific proteins. These two sides of the immune system act immediately (innate) to particular microbial antigens or evolve (adaptive) to attain high specificity and affinity to a much wider range of antigens. We also include examples of other key receptors in the immune system (cytokine receptors) that regulate immunity and inflammation. Furthermore, these antigen receptors use a limited set of protein folds to accomplish their various immunological roles. The other main players are the antigens themselves. We focus on surface glycoproteins in enveloped viruses including SARS-CoV-2 that enable entry and egress into host cells and are targets for the antibody response. This review covers what we have learned over the past half century about the structural basis of the immune response to microbial pathogens and how that information can be utilized to design vaccines and therapeutics.

Successes and challenges with retroviral enzymes

Collaborations between the Wlodawer and Skalka laboratories have covered a period of almost 30 years. During that time our groups have co-authored 18 publications, including several much cited journal articles, book chapters, and scholarly reviews. It has therefore been most rewarding for us to share enthusiasm, insights, and expertise with our Frederick colleagues over the years, and also to enjoy lasting friendships.

George Minot and Pernicious Anemia

George Minot (1885-1950) was born in Boston, Massachusetts. He was great grandson of James Jackson, co-founder of Massachusetts General Hospital in 1821. Graduating from Harvard College he enrolled at Harvard Medical School and obtained his MD in 1912. As a house pupil (intern) at the hospital he became interested in diseases of the blood and began taking meticulous histories of dietary habits of patients with anemia.

William Barlow and the Determination of Atomic Arrangement in Crystals

William Barlow (1845-1934) was an important if unconventional scientist, known for having developed the 'closest-packing' atomic models of crystal structure. He resumed an early nineteenth-century tradition of utilizing crystallographical and chemical data to determine atomic arrangements in crystals. This essay recounts Barlow's career and scientific activity in three parts: (a) His place in the tradition of determining atomic arrangement in context of this earlier tradition and of contemporaneous developments of crystallography and chemistry, (b) his unconventional career, and (c) the 'success' of his program to determine atomic arrangements in crystals and its influence on the work of William Lawrence Bragg.

The Protein Data Bank archive as an open data resource

The Protein Data Bank archive was established in 1971, and recently celebrated its 40th anniversary (Berman et al. in Structure 20:391, 2012). An analysis of interrelationships of the science, technology and community leads to further insights into how this resource evolved into one of the oldest and most widely used open-access data resources in biology.

Carl Friedrich Naumann and the introduction ofenantio terminology: A review and analysis on the 150th anniversary

Enantiomorphism and enantiomorphous were the first enantio-based terms, introduced 150 years ago, by Carl Friedrich Naumann, a German crystallographer, to refer to non-superposable mirror-image crystals. The terminology was not adopted by Pasteur, the discoverer of molecular chirality, and was not embraced at first in the stereochemical context, until it was accepted in 1877 by Van't Hoff in the German edition of his proposal for the tetrahedral asymmetric carbon atom. In the 1890s the use of enantio terms began to spread in the research literature, and many new derivatives of Naumann's original two terms were subsequently introduced. Problems in the usage of some of the terms are often found in the literature, e.g., enantiomorphism is sometimes confused with chirality; enantiomeric is often misused; the meaning of some of the many derived terms, e.g., enantiosymmetric, enantioposition, etc., is unclear. All in all, Naumann should be remembered as the creator of essential terminology in the realm of chirality.

Pictures of Dorothy Hodgkin

There are no established conventions for portraying scientific women. At the Royal Society, the first image of a female scientist was Henry Moore's drawing of Dorothy Hodgkin's hands, cruelly twisted by agonising arthritis. In her famous oil portrait, Maggi Hambling also focuses on Hodgkin's hands, thus symbolising the Nobel-prize winner's dedication to research and the importance of manual dexterity. Although Hambling's picture features a model of insulin, it is very different from photographs celebrating the discovery of DNA.

Recollections of the electron crystallographic heavy atom derivative search of purple membrane: the quest for EM structure determination

The use of multiple isomorphous replacement in protein electron crystallography for phase determination has been systematically studied only for purple membrane, even though the use of heavy atoms or heavy atom clusters has been used on many occasions in electron microscopy for locating domains or subunits in protein assemblies. The background behind the structure determination of bacteriorhodopsin, the protein component of purple membranes, is summarized and an evaluation of the strengths and weaknesses of using isomorphous replacement in electron crystallography is discussed.

Electron crystallography--accomplishments and challenges

Electron crystallography is a powerful tool for the quantitative structural characterization of substances that preferentially form thin microcrystals. Because multiple-beam dynamical scattering may cause observed diffraction intensities to deviate significantly from their kinematical values, it is necessary to demonstrate that the conditions favoring ab initio determinations can be established. Review of similar determinations made from electron and X-ray data make clear both the strengths and weaknesses of electron crystallography. With current instrumentation, the major onus now placed on the experimentalist is to optimize specimen preparation so that the resultant diffraction data can be directly interpreted.

The Hauptman-Woodward Medical Research Institute, Inc

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[Are liquid crystals living organisms?]

In 1888 the Austrian botanist F. Reinitzer made the observation that the solid compound cholesteryl-benzoate changes - when melting at 145.5 oC - into a cloudy liquid, that however, turns into a clear liquid at 178.5 oC and higher temperatures. The cloudy liquid seemed to be doubly refracting. Soon a number of these so-called 'liquid crystals' were discovered; in 1908 D. Vorländer, professor of organic chemistry at Halle, described more than 250 of these substances. It was O. Lehmann, professor of physics at Aachen (1885), Dresden (1888) and Karlsruhe (1889), who immediately after Reinitzer's observation began a systematic study of these liquid crystals. In The Netherlands the Amsterdam professor of physican chemistry H. W. Bakhuis Roozeboom was interested in liquid crystals, in particular because of their place in his phase system. F.M. Jaeger, at that time teaching chemistry in a secondary school in Zaandam (near Amsterdam) and working as an unpaid university lecturer at the Amsterdam university (by recommendation of Bakhuis Roozeboom), investigated liquid crystals (1906), as did a number of doctoral students (A.C. de Kock, 1903; A. Prins, 1907). At the university of Utrecht L.S. Ornstein, professor of physics, gave the study of liquid crystals a prominent place in his research programme. The discovery of liquid crystals, which seemed to be able to grow, move, divide, copulate, and so on, led to a discussion on the nature of these substances. Time and again Lehmann called them 'apparently living crystals', although without considering them as 'real living beings'. In his book Flüssige Kristalle und die Theorien des Lebens (1906), Lehmann proved to be an obvious adherent of the monistic views of the biologist E. Haeckel. Haeckel considered the existence of liquid crystals as proof of the unity between the inorganic and the organic world that he believed in so strongly. In his last book, Kristallseelen. Studien über das Anorganische Leben (1917), he considered liquid crystals a real form of life, as did F. Rinne, professor of mineralogy and petrography, as late as in the nineteen thirties.