Crystals of taka-amylase A, a cornerstone of protein chemistry in Japan.

In 1935, Shiro Akabori began research on the preparation of taka-amylase A with a purity suitable for chemical research, with the intention of elucidating the chemical nature of the enzyme. He succeeded in developing a method to efficiently obtain crystallized taka-amylase A from Aspergillus oryzae. Using crystallized taka-amylase A as the starting material, a series of studies were conducted to determine its amino acid composition and sequence, sugar chain structure, and three-dimensional structure. Based on these results, the molecular structure and catalytic mechanism of taka-amylase A were elucidated. The scientific achievements from research on taka-amylase A significantly enhanced Japan's capabilities in protein research, represented by the fact that taka-amylase A was the first amylase in the world for which both chemical and crystallographic structures were elucidated.

Isabella L. Karle: A Crystallography Pioneer.

The life and work of crystallography pioneer Isabella L. Karle is recounted (1921-2017), as researched from the literature and personal stories of colleagues and family. Her story includes her family background, education at the University of Michigan, research on the Manhattan Project, and 63 productive years at the Naval Research Laboratory. Her life-long partnership and scientific collaboration with husband Jerome Karle, 1985 Nobel Prize winner in Chemistry with Herbert Hauptman, is a big part of her story; however, Isabella has also established herself as a crystallographer extraordinaire through her Symbolic Addition Procedure to solve the phase problem, and her unique ability to solve the structures of complex biological molecules, including toxins, antibiotics, and peptides. Her rich family life with three daughters in a lake-front home, do-it-yourself attitude, and passions outside of science round up this portrait of a fascinating and brilliant woman.

History of DNA polymerase ß X-ray crystallography.

DNA polymerase ß (Pol ß) is an essential mammalian enzyme involved in the repair of DNA damage during the base excision repair (BER) pathway. In hopes of faithfully restoring the coding potential to damaged DNA during BER, Pol ß first uses a lyase activity to remove the 5'-deoxyribose phosphate moiety from a nicked BER intermediate, followed by a DNA synthesis activity to insert a nucleotide triphosphate into the resultant 1-nucleotide gapped DNA substrate. This DNA synthesis activity of Pol ß has served as a model to characterize the molecular steps of the nucleotidyl transferase mechanism used by mammalian DNA polymerases during DNA synthesis. This is in part because Pol ß has been extremely amenable to X-ray crystallography, with the first crystal structure of apoenzyme rat Pol ß published in 1994 by Dr. Samuel Wilson and colleagues. Since this first structure, the Wilson lab and colleagues have published an astounding 267 structures of Pol ß that represent different liganded states, conformations, variants, and reaction intermediates. While many labs have made significant contributions to our understanding of Pol ß, the focus of this article is on the long history of the contributions from the Wilson lab. We have chosen to highlight select seminal Pol ß structures with emphasis on the overarching contributions each structure has made to the field.

How computational chemistry develops: a tribute to Peter Goodford.

This editorial discusses the foundation of aspects of computational chemistry and is a tribute to Peter Goodford, one of those founders, who recently passed away. Several colleagues describe Professor Goodford's work and the person himself.

Biophysical Techniques in Structural Biology.

Over the past six decades, steadily increasing progress in the application of the principles and techniques of the physical sciences to the study of biological systems has led to remarkable insights into the molecular basis of life. Of particular significance has been the way in which the determination of the structures and dynamical properties of proteins and nucleic acids has so often led directly to a profound understanding of the nature and mechanism of their functional roles. The increasing number and power of experimental and theoretical techniques that can be applied successfully to living systems is now ushering in a new era of structural biology that is leading to fundamentally new information about the maintenance of health, the origins of disease, and the development of effective strategies for therapeutic intervention. This article provides a brief overview of some of the most powerful biophysical methods in use today, along with references that provide more detailed information about recent applications of each of them. In addition, this article acts as an introduction to four authoritative reviews in this volume. The first shows the ways that a multiplicity of biophysical methods can be combined with computational techniques to define the architectures of complex biological systems, such as those involving weak interactions within ensembles of molecular components. The second illustrates one aspect of this general approach by describing how recent advances in mass spectrometry, particularly in combination with other techniques, can generate fundamentally new insights into the properties of membrane proteins and their functional interactions with lipid molecules. The third reviewdemonstrates the increasing power of rapidly evolving diffraction techniques, employing the very short bursts of X-rays of extremely high intensity that are now accessible as a result of the construction of free-electron lasers, in particular to carry out time-resolved studies of biochemical reactions. The fourth describes in detail the application of such approaches to probe the mechanism of the light-induced changes associated with bacteriorhodopsin's ability to convert light energy into chemical energy.

Integrative Structure Modeling: Overview and Assessment.

Integrative structure modeling computationally combines data from multiple sources of information with the aim of obtaining structural insights that are not revealed by any single approach alone. In the first part of this review, we survey the commonly used sources of structural information and the computational aspects of model building. Throughout the past decade, integrative modeling was applied to various biological systems, with a focus on large protein complexes. Recent progress in the field of cryo-electron microscopy (cryo-EM) has resolved many of these complexes to near-atomic resolution. In the second part of this review, we compare a range of published integrative models with their higher-resolution counterparts with the aim of critically assessing their accuracy. This comparison gives a favorable view of integrative modeling and demonstrates its ability to yield accurate and informative results. We discuss possible roles of integrative modeling in the new era of cryo-EM and highlight future challenges and directions.

Visualization of biological macromolecules at near-atomic resolution: cryo-electron microscopy comes of age.

Structural biology is going through a revolution as a result of transformational advances in the field of cryo-electron microscopy (cryo-EM) driven by the development of direct electron detectors and ultrastable electron microscopes. High-resolution cryo-EM images of isolated biomolecules (single particles) suspended in a thin layer of vitrified buffer are subjected to powerful image-processing algorithms, enabling near-atomic resolution structures to be determined in unprecedented numbers. Prior to these advances, electron crystallography of two-dimensional crystals and helical assemblies of proteins had established the feasibility of atomic resolution structure determination using cryo-EM. Atomic resolution single-particle analysis, without the need for crystals, now promises to resolve problems in structural biology that were intractable just a few years ago.

X-Ray Free-Electron Lasers for the Structure and Dynamics of Macromolecules.

X-ray free-electron lasers provide femtosecond-duration pulses of hard X-rays with a peak brightness approximately one billion times greater than is available at synchrotron radiation facilities. One motivation for the development of such X-ray sources was the proposal to obtain structures of macromolecules, macromolecular complexes, and virus particles, without the need for crystallization, through diffraction measurements of single noncrystalline objects. Initial explorations of this idea and of outrunning radiation damage with femtosecond pulses led to the development of serial crystallography and the ability to obtain high-resolution structures of small crystals without the need for cryogenic cooling. This technique allows the understanding of conformational dynamics and enzymatics and the resolution of intermediate states in reactions over timescales of 100 fs to minutes. The promise of more photons per atom recorded in a diffraction pattern than electrons per atom contributing to an electron micrograph may enable diffraction measurements of single molecules, although challenges remain.

John Kendrew and myoglobin: Protein structure determination in the 1950s.

The essay reviews John Kendrew's pioneering work on the structure of myoglobin for which he shared the Nobel Prize for Chemistry in 1962. It reconstructs the status of protein X-ray crystallography at the time Kendrew entered the field in 1945, after distinctive service in operational research during the war. It reflects on the choice of sperm whale myoglobin as research material. In particular, it highlights Kendrew's early use of digital electronic computers for crystallographic computations and the marshaling of other tools and approaches that made it possible to solve the structure at increasing resolution. The essay further discusses the role of models in structure resolution and their broader reception. It ends by briefly reviewing Kendrew's other contributions in the formation and institutionalization of molecular biology.

Forty years of collaborative computational crystallography.

A brief overview is provided of the history of collaborative computational crystallography, with an emphasis on the Collaborative Computational Project No. 4. The key steps in its development are outlined, with consideration also given to the underlying reasons which contributed, and ultimately led to, the unprecedented success of this venture.

X-ray data processing.

The method of molecular structure determination by X-ray crystallography is a little over a century old. The history is described briefly, along with developments in X-ray sources and detectors. The fundamental processes involved in measuring diffraction patterns on area detectors, i.e. autoindexing, refining crystal and detector parameters, integrating the reflections themselves and putting the resultant measurements on to a common scale are discussed, with particular reference to the most commonly used software in the field.

100 years of X-ray crystallography.

The developments in crystallography, since it was first covered in Science Progress in 1917, following the formulation of the Bragg equation, are described. The advances in instrumentation and data analysis, coupled with the application of computational methods to data analysis, have enabled the solution of molecular structures from the simplest binary systems to the most complex of biological structures. These developments are shown to have had major impacts in the development of chemical bonding theory and in offering an increasing understanding of enzyme-substrate interactions. The advent of synchrotron radiation sources has opened a new chapter in this multi-disciplinary field of science.

Structural Molecular Biology-A Personal Reflection on the Occasion of John Kendrew's 100th Birthday.

Here, I discuss the development and future of structural molecular biology, concentrating on the eukaryotic transcription machinery and reflecting on John Kendrew's legacy from a personal perspective.

A Personal Perspective: My Four Encounters with John Kendrew.

By celebrating the 100th anniversary of John Kendrew's birth in 1917, the Journal of Molecular Biology recognizes his seminal contributions to science in general and structural biology in particular. John was first to use X-ray diffraction to solve the 3-dimensional structure of a protein, sperm-whale myoglobin, worthy of a Nobel Prize in Chemistry in 1962. John was the Founder and first Editor-in-Chief of the Journal of Molecular Biology, Deputy Chairman of the Laboratory of Molecular Biology and Head of its Division of Structural Studies, a Founder of the European Molecular Biology Organization, first Director-General of the European Molecular Biology Laboratory, and 33rd President of St. John's College, Oxford. In this personal perspective I relate how I came to know John as his postdoctoral fellow at the Laboratory of Molecular Biology in 1967 and as his biographer 45 years later.