X-Ray Structure Analysis of Bio-Macromolecular Crystals: Practical Methods and Basic Theory(23 International Union of Crystallography Texts on Crystallography)

Since the late 19th century, X-ray structural studies have forged ahead through technological progress and the creative ingenuity of researchers. As high intensity X-ray sources and increased speed and sensitivity of the detectors have emerged, it's now possible to image the atomic structure of complex bio-macromolecules, the orbital electron density of small molecules, and to even follow the dynamical behavior of bio-macromolecules. Textbooks from which junior researchers can grasp the current art have not kept pace with the technological developments and diversification of the field. X-ray studies of bio-macromolecules require a broad understanding of the theory and practical methodologies. A project can include isolating, crystalizing, and adjudicating suitable samples, obtaining and analysing the X-ray data, and finally publishing the results in a standard format. Early decisions in a project can become pitfalls that swallow the unwary. It is increasingly essential to become adept at managing both proteins and nucleic acids. Whereas software is available to help in the critical problem of resolving the phase, expedience often encourages treating such tools as a black-box. The aim here is to help navigate the researcher through these multifarious issues. The book is intended to serve as a "companion" to experimentalists. It is divided into a general overview of X-ray structural analysis techniques (chapters 1-2) and a detailed discussion (chapters 3-16) that begins with the preparation of proteins and (uniquely) nucleic acids and ends with publishing the results and is organized to lead the reader through the whole process.

Table of Contents:
1: Looking into the world of bio-macromolecules 2: Publication of structural analysis 3: Preparation of bio-macromolecules 4: Crystallization of bio-macromolecules 5: Symmetry of crystals 6: X-ray scattering and diffraction 7: Diffraction data collection and computer processing 8: Characteristics of structural factor 9: Phase Problem 10: Structural modeling and phase improvement 11: Structural refinements 12: Maximum likelihood estimation method and crystal structure analysis 13: Validation of analyzed structure 14: Deposition of analyzed structures into Protein Data Bank (PDB) 15: Software for structural analysis 16: Future prospects 17: Appendix

About the Author :
Akio Takénaka is a Senior Researcher at the Institute of Natural Sciences, College of Humanities and Sciences, Nihon University in Japan. After receiving a Doctor of Science degree from Kwansei Gakuin University, Akio Takénaka became interested in elucidating the mechanism by which proteins are synthesized according to the genetic code (composed of nucleic acid) at the Tokyo Institute of Technology. Most crystallographers have done X-ray structural analysis on proteins. Consequently, methods in X-ray analysis of nucleic acid molecules have progressed at a slower pace. He have focused X-ray analyses on both nucleic acids and proteins and he revealed various nucleic acid structures. In particular, he was awarded the IUCr prize for discovering the octaplex helical structure of DNA. Takashi Kumasaka is the Director of Center for Synchrotron Radiation Research and Structural Biology Division at Japan Synchrotron Radiation Research Institute (JASRI), which operates SPring-8 in Japan. He received his PhD in 1996 and contributed to the commissioning of the RIKEN structural biology beamlines at SPring-8 until 2002. After working as a lecturer at Tokyo Institute of Technology, he returned to SPring-8 in 2007 and continues to develop macromolecular crystallography beamlines and conduct structural biology research. Toshiyuki Chatake received a PhD degree with the title "X-ray analyses of DNA dodecamers containing 2'-deoxy-N6-methoxyadenosine" from Tokyo Institute of Technology and was awarded the Young Scientist Prize of the Crystallographic Society of Japan. He then worked on neutron crystallography of biomolecules at Japan Atomic Energy Research Institute. Finally, after working at Chiba Institute of Sciences, he is now working at Kyoto University on the development and application of neutron protein crystallography. In addition, he is carrying out structural studies of bioactive substances in the traditional Japanese food natto as another topic. Tomoko Sunami received a PhD degree in science for X-ray crystallographic study of DNA fragments under the supervision of Akio Takenaka at Tokyo Institute of Technology. Initially, she worked on crystallography of drug-target proteins with small compounds for drug discovery at Banyu Pharmaceutical. Later, she moved to the Japan Atomic Energy Agency (now National Institutes for Quantum Science and Technology). She returned to her original interest in DNA research, focusing on understanding the structure of DNA and the principles of interactions between DNA and proteins through several biophysical methods such as fluorescence and single molecule techniques like optical tweezers. Jiro Kondo is a professor at Sophia University. He obtained a PhD degree in 2004 from Tokyo Institute of Technology. From 2004 to 2010, He engaged in RNA structural biology at the Université de Strasbourg. He started his own lab at Sophia University in 2010. He received The Young Scientists' Award of The Commendation for Science and Technology by the Minister of Education, Culture, Sports, Science and Technology. His research interests include the structure-based design of nucleic acids for medical and nanotechnology applications. He has solved several exotic de-novo structures, such as a DNA octaplex, silver-DNA hybrid nanowires, and DNA-templated silver nanoclusters. Ella Morishita is a senior investigator at Veritas In Silico. She holds a PhD in Life Science from the Tokyo Institute of Technology, where she studied the structural basis for the therapeutic properties of oligonucleotide therapies. She then pursued postdoctoral fellowships at the University of Tokyo and RIKEN, where she worked on solving the structures of macromolecular complexes implicated in HIV infection and cancer. At her current position, Ella leads multiple drug discovery programs that focus on identifying small molecule drugs targeting disease-relevant RNA structures and continues to harness her structural biology expertise in target identification and structure-based drug design. Wayne Dawson is a software developer, currently working at Veritas In Silico. He obtained an MS at San Jose State University and a Doctor of Science at the University of Tokyo (experimental physics), in which he focused on using muon spin polarization to investigate solid state materials at the former UTMSL at KEK. His formal education includes condensed matter physics, chemistry, and the liberal arts. Since graduating, he has focused on biotechnology and has worked on problems in quantum chemistry and the thermodynamics of biomolecules. He is currently working on developing next generation RNA structure prediction software.