The Nuclear Magnetic Resonance Society of Japan Editor Experimental Approaches of NMR Spectroscopy Methodology and Application to Life Science and Materials Science Experimental Approaches of NMR Spectroscopy The Nuclear Magnetic Resonance Society of Japan Editor Experimental Approaches of NMR Spectroscopy Methodology and Application to Life Science and Materials Science 123 Editor The Nuclear Magnetic Resonance Society of Japan Kobe Japan ISBN 978-981-10-5965-0 ISBN 978-981-10-5966-7 (eBook) https://doi.org/10.1007/978-981-10-5966-7 Library of Congress Control Number: 2017950018 © Springer Nature Singapore Pte Ltd. 2018 This work is subject to copyright. 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The registered company address is: 152 Beach Road, #21-01/04GatewayEast, Singapore 189721, Singapore Member of the Editorial Board Akira Naito (Editor in Chief) Graduate School of Engineering, Yokohama National University, Yokohama, Japan Tetsuo Asakura Department of Biotechnology, Tokyo University of Agriculture and Technology, Tokyo, Japan Ichio Shimada Graduate School of Pharmaceutical Science, University of Tokyo, Tokyo, Japan Kiyonori Takegoshi Graduate School of Science, Kyoto University, Kyoto, Japan Yasuhiko Yamamoto Department of Chemistry, University of Tsukuba, Tsukuba, Japan v Preface This book describes the advanced developments in methodology and applications of NMR spectroscopy to life science and materials science. Experts who are leaders in the development of new methods and applications of life science and materials science have contributed an exciting range of topics that cover recent advances in structural determination and dynamic characterization of biological and material molecules, and development of novel NMR techniques, including resolution and sensitivity enhancement. First, this book particularly emphasizes the experimental details for new researchers to use NMR spectroscopy and also to pick up the potentials of NMR spectroscopy. Second, the book is designed for those who are involved in either developing the techniques or expanding the NMR application fields by applying them to specific samples. Third, the Nuclear Magnetic Resonance (NMR) Society of Japan has organized this book not only for NMR members of Japan but also for worldwide readers who are interested in using NMR spec- troscopy extensively. This book consists of two parts: methodology and application to life science and materials science. In Part I (Chaps. 1–9: Methodology), first, new concept of NMR experiment such as high pressure NMR and isotope-aided NMR methods are described. Second, advances in NMR data acquisition and processing methods are introduced. Third, advances in NMR hardware such as dynamic nuclear polariza- tion (DNP), photoirradiation and microwave irradiation NMR spectroscopies are emphasized. Fourth, recently developed solid-state NMR spectroscopy under ultrafast magic angle spinning (MAS) is focused in this book. Fifth, dynamics of biological molecules using relaxation dispersion NMR spectroscopy is particularly emphasized. Sixth, structure-determination experiments of biological molecules utilizing paramagnetic lanthanide probe methods and solid-state NMR spectroscopy are particularly highlighted. In Part II (Chaps. 10–22: Application to Life Science and Materials Science), advanced application to life science and materials science is described. First, as applications of solid-state NMR spectroscopy to materials science, studies on silk materials, polymer materials, functional materials and gaseous molecules in poly- mer materials are extensively described. Second, as applications of advanced NMR vii viii Preface techniques to life science, studies of natural products, glycoproteins and ribonucleic acid (RNA) are widely accounted. Third, metabolic profiling for small molecular complexity is introduced. Fourth, this book focuses on NMR studies of paramag- netic compounds. Fifth, NMR spectroscopy of quadrupole nuclei in organic com- pounds and inorganic materials is described. Sixth, advanced NMR spectroscopies are focused on characterization of protein–ligand interaction and determination of protein structure and dynamics. Kobe, Japan The NMR Society of Japan June 2017 Editorial board Akira Naito (Editor in Chief) Tetsuo Asakura Ichio Shimada Kiyonori Takegoshi Yasuhiko Yamamoto Acknowledgements We are deeply grateful to Dr. Tomohide Saio for completing Chap. 8 succeeded from late Prof. Fuyuhiko Inagaki. Unfortunately, Prof. Inagaki had passed away during the course of writing this book. Professor Inagaki was excited to write a chapter in this book and encouraged us to publish this book. We, therefore, sin- cerely dedicate this book to the late Prof. Inagaki. We would also like to acknowledge the council member of the NMR Society of Japan for their devoted help in the process of editing this book. Finally, we would like to thank Ms. Risa Takizawa and Mr. Shinichi Koizumi of the Springer Japan for their encouragement and assistance in editing the book. ix Contents Part I Methodology 1 Protein Studies by High-Pressure NMR . . . . . . . . . . . . . . . . . . . . . . 3 Kazuyuki Akasaka 2 Isotope-Aided Methods for Biological NMR Spectroscopy: Past, Present, and Future . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37 Masatsune Kainosho, Yohei Miyanoiri and Mitsuhiro Takeda 3 Advances in NMR Data Acquisition and Processing for Protein Structure Determination . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63 Teppei Ikeya and Yutaka Ito 4 Advances in High-Field DNP Methods . . . . . . . . . . . . . . . . . . . . . . . 91 Yoh Matsuki and Toshimichi Fujiwara 5 Photoirradiation and Microwave Irradiation NMR Spectroscopy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 135 Akira Naito, Yoshiteru Makino, Yugo Tasei and Izuru Kawamura 6 Solid-State NMR Under Ultrafast MAS Rate of 40–120 kHz. . . . . . 171 Yusuke Nishiyama 7 Elucidating Functional Dynamics by R1q and R2 Relaxation Dispersion NMR Spectroscopy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 197 Erik Walinda and Kenji Sugase 8 Structural Study of Proteins by Paramagnetic Lanthanide Probe Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 227 Tomohide Saio and Fuyuhiko Inagaki 9 Structure Determination of Membrane Peptides and Proteins by Solid-State NMR . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 253 Izuru Kawamura, Kazushi Norisada and Akira Naito xi xii Contents Part II Application to Life Science and Materials Science 10 NMR Studies on Silk Materials . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 297 Tetsuo Asakura and Yugo Tasei 11 NMR Studies on Polymer Materials . . . . . . . . . . . . . . . . . . . . . . . . . 313 Atsushi Asano 2 12 Solid-State H NMR Studies of Molecular Motion in Functional Materials . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 341 Motohiro Mizuno 13 NMR Spectral Observations of the Gases in Polymer Materials . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 365 Hiroaki Yoshimizu 14 NMR Studies on Natural Product—Stereochemical Determination and Conformational Analysis in Solution and in Membrane . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 383 Nobuaki Matsumori and Michio Murata 15 Technical Basis for Nuclear Magnetic Resonance Approach for Glycoproteins. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 415 Koichi Kato, Saeko Yanaka and Hirokazu Yagi 16 NMR Studies on RNA. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 439 Taiichi Sakamoto, Maina Otsu and Gota Kawai 17 NMR Analysis of Molecular Complexity . . . . . . . . . . . . . . . . . . . . . . 461 Jun Kikuchi 18 NMR of Paramagnetic Compounds . . . . . . . . . . . . . . . . . . . . . . . . . . 491 Yasuhiko Yamamoto and Tomokazu Shibata 19 NMR of Quadrupole Nuclei in Organic Compounds . . . . . . . . . . . . 519 Kazuhiko Yamada 20 Quadrupole Nuclei in Inorganic Materials . . . . . . . . . . . . . . . . . . . . 545 Toshikazu Takahashi 21 Protein–Ligand Interactions Studied by NMR . . . . . . . . . . . . . . . . . 579 Hidekazu Hiroaki and Daisuke Kohda 22 Protein Structure and Dynamics Determination by Residual Anisotropic Spin Interactions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 601 Shin-ichi Tate