Gauri Misra Editor Introduction to Biomolecular Structure and Biophysics Basics of Biophysics Introduction to Biomolecular Structure and Biophysics Gauri Misra Editor Introduction to Biomolecular Structure and Biophysics Basics of Biophysics Editor Gauri Misra Amity University Noida, Uttar Pradesh India ISBN 978-981-10-4967-5 ISBN 978-981-10-4968-2 (eBook) DOI 10.1007/978-981-10-4968-2 Library of Congress Control Number: 2017952062 # The Editor(s) (if applicable) and The Author(s) 2017 This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed. The use of general descriptive names, registered names, trademarks, service marks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. The publisher, the authors and the editors are safe to assume that the advice and information in this book are believed to be true and accurate at the date of publication. Neither the publisher nor the authors or the editors give a warranty, express or implied, with respect to the material contained herein or for any errors or omissions that may have been made. The publisher remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. Printed on acid-free paper This Springer imprint is published by Springer Nature The registered company is Springer Nature Singapore Pte Ltd. The registered company address is: 152 Beach Road, #21-01/04 Gateway East, Singapore 189721, Singapore Dedicated to The lotus feet of Shri Radha Krishna and Goverdhannathji Foreword by Prof. Joel L. Sussman Receiving is not always important; however, giving back to society can be incredi- bly significant. This book, Introduction to Biomolecular Structure and Biophysics: Basics of Biophysics, is an excellent volume of Dr. Gauri Misra to present the fundamentals and advances in the field of Biophysics to the scientific community. A journey beginning from the basic macromolecular structure, their functioning, interactions transcending to the methodology that includes the classical and new approaches makes this effort incredibly worthwhile. Contribution from the experts in the field enhances the quality of the content. Reading about new folds and structures, e.g., the Roadblock and Longin folds, is fascinating and will clearly stimulate the reader from neophyte through expert. The book goes from classical biochemistry, e.g., amino acids, primary through quaternary structures, to very recent discoveries such as intrinsically disordered proteins. New discoveries and creative thought process keep the flame of scientific curiosity ignited. The magnitude of work done to bring forth the new advancements in the field makes the book unique. The principles of the most complex of techniques, e.g., the latest developments of cryoEM and their impact on structural biology, are explained in a very clear manner so that the student’s enthusiasm remains intact while reading. This book will be useful to people working not only in biophysics but also in other scientific disciplines from chemistry through life sciences. The text is strengthened enormously by beautiful diagrams. I strongly believe this book will be a reader’s delight providing comprehensive understanding of macromolecular structure and functioning. It will be an excellent introduction for students towards biophysics and will clearly help them to develop a wider perspective of the field. Department of Structural Biology Joel L. Sussman Weizmann Institute of Science Rehovot, Israel vii Foreword by Shekhar C. Mande I am pleased to write this foreword on the book edited by Dr. Gauri Misra. Having browsed through the book, I am very happy to note that the book addresses several important aspects of modern Biophysics. Dr. Misra herself is a well-trained biophysicist; therefore she is in a good position to edit such a book. The field of Biophysics has seen several important developments in recent years, such as the advent of cryo-electron microscopy for determining high-resolution structures of proteins and macromolecular assemblies, super-resolution microscopy for high-end imaging of biological systems, hydrogen deuterium exchange, etc. For the students, to keep up with these developments is difficult, unless guided by trained biophysicists in these areas. Dr. Misra has clearly attempted to do so by bringing together experts in different fields and writing chapters on these aspects. Moreover, the fundamentals of biophysics have been well covered so that students do not miss the basics while trying to understand the modern developments. This book also provides insights into different kinds of biomolecules, including polypeptides, nucleotides, membranes, lipids, etc., in sufficient details. The structural insights into functioning of various macromolecules are explained with the help of several illustrations. Moreover, many useful resources are included as part of chapters. This book covers areas, such as protein folding, higher-order nucleic acid structures, new protein folds, conformational aspects of proteins with functional implications, thermodynamics of protein/DNA stability, etc. Dr. Misra’s creative contribution as an author on the chapter on protein structure is worthy of appreciation. Thus, a good blend of fundamental biophysics, structural biology, and modern developments in biophysics has been achieved in this book. This book has attempted to provide basic understanding of simple and complex experimental and theoretical aspects of biophysics. I am therefore sure that students of biophysics at the under- graduate, postgraduate, and doctoral levels will find this book very useful. Director, National Centre for Cell Science Shekhar C. Mande Pune, India ix Preface The present book is the beginning of a new chapter in my academic journey. A successful accomplished research career ignited within me the desire to disseminate the knowledge to young students which are desirous of building a career in science. I joined the university structure and started teaching biophysics and structural biology to the undergraduate, postgraduate, and doctoral students. Interaction with the students introduced me to the reality that they have an inherent apprehen- sion for these subjects as the available resources for most of the underlying concepts in these subjects were either research articles or academic reviews. They expressed their desire to have a reference book which could encompass a compre- hensive collection of basic principles in biophysics and recent research developments in the concerned field. This was the driving force behind the concep- tion of this book. The last few decades have evidenced tremendous growth in the macromolecular data supported by advances in technology and methodology. This upsurge in the information about proteins, DNA, and lipid structure along with fundamentals of various classical and advanced biophysical techniques used in drug discovery process needs to reach out to students in a language that is elucidating and does draw extensively upon academic jargon. This underlying motive is being attempted at in the treatment of ideas, concepts, and experiences presented in this book. There are nine chapters that form the framework of this book. The idea to encompass knowledge spanning from what is known to what is unknown in the writings from the experts in the field resulted in a concerted effort to justify the various topics. We sincerely hope our efforts will be embraced by students with appreciation and enthusiasm for learning. Organization of the Book I would like to present an overview of ideas that inform the organization of this book. In doing this, I would also like to foreground the salient and novel features that might draw the attention of readers and make it interesting and engaging. The book is structured in nine chapters that bring to students interesting dimensions of human understanding that relate to the subject in focus. xi xii Preface The first chapter highlights the fundamentals of protein structure and functioning with emphasis on the role of various structural folds and motifs. The recent research findings involving a new fold have now enhanced our knowledge in the field. The newer discovery and some implications from this work have been incorporated. The second chapter elaborates the basic process of protein folding which is responsible for attributing them with the multitude of functions. An additional information on the computational understanding of this process including the various intermediates involved is being explained. The third chapter navigates through the basics of DNA and RNA structure with underlying structural principles and properties. A brief outline toward the various methods used for the identification of these structures is presented in the last section of this chapter. The fourth chapter extends the basic knowledge of nucleic acid structure to higher-order structures considering the latest developments in this domain that involves the exhaustive details of various higher-order structures, chemical principles in higher-order