HIV-1 Proteomics: From Discovery to Clinical Application PDF
Preview HIV-1 Proteomics: From Discovery to Clinical Application
David R. M. Graham · David E. Ott Editors HIV-1 Proteomics From Discovery to Clinical Application HIV-1 Proteomics David R.M. Graham • David E. Ott Editors HIV-1 Proteomics From Discovery to Clinical Application Editors David R.M. Graham David E. Ott Department of Molecular and Comparative Leidos Biomedical Research, Inc. Pathobiology Frederick National Laboratory The Johns Hopkins University School of for Cancer Research Medicine Frederick , MD , USA Baltimore , MD , USA ISBN 978-1-4939-6540-3 ISBN 978-1-4939-6542-7 (eBook) DOI 10.1007/978-1-4939-6542-7 Library of Congress Control Number: 2016952094 © Springer Science+Business Media New York 2016 T his work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifi cally the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfi lms 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. T he use of general descriptive names, registered names, trademarks, service marks, etc. in this publication does not imply, even in the absence of a specifi c statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. T he 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. Printed on acid-free paper This Springer imprint is published by Springer Nature The registered company is Springer Science+Business Media LLC New York We dedicate this book to Louis Edwin Henderson Ph.D. (1934–2013). Lou: a pioneer in retroviral protein chemistry, a mentor to so many, trusted colleague, a friend, and a tireless AIDS fi ghter. Pref ace T he focus of this book is to provide a clear understanding of how the proteins in HIV-1 can be analyzed by proteomic approaches and cover some of the accomplish- ments produced by this powerful technique. Being in the fi eld, we believe that much can be learned from the comprehensive study of proteins and their modifi cations. Throughout our combined careers, we have seen many scientifi c advances that were initiated by protein-focused research of HIV-1. To convey this appreciation for this topic, we have set out to compile expert views of HIV-1 proteomics. The target audi- ences for this book are those non-expert readers who desire a comprehensive but technically understandable view of the fi eld, those in associated fi elds who want a deeper theoretical understanding and an entree into in-depth technical literature and resources through review references, and experts in the fi eld who are interested in key points of interest and confl ict in HIV-1 proteomics as well as current directions in the fi eld. We hope you enjoy this work. Baltimore, MD, USA David R. M. Graham Frederick, MD, USA David E. Ott vii Contents Part 1 Rebranding Classical Protein Chemistry: Proteomics of the Past 1 Introduction: HIV-1 Proteomics, Why Should One Care? . . . . . . . . . . . . 3 David E. Ott 2 HIV-1 Biology at the Protein Level . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5 David E. Ott 3 25 Years of HIV-1 Biochemistry . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27 David E. Ott Part 2 Modern HIV-1 Proteomics 4 Proteomic Studies of HIV-1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39 David R. M. Graham 5 HIV-1 Sequencing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59 Shelby L. O’Connor 6 Proteomic Studies of HIV-1 and Its Posttranslational Modifications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77 David R. Colquhoun and David R. M. Graham 7 Bioinformatics for Mass Spectrometry-Based Proteomics . . . . . . . . . . . 99 Rebekah L. Gundry ix Contributors David R. Colquhoun , Ph.D. Molecular and Comparative Pathobiology , The Johns Hopkins University School of Medicine , Baltimore , MD , USA David R. M. Graham , M.Sc., Ph.D. Department of Molecular and Comparative Pathobiology , The Johns Hopkins School of Medicine , Baltimore , MD , USA Rebekah L. Gundry , Ph.D. Department of Biochemistry , Medical College of Wisconsin , Milwaukee , WI , USA Shelby L. O’Connor , Ph.D. Department of Pathology and Laboratory Medicine , University of Wisconsin-Madison , Madison , WI , USA David E. Ott , Ph.D. Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research , Frederick , MD , USA xi Part 1 Rebranding Classical Protein Chemistry: Proteomics of the Past Chapter 1 Introduction: HIV-1 Proteomics, Why Should One Care? David E. Ott This book focuses on applying proteomics to the study of the HIV-1 virion and its associated proteins. Before we go further, it is important to understand why this topic is worthy of a book or a researcher’s effort to read it. Proteomics, the detection of the constellation of proteins and their posttranslational modifi cations in complex samples from organisms, has been used for years to comprehensively analyze pro- tein samples to better understand basic biology and for medical research aimed at developing new and improved diagnostic procedures and therapies. D espite the analytical power and potential of this important technology, these approaches have only recently been applied to the study of HIV-1 virions. HIV-1, like most RNA viruses, has a small genome, encoding just nine proteins. To com- pensate for this constraint, retroviruses use several unusual mechanisms to produce multifunctional proteins by differential splicing, alternative translational initiation/ internal ribosomal entry site (IRES) usage, protease processing, translation frame- shifting/nonsense codon suppression, and posttranslational modifi cation [1 , 2 ]. Many of these processes are well known now, but initially many of these now rou- tinely understood cellular mechanisms for maximizing protein expression from a limited genome and modifi cation in mammalian systems such as frameshifting [3 ] and myristylation [4 ] were initially observed in studying retroviral proteins. Thus, the study of retroviral proteins and their modifi cations has yielded many important discoveries. Yet these advances were made with traditional methods which, though still quite useful, remain constrained by relatively low sensitivity and limited throughput. Thus, even though much progress has been made in HIV-1 “pro- teomics,” there are still many potential modifi cations and secrets of HIV-1 proteins D. E. Ott , Ph.D. (*) Leidos Biomedical Research, Inc. , Frederick National Laboratory for Cancer Research, 1050 Boyles Street , Frederick , MD 21702 , USA e-mail: [email protected] © Springer Science+Business Media New York 2016 3 D.R.M. Graham, D.E. Ott (eds.), HIV-1 Proteomics, DOI 10.1007/978-1-4939-6542-7_1
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