{"product_id":"mass-spectrometry-analysis-for-protein-protein-interactions-and-dynamics-isbn-9780470258866","title":"Mass Spectrometry Analysis for Protein-Protein Interactions and Dynamics","description":"\u003cul\u003e \u003cli\u003ePresents a wide variety of mass spectrometry methods used to explore structural mechanisms, protein dynamics and interactions between proteins.\u003c\/li\u003e \u003cli\u003ePreliminary chapters cover mass spectrometry methods for examining proteins and are then followed by chapters devoted to presenting very practical, how-to methods in a detailed way.\u003c\/li\u003e \u003cli\u003eIncludes footprinting and plistex specifically, setting this book apart from the competition.\u003c\/li\u003e \u003c\/ul\u003e \u003cp\u003eForeword xiii\u003c\/p\u003e \u003cp\u003eContributors xv\u003c\/p\u003e \u003cp\u003e\u003cb\u003e1 Overview of Mass Spectrometry Technologies for Examining Protein Structure: Current and Future Directions 1\u003cbr\u003e \u003c\/b\u003e\u003ci\u003eShannon M. Swiatkowski and Mark R. Chance\u003c\/i\u003e\u003c\/p\u003e \u003cp\u003e1.1 Introduction 1\u003c\/p\u003e \u003cp\u003e1.2 Hydrogen\/Deuterium Exchange Mass Spectrometry 3\u003c\/p\u003e \u003cp\u003e1.3 Hydroxyl-Radical-Mediated Protein Footprinting 5\u003c\/p\u003e \u003cp\u003e1.4 Chemical Cross-linking 8\u003c\/p\u003e \u003cp\u003eReferences 8\u003c\/p\u003e \u003cp\u003e\u003cb\u003e2 Hydrogen Exchange Mass Spectrometry: Principles and Capabilities 11\u003cbr\u003e \u003c\/b\u003e\u003ci\u003eSébastien Brier and John R. Engen\u003c\/i\u003e\u003c\/p\u003e \u003cp\u003e2.1 The Chemistry of Hydrogen Exchange 11\u003c\/p\u003e \u003cp\u003e2.2 HX Mechanisms in Proteins 19\u003c\/p\u003e \u003cp\u003e2.3 Deuterium Incorporation into Proteins 23\u003c\/p\u003e \u003cp\u003e2.4 Measuring HX with Mass Spectrometry 26\u003c\/p\u003e \u003cp\u003e2.5 Capabilities of HX MS in Structural Biology 31\u003c\/p\u003e \u003cp\u003eAcknowledgment 36\u003c\/p\u003e \u003cp\u003eReferences 36\u003c\/p\u003e \u003cp\u003e\u003cb\u003e3 Covalent Labeling Methods for Examining Protein Structure and Protein Interactions 45\u003c\/b\u003e\u003cbr\u003e \u003ci\u003eKeiji Takamoto and Janna Kiselar\u003c\/i\u003e\u003c\/p\u003e \u003cp\u003e3.1 Introduction 45\u003c\/p\u003e \u003cp\u003e3.2 Chemistry of Hydroxyl Radical Footprinting 46\u003c\/p\u003e \u003cp\u003e3.3 Mass Spectrometry Approaches for Quantitative Protein Footprinting 52\u003c\/p\u003e \u003cp\u003e3.4 Examples of Various Methods that Generate Hydroxyl Radicals in Solution to Examine Protein Structure 55\u003c\/p\u003e \u003cp\u003e3.5 The Future: Hybrid Approaches that Combine Experimental and Computational Data 62\u003c\/p\u003e \u003cp\u003eReferences 63\u003c\/p\u003e \u003cp\u003e\u003cb\u003e4 Complementary Methods for Structure Determination: Hydroxyl-Radical-Mediated Footprinting and Deuterium Exchange Mass Spectrometry as Applied to Serpin Structure 69\u003cbr\u003e \u003c\/b\u003e\u003ci\u003eXiaojing Zheng and Patrick L. Wintrode\u003c\/i\u003e\u003c\/p\u003e \u003cp\u003e4.1 Introduction 69\u003c\/p\u003e \u003cp\u003e4.2 Technical Comparison of Hydroxyl-Radical-Mediated Footprinting and H\/D Exchange Methodologies 73\u003c\/p\u003e \u003cp\u003e4.3 Structural Mass Spectrometry Data 76\u003c\/p\u003e \u003cp\u003e4.4 Solvent Accessibility 79\u003c\/p\u003e \u003cp\u003e4.5 Dynamics 84\u003c\/p\u003e \u003cp\u003e4.6 Significance for Serpin Structure and Function 87\u003c\/p\u003e \u003cp\u003e4.7 Summary 87\u003c\/p\u003e \u003cp\u003eAcknowledgment 88\u003c\/p\u003e \u003cp\u003eReferences 88\u003c\/p\u003e \u003cp\u003e5 Deuterium Exchange Approaches for Examining Protein Interactions: Case Studies of Complex Formation 91\u003cbr\u003e \u003ci\u003eElizabeth A. Komives\u003c\/i\u003e\u003c\/p\u003e \u003cp\u003e5.1 Interactions of Regulatory and Catalytic Subunits of Protein Kinase A 91\u003c\/p\u003e \u003cp\u003e5.2 Allostery in Protein–Protein Interactions Revealed by H\/D Exchange 95\u003c\/p\u003e \u003cp\u003e5.3 Interactions of the Inhibitor IκBα with the Transcription Factor NF-κB 97\u003c\/p\u003e \u003cp\u003eReferences 101\u003c\/p\u003e \u003cp\u003e\u003cb\u003e6 Hydrogen\/Deuterium Exchange Studies of Viruses 105\u003c\/b\u003e\u003ci\u003e\u003cbr\u003e Sebyung Kang and Peter E. Prevelige Jr.\u003c\/i\u003e\u003c\/p\u003e \u003cp\u003e6.1 Overview of Virus Lifecycles 105\u003c\/p\u003e \u003cp\u003e6.2 Structural Investigations of Viral Capsids 105\u003c\/p\u003e \u003cp\u003e6.3 Dynamics of Viral Capsids 106\u003c\/p\u003e \u003cp\u003e6.4 Hydrogen\/Deuterium Exchange Studies of Virus Capsid Structure 107\u003c\/p\u003e \u003cp\u003e6.5 Hydrogen\/Deuterium Exchange Studies of Viral Protein Dynamics 114\u003c\/p\u003e \u003cp\u003e6.6 Technical Aspects of Performing Hydrogen\/Deuterium Exchange Experiments on Viruses 118\u003c\/p\u003e \u003cp\u003eReferences 119\u003c\/p\u003e \u003cp\u003e\u003cb\u003e7 Use of Enhanced Peptide Amide Hydrogen\/Deuterium Exchange-Mass Spectrometry (DXMS) in the Examination of Protein–Protein Interactions 123\u003cbr\u003e \u003c\/b\u003e\u003ci\u003eYoshitomo Hamuro, Stephen J. Coales, Lora L. Hamuro, and Virgil L. Woods Jr.\u003c\/i\u003e\u003c\/p\u003e \u003cp\u003e7.1 Introduction 123\u003c\/p\u003e \u003cp\u003e7.2 Theory of H\/D Exchange 124\u003c\/p\u003e \u003cp\u003e7.3 Overview of DXMS Technology for Protein–Protein Interactions 126\u003c\/p\u003e \u003cp\u003e7.4 DXMS of Human Growth Hormone and Its Binding Protein 129\u003c\/p\u003e \u003cp\u003e7.5 DXMS of PKA Regulatory Subunits 133\u003c\/p\u003e \u003cp\u003e7.6 DXMS of PKA R-Subunit D\/D Domains and D-AKAP2 AKB Domain 139\u003c\/p\u003e \u003cp\u003e7.7 Epitope Mapping by DXMS 146\u003c\/p\u003e \u003cp\u003e7.8 Conclusions 148\u003c\/p\u003e \u003cp\u003eAbbreviations 149\u003c\/p\u003e \u003cp\u003eAcknowledgments 150\u003c\/p\u003e \u003cp\u003eReferences 150\u003c\/p\u003e \u003cp\u003e\u003cb\u003e8 Cross-linking as a Tool to Examine Protein Complexes: Examples of Cross-linking Strategies and Computational Modeling 157 \u003cbr\u003e \u003c\/b\u003e\u003ci\u003eEvgeniy V. Petrotchenko and Christoph H. Borchers\u003c\/i\u003e\u003c\/p\u003e \u003cp\u003e8.1 Introduction 157\u003c\/p\u003e \u003cp\u003e8.2 Cross-linking Strategies 157\u003c\/p\u003e \u003cp\u003e8.3 Cross-linking Methodology 158\u003c\/p\u003e \u003cp\u003e8.4 Challenges Associated with Combining Cross-linking with Mass Spectrometry 159\u003c\/p\u003e \u003cp\u003e8.5 Advances in Mass Spectrometry Instrumentation and Capabilities 160\u003c\/p\u003e \u003cp\u003e8.6 Novel Cross-linking Reagents for Mass Spectrometry Applications 162\u003c\/p\u003e \u003cp\u003e8.7 Analytical Software 165\u003c\/p\u003e \u003cp\u003e8.8 Using Cross-linking Distance Constraints to Build Experimental Models of Protein Complexes 167\u003c\/p\u003e \u003cp\u003eReferences 167\u003c\/p\u003e \u003cp\u003e\u003cb\u003e9 Complex Formation in the Actin Cytoskeleton: Cross-linking Tools to Define Actin Protein Structure and Interactions 169 \u003cbr\u003e \u003c\/b\u003e\u003ci\u003eSabrina Benchaar and Emil Reisler\u003c\/i\u003e\u003c\/p\u003e \u003cp\u003e9.1 Introduction 169\u003c\/p\u003e \u003cp\u003e9.2 Mapping Cross-linking with Methods Other than Mass Spectrometry 171\u003c\/p\u003e \u003cp\u003e9.3 Actin-Actin Cross-linking 171\u003c\/p\u003e \u003cp\u003e9.4 Intrastrand Cross-linked Actin between GLN41 and CYS374 174\u003c\/p\u003e \u003cp\u003e9.5 Regulation of Cytoskeleton by ABPs and Mapping their Interfaces with Actin by Cross-linking 175\u003c\/p\u003e \u003cp\u003e9.6 Cross-linking of Actin and Muscle Proteins—Examples of Experimental Approaches 181\u003c\/p\u003e \u003cp\u003e9.7 Concluding Remarks 182\u003c\/p\u003e \u003cp\u003eAcknowledgment 183\u003c\/p\u003e \u003cp\u003eReferences 183\u003c\/p\u003e \u003cp\u003e\u003cb\u003e10 Computational Approaches to Examining Protein–Protein Interactions: Combining Experimental and Computational Data in the Era of Structural Genomics 189\u003cbr\u003e \u003c\/b\u003e\u003ci\u003eJ.K. Amisha Kamal\u003c\/i\u003e\u003c\/p\u003e \u003cp\u003e10.1 Interactome in Structural Genomics 189\u003c\/p\u003e \u003cp\u003e10.2 Importance of Computational Methods in Structural Genomics 190\u003c\/p\u003e \u003cp\u003e10.3 Combining Computational Method with Experimental Data in Modeling the Structure of Protein Binary Complex 190\u003c\/p\u003e \u003cp\u003e10.4 Method Summary 208\u003c\/p\u003e \u003cp\u003e10.5 Experimental Methods 210\u003c\/p\u003e \u003cp\u003eAcknowledgment 212\u003c\/p\u003e \u003cp\u003eReferences 213\u003c\/p\u003e \u003cp\u003e\u003cb\u003e11 Studies of Intact Proteins and Protein Complexes: ESI MS Approaches 217 \u003cbr\u003e \u003c\/b\u003e\u003ci\u003eIgor A. Kaltashov, Rinat R. Abzalimov, Agya K. Frimpong, and Stephen J. Eyles\u003c\/i\u003e\u003c\/p\u003e \u003cp\u003e11.1 Introduction 217\u003c\/p\u003e \u003cp\u003e11.2 Tertiary Structure Integrity and Conformational Heterogeneity (Charge State Distributions) 220\u003c\/p\u003e \u003cp\u003e11.3 Quaternary Structure Integrity and Composition of Non-Covalent Complexes 224\u003c\/p\u003e \u003cp\u003e11.4 Functional Competence 226\u003c\/p\u003e \u003cp\u003e11.5 Flexibility Maps and Binding Interfaces 229\u003c\/p\u003e \u003cp\u003e11.6 Gas Phase Ion Chemistry and Its Influence on the Measurement of Protein Properties in Solution 231\u003c\/p\u003e \u003cp\u003e11.7 Challenges and Future Outlook 234\u003c\/p\u003e \u003cp\u003eAcknowledgments 237\u003c\/p\u003e \u003cp\u003eReferences 237\u003c\/p\u003e \u003cp\u003e\u003cb\u003e12 Two Approaches to Mass Spectrometric Protein Footprinting: PLIMSTEX and FPOP 243 \u003cbr\u003e \u003c\/b\u003e\u003ci\u003eMichael L. Gross, Mei M. Zhu, and David M. Hambly\u003c\/i\u003e\u003c\/p\u003e \u003cp\u003e12.1 Introduction: Protein–Ligand Interactions by Mass Spectrometry, Titration, and Hydrogen\/Deuterium Amide Exchange and Fast Photochemical Oxidation of Proteins 243\u003c\/p\u003e \u003cp\u003e12.2 Protein–Ligand Interactions by Mass Spectrometry, Titration, and H\/D Amide Exchange (PLIMSTEX) 245\u003c\/p\u003e \u003cp\u003e12.3 Applications of PLIMSTEX 247\u003c\/p\u003e \u003cp\u003e12.4 Self-Association of Insulin: A Protein\/Protein Interaction 253\u003c\/p\u003e \u003cp\u003e12.5 Features of PLIMSTEX 254\u003c\/p\u003e \u003cp\u003e12.6 Fast Photochemical Oxidation of Proteins: An Example of Fast Protein Footprinting 256\u003c\/p\u003e \u003cp\u003e12.7 Features of FPOP 263\u003c\/p\u003e \u003cp\u003e12.8 Future 264\u003c\/p\u003e \u003cp\u003eAbbreviations 265\u003c\/p\u003e \u003cp\u003eAcknowledgments 265\u003c\/p\u003e \u003cp\u003eReferences 265\u003c\/p\u003e \u003cp\u003eIndex 271\u003c\/p\u003e \u003cb\u003eMark Chance, PhD\u003c\/b\u003e, is the Director of the Case Center for Proteomics and Professor of Physiology and Biophysics at Case Western Reserve University. He also directs the Case Center for Synchrotron Biosciences, located at the National Synchrotron Light Source at Brookhaven National Laboratory, New York. Dr. Chance received his bachelor's degree in biology from Wesleyan University and his PhD in biophysics from the University of Pennsylvania. He furthered his training as a postdoctoral research associate at AT\u0026amp;T Bell Laboratories, then went on to become assistant professor in the department of chemistry at Georgetown University. He moved to Albert Einstein College of Medicine in the Bronx, New York, in 1992, and was soon promoted to associate professor of the departments of physiology \u0026amp; biophysics and biochemistry, and full professor in 1998. While at AECOM, he was the Joseph and Anne Wunsch fellow in biophysical engineering and recipient of the Irma Hirschl Career Scientist Award. In 2005, he moved to Case Western Reserve University as the founding director of the Center for Proteomics. His research primarily concerns development of structural and cellular proteomics technologies to understand protein structure-function.  \u003cp\u003eA how-to guide that helps you take advantage of the latest mass spectrometry methods\u003c\/p\u003e \u003cp\u003eThis book brings together and examines the latest mass spectrometry methods used to investigate proteins, including structural mechanisms, protein dynamics, and interactions among proteins. Written by a team of experts with many years of hands-on experience developing and working with mass spectrometry methods, the book offers a wealth of practical advice and tips to help readers fully exploit the capabilities of a mass spectrometer.\u003c\/p\u003e \u003cp\u003eThe book begins with an overview of mass spectrometry technologies, including an expert forecast of future directions. Next, the authors offer step-by-step guidance for such topics as:\u003c\/p\u003e \u003cul\u003e \u003cli\u003e \u003cp\u003eComplementary methods for structure determination: hydroxyl radical-mediated footprinting and deuterium exchange mass spectrometry as applied to serpin structure\u003c\/p\u003e \u003c\/li\u003e \u003cli\u003e \u003cp\u003eCovalent labeling methods for examining protein structure and protein interactions\u003c\/p\u003e \u003c\/li\u003e \u003cli\u003e \u003cp\u003eComputational approaches to examine protein-protein interactions: combining experimental and computational data in the era of structural genomics\u003c\/p\u003e \u003c\/li\u003e \u003cli\u003e \u003cp\u003eTwo approaches to mass spectrometric protein footprinting: PLIMSTEX and FPOP\u003c\/p\u003e \u003c\/li\u003e \u003cli\u003e \u003cp\u003eHydrogen\/deuterium exchange studies of viruses\u003c\/p\u003e \u003c\/li\u003e \u003c\/ul\u003e \u003cp\u003eCarefully edited, the book presents a uniform standard of high quality and thoroughness throughout all the chapters. References to the literature enable readers to explore each individual topic in greater depth.\u003c\/p\u003e \u003cp\u003eAny researcher seeking to advance his or her own protein research will benefit from this book's insights and how-to guidance. The spectrometry methods can be applied to support investigations in such fields as biomedicine, biotechnology, and pharmaceutical research.\u003c\/p\u003e","brand":"Wiley","offers":[{"title":"Default Title","offer_id":47989578727653,"sku":"NP9780470258866","price":136.95,"currency_code":"USD","in_stock":false}],"thumbnail_url":"\/\/cdn.shopify.com\/s\/files\/1\/1842\/7735\/files\/9780470258866.jpg?v=1761784673","url":"https:\/\/k12savings.com\/es\/products\/mass-spectrometry-analysis-for-protein-protein-interactions-and-dynamics-isbn-9780470258866","provider":"K12savings","version":"1.0","type":"link"}