Protein Complex Assembly, Softcover reprint of the original 1st ed. 2018
Methods and Protocols
Methods in Molecular Biology Series, Vol. 1764

This volume details the importance of multiple experimental techniques and computational methods needed to obtain the comprehensive picture of protein complex structure, dynamics and assembly afforded by the emerging field of integrative structural biology. Chapters guide readers through the broad spectrum of approaches required for a complete representation of protein complexes, including expression and purification, experimental characterization of structure and assembly, and computational methods for identifying protein complexes and modelling their assembly. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.

Authoritative and cutting-edge, Protein Complex Assembly: Methods and Protocols aims to ensure successful results in the further study of this vital field.

PART I – Experimental methods

1.      Experimental Characterisation Of Protein Complex Structure, Dynamics, and Assembly

Jonathan N. Wells and Joseph A. Marsh

2.      High-Throughput Electron Cryo-Tomography of Protein Complexes and their Assembly

Louie D. Henderson and Morgan Beeby

3.      Preparation of Tunable Microchips to Visualize Native Protein Complexes for Single Particle Electron Microscopy

Brian L. Gilmore, A. Cameron Varano, William Dearnaley, Yanping Liang, Bridget C. Marcinkowski, Madeline J. Dukes, and Deborah F. Kelly

4.      Time-resolved Cryo-Electron Microscopy Using a Microfluidic Chip

Sandip Kaledhonkar, Ziao Fu, Howard White and Joachim Frank

5.      Characterizing Protein-protein Interactions using Solution NMR
Spectroscopy

Jose Luis Ortega-Roldan, Martin Blackledge and Malene Ringkjøbing Jensen

6.      Reconstitution of Isotopically Labeled Ribosomal Protein L29 in the 50S Large Ribosomal Subunit For Solution-state and Solid-state NMR

Emeline Barbet-Massin, Eli van der Sluis, Joanna Musial, Roland Beckmann, and Bernd Reif

Angelica V. Medina-Cucurella and Timothy A. Whitehead

8.      Structurally Guided In Vivo Crosslinking

Johanna C. Scheinost and Thomas G. Gligoris

9.      Characterising Intact Macromolecular Complexes using Native Mass Spectrometry Elisabetta Boeri Erba, Luca Signor, Mizar F. Oliva, Fabienne Hans, and Carlo Petosa

Brent A. Kochert, Roxana E. Iacob, Thomas E. Wales, Alexandros Makriyannis, and John R. Engen

11.  Structural Analysis of Protein Complexes by Cross-linking and Mass-spectrometry

Moriya Slavin and Nir Kalisman

12.  Global Characterization of Protein Complexes by Biochemical Purification-mass Spectrometry (BP/MS)

Reza Pourhaghighi and Andrew Emili

13.  Proteomic Profiling of Integrin Adhesion Complex Assembly

Adam Byron

14.  Dual-Color and 3D Super-Resolution Microscopy of Multi-protein Assemblies

Philipp Hoess, Markus Mund, Manuel Reitberger and Jonas Ries

15.  Correlative 3D Structured Illumination Microscopy and Single Molecular Localisation Microscopy for Imaging Cancer Invasion

16.  Observing the Assembly of Protein Complexes In Living Eukaryotic Cells In Super-resolution using refSOFI

Fabian Hertel, Gary C.H. Mo, Peter Dedecker and Jin Zhang

17.  Detecting Purinosome Metabolon Formation with Fluorescence Microscopy

Anthony M. Pedley and Stephen J. Benkovic

18.  Analysis of Bacterial pilus Assembly by Shearing and Immunofluorescence Microscopy

Areli Luna-Rico, Jenny-Lee Thomassin and Olivera Francetic

19.  Expression, Purification and Assembly of Archaellum Subcomplexes of Sulfolobus Acidocaldarius

Paushali Chaudhury, Patrick Tripp, and Sonja-Verena Albers

20.  Unstable Protein Purification through the Formation of Stable Complexes

Sylvia Eiler, Nicolas Levy, Benoit Maillot, Julien Batisse, Karine Pradeau Aubreton, Oyindamola Oladosu, and Marc Ruff

21.  Expressing Multi-subunit Complexes using biGBac

Florian Weissmann and Jan-Michael Peters

PART II – Computational Methods

22.  Computational Modelling of Protein Complex Structure and Assembly

Jonathan N. Wells, L. Therese Bergendahl, and Joseph A. Marsh

23.  Inferring and using Protein Quaternary Structure Information from Crystallographic Data Sucharita Dey and Emmanuel D. Levy

Birgit H. M. Meldal and Sandra Orchard

Florian Goebels, Lucas Hu, Gary Bader, and Andrew Emili

26.  A Multi-scale Computational Model for Simulating the Kinetics of Protein Complex Assembly

Jiawen Chen and Yinghao Wu

27.  Flexible Protein-protein Docking with SwarmDock

Iain H. Moal, Raphael A.G. Chaleil, and Paul A. Bates

28.  Protein-protein Docking using Evolutionary Information

Aravindan Arun Nadaradjane, Raphael Guerois, and Jessica Andreani

29.  Modeling Structure and Dynamics of Protein Complexes with SAXS Profiles

Dina Schneidman-Duhovny and Michal Hammel

30.  Modeling the Structure of Helical Assemblies with Experimental Constraints in Rosetta Ingemar André

Loïc Salmon, Logan S Ahlstrom, James C.A. Bardwell, and Scott Horowitz

Includes cutting-edge methods and protocols

Provides step-by-step detail essential for reproducible results

Contains key notes and implementation advice from the experts