Chapter 12
Integrative Mass Spectrometry–Based Approaches
for Modeling Macromolecular Assemblies
Andy M. Lau and Argyris Politis
Abstract
Mass spectrometry (MS)–based strategies have emerged as key elements for structural modeling of proteins
and their assemblies. In particular, merging together complementary MS tools, through the so-called
hybrid approaches, has enabled structural characterization of proteins in their near-native states. Here,
we describe how different MS techniques, such as native MS, chemical cross-linking MS, and ion mobility
MS, are brought together using sophisticated computational algorithms and modeling restraints. We
demonstrate the applicability of the strategy by building accurate models of multimeric protein assemblies.
These strategies can practically be applied to any protein complex of interest and be readily integrated with
other structural approaches such as electron density maps from cryo-electron microscopy.
Key words Structural mass spectrometry, Computational modeling, Protein complexes, Hybrid
approaches, Modeling restraints
1 Introduction
Integrative structural methods has come of age in building 3D
model ensembles of proteins and their complexes [1]. These methods allow bringing together data sets sourced from diverse structural methods that otherwise will be reported independently
[2]. Such integration can be achieved through the use of modeling
restraints obtained directly from the experimental data [1, 2]
(Fig. 1). Recent innovative studies have led to the expansion of the
integrative structural toolkit to incorporate a variety of MS-based
methods. These include powerful methods such as chemical crosslinking [3–6], ion mobility [7, 8], and native MS [9]. Moreover,
these methods can be integrated with other powerful methods such
as X-ray crystallography [10], cryo-EM [11], and hydrogen–deuterium exchange (HDX)-MS [11] structural approaches. Impressive
examples of the integrative structural toolkit include the elucidation
of many structural aspects of large complexes such as the proteasome [5, 6], ATP synthase [12], and nuclear pore complex [13].
Arnaud Poterszman (ed.), Multiprotein Complexes: Methods and Protocols, Methods in Molecular Biology, vol. 2247,
https://doi.org/10.1007/978-1-0716-1126-5_12, © Springer Science+Business Media, LLC, part of Springer Nature 2021
221
Integrative Mass Spectrometry–Based Approaches
for Modeling Macromolecular Assemblies
Andy M. Lau and Argyris Politis
Abstract
Mass spectrometry (MS)–based strategies have emerged as key elements for structural modeling of proteins
and their assemblies. In particular, merging together complementary MS tools, through the so-called
hybrid approaches, has enabled structural characterization of proteins in their near-native states. Here,
we describe how different MS techniques, such as native MS, chemical cross-linking MS, and ion mobility
MS, are brought together using sophisticated computational algorithms and modeling restraints. We
demonstrate the applicability of the strategy by building accurate models of multimeric protein assemblies.
These strategies can practically be applied to any protein complex of interest and be readily integrated with
other structural approaches such as electron density maps from cryo-electron microscopy.
Key words Structural mass spectrometry, Computational modeling, Protein complexes, Hybrid
approaches, Modeling restraints
1 Introduction
Integrative structural methods has come of age in building 3D
model ensembles of proteins and their complexes [1]. These methods allow bringing together data sets sourced from diverse structural methods that otherwise will be reported independently
[2]. Such integration can be achieved through the use of modeling
restraints obtained directly from the experimental data [1, 2]
(Fig. 1). Recent innovative studies have led to the expansion of the
integrative structural toolkit to incorporate a variety of MS-based
methods. These include powerful methods such as chemical crosslinking [3–6], ion mobility [7, 8], and native MS [9]. Moreover,
these methods can be integrated with other powerful methods such
as X-ray crystallography [10], cryo-EM [11], and hydrogen–deuterium exchange (HDX)-MS [11] structural approaches. Impressive
examples of the integrative structural toolkit include the elucidation
of many structural aspects of large complexes such as the proteasome [5, 6], ATP synthase [12], and nuclear pore complex [13].
Arnaud Poterszman (ed.), Multiprotein Complexes: Methods and Protocols, Methods in Molecular Biology, vol. 2247,
https://doi.org/10.1007/978-1-0716-1126-5_12, © Springer Science+Business Media, LLC, part of Springer Nature 2021
221