Mass spectrometry: come of age for structural and dynamical biology

Abstract

Over the past two decades, mass spectrometry (MS) has emerged as a bone fide approach for structural biology. MS can inform on all levels of protein organization, and enables quantitative assessments of their intrinsic dynamics. The key advantages of MS are that it is a sensitive, high-resolution separation technique with wide applicability, and thereby allows the interrogation of transient protein assemblies in the context of complex mixtures. Here we describe how molecular-level information is derived from MS experiments, and how it can be combined with spatial and dynamical restraints obtained from other structural biology approaches to allow hybrid studies of protein architecture and movements.

Figure 1. Structure and dynamics space accessible to MS-based approaches

Proteins undergo a range of dynamical fluctuations, from folding of the polypeptide to changes in the composition of the proteome (indicated upper left). These processes span not only a wide range of timescales, but also all aspects of protein organisation, from primary to quinary (clockwise around wheel). A plethora of MS-based approaches can inform on many of these structural dynamics, and are indicated as overlapping coloured wedges, with their tractability in the temporal dimension indicated by shading and the radial scale bar (faster towards centre of wheel). These include ‘bottom-up’ experiments in which peptides, produced by proteolysis of cell extracts or purified components, are interrogated; and ‘top-down’ methodologies which rely on the examination of the proteins or assemblies intact in the gas-phase. Here we have grouped them according to their approximate feasibility as a function of mass (blue = easier as mass increases, orange = more difficult as mass increases, purple = independent of mass).

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