Protein Complexes Are under Evolutionary Selection to Assemble via Ordered Pathways

Joseph A. Marsh,Sarah A. Teichmann,Zoe Hall,Sebastian E. Ahnert,Carol V. Robinson,Helena Hernández,Tina Perica

doi:10.1016/j.cell.2013.02.044

Abstract

SummaryIs the order in which proteins assemble into complexes important for biological function? Here, we seek to address this by searching for evidence of evolutionary selection for ordered protein complex assembly. First, we experimentally characterize the assembly pathways of several heteromeric complexes and show that they can be simply predicted from their three-dimensional structures. Then, by mapping gene fusion events identified from fully sequenced genomes onto protein complex assembly pathways, we demonstrate evolutionary selection for conservation of assembly order. Furthermore, using structural and high-throughput interaction data, we show that fusion tends to optimize assembly by simplifying protein complex topologies. Finally, we observe protein structural constraints on the gene order of fusion that impact the potential for fusion to affect assembly. Together, these results reveal the intimate relationships among protein assembly, quaternary structure, and evolution and demonstrate on a genome-wide scale the biological importance of ordered assembly pathways.

Highlights

In order to function, most proteins assemble into complexes— either homomers, comprised of self-interacting copies of a single type of subunit, or heteromers, composed of two or more distinct polypeptide chains
These results demonstrate the role of protein complex assembly in evolution and provide fundamental insight into the biophysics and biological importance of ordered assembly pathways
Prediction of Heteromer Assembly Pathways and Characterization by Nanoelectrospray Ionization mass spectrometry (MS) We first searched the Protein Data Bank (Berman et al, 2000) for heteromeric complexes for which there is genomic evidence of fusion occurring between subunits in the STRING database (Szklarczyk et al, 2011)

Summary

Introduction

Most proteins assemble into complexes— either homomers, comprised of self-interacting copies of a single type of subunit, or heteromers, composed of two or more distinct polypeptide chains. Is the order in which protein subunits associate important for the formation and biological function of the final complex? By analogy to Levinthal’s paradox of protein folding (Levinthal, 1969), we can presume that assembly must proceed via energetically favorable intermediate subcomplexes, lest the time required for productive multisubunit complex formation be prohibitively long. Electrospray mass spectrometry (MS) has emerged as an extremely useful method for studying assembly, having the distinct advantage of being able to probe the oligomeric states of multiple subcomplex intermediates simultaneously, allowing in vitro ordered assembly pathways to be elucidated in detail (Sobott et al, 2002; Hernandez and Robinson, 2007; Levy et al, 2008)

Results

Discussion

Conclusion