Periodic table of protein complexes

New tool helps to visualise, understand and predict how proteins combine to drive biological processes

Periodic table of protein complexes

Newpic1.jpgEMBL-EBI

A new ‘periodic table’ of protein complexes has been developed that provides a unified way to classify and visualise protein complexes, providing a valuable tool for biotechnology and the engineering of novel complexes.

This study also provides insights into evolutionary distribution of different types of existing protein complexes.

The Periodic Table of Protein Complexes, published in Science, offers a new way of looking at the enormous variety of structures that proteins can build in nature, which ones might be discovered next, and predicting how entirely novel structures could be engineered. Created by an interdisciplinary team led by researchers at the Wellcome Genome Campus and the University of Cambridge, the Table provides a valuable tool for research into evolution and protein engineering.

Almost every biological process depends on proteins interacting and assembling into complexes in a specific way, and many diseases are associated with problems in complex assembly. The principles underpinning this organisation are not yet fully understood, but by defining the fundamental steps in the evolution of protein complexes, the new ‘periodic table’ presents a systematic, ordered view on protein assembly, providing a visual tool for understanding biological function.

“Evolution has given rise to a huge variety of protein complexes, and it can seem a bit chaotic. But if you break down the steps proteins take to become complexes, there are some basic rules that can explain almost all of the assemblies people have observed so far.”

Dr Joe Marsh, formerly of the Wellcome Genome Campus and now of the MRC Human Genetics Unit at the University of Edinburgh.

table3.pngScience
Part of the Periodic Table of Protein Complexes. The table shows how all bijective protein complex topologies can be arranged according to the number of different subunit types (s) and the number of times these subunits are repeated (r).

Different ballroom dances can be seen as an endless combination of a small number of basic steps. Similarly, the ‘dance’ of protein complex assembly can be seen as endless variations on dimerization (one doubles, and becomes two), cyclisation (one forms a ring of three or more) and subunit addition (two different proteins bind to each other). Because these happen in a fairly predictable way, it’s not as hard as you might think to predict how a novel protein would form.

“We’re bringing a lot of order into the messy world of protein complexes. Proteins can keep go through several iterations of these simple steps, adding more and more levels of complexity and resulting in a huge variety of structures. What we’ve made is a classification based on these underlying principles that helps people get a handle on the complexity.”

Dr Sebastian Ahnert of the Cavendish Laboratory at the University of Cambridge

The exceptions to the rule are interesting in their own right, as are the subject of on-going studies.

“By analysing the tens of thousands of protein complexes for which three-dimensional structures have already been experimentally determined, we could see repeating patterns in the assembly transitions that occur – and with new data from mass spectrometry we could start to see the bigger picture."

Dr Joe Marsh

“The core work for this study is in theoretical physics and computational biology, but it couldn’t have been done without the mass spectrometry work by our colleagues at Oxford University. This is yet another excellent example of how extremely valuable interdisciplinary research can be.”

Dr Sarah Teichmann, Research Group Leader at the Wellcome Trust Sanger Institute and the European Bioinformatics Institute (EMBL-EBI)

Notes to Editors
Publications
  • Principles of assembly reveal a periodic table of protein complexes.

    Ahnert SE, Marsh JA, Hernández H, Robinson CV and Teichmann SA

    Science (New York, N.Y.) 2015;350;6266;aaa2245

Interactive online version of the table

An interactive version of this table with information on the structures represented by each topology can be found at http://www.periodicproteincomplexes.org/

Funding

This work was funded by the Royal Society (S.E.A. and C.V.R.), the Human Frontier Science Program (J.A.M.), the Medical Research Council grant G1000819 (H.H. and C.V.R.) and the Lister Institute for Preventative Medicine (S.A.T.).

Participating Centres
  • Theory of Condensed Matter, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE
  • MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU
  • European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI) Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD
  • Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford,South Parks Road, Oxford OX1 3QZ
  • Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA
Selected Websites
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