Periodic Table of Protein Complexes
News Dec 14, 2015
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 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.
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)
A team led by Johns Hopkins Medicine researchers says it has identified two protein biomarkers in urine that may one day be used to better diagnose acute interstitial nephritis, an underdiagnosed but treatable kidney disorder that impairs renal function in the short term and can lead to chronic kidney disease, permanent damage or renal failure if left unchecked.READ MORE