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Water lends a helping hand in folding

New work from EPSRC Research Fellow Dr Sylvia McLain in the Department has challenged a long-held assumption about how proteins fold.

The work provides the first evidence for water’s active role in helping proteins attain their folded structure and could help in our understanding of the part that water plays in many cellular functions.

Model of the GPG-NH<sub>2</sub> peptide and water showing a water-mediated peptide folding interaction. The single bridging water is shown interacting with an oxygen molecule and with the NH<sub>2</sub> cap (oxygen in red, nitrogen in blue)

Model of the GPG-NH2 peptide and water showing a water-mediated peptide folding interaction. The single bridging water is shown interacting with an oxygen molecule and with the NH2 cap (oxygen in red, nitrogen in blue)
(Click to enlarge)

Dr Sylvia McLain and her group carried out the research with collaborators at Oxford, Kings College London, and at the John Carroll University in the States. They published their findings in a paper in Angewandte Chemie (1).

Despite knowing a considerable amount about the structure of folded proteins, we still do not understand how a polypeptide sequence translates into a fully folded structure that is necessary for the protein to be functional.

‘Historically, the driving force for protein folding has been attributed largely to the ‘hydrophobic effect’,’ explains Dr McLain. ‘Protein folding is believed to take place because water is expelled from around the hydrophobic parts of the protein, decreasing the entropy of the system and inducing the protein to fold.’

But she adds that there is no experimental data to support this and that we know little about the fundamental interactions causing proteins to fold. Just as important to the folding process as the hydrophobic interactions may be the interactions between the protein and water.

One commonly occurring folding pattern in proteins is the ß-turn, in which the polypeptide turns tightly back on itself. The turn is often found on the surface of proteins where it is exposed to the surrounding water.

The ß-turn is thought to be nucleated by the amino acid sequences within it. But researchers do not know whether the amino acid sequences alone can initiate the formation of the ß-turn or whether water may play a fundamental role in the process.

Dr McLain was interested to find out if she could directly explore the role of water in initiating the ß-turn fold. She and Dr Sebastian Busch, a postdoc in the lab who carried out much of the work, chose to study the turn’s structure in a simple model peptide GPG-NH2. This contains the sequence glycine-proline-glycine, known to occur in ß-turns in proteins, and a NH2 cap.

In collaboration with others, they tackled the problem using a comprehensive set of techniques - NMR, carried out in the Department with Professor Christina Redfield, neutron diffraction carried out at the ISIS facility, and computer simulations in conjunction with a colleague from KCL. Together, this unique combination of approaches allowed them to explore the structural interactions between peptide and water on the atomic scale.

NMR analysis of the peptide pointed to an interaction between its ends, even though the residues are some distance apart, suggesting that the peptide adopts a specific structure. Neutron diffraction was used to reveal further details about the structure and its interaction with surrounding water molecules. From this, the researchers could determine that the oxygens in the different positions along the peptide interact differently with water.

Together, the approaches build up a picture of the structure in which water is mediating the interaction between the ends of the peptide, nucleating the turn. Water is able to act in this way by virtue of hydrogen bonding interactions - between the oxygen on Gly1 and with the NH2 cap of the peptide.  

The results point to water being a fundamental part of the folded structure and mediating folding in the early stages. None of the approaches alone, Dr McLain comments, would have yielded this structural understanding of the interaction between water and peptide.

The next steps, she hopes, will reveal what is going on in more detail. ‘There are lots of experiments to do to explore the role of water better,’ she says. ‘We’d like to capture the structure, for example freeze it and see what’s happening to the water around the groups. We can also extend the study to larger peptides.’

As well as highlighting water’s more active role in protein folding, the research has the potential to provide an insight into fundamental interactions in living cells such as those between peptides.

Reference
  1. Busch, S., Bruce, C. D., Redfield, C., Lorenz, C. D. and McLain, S. E. (2013). Water mediation is essential to nucleation of β-turn formation in peptide folding motifs. Angew. Chem. Int. Ed.. doi: 10.1002/anie.201307657

 

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