Origami for proteins
One of SULSA’s latest recruits, Professor Neil Bulleid recently returned to Glasgow where he did his PhD in biochemistry in 1985. In his new job at the Division of Molecular & Cellular Biology (in the Faculty of Biomedical and Life Sciences), he is looking forward to exploring new frontiers in life sciences and breaking down the barriers between the different scientific disciplines in his quest for the truth about how proteins get into shape……
When Neil Bulleid talks about proteins, he uses more metaphors than the average poet. One moment, he is talking about “posting a letter” and the “postcode” which makes sure that molecules get to the right destination. The next moment, he is talking about the “factories” that manufacture proteins, and the “quality control” systems that reject faulty proteins. Then he explains how polypeptides (made from chains of amino acids) form themselves into a particular shape by folding themselves into proteins – like microscopic origami. But how else do you describe the highly complex creation of proteins, without which there would be no life on earth?
The “folding” process used in the manufacturing of proteins has been known about for decades, but biologists are only now beginning to understand how it works – and Bulleid is one of the scientists leading the way, shedding light on how proteins are formed and how they are transported from the inside to the outside of a cell, moving through the secretory pathway to populate the surface.
Human beings have at least 25,000 genes and about a third of them are designed to make the proteins which enter the secretory pathway. The first stage of their journey through the pathway is a cellular organelle called the endoplasmic reticulum. It is within this organelle that proteins entering the pathway are folded and assembled into their correct functional form. Only the correctly folded protein is allowed to exit the endoplasmic reticulum, giving rise to the idea that the organelle acts as a quality control point in the secretory pathway. Proteins that do not attain their correct shape are degraded, thereby preventing their build-up in the cell. And as Bulleid explains it, the way that the protein chain adopts the correct shape involves mind-boggling mathematics. For example, the number of possible shapes that the chains could form could be as many as 1047 – more than the number of atoms in the whole human body. And the fact that each chain does form a particular shape a few seconds after it comes into being is a “marvel of biology,” according to Bulleid.
In the 1960s, says Bulleid, scientists believed that all the information needed for proteins to fold correctly was contained in the amino acid sequence, like the code in a smart piece of software, but the mathematics suggest that if this were the case, the process may take several years. It was only later they discovered that “chaperone” proteins were needed to facilitate the process, not only helping the proteins to form the right shapes but also looking after quality control. If the proteins don’t meet the quality standard, the chaperones will bind to them and make sure they don’t go anywhere else. The downside to this binding is that if the proteins are not degraded, this can result in a build-up of toxic proteins which may lead to the development of diseases like Parkinson’s or Alzheimer’s. For example, cystic fibrosis is caused by a protein not arriving at the right destination because the quality control system has detected a minor difference in its shape and prevented it from going where it should go. If the “slightly faulty” protein was “passed” by the quality control system, the sufferer may lead a more normal life, but the system has strict rules and sticks to the rulebook. And as we get older, these problems get worse.
Ultimately, scientists like Bulleid want to understand the fundamental processes involved so they can cure or prevent these diseases, and huge advances have been made over the last 15 years, since Bulleid first set up his lab. As an example, one of the more recent breakthroughs is the development of a treatment for Gaucher’s disease, using drugs that bind to mutant proteins so they form the right shape, and drugs for cystic fibrosis which “bend the rules” of the quality control system to allow imperfect proteins out of the cell. The development of these drugs would not have occurred if we did not understand the link between protein folding, quality control and cellular stress.
According to Bulleid, his primary interest is “biochemical reactions in a cellular context,” but he does not like to be pigeon-holed as a cell biologist or biochemist because he sees the future in a broader approach. Even though the questions asked are specialist in nature, says Bulleid, we must adopt a multidisciplinary approach to come up with solutions.
What sets Bulleid apart from many other biologists is the way that he investigates the microscopic universe of proteins, cells and molecules “to look at what really happens” when proteins are formed – something which is technically very difficult to do. “We try to use approaches which will reproduce what happens in the cell,” he explains, “without using an intact cell.” And to do this, he uses a technique which creates naked or “ghost” cells which have no plasma membrane.
To be able to study the initial stages in the life of a protein within the endoplasmic reticulum and watch it in action in an environment in which it is able to fold, Bulleid and his team use a special detergent to “wash away” or “punch holes” in the cholesterol-rich plasma membrane which surrounds the cell. This releases all the cytosolic components but leaves the endoplasmic reticulum intact. These ghost cells can then be used to study the synthesis of individual proteins. One of the proteins he has worked with is procollagen (collagen being the most common protein in our bodies, helping to form bones and skin), which in the past could only be studied by looking at cells grown in culture. Using his “ghost cell” approach in the lab, Bulleid was able to determine which chaperones were needed to fold this protein and has developed a “non-natural” form of collagen, since patented, which could be used in tissue engineering for applications such as skin replacement and ulcerations.
More recently, he has been carrying out research into 17 similar proteins which belong to the same enzyme family. These enzymes are responsible for forming linkages within and between protein chains. No one knows why there are so many enzymes which catalyse the same reaction, but it could be due to each enzyme only working with a distinct set of substrates. Bulleid has used an approach which traps the enzyme with its substrate so that he can identify which proteins are substrates for each enzyme. “We are now beginning to understand which folding enzymes or chaperones are needed to make each protein that enters the secretory pathway,” says Bulleid. “This knowledge is crucial if we are to optimise the production of proteins for therapeutic purposes as many of these proteins enter the secretory pathway.”
In the last few years, says Bulleid, there have been some significant discoveries, including the fact that we now know much more about the by-products involved in the formation of proteins and how they relate to disease – for example, reactive oxygen species (ROS) like hydrogen peroxide which can damage our cells. It is now recognised that the process of protein folding in the endoplasmic reticulum can lead to oxidative stress and cell death. Our increased understanding of the link between protein folding and oxidative stress is crucial if we are to fully understand how many disease pathologies originate.
So why has Bulleid joined the growing number of researchers moving to Scotland under the SULSA scheme? He is keen to plug himself into the network created by SULSA and sees it as a great opportunity to establish a new direction in his research, collaborating with other researchers in Scotland and having easier access to costly equipment and facilities. By joining together and pooling resources, Scottish Universities can provide sophisticated research facilities in the biological sciences and avoid competing against each other for diminishing resources, says Bulleid. He is also looking forward to the “greater degree of freedom” he will get as a SULSA researcher, and to interacting with the wealth of talented researchers at the University of Glasgow.“My focus is on fundamental research,” Bulleid says “I’ve always been interested in how things work.” And as part of SULSA, Bulleid will be given every chance to succeed – and find out more about how proteins that enter the secretory pathway keep themselves in shape.