New Danish research centre to make designed proteins with vast potential

(Press-News.org) Proteins are the workhorses of biology. They perform virtually every important function in living organisms. They store, copy and protect our DNA, digest food to give us energy, and harness this energy to make our cells and muscles work.

But imagine if proteins could be specifically designed to provide even more versatile molecular toolboxes for science, technology and healthcare. In essence, this is what protein design is all about. It is a growing field that allows scientists to create entirely new proteins - including those that nature itself has not explored - and to tailor them to solve specific challenges.

Protein design could lead to artificial proteins that are able to detect diseases, and others to cure those diseases directly in the body. It could also produce proteins with industrial and environmental applications such as greener production of pharmaceuticals or the ability to break down plastics and other pollutants. A new centre at the University of Copenhagen will drive efforts to realise this potential.

CPD to play international key role in protein design Proteins are large chain-like molecules made of building blocks called amino acids. In nature there are 20 different amino acids, and the order of these along the chain (the protein sequence) determines the shape that a protein forms, and, in turn, the job that it does.

The 2024 Nobel Prize in Chemistry was awarded to two artificial intelligence (AI) researchers who helped crack the code that links a protein’s sequence to its three-dimensional structure, and to a biochemist who with many others showed that it is possible to design proteins from scratch using computers. It is this work that Dek Woolfson and the University of Copenhagen will now build on to open a whole new chapter in the story.

The Novo Nordisk Foundation Center for Protein Design (CPD) will launch in August 2025, marking the beginning of an ambitious endeavour that will bring together a diversity of disciplines from biology, chemistry and drug design to computer science spread across two faculties to create a world-leading hub for protein design.

The CPD’s Director will be Dek Woolfson, a world-renowned and leading scientist in the field. The chance to lead protein design research in Copenhagen was an offer that he couldn't refuse.

“The great leaps in understanding proteins and in computational design, including AI, that have been made recently give us tools to start designing artificial proteins with confidence, and the resulting possibilities seem almost endless,” says Dek Woolfson. “However, there is still a lot of work to do before the full potential of protein design is realised. The CPD will play a key role in this, including driving fundamental research, and translating it into real-life applications. I am very excited by this opportunity, and I’m looking forward to establishing and leading the centre.”

Dek Woolfson comes from a position at the University of Bristol, UK, where he has pioneered protein design and led initiatives such as BrisSynBio, a Synthetic Biology Research Centre.

The Novo Nordisk Foundation has long recognised the great potential of protein design. 

“De novo protein design opens possibilities for entirely new solutions to global challenges - from the development of targeted drugs and vaccines to sustainable biomaterials and enzymes that can degrade microplastics,” says Lene Oddershede, Chief Scientific Officer, Novo Nordisk Foundation. “Recently the field has made significant strides, and Denmark has a strong starting point with its long tradition of protein research. With this grant, we want to help translate groundbreaking basic research into concrete solutions, train the next generation of researchers in this crucial field, and ultimately establish a powerhouse for protein design here in Europe.”

Producing knowledge, researchers and actual proteins A lot of understanding about how proteins work is still missing. Fundamental knowledge of the chemistry and physics at play within proteins will therefore be an early targeted effort of the CPD, along with advancing understanding of how proteins can be made to work in specified conditions and environments.

“The CPD will design novel proteins with specific properties to work under desired conditions,” says Dek Woolfson. “To do this, we will develop and use the latest computational methods, including generative AI. However, it will be critical to combine this with chemistry and physics to gain a more complete picture of proteins, how they function, and how we can design them. All the time, we will be training new research talent in the field – from biochemists, chemists, and computer scientists to pharmacists, and drug designers.”

The CPD will have its main operation between the Department of Biology and the Department of Drug Design and Pharmacology at UCPH, and with additional activities at the Departments of Chemistry and Computer Science. In addition to a strong core team of experienced researchers, it will host and train a large number of PhD students and post-doctoral researchers. It will also be open to visiting Danish and international guest researchers to ensure the centre’s activities are of the highest standard.

The core strength: Interdisciplinary collaboration on a clear mission The CPD will bring together researchers from a wide range of disciplines on the common mission of protein design, and this is the great strength of the centre, according to Dean Bo Jellesmark-Thorsen from the Faculty of Science.

“This complex new field does not sit comfortably alone in any of the classical scientific disciplines,” he says. “Interdisciplinary collaboration between biochemists, computer scientists, and pharmaceutical researchers is essential for mastering it. Fortunately, the collaboration across the Faculty of Health and Medical Sciences and the Faculty of Science to pave the way for the CPD has been extremely positive. It is the same mindset that will carry the CPD forward and ensure that the great potential is also realised.”

At the Faculty of Health and Medical Sciences this view is strongly supported.

“The CPD has been created precisely to bring together expertise across disciplines and institutions,” says the faculty’s Dean, Bente Stallknecht. “Based on collaboration between the departments, the centre will enhance synergy between the best in the field from both faculties. This collaboration extends both nationally and internationally. We are very pleased to have attracted Dek Woolfson, an internationally recognised leader in the field. Under his leadership, the centre will become a hub with strong links to the international research community and have an exchange of both ideas and people through partnerships with collaborating universities working on common projects and grand challenges.”

Dek Woolfson is extremely experienced in collaborative and interdisciplinary research. He has recently been elected a Fellow of the Royal Society, a highly renowned scientific academy in the UK. Currently, Dek works across the Schools of Chemistry and Biochemistry at the University Bristol, where he established BrisSynBio and promoted collaborations that bring protein design to cell biology, materials science and other fields. He will maintain these links and forge new international partnerships by creating several CPD spokes, including one in Engineering Biology at the University of Bristol.

 

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Facts about protein design Proteins are chain-like molecules made of building blocks called amino acids. The chains fold up into three-dimensional structures that determine the functions of the proteins.

Our genes determine the order in which the amino acids are linked together, called the protein sequence. This is crucial for correct protein folding. Understanding the connections between protein sequence on the one hand and protein structure and function on the other has been a massive challenge for science since the 1960’s.

In 2024, the Nobel Prize in Chemistry was awarded for two pieces of pioneering work that applied advances in computation to the protein folding problem. One half of the prize was awarded to Demis Hassabis and John Jumper at Google DeepMind in the UK. They led the team that developed AlphaFold, an AI that accurately predicts protein structure from sequence. The second half went to biochemist David Baker from the University of Washinton, who made computational breakthroughs to do the reverse: that is, for a targeted protein structure, what is the sequence needed to form it?

Their work has established and accelerated the field of protein design, in which synthetic or artificial proteins are made from scratch. These designed proteins have the potential to perform entirely new functions and can be made relatively easily by introducing synthetic genes that encode them into bacteria.

The next steps of making protein design mainstream, and to generate new protein structures and functions to order are considerable challenges, but it is exciting frontier science with enormous potential.

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