Publication highlights

Researchers at the Crick and Imperial College report a method to characterise and track sugar-coated cell sensors called proteoglycans using click chemistry. Through a 'bump and hole' engineering technique, they modified a hole in an enzyme and a bump in a sugar, to alter an enzyme that glues the two together so it accepts a bumped version of the sugar. This modified sugar contains a chemical tag which means it can be traced using click chemistry, such as attaching a fluorescent molecule to 'see' the molecule by imaging, or a molecule acting like an anchor to isolate and further study it. In the future, these molecules could be tagged and tracked in different contexts, or proteoglycan function could be altered by replacing the sugar chain with a different biological or synthetic molecule.

Researchers at the Crick and King's College London have used phototherapy to inhibit a protein in E. Coli bacteria that makes them resistant to antibiotics. They designed a new chemical tool, Ru1, composed of a light-activated ruthenium metal complex attached to an organic ligand that binds to NDM-1, an enzyme in drug-resistant bacteria that breaks down common beta-lactam antibiotics like penicillin. When exposed to blue light, the metal complex produces reactive oxygen species that cause damage to NDM-1, preventing it from binding and destroying an antibiotic. They showed that Ru1 can boost the activity of meropenem antibiotic against E. Coli by 53 times, without showing toxicity to human cells.

Researchers at the Crick and the University of Pittsburgh have used x-ray crystallography and cryo-electron microscopy to determine the structures of betaglycan - a co-receptor involved in cell signalling - in complex with the TGF-β protein and its signalling receptors. They found that both domains in betaglycan are involved in ligand binding, demonstrated how this occurs, and revealed that their arrangement also allows for signalling receptor recruitment. The results provide a structural explanation for how betaglycan functions to capture the ligand and hand it over to the receptors in a sequential manner, to selectively enhance TGF-β signalling.

Dysregulation of an enzyme called peptidyl arginine deiminase IV (PADI4) has been linked to many diseases including various cancers and atherosclerosis. However, little is known about its regulation within cells, largely due to al ack of appropriate chemical tools. In this study researchers at the Crick used the RaPID system, a very powerful screening technology, to identify binders of PADI4 from DNA-encoded libraries of more than a trillion cyclic peptides. We developed these binders into three novel cyclic peptide chemical tools that modulate PADI4 activity: one to target the active conformation of PADI4, one to bind to the allosteric site and activate PADI4, and a third to use as a tool to identify different PADI4 protein binding partners that may regulate its activity. Together these peptides provide a new toolkit for the study of PADI4 in the context of health and disease.

During cell division, the accurate separation of duplicated chromosomes relies on a protein complex called cohesin, which forms ring-like structures to hold together identical sister DNAs. Although cohesion's role is established during DNA replication, the coordination between DNA replication and cohesion remained unclear.

Through single-molecule imaging, researchers at the Crick revealed that cohesins are pushed along DNA by the replication machinery, known as the replisome, until they meet with another replisome. While replisomes disassemble once DNA replication is complete, cohesins persist, anchoring sister DNAs together at replication termination sites. In living cells, disrupting replisome disassembly stops cohesin from being able to link sister DNAs together, underscoring the critical connection between sister chromatid cohesion and DNA replication termination.

Enzymes called ZDHHCs are responsible for directing a type of regulatory modification, palmitoylation, that adds a lipid to specific proteins, but humans have 23 different ZDHHCs, and understanding which proteins each one modifies has been very challenging. A team led by satellite group leader Ed Tate have developed a new method that identifies the set of proteins just one ZDHHC acts on, which has ramifications not just for our understanding of lipid biology, but also for therapeutic strategies targeting proteins whose activity depends on palmitoylation. To progress the research into drug discovery, the researchers have also screened a very large library of compounds to find effective ZDHHC inhibitors.

Cell-surface and secreted proteins play critical roles in human development, growth factor signalling, and cell adhesion. Proteoglycans are an important subset of these proteins and are modified with long chains of sugar molecules called Glycosaminoglycans (GAGs) such as heparan sulphate (HS) or chondroitin sulphate (CS), but they all start with the same four sugars – only after the addition of the fifth sugar is the fate of the growing chain sealed.

While protein and DNA synthesis are template-driven, from DNA or RNA, synthesis of the proteoglycan GAG chains are not. In a collaboration between the Crick and Imperial, the researchers devised a synthesis system to allow precise control of eight of the enzymes in the biosynthesis pathway. They discovered that chrondroitin sulphate is the “default” modification, and that the enzyme responsible for priming chrondroitin sulphate synthesis modifies all sites equally. They also found that the enzyme responsible for priming heparan sulphate synthesis (EXTL3) has a positively charged patch that interacts with negatively charged amino acids near the attachment site and will only modify certain substrates. This will help to predict how mutations surrounding the glycosaminoglycan attachment sites could be implicated in diseases like cancer or developmental conditions.