Commentaries

Dec

2022

Trainspotting within the cell’s antenna

New research, published in Cell, illuminates the molecular “trains” that transport cargoes essential for human health and development.

Virtually every cell in the human body grows an antenna-like structure on its surface, which is used to receive vital signals from the body and the outside world. Perturbations in this process cause a wide range of human disorders spanning loss of eyesight, cystic kidneys, breathing problems, and infertility, among other conditions.

New research from the Institute of Structural and Molecular Biology has shed new light on the molecular “trains” that underpin this process, and how they misfunction in disease. Using cryo-election microscopy, a powerful technique for determining the three-dimensional shape of biological molecules, the team was able to see the structure of the proteins that make up the trains and how they carry their vital cargoes. Cell biology experiments showed that the range of cargoes transported by the trains is even wider than anticipated. The findings will help researchers to interpret patient mutations in the proteins that cause disease and design new experiments.

This research, funded by the Wellcome Trust and BBSRC with co-first authors Dr. Sophie Hesketh and Dr. Aakash Mukhopadhyay and co-senior authors Dr. Katerina Toropova and Dr. Anthony Roberts, was published in Cell on 2 December 2022: https://www.cell.com/cell/fulltext/S0092-8674(22)01422-2

Feb

2022

The killer weapon of the immune system

Researchers in Biological Sciences at Birkbeck, in collaboration with a group at the Peter MacCallum Cancer Centre in Melbourne, have determined the structure of a protein assembly used by the immune system to kill unwanted cells. The immune system uses cytotoxic T lymphocytes and natural killer cells to act as executioners when it detects the presence of virally infected or cancerous cells. The cytotoxic and killer cells contain small membrane parcels filled with the protein perforin, which can punch holes through cell membranes, along with the toxic granzyme enzymes. When an infected cell is detected, the killer cell latches onto it and ejects some of the membrane parcels with their toxic contents so that the perforin protein punches holes in the target cell membrane, through which the toxic granzymes enter, rapidly causing the target cell to die (Figure 1). The cytotoxic and killer cells are professional assassins that can kill many victims in rapid succession, briefly attaching, ejecting their lethal cargo, and then moving on to the next victim. Perforin is an essential protein for survival, and unfortunate individuals who lack functional perforin usually die of infection or cancer in early childhood. On the other hand, over active killer cells can also cause serious damage, by triggering inflammation and killing healthy cells.

A former postdoctoral researcher, Marina Ivanova (now at Imperial College), determined the perforin structure in the group of Professor Helen Saibil, and the paper has been published in Science Advances. Perforin is made as single protein molecules that are stored inside their membrane compartment until they are needed, but when they are released, they join up into rings of around 22 molecules and undergo a dramatic shape change in order to punch the hole through the target membrane. Two parts of the protein that are at first coiled up in the molecule extend and join up into the ring to punch through the membrane. This shape change is shown in Figure 2, with the part of the protein that makes the big change highlighted in pink.

Figure 3 shows two views of a perforin ring (multicoloured molecules) enclosing a hole in a cell membrane (shown as a pale blue slab). Now that we know the details of the pore structure, it will be possible to think about designing drugs to either enhance or prevent its activity. This could eventually lead to new therapeutics for certain autoimmune diseases and the condition familial hemophagocytic lymphohistiocytosis.

Ivanova, M.E., Lukoyanova, N., Malhotra, S., Topf, M., Trapani, J.A., Voskoboinik, I., Saibil, H.R. (2022) The pore conformation of lymphocyte perforin. Science Advances 8, eabk3147.

Jan

2022

Nobel Prize in Chemistry for Bio-Inspired Catalysts

The Nobel Prize in Chemistry in 2021 has been awarded to German Benjamin List and British David MacMillan.
Prof Stefan Howorka from the ISMB at UCL Chemistry explains: ‘The two researchers have developed a new class of catalysts that are inspired by Nature. Enzymes are widely used in biology as they initiate and specifically control biochemical reactions to achieve the desired stereochemistry while limiting the creation of undesirable by-products. Reconstructing these catalytic functions with smaller and cheaper synthetic units is of considerable scientific and industrial interest. Ideally, synthetic catalysts should also avoid precious metals such as platinum which are not environmentally friendly.
List and MacMillan succeeded independently of each other in developing efficient biomimetic and “green” catalysts. In the late 1990s, List wondered whether amino acids found in the enzymes’ active site would also be able to achieve part of the same catalytic role if added in isolation. As proof-of-principle, List tested the catalytic properties of proline and related compounds in an aldol reaction. The specific question was whether the use of a chiral proline would control the stereochemical outcome of the reaction. Indeed, the chirality of the catalyst controlled which enantiomer of the aldol products was formed.
MacMillan was working in the same field. MacMillan was motivated to develop new catalysts that avoid the widely used metals. Rather, he focused on environmentally harmless and inexpensive organic frameworks that contain -in addition to carbon- oxygen, nitrogen, sulphur or phosphorous. Similar to List, MacMillan also tested chiral versions of his organic catalysts but with a different reaction, the Diels-Alder cycloaddition. The reaction was successful as enantiopure products formed depending on the chirality of the catalysts.
Reflecting the catalysts’ composition and enantioselective control, MacMillan coined the term ‘asymmetric organocatalysis’ This new field has grown dramatically and develops simple, easy-to-manufacture and environmentally friendly catalyst. This has a huge impact in science and industry to produce new pharmaceuticals or molecules that can capture light in solar cells. This year’s Nobel prize and the Nobel prize given in 2018 for ‘the directed evolution of enzymes’ underscore the importance of developing new catalytic tools, Prof Howorka concludes.

References:
J. Am. Chem. Soc. 2000, 122, 2395-2396; J. Am. Chem. Soc. 2000, 122, 4243-4244

Oct

2018

ISMB Commentary: An unexpected role for the enzyme Glutamine Synthetase

October 2018

Prof Francesco Gervasio’s group has contributed to the discovery and clarification of an unexpected, yet fundamental, role of the enzyme glutamine synthetase.

Glutamine synthetase (GS) is an enzyme that converts glutamate and ammonia to glutamine. GS is expressed in endothelial cells, fundamentally regulating vascular development. However, a group of scientists led by Prof Peter Carmeliet at VIB in Belgium together with Prof Francesco L. Gervasio found that it surprisingly shows little glutamine synthetizing activity in these cells. Instead, GS localizes in membranes due to an expected (and so-far, unknown) auto-palmitoylation activity. This moonlighting activity turns out to be fundamental for vessel sprouting. However, it was unclear how it happens and which residues are involved. The state-of-the art models and simulations by Prof. Gervasio’s group were able to solve the mystery, showing how palmitoyl-COA binds to the active site (see figure, left) and reacts with cysteine 209 to form a covalent bond. Site-directed mutagenesis of Cys209 later confirmed the computational prediction and validated the proposed mode of action. This new finding, published by Nature at the beginning of September, has important implications for anti-cancer drug discovery, as it might lead to new drugs blocking the vascular development in solid cancers.

Role of glutamine synthetase in angiogenesis beyond glutamine synthesis
Eelen, G.,…, Gervasio, F.L.,…, Carmeliet, P.
Nature (2018) 561, 63-69

Aug

2018

ISMB Commentary: Using deep learning and single cell tracking to understand competitive interactions in cell populations

June 2018

Cell competition is a quality-control mechanism through which tissues eliminate unfit cells. Cell competition can result from short-range biochemical inductions or long-range mechanical cues. However, little is known about how cell-scale interactions give rise to population shifts in tissues, due to the lack of experimental and computational tools to efficiently characterize interactions at the single-cell level. Here, we address these challenges by combining long-term automated microscopy with deep-learning image analysis to decipher how single-cell behavior determines tissue makeup during competition. Using our high-throughput analysis pipeline, we show that competitive interactions between MDCK wild-type cells and cells depleted of the polarity protein scribble are governed by differential sensitivity to local density and the cell type of each cell’s neighbors. We find that local density has a dramatic effect on the rate of division and apoptosis under competitive conditions. Strikingly, our analysis reveals that proliferation of the winner cells is up-regulated in neighborhoods mostly populated by loser cells. These data suggest that tissue-scale population shifts are strongly affected by cellular-scale tissue organization. We present a quantitative mathematical model that demonstrates the effect of neighbor cell–type dependence of apoptosis and division in determining the fitness of competing cell lines.

Dr Alan Lowe

Ref: Local cellular neighbourhood controls proliferation in cell competition
Bove, A., Gradeci, D., Fujita, Y., Banerjee, S., Charras, G., Lowe, A.R.
Mol. Biol. Cell (2017) 28: 3215-3228

This video by the Alan Lowe lab demonstrates the data acquired and software developed as part of the work.

Commentaries

Trainspotting within the cell’s antenna

The killer weapon of the immune system

Nobel Prize in Chemistry for Bio-Inspired Catalysts

ISMB Commentary: An unexpected role for the enzyme Glutamine Synthetase

ISMB Commentary: Using deep learning and single cell tracking to understand competitive interactions in cell populations

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