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Detection of the way an important enzyme works in the cell

Acyl S is the process of chemically binding lipid to protein via thioester bond. It is an important cell process that regulates the localization and function of many proteins. It enhances the binding of the lipid membrane to the protein, for example to the plasma membrane, the Golgi apparatus, or the inner nuclear membrane.

Like most biochemical processes in the cell, protein S acyl can be reversed to regulate the functions of named proteins. Acyl S is reversed by protein acyl thioesterases (APTs).

To do their job, APTs must interact with the lipid membranes that the target proteins bind to. But although APTs are central to the important depleting process, little is known about how APTs do their job.

Scientists led by Jisoo van der Goet and Matteo Dal Beraro at the EPFL School of Life Sciences have made significant advances in our understanding of how APT2, a major acylthiosterase, works in the cell. The work was published on Biology of Chemical Nature.

First, the researchers showed that APTs have an intrinsic membrane-binding capacity. By combining X-ray crystallography with simulation of molecular dynamics, they showed that APTs contain in their structure positively charged spots that allow them to electrically attract the lipid bimembrane layer.

The team also discovered a slightly hydrophobic ring on the surface of APTs they called “tongue,” which allows the enzyme to perform hydrophobic reactions with the membrane. The researchers made APT2 mutations with imperfect tongues and found that they became unable to bind to the membranes, leading them to the conclusion that the ability of APT2 (and other by extension thioesterases) to bind to the membranes is mediated by the tongue sequence.

By analyzing the architecture of APT2, the researchers also identified a site that could degrade it. The site allows the enzyme to attach to ubiquitin, a protein that the cell uses to mark molecules for breakdown. Essentially, APT2 has a built-in control mechanism for its own degradation – but this can only happen after its target is de-traitized and APT2 is freed from it. Alternatively, after one task is complete, APT2 can travel to another membrane, bind it, and elute another protein there.

The researchers then switched to the S acylate of APT2 itself. Previous studies have shown that the enzyme accumulates significantly in the cell’s Golgi apparatus, the organelle that packs a new protein into vesicles before sending it to the cell membrane.

Using another APT2 mutation, the researchers were able to determine that this accumulation is dependent on the S acylate of APT2 itself – on the amino acid cysteine ​​along its sequence (Cys2). In summary, the S acylate on Cys-2 is essential for APT2 to be able to stably bind to lipid membranes and to remove adenoids from their targets in the cell.

Next, the team looked for potential candidate enzymes that could secrete APT2. To do this, they examined all palmitoyltransferase enzymes. The results indicated that APT2 could be corroded as S-shaped by either of two types of palm vectors, ZDHHC3 or ZDHHC7.

Finally, the scientists gathered their data together to find out how APT2 binds to lipid membranes, which is essential for its ability to function in the cell.

What they found is that APT2 binds to membranes in a three-step process. First, long-term electrostatic reactions attract, through its positive stain, the enzyme to the lipid membrane. There, the tongue “dips” into the membrane and temporarily holds APT2 in place, which is necessary for its “fulfillment” by the enzymes that will synthesize it. This causes APT2 to bind to the membrane steadily and ready to perform acetylated functions.

“This study shows that APT2 is actually a hybrid between a lipid-carrying protein, which can extract lipids from membranes, and hydrolase, which can cut protein fats,” says Gisou van der Goot.

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Other contributors

EPFL Protein Production Facility and Structure

Swiss Institute for Bioinformatics

Reference

Lawrence Abrami, Martina O’Dagno, Silvia Hu, Maria José Markida, Francisco S. Mesquita, Muhammad Yu Anwar, Patrick A. Sandoz, Julia Fonte, Florence Pugher, Matteo D. Piraro, F. Jisoo van der Gout. Molecular mode of action of the protein acylthioesterase. Biology of Chemical Nature March 11, 2021. DOI: 10.1038 / s41589-021-00753-2

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