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Proteins are the workhorses of the body, fulfilling many roles essential for life processes. These molecules are made up of hundreds or thousands of small units called amino acids, which attach to each other to form a long chain. The exact sequence of amino acids determines how the protein will then fold to acquire its final, three-dimentional shape.
Enzymes called proteases can degrade unneeded or faulty proteins so that the amino acids can be recycled. For instance, in bacteria, the AAA+ protease ClpXP can recognize and ‘grab’ specific patterns of amino acids at the ends of a protein. This molecular machine then tugs on the segment and unfold the protein, the way a ball of yarn unwinds when pulled from one end. The unfurled protein is then fed into a different section of ClpXP, where it is chopped into short segments for recycling.
ClpXP is the best-characterized enzyme amongst AAA+ proteases. However, it is still unclear how it can grip target proteins tightly enough to allow unfolding. To investigate, Bell et al. attached different patterns of 12 amino acids to the end of a folded protein. How well ClpXP grasped each of these proteins was then measured in bacteria and in test tubes. This revealed that ClpXP attaches to six to eight amino acids at a time, suggesting that only part of the enzyme clasps on the protein. Large amino acids are better gripped than small amino acids, similar to how a knotted string is easier to hold than a smooth rope. Amino acids that are electrically charged also interfere with ClpXP attaching to the protein. Finally, ClpXP grasps multiple amino acids at the same time, which dramatically increases grip strength.
Many proteins, including some found in viruses, use ‘slippery’ patterns of amino acids to avoid being gripped and unfolded by proteases. By understanding how different patterns of amino acids are grasped, it may someday be possible to engineer enzymes able to target dangerous proteins.
