Bounty Hunter, Protein Edition

CDC48 is an all-purpose protein extractor, bringing reluctant proteins in from far-flung parts of the cell, to be executed at the proteosome.

Every cell needs a recycling bin. While DNA lives forever, other molecules like membrane lipids, RNAs, and proteins do not. They are chemically less stable. They may also have functions that are sufficiently fleeting or conditional that they need to be turned off  quickly and specifically, one common method of which is to dispose of them entirely. For proteins, a vast infrastructure exists to identify and recycle them for these various reasons, involving hundreds of genes. A central character in this story is ubiquitin, a small protein that is, as its name implies, ubiquitous. It is used as a flag to mark proteins, usually for degradation, but also for other regulatory events. 

For example, one mechanism that sets protein lifespans is the N-end rule. A set of enzymes recognize the amino acid on the very N-terminus of each protein in the cell (if it is accessible). Different amino acids determine different life spans, from days (M, G, A, S, T, V, P), to a fleeting couple of minutes (R). These enzymes then ligate a ubiquitin to the protein, and leave it to be found by the next actor in the system, the bounty hunter of the cell, CDC48. Not all proteins need to be tracked down. Many diffuse on their own over to the proteosome, where they are willingly digested for the greater good. (Think Soylent Green, at risk of mixing metaphors) Some ubiquitin-flagged proteins are more reluctant, however. They may be stuck in one of many cellular membranes, or part of a big protein complex, or in a misfolded protein glob. Biology has become awfully complex in the last few billion years, and proteins find themselves in all sorts of tight spots.

The euthanasia processing center.

Most of the hundreds of genes devoted to this protein disposal process encode proteins (called E3 ligases) that attach ubiquitin to target proteins based on various rules such as the one above. Another recently described rule and protein (FBXL17) evaluates the quality of a particular family of protein dimers. If such a dimer is slightly misaligned or misfolded, a patch on its surface (called a degron) is exposed that interacts with this protein, which attaches a chain of ubiquitins, putting up the wanted poster that CDC48 and its colleagues later come around to collect.

CDC48 eventually arrives, as a special extractor of reluctant proteins, crow-barring them out of wherever they happen to be hiding so that they can be ferried over to the proteasome / recycling center. Its structure is a complex hexameric donut, and it has not one, but two ATPase activities, so one might say it comes equipped with two six-shooters. It collaborates with a large number of other proteins that help identify and track down squirrely proteins, as well as to help transfer them onwards. (CDC stands for cell division cycle, a famous series of mutants in yeast that won a Nobel prize in 2001 for their elucidation of the mechanics of cell division regulation. Many key cell division proteins have very short and closely regulated lifespans. The human version of CDC48 is named VCP and p97.)

Structure of CDC48 (green, blue, and purple portions) with a small inhibitor (red) jammed in that gums up its activity.

As do many interesting protein complexes, CDC48 has a hole in the middle. This is where the tagged proteins get pulled through, yanking them right out of wherever they are, guns blazing. Which is to say, with plenty of ATP powering the process. The top part of the complex recognizes ubiquitin in the form of polyubiquitin chains, which is the typical degradation tag. The two rings, which are the meat of the CDC48 protein, each have an ATPase activity, and engage in a subtle hokey-pokey as they operate, (below) which is assumed to constitute the extraction process, pulling proteins bit by bit through the center. Since the target protein is covalently tagged with ubiquitin, it has been found that this central hole is big enough to accommodate two protein chains going through at the same time, either a hairpin shaped substrate following a leading ubiquitin chain, or ubiquitin and the target protein travelling alongside each other.

A very rough model of the structural changes of CDC48 as it burns ATP to pull protein chains through its inner ring, from top to bottom. 

"After interaction of the polyubiquitin chain with UN, [an accessory protein docked to the top of CDC48 that helps recognize the ubiquitin tag], Cdc48 uses ATP hydrolysis in the D2 domain to move and unfold the polypeptide substrate through its central pore. ATP hydrolysis in the D1 domain is involved in substrate release from Cdc48, a process that requires the cooperation of the ATPase with a DUB. The DUB trims the polyubiquitin chain, and the remaining oligoubiquitin chain is then also translocated through the pore."

When the protein gets to the other side, it is not quite clear what happens next. Most likely is that CDC48 waits till directly docked with a cytoplasmic proteasome before fully unfolding its captured culprit into the proteasome's maw. But there are likely to be partner proteins involved in this process as well, at least as helpers. This is an ancient and ubiquitous process, conserved from bacteria to humans. CDC48 makes up about one percent of proteins in a typical cell, a very prominent role in line with the minor, though critical, role, of bounty hunters in our legal and dramatic worlds.

• Stiglitz on the election.
• On the economic Nobels: " ... running out of resources is not a huge concern, but rather the exact opposite, that we will have access to and use too many polluting resources, should worry us. That is tremendous foresight for someone writing in 1974!"
• Also, inventors and innovators never get a break- their profits are small and fleeting. "I estimate that innovators were able to capture about 4 percent of the total social surplus from innovation."
• Do driverless cars want to avoid getting hurt?
• The Taliban may be winning ground, but hearts, not so much. For Pakistan, however, they are the ideal tool.
• Social dominance feeds on itself. Thus every family's quest to scrabble up the social tree.
• Ditto from Adam Smith.
• It remains odd to have a Russian operative in the White House.
• Is economics monotheistic?
• Dr. John McLaughlin.