April 24, 2018 | David F. Coppedge

More Cool Cell Tricks Discovered

Watching molecular machines at work in living cells should be as fascinating as watching a city through a magnifying glass.

Observing biological nanotransporters (Science Daily). What if you could watch drawbridges working on the head of a pin? Something like that, but far smaller, works inside your cells. There’s a “nanoporter” that uses ATP to transport cargo in and out of cell membranes. This system is not as simple as A-B-C, even though it has that name.

“ABC transporters are fascinating biological nanomachines,” says Lars Schäfer, head of the Molecular Simulation research group [at Ruhr-University Bochum]. These proteins couple the binding and chemical cleavage of ATP molecules, the chemical energy unit of the cell, with the transport of molecules through biological membranes….

“Our results show how the binding of ATP molecules induces structural changes in the transporter that are ultimately required to carry substrate molecules through the membrane,” explains Hendrik Göddeke, co-author and doctoral researcher in Lars Schäfer’s group.

Study reveals the inner workings of a molecular motor that packs and unpacks DNA (Phys.org). A chromosome remodeler named INO80 is performing onstage at the Ludwig Maximilian University of Munich: on the microscope stage, that is. Researchers at LMU watched the act of “astonishing precision” as it worked on its “heavy-duty reorganizational task” of wrapping DNA around chromatin.

Chromatin remodelers have an essential role as they are molecular machines: they unpick and unpack segments of the DNA by sliding nucleosome spools back and forth, replacing individual histones, freeing up the DNA for transcription, and finally compacting it again, when the job is done. Since all of this happens in a highly dynamic fashion, chromatin remodelers enable cells to react rapidly to alterations in their environment – and this holds for brewer’s yeast as well as for human cells.

The clouds of spaghetti that keep DNA data safe (Science Daily). Computer systems worry about data breaches, and so do cells. The cell nucleus is like a massive library read by numerous machines. They deliver information to the cytoplasm outside the nucleus, but only certain molecules can get in or out. This article describes some of the data protection systems provided by the Nuclear Pore Complexes (NPCs), some of the most complex machine systems in cells.

Molecular machines (Illustra Media)

Cells can avoid “data breaches” when letting signaling proteins into their nuclei thanks to a quirky biophysical mechanism involving a blur of spaghetti-like proteins, researchers from the Rockefeller University and the Albert Einstein College of Medicine have shown. Their study appears in the March 23 issue of the Journal of Biological Chemistry….

To travel through NPCs, many molecules must be attached to proteins called transport factors (TFs), which act as shuttles that the NPC recognizes. But the NPC faces a challenge: It must accurately recognize and bind to TFs to let them through without admitting unwanted traffic, but it must let them through quickly — in a matter of milliseconds — in order for the cell to be able to do its duties. Proteins known to accurately bind to specific molecules, like antibodies, normally stay stuck to their targets for periods of up to months.

How on Earth do you have the kind of specificity that we see in protein-protein interactions like antibodies, and yet have the kind of speed that we see with water off a Teflon pan?” asked Michael Rout, professor at Rockefeller University who was one of the co-lead authors of the work.

The spaghetti trick involves many intrinsically-disordered proteins in the NPC, looking somewhat like strands of spaghetti, making “many quick, transient contacts between transport factors” and nuclear proteins. How can we visualize this? “I can’t think of any analogy in normal life that does what this does,” Rout said. “You’ve got this blur of (amino acids) coming on and off (the transport factor) with extraordinary speed.” Maybe security engineers could learn something from this technique.

Scientists map the portal to the cell’s nucleus (Science Daily). In this second article from Rockefeller University about the NPC, Rout did find one analogy:

It reminds us of a suspension bridge, in which a combination of sturdy and flexible parts produce a stress-resilient structure, says Michael P. Rout, who led the work together with Brian T. Chait.

The pore complex contains 552 component proteins, called nucleoporins, and scientists hadn’t previously known how they all fit together. It took a combination of approaches to assemble a comprehensive map of these pieces.

Sadly, after comparing the NPC to lesser systems designed intelligently by humans, Rout ascribes it all to evolutionary chance. “Evolution has enclosed it with a double membrane, the nuclear envelope,” the article says, going on to visualize some unobserved miracles:

The pore complex first emerged when single-celled organisms — the only living things at the time — acquired special compartments containing organ-like structures, including the nucleus, which houses the cell’s genetic code.

Strings of electron-carrying proteins may hold the secret to ‘electric bacteria’ (Phys.org). This article suggests that some bacteria may have the ability to transfer electrons from the inside to the outside environment, using “micro machines” that turn on the power to extract energy from the environment. “Could a unique bacterium be nature’s microscopic power plant?” asks Moh El-Naggar, scientist at USC. Isn’t it nice to know that bacteria, “wired for survival” as among the smallest organisms on earth, are “highly evolved machines”?

Microbiologists, can you please please turn off the obligatory Darwinspeak and just tell us the facts of what you are looking at? You’re beginning to sound like comedians.

 

 

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