In 1998, former AAAS president Bruce Alberts contemplated what “the next generation of molecular biologists” needed to study. Evidence had been mounting that proteins don’t just undergo chemical reactions, but actually perform physical work with moving parts. “Indeed,” he said in the journal Cell, “the entire cell can be viewed as a factory that contains an elaborate network of interlocking assembly lines, each of which is composed of a set of large protein machines.”
At the time, he acknowledged that “we still have an enormous amount to learn,” but also invited young molecular biologists to engage the factory metaphor, saying, “the great future in biology lies in gaining a detailed understanding of the inner workings of the cell’s many marvelous protein machines.” Now, almost twenty years later, the lights on this factory are much brighter. Let’s look at some of the machinery with the unprecedented detail provided by advances in imaging.
Kinesin with gear switch. What’s more machine-like than gears? One of the kinesin “walking” motors has a gear switch that lets it change direction. This impressed molecular biologists at Oregon State. We read, “Scientists discover a molecular motor has a ‘gear’ for directional switching.” The particular kinesin, named KlpA, helps pull chromosomes apart during cell division. Most kinesins are like one-way roller-coaster cars on their tracks, but this one “contains a gear-like component that enables it to switch direction of movement.”
“KlpA is a fascinating motor protein because it is the first of its kind to demonstrate bidirectional movement,” [Weihong] Qiu said. “It provides a golden opportunity for us to learn from Mother Nature the rules that we can use to design motor protein-based transport devices. Hopefully in the near future, we could engineer motor protein-based robotics for drug delivery in a more precise and controllable manner.” [Emphasis added.]
For more on this amazing molecular machine, see our video, “The Workhorse of the Cell: Kinesin.”
Perfectionist editor. Like a picky newspaper editor, the spliceosome goes to work on “text” transcribed from DNA. This large machine has been hard to study because it is so complicated. Two papers in Nature discuss new findings about it. In “Structure of a spliceosome remodelled for exon ligation,” Fica and team use words like “lariat” and “attack” to show how the spliceosome spends ATP currency as it docks the target, slices and rotates messenger-RNA ‘paragraphs’ for rearrangement. In “Cryo-EM structure of a human spliceosome activated for step 2 of splicing,” Bertram and team describe how one portion of the complex grabs an intron and a base and moves them out of the catalytic core, thereby opening up space for the exon to dock in the right position before it is spliced in. How this multi-component machine knows what to grab, where to position it, and what sequence to follow should strike anyone as fascinating. It’s a molecule, but it acts like a precision robot with moving parts!
Power walkers. Myosins comprise a family of transport machines that use a hand-over-hand ‘walking’ motion. Labeled with Roman numerals, such as myosin-VI, they perform numerous important functions in the cell. In recent weeks, four papers about myosins appeared in the Proceedings of the National Academy of Sciences. First, a review of the other papers by Citovsky and Liu compares the activity of myosins in animals vs plants, finding surprises in how unique the myosins in plants are. Should you care? They think so. They say, “we all should care for the workings of the plant cell because plants sustain life on Earth.”
- Elizabeth Kurth is joined by Eugene Koonin and others in a paper about “Myosin-driven transport network in plants,” focusing on myosin-IX involved in the ‘cytoplasmic streaming’ so characteristic of plant cells. They find hints of “a myosin-dependent nucleocytoplasmic trafficking pathway.”
- Mukherjee and two others describe the “dynamics of the mechanochemical cycle of myosin-V” with descriptive terms like powerstroke, hand-over-hand motion, and force generation.
- French, Sosnick, and Rock investigate “human myosin VI targeting using optogenetically controlled cargo loading.” To watch these motors, they tagged their cargoes with glowing molecules and found new clues to how the cargoes cooperate with the motors and signal each other in a site-specific manner. “Myosins play countless critical roles in the cell, each requiring it to be activated at a specific location and time,” they say.
Speaking of walking machines, if the smart guys at Purdue University design a molecular walking machine made of DNA that we know is intelligently designed, is it fair to attribute intelligent design to the natural walkers in the cell that perform much better? Yet they say, “The designs are inspired by natural biological motors that have evolved to perform specific tasks critical to the function of cells.” Go figure.
Dedicated translator. We know about the ribosome–one of the most intricate machines in the cell — with its RNA and protein parts that translate messenger RNA into proteins. But did you know that mitochondria (the power plants of the cell) have dedicated ribosomes that are smaller? In Science Magazine, a European team studied the “mitoribosome” in yeast and found that it has a distinct architecture, including a large RNA component and 34 proteins, “including 14 without homologs in the evolutionarily related bacterial ribosome.” (How they know it is “evolutionarily related” if it is so different is a conundrum for another time.) Like cytoplasmic ribosomes, the mitoribosome threads messenger RNAs into an entrance channel into the interior, where transfer RNAs line up their corresponding amino acids into proteins. Then the mRNA strand is fed out an exit channel, where folding begins. The team found that the mitoribosome adopts three distinct conformations as it works, but with more subtle motions than the cytoplasmic ribosomes.
Turnstiles. Channels form a large, important class of molecular machines. These are the gates embedded in membranes for purposes of import and export: i.e., “active transport” that goes against the concentration gradient to give a cell control of its interior. Each channel is specific for its own type of molecule: some for ions, some for nutrients, some for expelling toxins, and more. Channels employ several types of “selectivity filters” to ensure only the correct molecules get through.
- Researchers at Ludwig Maximilian University in Munich reported on “adaptor proteins” that act like tickets for getting through certain channels that control the flow of sodium and calcium ions. They “uncovered an activation mechanism in which an accessory molecular adaptor acts as a fail-safe mechanism to prevent inappropriate opening of two related ion channels.” The details are published in PNAS.
- Roderick MacKinnon, who won a Nobel Prize for his work on ion channels, is back with two colleagues describing more details on how a high-throughput calcium-ion channel guarantees passage to only the correct ions. Writing in Nature, they begin, “The precise control of an ion channel gate by environmental stimuli is crucial for the fulfilment of its biological role.” That precision is maintained by moving parts in the selectivity filter “through covalent linkers and through protein interfaces formed between the gating ring and the voltage sensors.” Consequently, membrane voltage regulates the gating of the pore by influencing calcium-ion sensors. A second paper by the team in Nature describes the structure of the high-conductance potassium channel.
- A team of three at University of Texas describes how “two-pore channels” tune their selectivity filters. Writing in PNAS, they first mention that these two-pore channels are ubiquitous throughout the living world. “Interestingly,” they remark, “plant and animal TPCs share high sequence similarity in the filter region, yet exhibit drastically different ion selectivity.” In one mutation experiment, a change of one amino acid changed the filter’s selectivity from potassium to sodium. In another case, “the carboxamide groups of the two symmetrical Asn630 residues are in a defined position with less mobility, allowing them to exert stringent size selection for the crossing ions.”
Well, we’re out of space for this quick tour of the molecular machine menagerie, but not out of examples. More tomorrow. Some take-home lessons so far:
- Each machine is extremely well built for its function.
- The machines are very complex, consisting of multiple protein and/or RNA molecules.
- They often have moving parts that interact with other machines in precise ways.
- They work in specific locations at specific times.
- Minor changes can have deleterious effects, or even cause failure.
- ‘Fail-safe’ mechanisms ensure proper operation.
- They are built from complex specified information in genes.
That list has intelligent design written all over it.