Photo credit: Jude Beck via Unsplash. A Physician Describes How Behe Changed His MindLife’s Origin — A “Mystery” Made AccessibleCodes Are Not Products of PhysicsIxnay on the Ambriancay PlosionexhayDesign Triangulation: My Thanksgiving Gift to All Origin of Life: Brian Miller Distills a Debate Between Dave Farina and James Tour Requesting a (Partial) Retraction from Darrel Falk and BioLogos Intelligent Design Molecular Motor Threads a Spiral StaircaseEvolution News @DiscoveryCSCAugust 29, 2019, 5:57 AM Email Print Google+ Linkedin Twitter Share Tagsamino acidsATP synthaseATPasebacterial flagellumbiochemistryCdc48 ATPase complexcryo-electron microscopyDarwin DevolvesDarwin’s Black BoxDarwinian mechanismEdward Twomeyintelligent designJerry CoynekinesinMichael Behemolecular motorpeptide bondpolypeptide chainproteasomeproteinsRichard DawkinsScience (journal)ubiquitin,Trending Jane Goodall Meets the God Hypothesis Evolution NewsEvolution News & Science Today (EN) provides original reporting and analysis about evolution, neuroscience, bioethics, intelligent design and other science-related issues, including breaking news about scientific research. It also covers the impact of science on culture and conflicts over free speech and academic freedom in science. Finally, it fact-checks and critiques media coverage of scientific issues. Share “A Summary of the Evidence for Intelligent Design”: The Study Guide Recommended Let’s get acquainted with another irreducibly complex molecular motor. This one is a master at unfolding proteins, even the tough nuts that are hard to crack. Its method is ingenious.One shouldn’t think that icons of intelligent design in biochemistry are restricted to the few favorites, like the bacterial flagellum, kinesin, and ATP synthase. There are thousands of them — tens of thousands! Each one is fascinating in its own way. Today’s focus is on one, called the “Cdc48 ATPase complex,” or Cdc48 for short. It’s another ATPase (meaning, it uses ATP for energy) with an important job: unfolding proteins. Most proteins, you recall, are folded into globular shapes. Some of those can get pretty tightly wound, held together with electrical charges and mechanical forces. Anyone who has tried to untangle threads, ropes, or fish lines knows that the tighter the wad, the harder it is to untangle. Here is how Cdc48 does its job — with finesse.Ubiquitin, as in UbiquitousBefore getting into the mechanics of Cdc48, it would help to learn about another protein called ubiquitin. As the name implies, it is ubiquitous in the cell. Because ubiquitin fastens easily to many domains on other proteins, it often “tags” them so that they get noticed by other enzymes. Ubiquitins can be chained together easily, conferring additional tagging messages. Some poly-ubiquitin tags tell the proteasome (the cell’s garbage disposal) that the substrate needs to be recycled. The proteasome removes the poly-ubiquitin tag before stuffing the spent or damaged protein into the barrel-shaped slicer-dicer, where its amino acids are separated for recycling.Another poly-ubiquitin tag informs Cdc48 that “this substrate needs unfolding.” Such a situation can occur when a protein is too tightly wound for the proteasome, when it is part of a multi-protein complex, or when it is in a hard-to-access area, such as embedded in a membrane. What happens when the protein fastens to the enzyme is quite amazing. The action was recently deciphered in more detail than ever by Edward Twomey et al. who describe their findings in Science. Get ready for a trip down a spiral staircase inside another molecular machine! Visualize Its ShapeTo visualize its shape, think of two hexagonal tires stacked on top of each other. A hand from inside grabs the end of the first ubiquitin, and pulls on it. Out the bottom tire comes an unfolded protein. Presto! What happened inside?Cdc48/p97 belongs to the AAA+ (ATPases associated with diverse cellular activities) family. It contains an N-terminal domain and two tandem ATPase domains (D1 and D2). Six monomers form a double-ring structure, with a central pore. Cdc48 often collaborates with the heterodimeric cofactor Ufd1/Npl4. Substrate initially binds through the attached polyubiquitin chain to Ufd1/Npl4 and then moves through the pore of the ATPase rings and is thereby unfolded. This translocation process requires adenosine 5′-triphosphate (ATP) hydrolysis by the D2 domains and involves their pore loop residues. [Emphasis added.]In short, Cdc48 literally pulls its substrate through a central pore with force. The pore, they say, is shaped like a spiral staircase. Finely-placed amino acids that look like loops within the pore grab onto the substrate and pull it through in a “hand-over-hand” manner. It’s a powered string untangler!Where does the ubiquitin come in? The machine grabs the poly-ubiquitin “tag” first, and pulls it into a special groove in the machine. This gives Cdc48 both a signal to proceed, and also something to grab onto for recognizing the substrate coming in behind. An Amazing MotorTwomey et al. wanted to know more about this amazing motor.The mechanism of substrate processing by Cdc48 is poorly understood. For example, it is unknown how Cdc48 can deal with a broad range of even well-folded substrates, the only requirement being an attached polyubiquitin chain. Specifically, it remains unclear how a segment of a folded substrate can pass through the D1 ring to contact the D2 pore loops that power translocation. How these D2 subunits then translocate the substrate is also not known. Structures of related hexameric ATPases indicate a spiral-staircase arrangement of pore loops around the substrate, but structures of the Cdc48 ATPase engaged with a polyubiquitinated substrate have not yet been determined.The biochemists found a way to slow down the action so that they could watch it. To do this, they had to mutate the enzyme so that it didn’t operate so fast. Then, they captured “movie frames” using cryo-electron microscopy. Then they could put the frames together and see what was going on.The structures show two folded ubiquitin molecules bound to Npl4 located on top of Cdc48’s D1 ring. Hydrogen-deuterium exchange experiments indicate additional ubiquitin-binding sites on Ufd1. Surprisingly, one ubiquitin molecule is unfolded and bound to a groove of Npl4, which contains conserved amino acids required for substrate unfolding. Unfolding of ubiquitin is remarkable, given that it is an extremely stable protein that can survive boiling. The unfolded ubiquitin molecule projects its N-terminal segment through the D1 ATPase ring and engages the pore loops of the D2 ATPases. These pore loops form a staircase that acts as a “conveyer belt” to move the polypeptide through the central pore.Illustrations in the paper show the ubiquitins fitting tightly into a special groove made to order for them. The machine unfolds the first ubiquitin (like they say, quite a feat for a stable protein that can survive boiling!). This gives the substrate that follows a “handle” that the machine can pull on. The ubiquitins engage both the specialized groove in D1, but also the “conveyor belt” in D2, where a spiral staircase of six loops named A to F pull on the substrate, unfolding it in a hand-over-hand manner. The sequence of peptides coming in doesn’t matter to this general-purpose unfolding machine; it can handle them all. Particularly tough nuts may require additional ubiquitin “leader” chains:Our results explain why the Cdc48 ATPase can act on a broad range of even well-folded proteins: It uses ubiquitin binding and unfolding to initiate substrate processing. Cdc48 first pulls on the N terminus of the unfolded ubiquitin molecule. The structure implies that if substrate is directly attached to the unfolded ubiquitin, it will next translocate through the central pore; otherwise, Cdc48 has to successively unfold the intervening ubiquitin molecules until it reaches and unfolds the substrate.Why the Machine Is ImportantThis machine is important. Defects in Cdc48 can cause neurological diseases. Surely this must be a crown product of late evolution, right? No; the scientists did their work with yeast, one of the very simplest eukaryotes. And it is also found in archaea, considered by some to be the most primitive life forms on earth. One could rightly suspect that without this general-purpose untangler present at the beginning, the first cells would quickly become clogged with tangled wads of useless polypeptides. Need more amazement? The scientists found that this machine has moving parts. If you recall those old hand-operated label-makers, it’s a bit like that: the user would crank a handle to send the tape moving along with each letter. Here’s what the researchers found:The D1 and D2 domains both behave as rigid bodies (fig. S11). Superposition of the Cdc48 monomers on the basis of the D1 domains shows that the staircase arrangement of the D2 domains is caused by rigid body movements relative to D1 (fig. S11B). The angle between the D1 and D2 subunits changes dramatically from subunits B to E, causing a displacement of the D2 pore loop by more than 18 Å (fig. S11B).That’s a pretty large motion for a molecule. Here is how the general-purpose unfolding machine handles any chain:Five of the subunits (A to E) contact the polypeptide and form a pronounced staircase, with subunit A on top and subunit E on the bottom…. All substrate-engaged subunits contact the polypeptide through the Trp561 and Tyr562 residues in their pore loops (Fig. 6B). These residues “pinch” every other peptide bond of the extended polypeptide substrate. Thus, each power stroke of the hexameric ATPase moves two amino acids of the substrate, and the intercalation of pore loops between side chains allows translocation of a polypeptide regardless of its specific amino acid sequence.Where to GrabIn other words, regardless of the shapes or sizes of the amino acids, the machine knows where to grab. It “feels” for the peptide bond common to all amino acid residues, pinches it, and pulls with a “power stroke,” resulting in a large motion between D1 and D2. The subunit loops are in contact with the substrate all the way through, making sure it unfolds properly. But why doesn’t the pulling motion dislocate the machine as well? Therein likes another wonder. Think of a conveyor belt. The belt eventually moves back to its starting position. Together, our structures reveal that the D2 ATPases use a “conveyor belt” mechanism to translocate a polypeptide chain through the central pore (Fig. 6D). In this model, subunit A binds to the top of the polypeptide chain when it converts from the ADP-bound or nucleotide-free state to the ATP-bound state. The subunits then move downward, dragging the polypeptide chain with them. At the lowest substrate-engaged position, subunit E hydrolyzes ATP. Subsequently, in the ADP-bound or nucleotide-free state, subunit F disengages from the substrate so that it can move to the top position and start a new cycle. This is so like macro-machines we are familiar with: conveyor belts, windmills, sewing machines, and other devices that continually reposition themselves for continuous action. Other molecular machines use a similar conveyor-belt mechanism, the authors say, but Cdc48 seems to be the deluxe model with an added contact that “may allow Cdc48 (p97) to exert more force to unfold its substrates.” This is not simple chemistry. This is machinery with moving parts, forces and interacting subunits!As expected, the mechanism is even more complex than described here. And, again as expected, the authors have nothing to say about evolution.Would They Dare?Behe notes in his Appendix to Darwin Devolves that evolutionists have failed to explain the bacterial flagellum or the blood clotting cascade with a Darwinian mechanism. He gave them that challenge to Darwinism in Darwin’s Black Box twenty years ago. A couple of teams tried, but dodged the issue. The rest have remained silent. And yet they still keep their jobs, demanding sole authority for Darwinism in science. It’s time for some overkill: not just one or two molecular machines, but thousands of them, including Cdc48. Show them all, day after day, incessantly, faster and faster, until the most ardent Darwinist cries uncle. At first, if you have seen the old I Love Lucy episode, Lucy and Ethel could handle the conveyor belt of chocolates. They could excuse the occasional missed one, or swallow another. Let’s put Jerry Coyne and Richard Dawkins in their places and watch the fun as we send molecular machines down the conveyor belt for them to wrap in Darwinian explanations, and when they are really sweating, shout, “Speed ’er up, all!” Congratulations to Science Magazine for an Honest Portrayal of Darwin’s Descent of Man Email Print Google+ Linkedin Twitter Share
BROOKLYN, Mich. – According to Daniel Suarez, if you want to win races, a drastic change in behavior among competitors leaves no room for kindness on the race track.During the Stewart-Haas Racing driver’s media availability Friday at Michigan International Speedway, Suarez dove into detail regarding how much driver etiquette has changed since he first came onto the Monster Energy NASCAR Cup Series scene, a conversation he and Ryan Blaney and Corey LaJoie actually had at dinner with fellow Ford Performance drivers Thursday night.“In today’s racing, nobody gives respect,” Suarez said. “It’s way different than two years ago. When I came to the Cup Series in 2017, everyone was very polite. In the first half of the race, if someone was faster than me, I would let the guy go. But right now, … Lap 2 … we’re driving it with everything.RELATED: Suarez fast early at Michigan | Full schedule for Michigan, Texas“That’s how it is,” Suarez continued. “There’s just no more respect or polite drivers out there. If you’re polite, you won’t last.”With track position at a premium based on how competitive the Cup Series field has become, Suarez noted restarts have become more aggressive, with drivers jockeying to gain every position possible.“Everyone has to make positions,” Suarez said. “If you don’t make positions, you’re going to lose positions. You have to have that mentality.“I’ve had a lot of good race cars in the past where I’m good on the long run, but on the restarts I’m not great,” he added. “It takes me seven laps to finally get going. In today’s racing, you can’t have that. It’s one of those things where you have to be at least decent on restarts to have a good trade off.”Although Suarez acknowledged being nice doesn’t get you very far in today’s day and age, he’s also not complaining about it. He actually enjoys it.“Nobody gives anyone a break,” Suarez said. “It’s very hard, but it’s fun. I like it, driving hard; I don’t have a problem with that. It’s just a different style of racing now.“The lead cars — the guys out running the top 15, top 10 – I think it’s how it’s supposed to be. I don’t mind driving hard. That’s what we get paid for, right?”RELATED: SHR cars lead 10-lap averages in Michigan practiceDespite the lack of give-and-take on the race track, Suarez believes firmly in drawing a line in the sand to separate what happens on the race track from relationships in the motor coach lots.“Personally, I try to be good with everyone, but on the race track it’s a whole different deal,” Suarez said. “There’s a lot of drivers like that. Joey Logano … he’s a great friend of mine and we get along extremely well off the race track. But when we’re on the race track, we’re always banging and hitting and talking trash on the radio. That’s how it is and that’s how I like it to be.“It has to be that way. He (Logano) does a good job on that. He’s an extremely aggressive driver. I will say, I’m the same way. Maybe some people will say sometimes it’s too much, I prefer to be on the too much side and not too little.”If there’s any doubt that Suarez gets a thrill out of ultra-aggressive racing and standing up to his competition, he’s quick to remind of his scuffle with Michael McDowell at ISM Raceway in March.“Do you see when I was fighting in Phoenix, I was smiling, too,” Suarez said with a grin. “I don’t have a problem with that. I’ve been in tougher situations, believe me.”
A specialist list hosted at the Rolls Building to deal with financial market cases has taken a further step towards full operation with the publication of practice directions at a formal unveiling last night. Speaking before representatives from the legal and financial professions, lord chancellor Michael Gove praised the financial list, which launched on 1 October, as one of the most ‘exciting innovations in the field of British justice’. The list was a key part in ensuring the modernisation of the legal system, he said.Bank of England deputy governor Sir Jon Cunliffe said the central bank ‘wholeheartedly supports’ the initiative for financial stability and competitive reasons.‘This isn’t just something that matters for the UK and UK financial stability. It is something that matters [for] international financial stability as well,’ he said.Lord chief justice Lord Thomas of Cwmgiedd said that the list would be kept under review, but added: ‘I do hope this initial experiment will work and we will try and improve it wherever possible.’The financial list will initially run as a two-year pilot until the end of September 2017. Cases will be heard by 12 judges from the Commercial Court and Chancery Division.Alasdair Douglas, chair of the City of London Law Society, said: ‘The facility to bring market test cases, where authoritative legal guidance is needed, will be an important feature of the financial list initiative. ‘Litigants expect judges to be familiar with the subject matter of a case, and the financial list will offer the assurance that these significant cases will be heard by a high-calibre judge who, for example, has an understanding of the global financial markets.‘The financial list will improve, and be seen to improve, the service provided by the English courts to international litigants.’The first case, between foreign parties and concerning derivatives transactions, was transferred onto the financial list last week and is in the course of being tried by Mr Justice Blair.