Biomolecular machines

[semaphore]

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[Techne]

Phylogenetic analysis, this was a while ago. I'm now in finance lol.

Bah, sell-out .

 

[Techne]

How cells take out the trash

Date:
April 22, 2014
Source:
NIH, National Institute of General Medical Sciences (NIGMS)
Summary:
As people around the world mark Earth Day (April 22) with activities that protect the planet, our cells are busy safeguarding their own environment. To keep themselves neat, tidy and above all healthy, cells rely on a variety of recycling and trash removal systems. If it weren't for these systems, cells could look like microscopic junkyards -- and worse, they might not function properly.

When proteins enter the proteasome, they're chopped into bits for re-use.
Credit: Office of Biological and Environmental Research of the U.S. Department of Energy Office of Science.​

As people around the world mark Earth Day (April 22) with activities that protect the planet, our cells are busy safeguarding their own environment.

To keep themselves neat, tidy and above all healthy, cells rely on a variety of recycling and trash removal systems. If it weren't for these systems, cells could look like microscopic junkyards -- and worse, they might not function properly. Scientists funded by the National Institutes of Health are therefore working to understand the cell's janitorial services to find ways to combat malfunctions.

Garbage Disposal and Recycling Plant
One of the cell's trash processors is called the proteasome. It breaks down proteins, the building blocks and mini-machines that make up many cell parts. The barrel-shaped proteasome disassembles damaged or unwanted proteins, breaking them into bits that the cell can re-use to make new proteins. In this way, the proteasome is just as much a recycling plant as it is a garbage disposal.

How does the cell know which proteins to keep and which to trash? The 2004 Nobel Prize in chemistry went to three scientists for answering that question. They found that the cell labels its refuse with a tiny protein tag called ubiquitin. Once a protein has the ubiquitin label, the proteasome can grab it, put it inside the barrel, break it down and release the pieces.

Because diseases like Alzheimer's involve the accumulation of excess proteins, researchers are trying to develop medicines to help the proteasome out. They hope such a treatment would keep brain cells clean and healthy.
Scientists are also interested in designing medicines that turn off the proteasome. Cancer cells, for instance, make a lot of abnormal proteins that their proteasomes have to remove. A proteasome-clogging medicine could prevent cancer cells from recycling their own garbage, leaving them without reusable resources for survival and growth. This is the approach behind the proteasome inhibitor drug bortezomib, which is used for the blood cancer multiple myeloma.

Cellular Stomach
Proteins aren't the only type of cellular waste. Cells also have to recycle compartments called organelles when they become old and worn out. For this task, they rely on an organelle called the lysosome, which works like a cellular stomach. Containing acid and several types of digestive enzymes, lysosomes digest unwanted organelles in a process termed autophagy, from the Greek words for "self" and "eat." The multipurpose lysosome also processes proteins, bacteria and other "food" the cell has engulfed.

An inability to make one of the lysosomal enzymes can lead to a rare, life-threatening sickness called a lysosomal storage disease. There are more than 40 different lysosomal storage diseases, depending on the kind of trash that's unprocessed. These diseases can affect many organs, including the brain, heart and bones.
Lysosomes also gobble up viruses, an activity important to fighting infections. A drug that activates lysosomes protects mice from diseases like West Nile virus. It's possible that the same or similar medications might treat diseases in which cellular trash piles up, including Alzheimer's and other diseases of aging.

Scrap Pile
While cells mainly use proteasomes and lysosomes, they have a couple of other options for trash disposal.
Sometimes they simply hang onto their trash, performing the cellular equivalent of sweeping it under the rug. Scientists propose that the cell may pile all the unwanted proteins together in a glob called an aggregate to keep them from gumming up normal cellular machinery.

For example, a protein called islet amyloid polypeptide builds up in aggregates in the pancreas of people with type 2 diabetes. Other proteins form aggregates in certain brain diseases. Scientists are still trying to understand what these trash piles do and whether they're helpful or harmful.

If the garbage can't be digested by lysosomes, the cell can sometimes spit it out in a process called exocytosis. Once outside the cell, the trash may encounter enzymes that can take it apart, or it may simply form a garbage heap called a plaque. Unfortunately, these plaques outside the cell may be harmful, too.

The cell also has ways to toss out some poisons that get inside. This means that cancer cells may pump out cancer drugs that are meant to destroy them, and bacteria may do the same with antibiotics. Scientists are studying how these pumps work, looking for ways to keep the medicines inside where they can do their job.
Further study of the many ways cells take out the trash could lead to new approaches for keeping them healthy and preventing or treating disease.

 

[Techne]

The ribosome uses cooperative conformational changes to maximize and regulate the efficiency of translation

Significance

The catalytic cycle of many enzymes often requires that several, spatially remote enzyme structural elements undergo functionally important conformational changes. To maximize and regulate the efficiency of catalysis, therefore, considerable evidence suggests that small protein enzymes can coordinate the conformational changes of multiple structural elements. Whether and how larger, multicomponent biomolecular machines such as the ribosome also exhibit such coordination, however, remains unknown. Here, we demonstrate that the ribosome coordinates multiple, functionally important conformational changes to maximize and regulate the efficiency with which it translocates along its messenger RNA template. Our findings suggest that such coordination is likely to be a general and important mechanism through which all biomolecular machines maximize and regulate their functional efficiencies.

Nice video demonstrating translation in ribosomes.
[video=youtube;TfYf_rPWUdY]https://www.youtube.com/watch?v=TfYf_rPWUdY[/video]

 

[Techne]

Biomotor discovered in many bacteria and viruses

Nano-biotechnologists have reported the discovery of a new, third class of biomotor, unique in that it uses a "revolution without rotation" mechanism. These revolution biomotors are widespread among many bacteria and viruses.

Illustration of rotation motions and revolution motions using Phi29 revolution motor as an example. (A) 3D structure of Phi29 dsDNA packaging motor in a side view and top view with a pRNA hexamer derived from the crystal structure [16], and the AFM images of the pRNA hexamer with extended loops. (B) Illustration of rotation motors like the Earth rotates around its own axis. (C) Illustration of revolution motors like the Earth revolves around the Sun without rotation. (D) Illustration of the dsDNA revolution inside the hexameric ATPase channel. Only three of the six steps are shown. (E) Illustration of the dsDNA revolution inside the dodecameric connector channel, only four of the twelve steps are shown. Neither the channel nor the dsDNA needs to rotate during the revolution through channels.​

Scientists at the University of Kentucky, led by nano-biotechnologist Peixuan Guo, have made some critical discoveries over the past year into the operation of biomotors, the molecular machines used by viruses and bacteria in the packaging of DNA.

Biomotors function similarly to mechanical motors but on a nano-scale. Last year, Guo's team reported the discovery of a new, third class of biomotor, unique in that it uses a "revolution without rotation" mechanism. Rotation is the turning of an object around its own axle, as Earth does every 24 hours. Revolution is the turning of an object around a second object, as Earth does around the sun.

Recently, Guo's team reported that these revolution biomotors are widespread among many bacteria and viruses.
Guo, director of the Nanobiotechnology Center and the William Farish Endowed Chair of Nanobiotechnology at the Markey Cancer Center and UK College of Pharmacy said these biomotors are of great interest to medical researchers.

"DNA-packaging technology has tremendous potential applications in the diagnosis and treatment of viral diseases and cancers, as well as in personalized medicine and high-throughput human genome sequencing," he said. "The DNA packaging motor itself can serve as a high efficient drug target for the development of anti-viral and anti-bacterial therapy."

Guo hopes the current findings will generate new momentum in the viral-assembly field among young scientists.
In his early career, as a graduate student in Dwight Aderson's lab, Guo constructed the first viral motor outside the cell, the DNA-packaging motor of bacteria virus phi29. He also discovered one of the vital components of the motor, the six-membered RNA ring that gears the phi29 DNA-packaging motor. His postdotoral experience at NIH with Bernard Moss, a scientist in vaccinia virus studies and a member of the National Academy of Sciences, expanded his vision on the DNA packaging of animal and human viruses.

Research on this motor led to dozens of papers published and debated in many prominent journals such as Nature, Science, Cell, PNAS, Molecular Cell, PLOS Biology, EMBO J, Virology, ACS Nano, RNA, Nature Nanotechnology, Nature Protocol, Cell and Bioscience, Biotechnology Advances, Current Opinion of Biotechnology, Advanced Virus Research, Biophysical Journal and the Journal of Virology.

However, the main mechanism of motor action over many years of studies has not been elucidated until recently, Guo says.

In 1998, Guo and his lab began to test a new hypothesis. Guo's research has persisted, and it continues to strongly support the ATPase hexameric model in viral DNA packaging. Now, discovery of the revolution motor has solved many puzzles that have eluded researchers throughout the 35 years of investigations of the mechanism of dsDNA translocation motors.

Three recent publications coming out of the Guo lab provide new evidence and support for Guo's widespread revolution mechanism.

Journal References:

1. Gian Marco De-Donatis, Zhengyi Zhao, Shaoying Wang, Lisa P Huang, Chad Schwartz, Oleg V Tsodikov, Hui Zhang, Farzin Haque, Peixuan Guo. Finding of widespread viral and bacterial revolution dsDNA translocation motors distinct from rotation motors by channel chirality and size. Cell & Bioscience, 2014; 4 (1): 30 DOI: 10.1186/2045-3701-4-30
2. Peixuan Guo. Biophysical Studies Reveal New Evidence for One-Way Revolution Mechanism of Bacteriophage ϕ29 DNA Packaging Motor. Biophysical Journal, 2014; 106 (9): 1837 DOI: 10.1016/j.bpj.2014.03.041
3. Peixuan Guo, Zhengyi Zhao, Jeannie Haak, Shaoying Wang, Dong Wu, Bing Meng, Tao Weitao. Common mechanisms of DNA translocation motors in bacteria and viruses using one-way revolution mechanism without rotation. Biotechnology Advances, 2014; 32 (4): 853 DOI: 10.1016/j.biotechadv.2014.01.006:

 

[Techne]

Hybrid-motor helps cells push their way through tissues

Research has uncovered how two cellular motors, previously thought to compete with each other, can actually work together to help cells squeezing through a crowded mass of cells. The study provides fresh understanding of how cells can combine accurate steering with a brute force mechanism in order to push through our body, essential when cells of our immune defense need to reach sites of inflammation, but detrimental during tumor metastasis or parasitic infection.

Cell blebbing.
Credit: University of Warwick​

Research has uncovered how two cellular motors, previously thought to compete with each other, can actually work together to help cells squeezing through a crowded mass of cells.

The study published in PNAS provides fresh understanding of how cells can combine accurate steering with a brute force mechanism in order to push through our body, essential when cells of our immune defense need to reach sites of inflammation, but detrimental during tumor metastasis or parasitic infection. The work was conducted by Dr Till Bretschneider and Dr Richard University of Warwick's Systems Biology Centre and a team at the Medical Research Laboratory of Molecular Biology in Cambridge.

One of the cellular motors causes the cell membrane, the flexible envelope encasing all cells, to bulge out by forming so-called pseudopods. "In this instance, cell locomotion is driven by the localised growth of a dynamic protein scaffold pushing against the cell membrane from the inside," says Dr Tyson, continuing, "Cells employ complex regulation, linked to environmental sensing, to make pseudopods highly accurate steering devices, which are of limited power though."

The second motor entails faster, pressure-driven protrusions in form of cellular blebs. These provide higher force, working like a battering ram to open up gaps for cells to squeeze in-between other tightly connected cells. "Like a muscle, a cell is able to contract itself, increasing its internal pressure and causing the cell membrane to locally tear away from the underlying cytoskeletal scaffold. Pressure then blows it outwards to force aside other cells or to create footholds for traction as a rock climber would," says Dr Tyson. In contrast to pseudopods, blebs appeared to be under less precise control as to where they form on a cells' surface, making the impression of a loose cannon.

Recently Evgeny Zatulovskiy and Rob Kay from Cambridge have shown that Dictyostelium cells, a popular model organism for studying cell locomotion, can employ both motors simultaneously[2], raising the question of how they might interact.

To address this question Richard Tyson and Till Bretschneider from Warwick University developed new computer algorithms capable of tracking large numbers of both blebs and pseudopods in microscopy movies of Dictyostelium cells. In the current study, How blebs and pseudopods cooperate during chemotaxis, they demonstrate that cell shape influences how these motors interact. When slow pseudopods extend they deform the cell membrane creating an inward-curved regions at their base.

A biophysical model shows that the cell membrane, which is under tension, experiences an outward directed force in these regions, facilitating the tearing away of membrane, which precedes the formation of a bleb. "Thus, membrane geometry turns out to be an important, previously overlooked factor coupling both types of protrusions and helping to indirectly orient blebs," says Dr Bretschneider. This mechanism is similar to blistering of an overly thick coat of drying paint where moisture is trapped underneath and expands when the temperature increases.

Like the cell membrane, drying paint is also under tension, which is more easily released on inward curved surfaces, where it preferably causes paint to blister or flake off. An example of an inward curved surface where this applies would be a ceiling coving, as opposed to a plane wall. Cellular pseudopods can actively create inward curved surfaces and consequently direct where blebs form.

"The significance of this work is two-fold," Dr Bretschneider explains, "Firstly, the underlying mechanism is a generic physical one, similar to the example of drying paint. It has been confirmed to exist in different cell types and is independent of a cell's sensory system. Secondly, until now the common picture was that the requirements for forming one type of protrusion or the other are mutual exclusive. The current study shows that both motors can actually work together to make cell motility more effective by providing accurate steering to a high power motor."

Journal References:

1. R. A. Tyson, E. Zatulovskiy, R. R. Kay, T. Bretschneider. How blebs and pseudopods cooperate during chemotaxis. Proceedings of the National Academy of Sciences, 2014; DOI: 10.1073/pnas.1322291111
2. E. Zatulovskiy, R. Tyson, T. Bretschneider, R. R. Kay. Bleb-driven chemotaxis of Dictyostelium cells. The Journal of Cell Biology, 2014; 204 (6): 1027 DOI: 10.1083/jcb.201306147

 

[Techne]

Pretty good documentary from BBC.
Hidden life of the cell.
[video=dailymotion;x1f26gz]http://www.dailymotion.com/video/x1f26gz_bbc-our-secret-universe-the-hidden-life-of-the-cell-720p-hdtv_tech[/video]

 

[Techne]

Key moment mapped in assembly of DNA-splitting molecular machine

Scientists reveal crucial steps and surprising structures in the genesis of the enzyme that divides the DNA double helix during cell replication. The research combined electron microscopy, perfectly distilled proteins, and a method of chemical freezing to isolate specific moments at the start of replication.

Three-dimensional model (based on electron microscopy data) of the double-ring structure loaded onto a DNA helix.​

 

[Techne]

Humans' tiny cellular machines: Spliceosomes in detail

Like exploring the inner workings of a clock, researchers are digging into the inner workings of the tiny cellular machines called spliceosomes, which help make all of the proteins our bodies need to function. They have now captured images of this machine, revealing details never seen before.

Structure of the U6 complex. U6 RNA is red and the four RRMs of Prp24 protein are beige, orange, aqua and purple, with linkers in gray.
Credit: Brow and Butcher Labs​

A grandfather clock is, on its surface, a simple yet elegant machine. Tall and stately, its job is to steadily tick away the time. But a look inside reveals a much more intricate dance of parts, from precisely-fitted gears to cable-embraced pulleys and bobbing levers.

Like exploring the inner workings of a clock, a team of University of Wisconsin-Madison researchers is digging into the inner workings of the tiny cellular machines called spliceosomes, which help make all of the proteins our bodies need to function. In a recent study published in the journal Nature Structural and Molecular Biology, UW-Madison's David Brow, Samuel Butcher and colleagues have captured images of this machine, revealing details never seen before.

In their study, they reveal parts of the spliceosome -- built from RNA and protein -- at a greater resolution than has ever been achieved, gaining valuable insight into how the complex works and also how old its parts may be.
By better understanding the normal processes that make our cells tick, this information could some day act as a blueprint for when things go wrong. Cells are the basic units of all the tissues in our bodies, from our hearts to our brains to our skin and lungs.

It may also help other scientists studying similar cellular machinery and, moreover, it provides a glimpse back in evolutionary time, showing a closer link between proteins and RNA, DNA's older cousin, than was once believed.
"It gives us a much better idea of how RNA and proteins interact than ever before," says Brow, a UW-Madison professor of biomolecular chemistry.

The spliceosome is composed of six complexes that work together to edit the raw messages that come from genes, cutting out (hence, splicing) unneeded parts of the message. Ultimately, these messages are translated into proteins, which do the work of cells. The team created crystals of a part of the spliceosome called U6, made of RNA and two proteins, including one called Prp24.

Crystals are packed forms of a structure that allow scientists to capture three-dimensional images of the atoms and molecules within it. The crystals were so complete, and the resolution of the images so high, the scientists were able to see crucial details that otherwise would have been missed.

The team found that in U6, the Prp24 protein and RNA -- like two partners holding hands -- are intimately linked together in a type of molecular symbiosis. The structure yields clues about the relationship and the relative ages of RNA and proteins, once thought to be much wider apart on an evolutionary time scale.

"What's so cool is the degree of co-evolution of RNA and protein," Brow says. "It's obvious RNA and protein had to be pretty close friends already to evolve like this." The images revealed that a part of Prp24 dives through a small loop in the U6 RNA, a finding that represents a major milestone on Brow and Butcher's quest to determine how U6's protein and RNA work together. It also confirms other findings Brow has made over the last two decades.

"No one has ever seen that before and the only way it can happen is for the RNA to open up, allow the protein to pass through, and then close again," says Butcher, a UW-Madison professor of biochemistry.
Ultimately, Butcher says they want to understand what the entire spliceosome looks like, how the machines get built in cells and how they work.

While this is the first protein-RNA link like this seen, Brow doesn't believe it is unique. Once more complete, high-resolution images are captured of other RNA-protein machines and their components, he thinks these connections will appear more commonly. He hopes the findings mark a transition in the journey to understand these cellular workhorses.

"It's exciting studying these machines," he says. "There are only three big RNA machines. Ours evolved 2 billion years ago. But once it's figured out, it's done."

The U6 crystal structure was imaged using the U.S. Department of Energy Office of Science's Advanced Photon Source at Argonne National Laboratory. The work was funded by a joint grant from the National Institutes of Health shared by Brow and Butcher.

Journal Reference:
Eric J Montemayor, Elizabeth C Curran, Hong Hong Liao, Kristie L Andrews, Christine N Treba, Samuel E Butcher, David A Brow. Core structure of the U6 small nuclear ribonucleoprotein at 1.7-Å resolution. Nature Structural & Molecular Biology, 2014; DOI: 10.1038/nsmb.2832

These molecular complexes are absolutely fascinating:

[video=youtube;q63JCoLDR2w]https://www.youtube.com/watch?v=q63JCoLDR2w[/video]

Knowing more about them has the potential to develop better treatments for cancer:
Multiple components of the spliceosome regulate Mcl1 activity in neuroblastoma

Targeting the Deregulated Spliceosome Core Machinery in Cancer Cells Triggers mTOR Blockade and Autophagy