Scientists watch proteins self-assemble

Jun 10, 2012
Vallée-Bélisle and Michnick have developed a new approach to visualize how proteins assemble, which may also significantly aid our understanding of diseases such as Alzheimer’s and Parkinson’s, which are caused by errors in assembly. Here shown are two different assembly stages (purple and red) of the protein ubiquitin and the fluorescent probe used to visualize these stage (tryptophan: see yellow). Print resolution available on request. Credit: Credit: Peter Allen

Enabling bioengineers to design new molecular machines for nanotechnology applications is one of the possible outcomes of a study by University of Montreal researchers that was published in Nature Structural and Molecular Biology today.

The scientists have developed a new approach to visualize how proteins assemble, which may also significantly aid our understanding of diseases such as Alzheimer's and Parkinson's, which are caused by errors in assembly.

"In order to survive, all creatures, from to humans, monitor and transform their environments using small protein nanomachines made of thousands of atoms," explained the senior author of the study, Prof. Stephen Michnick of the university's department of biochemistry. "For example, in our sinuses, there are complex that are activated in the presence of different . Some of those scents warn us of danger; others tell us that food is nearby." Proteins are made of long linear chains of , which have evolved over millions of years to self-assemble extremely rapidly – often within thousandths of a split second - into a working nanomachine. "One of the main challenges for biochemists is to understand how these linear chains assemble into their correct structure given an astronomically large number of other possible forms," Michnick said.

"To understand how a protein goes from a linear chain to a unique assembled structure, we need to capture snapshots of its shape at each stage of assembly said Dr. Alexis Vallée-Bélisle, first author of the study. "The problem is that each step exists for a fleetingly short time and no available technique enables us to obtain precise structural information on these states within such a small time frame. We developed a strategy to monitor protein assembly by integrating fluorescent probes throughout the linear protein chain so that we could detect the structure of each stage of protein assembly, step by step to its final structure." The protein assembly process is not the end of its journey, as a protein can change, through chemical modifications or with age, to take on different forms and functions. "Understanding how a protein goes from being one thing to becoming another is the first step towards understanding and designing protein nanomachines for biotechnologies such as medical and environmental diagnostic sensors, drug synthesis of delivery," Vallée-Bélisle said.

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More information: "Visualizing transient protein folding intermediates by tryptophan scanning mutagenesis," published in Nature Structural & Molecular Biology.

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kevinrtrs
1.2 / 5 (17) Jun 10, 2012
Proteins are made of long linear chains of amino acids, which have evolved over millions of years to self-assemble extremely rapidly

The researcher is surely talking pseudo-science here.

Firstly, if the proteins didn't self-assemble extremely rapidly in the first place, life would not be possible as we know it.

Secondly, just how does he know that it took millions of years to "evolve"? Was he there to observe and record that process in which they "evolved"? No. No one was there to see it and record it for posterity. Saying that it "evolved" over millions of years doesn't make it so. It's just a superflous guess that cannot be verfied or falsified in any way since no one can travel back into the past.
These kind of statements is not scientific in any way, shape of form. It's just plain junk.
Terriva
2.7 / 5 (7) Jun 10, 2012
It's just plain junk.
The proteins self-assemble at many geometric levels. We do recognize the primary, secondary, tertiary structure of protein folding, but this is not all. For example many organelles like the ribosomes, chromosomes and/or kinesin fibers are able to fold spontaneously as well, so there's is no exact boundary for the protein folding at the organic chemistry level (which requires only physical laws) and cellular level (which requires some evolution too). From certain perspective we are all the complex product of the spontaneous protein folding and after then the above sentence criticized by you will remain perfectly valid.
Mike_Massen
2.5 / 5 (8) Jun 10, 2012
kevinrtrs has lost
These kind of statements is not scientific in any way, shape of form. It's just plain junk.
Are you scientific ?

How do "Voices in the Head" in a book from a deity that cannot communicate count for Science or even any sort of functional useful foundation for religion ?

You realise there can never be any true religion ever, that horse has bolted with Moses & his associates and Jesus & his associates & Mohammed & his associates also Joseph Smith & many others, even GW Bush claimed a deity told him to invade Iraq!

Are you so happy & comfortable kevinrtrs with "Voices in the Head" with no consistency through the millenia that it quells your intellectual rigour to such a degree you are showing up your only focus, that is the emotional attachment or rather hypnosis to & of a book which can never ever have its contents verified ?

Biological evolutionary history has its markers and there are many with a beautiful consistency with more work being added often monthly.
jibbles
4 / 5 (4) Jun 10, 2012
kevinretards, it would be better to save your fatuous bloviating demagoguery for another site, preferably one where you and your jeebus-loving friends can circle-jerk each other to your heart's content. really, you're just wasting your precious spunk on physorg.
trekgeek1
5 / 5 (3) Jun 11, 2012
Proteins are made of long linear chains of amino acids, which have evolved over millions of years to self-assemble extremely rapidly

The researcher is surely talking pseudo-science here.

Firstly, if the proteins didn't self-assemble extremely rapidly in the first place, life would not be possible as we know it.

Secondly, just how does he know that it took millions of years to "evolve"? Was he there to observe and record that process in which they "evolved"? No. No one was there to see it and record it for posterity. Saying that it "evolved" over millions of years doesn't make it so. It's just a superflous guess that cannot be verfied or falsified in any way since no one can travel back into the past.
These kind of statements is not scientific in any way, shape of form. It's just plain junk.


I think I've decided that this guy is just trolling us. He's too far gone and I think he's just some guy getting a kick out of messing with us.
kevinrtrs
1 / 5 (12) Jun 11, 2012
Thank you all for your dismissal of the statements I made.
Perhaps you'd like to think about how the proteins inside the cell came about in the first place. Please explain in accepted scientific terms, just how those proteins arose in the first place. Once you start looking at the actual, physical barriers [left-handedness, coding, decoding, stability inside the cell etc.] you might want to take astep back from believing it somehow "evolved".
Since life requires proteins to be in place for there to be any life in the the first place, please explain how life came to exist without it.
Go ahead, knock yourselves out - there's a million dollar prize just waiting to be claimed for anyone who can give a scientifically plausible and acceptable explanation for how it arose. Have fun.

You deride my statements but it's actually YOU who believe in the sanguine tooth-fairy when you think it[life] all just jumped out of a deep dark swamp sometime in the past.
Origin
2.3 / 5 (3) Jun 11, 2012
Since life requires proteins to be in place for there to be any life in the the first place, please explain how life came to exist without it.
IMO it's good to ask such a questions. But we know, that the proteins can form spontaneously with polymerization of aminoacids, which can form spontaneously from mixture of some precursors (compare the Miller-Urey experiments). In my theory this polymerization was initiated with chiraly specific absorption of curved surfaces of liposomes, i.e. tiny droplets of phospholipids and another oily substances. The RNA like molecules could serve as an agents, which catalysed this polymerization and when the liposomes splitted, they maintained the inheritance of their surface reactions. IMO this mechanism appears feasible for me.
Origin
2.3 / 5 (3) Jun 11, 2012
The another studies consider the polymerization of aminoacids catalysed with surfaces of minerals, like the clays with high specific surface. IMO the presence of such surfaces wasn't strictly necessary and it slowed down the another evolution of the molecules immobilized in this way. Whereas the emulsion of droplets is behaving like living cells in many aspects, including their autonomous locomotion and solving intelligent task regarding the search for food sources.
aroc91
5 / 5 (4) Jun 11, 2012
I've thoroughly debunked the chirality "problem" in a previous article where you brought it up, kevin. You're trolling and everybody knows it.
Origin
1.6 / 5 (5) Jun 11, 2012
The tiny liposome model of eobion formation just solves the problem of chirality of life well, because the curved surface attracts the hydrophobic molecules (aminoacids) and repels the hydrophilic ones (sugars) in chirally selective way: the L-aminoacids are preferably adsorbed more onto inner surface of liposomes and D-sugars are concentrated on their outer surfaces instead. The symmetric way is indeed possible too, but the living cells do need to concentrate their construction material (proteins) inside and the renewable energy resources (sugars) outside of their cells, not vice-versa. So until the first living cells were of positive curvature, they selected the chiral molecules purely by physical adsorption mechanism.
Origin
1 / 5 (3) Jun 11, 2012
This chirality is hardwired in universe at many geometric levels. For example, even the curved gravity field around planets is separating particle by their chirality: the material particles are transported inside, whereas the antiparticles which are more similar to the hollow bubbles are repelled and kept at the distance like the "particles of energy". Note that the antiparticles don't condense and they remain in diaspora (i.e. neutrinos) in similar way, like the sugars around living cells.

Analogously the men and women are chiral objects in certain extent too. The women tend to condense inside of their homes and they're collecting building materials here, whereas the men are more asocial, movable and volatile and they're collecting energy (i.e. food resources) into their houses from distance like the hunters.

In dense aether model all particles are living or physical - they just differ in their complexity.
aroc91
not rated yet Jun 11, 2012
The tiny liposome model of eobion formation just solves the problem of chirality of life well, because the curved surface attracts the hydrophobic molecules (aminoacids) and repels the hydrophilic ones (sugars) in chirally selective way: the L-aminoacids are preferably adsorbed more onto inner surface of liposomes and D-sugars are concentrated on their outer surfaces instead. The symmetric way is indeed possible too, but the living cells do need to concentrate their construction material (proteins) inside and the renewable energy resources (sugars) outside of their cells, not vice-versa. So until the first living cells were of positive curvature, they selected the chiral molecules purely by physical adsorption mechanism.


Not all amino acids are hydrophobic.
Mike_Massen
2 / 5 (4) Jun 12, 2012
Emotionally attached & hypnotised kevinrtrs again made negligent claims
..if the proteins didn't self-assemble extremely rapidly in the first place, life would not be possible as we know it.
When you see a functioning building, you dont see the scaffolding, its gone.

Similarly in the various chemico-life processes very early on, there are likely to be any number of chemical structures that dont survive today, that potential scaffolding has gone long ago & is unlikely to recur & if it did it could be anywhere and be very quickly displaced or eaten by "the children of it's process" !

All life on earth has a reliance on amines !

We all need amino acids in our food, they make our proteins.

Amines come from Ammonia, early earth had a tremendous amount of Ammonia, some methane, water and lightning & I might add less likely to form proportionately when more oxygen is available.

More can be found here:-
phys.org/news/2012-06-basic-blocks-life-rethought.html