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Eric Francouer helped rescue this crucial archive of early uses of interactive computer graphics in understanding the molecular realm of intracellular biology. These movies document the very early days of interactive computer graphics and their maiden scientific use (in practical science at least) in working out macromolecular structures.

The first system for the interactive display of molecular structures was devised at MIT in the mid-1960s.

Cyrus Levinthal and his colleagues designed a “model-building” program to work with protein structures (Levinthal 1966). This program allowed the study of short-range interaction between atoms and the “online manipulation” of molecular structures. The display terminal (nicknamed Kluge) was a monochrome oscilloscope, showing the structures in wireframe fashion.

Three-dimensional effect was achieved by having the structure rotate constantly on the screen. To compensate for any ambiguity as to the actual sense of the rotation, the rate of rotation could be controlled by globe-shaped device on which the user rested his/her hand (an ancestor of today’s trackball) (NOTE - this is a fantastic historical parallel to the use of the Leap Motion to control data from the Protein Data bank [link])

Speaking of his invention Levinthal said:

"It is too early to evaluate the usefulness of the man-computer combination in solving real problems of molecular biology. It does seems likely, however, that only with this combination can the investigator use his "chemical insight" in an effective way. We already know that we can use the computer to build and display models of large molecules and that this procedure can be very useful in helping us to understand how such molecules function. But it may still be a few years before we have learned just how useful it is for the investigator to be able to interact with the computer while the molecular model is being constructed."

Proteins

We’ve talked about amino acids before, but this is where they get interesting. Amino acids combine to make up proteins: proteins are polymers and amino acids are its monomers. There are twenty amino acids, which would be useful to memorise if you’re continuing with biology. At pH 7, ten are non-polar and uncharged, five are polar and uncharged, three are polar and charged positive, and two are polar and charged negative. This is a handy table:

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(Source: Pearson Ed via University of Illinois at Chicago)

These amino acids have structures that generally look like this:

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The “R” group is a specific side chain that varies among the amino acids, making each one unique—and hence determines their charge.

Amino acids joined together through a dehydration reaction, where a water molecule is formed and removed to form a covalent bond called a peptide bond. A structure resulting from a bunch of these bonds repeating over and over is called a polypeptide. Like DNA molecules, polypeptides have a direction: they’ve got an amino acid at one end (the N-terminus) and a carboxyl group at the other (the C-terminus).

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Proteins are polypeptides, accounting for 50% of dry mass in almost all cells. They’re incredibly diverse, and are instrumental in almost everything that organisms do, so it’s only natural that there must be a whole lot of different types—enzymatic proteins which accelerate chemical reactions, receptor proteins which respond to chemical stimuli, defensive proteins that protect against disease… And that just scratches the surface.

Protein function is dictated by structure, and proteins structures are hierarchical in nature—there are four different levels:

  1. Primary: This is the amino acid sequence. There are twenty types of amino acids, and proteins are chains of 127 of them, so there are thousands of different combinations. The particular sequence of amino acids is determined by genetic information, so essentially, DNA dictates how proteins are built.
  2. Secondary: This is the way the amino acids are folded into regular units. These are the result of hydrogen bonds between the backbones of the amino acid and carboxyl groups. These bonds are usually formed to keep non-polar parts away from water. There are two main types: alpha helix and beta pleated sheet.
  3. Tertiary: The overall 3D way the polypeptide folds up. This is the result from the interactions between the side chains (R groups) of the amino acids, and the whole tertiary structure is held together by a bunch of different forces, such as hydrogen bonding, weak dispersive forces, and disulphide bonds.
  4. Quaternary: Some proteins stop at the tertiary structure, but others go further, joining up a bunch of 3D units to form a larger functional molecule, held together by weak interactions like the forces listed above.

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The kind of structure a protein has fully determines what function it serves. The structure depends on a variety of different conditions—if the chemical and physical environment, pH, salt concentration or temperature change, the protein structure might unravel and denature, and thus become unable to perform its function.

Body images sourced from Wikimedia Commons

Further resources: Video to get your head around the levels of structure and another about function

New front in war on Alzheimer’s, other protein-folding diseases

A surprise discovery that overturns decades of thinking about how the body fixes proteins that come unraveled greatly expands opportunities for therapies to prevent diseases such as Alzheimer’s and Parkinson’s, which have been linked to the accumulation of improperly folded proteins in the brain.

“This finding provides a whole other outlook on protein-folding diseases; a new way to go after them,” said Andrew Dillin, the Thomas and Stacey Siebel Distinguished Chair of Stem Cell Research in the Department of Molecular and Cell Biology and Howard Hughes Medical Institute investigator at the University of California, Berkeley.

Dillin, UC Berkeley postdoctoral fellows Nathan A. Baird and Peter M. Douglas and their colleagues at the University of Michigan, The Scripps Research Institute and Genentech Inc., will publish their results in the Oct. 17 issue of the journal Science.

Cells put a lot of effort into preventing proteins – which are like a string of beads arranged in a precise three-dimensional shape – from unraveling, since a protein’s activity as an enzyme or structural component depends on being properly shaped and folded. There are at least 350 separate molecular chaperones constantly patrolling the cell to refold misfolded proteins. Heat is one of the major threats to proteins, as can be demonstrated when frying an egg – the clear white albumen turns opaque as the proteins unfold and then tangle like spaghetti.

Heat shock

For 35 years, researchers have worked under the assumption that when cells undergo heat shock, as with a fever, they produce a protein that triggers a cascade of events that field even more chaperones to refold unraveling proteins that could kill the cell. The protein, HSF-1 (heat shock factor-1), does this by binding to promoters upstream of the 350-plus chaperone genes, upping the genes’ activity and launching the army of chaperones, which originally were called “heat shock proteins.”

Injecting animals with HSF-1 has been shown not only to increase their tolerance of heat stress, but to increase lifespan.

Because an accumulation of misfolded proteins has been implicated in aging and in neurodegenerative diseases such as Alzheimer’s, Parkinson’s and Huntington’s diseases, scientists have sought ways to artificially boost HSF-1 in order to reduce the protein plaques and tangles that eventually kill brain cells. To date, such boosters have extended lifespan in lab animals, including mice, but greatly increased the incidence of cancer.

Dillin’s team found in experiments on the nematode worm C. elegans that HSF-1 does a whole lot more than trigger release of chaperones. An equal if not more important function is to stabilize the cell’s cytoskeleton, which is the highway that transports essential supplies – healing chaperones included – around the cell.

“We are suggesting that, rather than making more of HSF-1 to prevent diseases like Huntington’s, we should be looking for ways to make the actin cytoskeleton better,” Dillin said. Such tactics might avoid the carcinogenic side effects of upping HSF-1.

Dillin is codirector of the Paul F. Glenn Center for Aging Research, a new collaboration between UC Berkeley and UC San Francisco supported by the Glenn Foundation for Medical Research. Center investigators will study the many ways that proteins malfunction within cells, ideally paving the way for novel treatments for neurodegenerative diseases.

A cell at war

Dillin compares a cell experiencing heat shock to a country under attack. In a war, an aggressor first cuts off all communications, such as roads, train and bridges, which prevents the doctors from treating the wounded. Similarly, heat shock disrupts the cytoskeletal highway, preventing the chaperone “doctors” from reaching the patients, the misfolded proteins.

“We think HSF-1 not only makes more chaperones, more doctors, but also insures that the roadways stay intact to keep everything functional and make sure the chaperones can get to the sick and wounded warriors,” he said.

The researchers found specifically that HSF-1 up-regulates another gene, pat-10, that produces a protein that stabilizes actin, the building blocks of the cytoskeleton.

By boosting pat-10 activity, they were able to cure worms that had been altered to express the Huntington’s disease gene, and also extend the lifespan of normal worms.

Dillin suspects that HSF-1’s main function is, in fact, to protect the actin cytoskeleton. He and his team mutated HSF-1 so that it no longer boosted chaperones, demonstrating, he said, that “you can survive heat shock with the normal level of heat shock proteins, as long as you make your cytoskeleton work better.”

He noted that the team’s results – that boosting chaperones is not essential to surviving heat stress – were so contradictory to current thinking that “I made my post-docs’ lives hell for three years” insisting on more experiments to rule out errors. Yet, when Dillin presented the results recently to members of the protein-folding community, he said the first reaction of many was, “That makes perfect sense.”

A Moveable Yeast: modeling shows proteins never sit still

Our body’s proteins – encoded by DNA to do the hard work of building and operating our bodies – are forever on the move. Literally, according to new findings reported by Trey Ideker, PhD, chief of the Division of Genetics in the UC San Diego School of Medicine, and colleagues in a recent issue of the Proceedings of the National Academy of Sciences.

Hemoglobin protein molecules, for example, continuously transit through our blood vessels while other proteins you’ve never heard of bustle about inside cells as they grow, develop, respond to stimuli and succumb to disease.

To better understand the role of proteins in biological systems, Ideker and colleagues developed a computer model that can predict a protein’s intracellular wanderings in response to a variety of stress conditions.

To date, the model has been used to predict the effects of 18 different DNA-damaging stress conditions on the sub-cellular locations and molecular functions of more than 5,800 proteins produced by yeasts. They found, for example, that yeast proteins could move from mitochondria to the cell nucleus and from the endoplasmic reticulum to Golgi apparatus.

Though the model debut involved yeasts, researchers said the coding can be adapted to study changes in protein locations for any biological system in which gene expression sequences have been identified, including stem cell differentiation and drug response in humans.

Image courtesy of Material Mavens

La sinfonía de las proteínas 

/ Todo aquello que esté compuesto por moléculas, vibra. Y así como las cuerdas de los violines vibran de manera distinta a las cuerdas de las arpas cuando interpretan la Sinfonía No. 9 de Mahler, las proteínas de nuestros cuerpos vibran con diferentes patrones. 

La comunidad científica sabe de este fenómeno desde hace tiempo, pero los científicos creían que este movimiento, semejante al del tintineo de una campana, se disipaba. Esta vibración les permite a las proteínas cambiar de forma rápidamente y facilita que se unan con otras. Así se pueden llevar a cabo funciones biológicas fundamentales, como la reparación celular o la replicación del DNA.

Para medir el movimiento de las proteínas, en el pasado los científicos necesitaban condiciones extremadamente secas y ambientes sumamente fríos, cosa que resultaba carísima. Ahora, es posible observar este fenómeno gracias a una propiedad fundamental de estas moléculas: las proteínas vibran a la misma frecuencia que la luz que absorben. 

¿Qué significa esto? Cuando una cantante de ópera rompe una copa de cristal con su voz,  se debe a que la copa absorbió las ondas del sonido y ambos alcanzaron la misma frecuencia. Así que cuando los científicos quieren estudiar la vibración de las proteínas, las exponen a diferentes frecuencias para medir los tipos de luz que absorben y qué partes de la molécula vibran.

Gracias a estos estudios, se puede comprender cómo es que ciertas proteínas desempeñan funciones bajo características ambientales específicas. En un futuro, se podrán crear maneras de activarlas o inhibirlas al cambiar o bloquear determinadas vibraciones.

_______________

Fuentes:

Artículo publicado el 16 de enero, en el que se habla de una nueva tecnología empleada para medir la vibración de las proteínas. 

Nota de Eurekalert! Que habla de este tema.

Sinfonía No. 9 de Mahler.

Imagen tomada de este sitio.

 

Protein researchers closing in on the mystery of schizophrenia

Seven per cent of the adult population suffer from schizophrenia, and although scientists have tried for centuries to understand the disease, they still do not know what causes the disease or which physiological changes it causes in the body. Doctors cannot make the diagnosis by looking for specific physiological changes in the patient’s blood or tissue, but have to diagnose from behavioral symptoms.

In an attempt to find the physiological signature of schizophrenia, researchers from the University of Southern Denmark have conducted tests on rats, and they now believe that the signature lies in some specific, measurable proteins. Knowing these proteins and comparing their behaviour to proteins in the brains of not-schizophrenic people may make it possible to develop more effective drugs.

It is extremely difficult to study brain activity in schizophrenic people, which is why researchers often use animal models in their strive to understand the mysteries of the schizophrenic brain. Rat brains resemble human brains in so many ways that studying them makes sense if one wants to learn more about the human brain.

Schizophrenic symptoms in rats

The strong hallucinogenic drug phenocyclidine (PCP), also known as “angel’s dust”, provides a range of symptoms in people which are very similar to schizophrenia.

“When we give PCP to rats, the rats become valuable study objects for schizophrenia researchers,” explains Ole Nørregaard Jensen, professor and head of the Department of Biochemistry and Molecular Biology.

Along with Pawel Palmowski, Adelina Rogowska-Wrzesinska and others, he is the author of a scientific paper about the discovery, published in the international Journal of Proteome Research.

Among the symptoms and reactions that can be observed in both humans and rats are changes in movement and reduced cognitive functions such as impaired memory, attention and learning ability.

"Scientists have studied PCP rats for decades, but until now no one really knew what was going on in the rat brains at the molecular level. We now present what we believe to be the largest proteomics data set to date," says Ole Nørregaard Jensen.

PCP is absorbed very quickly by the brain, and it only stays in the brain for a few hours. Therefore, it was important for researchers to examine the rats’ brain cells soon after the rats were injected with the hallucinogenic drug.

"We could see changes in the proteins in the brain already after 15 minutes. And after 240 minutes, it was almost over," says Ole Nørregaard Jensen.

The University of Southern Denmark holds some of the world’s most advanced equipment for studying proteins, and Ole Nørregaard Jensen and his colleagues used the university’s so-called mass spectrometres for their protein studies.

352 proteins cause brain changes

"We found 2604 proteins, and in 352 of them, we saw changes that can be associated with the PCP injections. These 352 proteins will be extremely interesting to study in closer detail to see if they also alter in people with schizophrenia - and if that’s the case, it will of course be interesting to try to develop a drug that can prevent the protein changes that lead to schizophrenia," says Ole Nørregaard Jensen about the discovery and the work that now lies ahead.

The 352 proteins in rat brains responded immediately when the animals were exposed to PCP. Roughly speaking, the drug made proteins turn on or off when they should not turn on and off. This started a chain reaction of other disturbances in the molecular network around the proteins, such as changes in metabolism and calcium balance.

"These 352 proteins are what causes the rats to change their behaviour - and the events are probably comparable to the devastating changes in a schizophrenic brain," explains Ole Nørregaard Jensen.

The protocol for studying rat brain proteins with mass spectrometry, developed by Ole Nørregaard Jensen and his colleagues, is not limited to schizophrenia studies - it can also be used to explore other diseases.

The research was a collaboration between the University of Southern Denmark, the Danish Technological Institute and NeuroSearch A/S.

Details about the experiment
Twelve rats were used for the experiment. Six received an injection with the hallucinogenic drug PCP (10 mg/kg body weight), and six were injected with a saline solution to serve as controls. After 15 minutes, the first two animals in each group were killed and within less than two minutes, samples of their brains (temporal lobes) were taken and quickly frozen in liquid nitrogen.

After 30 and 240 minutes, respectively, the same was done to other rats. All experiments were conducted in accordance with Danish and EU guides for the handling of laboratory animals. The collected tissue samples were then subjected to various mass spectrometric protein analyses. The analyses revealed differences in the phosphorylation of proteins indicating which proteins had been affected by the drug PCP.

Interpretation of the complex protein data set suggest that PCP affects a number of processes in brain cells and leads to changes in calcium balance in the brain cells, changes in the transport of substances into and out of cells, changes in cell metabolism and changes in the structure of the cell’s internal skeleton, the cytoskeleton.

'First drafts' of human protein catalogue published

"The first two attempts at a database of every single human protein - the "proteome" - have been made public.

This builds on our knowledge of the genome by showing which genes actually produce proteins in which tissues.

One team in Germany and one spanning the US and India have published their proteome maps in the journal Nature, and on searchable, public websites.”

Learn more from bbcnews.

Researchers find clue to stopping Alzheimer’s-like diseases

Tiny differences in mice that make them peculiarly resistant to a family of conditions that includes Alzheimer’s, Parkinson’s and Creutzfeldt-Jakob Disease may provide clues for treatments in humans.

Amyloid diseases are often incurable because drug designers cannot identify the events that cause them to start.

Professor Sheena Radford, Astbury Professor of Biophysics at the University of Leeds, said: “Amyloid diseases are associated with the build-up of fibrous plaques out of long strings of ‘misfolding’ proteins, but it is not clear what kicks the process off. That means the normal approach of designing a drug to destroy or disable the species that start the disease process does not work.

“We have to take a completely different tack: instead of targeting the cause of the disease, we need to disrupt the plaque building process.”

The University of Leeds-led team’s study, published in the journal Molecular Cell, looked to mice for a way forward.

“We already knew that mice were not prone to the build up of some of these plaques. This study, for the first time, observed the building happening and saw the differences between the mice proteins and their almost identical human equivalents,” Professor Radford said.

She added: “We mixed the mice and human proteins and found that the mice protein actually stopped the formation of the plaque-forming fibrils by the human protein.”

The research was conducted completely in the test-tube using human and mice beta-2 microglobulin proteins produced in the laboratory. Plaques made up of beta-2 microglobulin are associated with Dialysis Related Amyloidosis (DRA). Instead of being a neurodegenerative condition like Alzheimer’s or Parkinson’s, DRA primarily affects the joints of people on kidney dialysis.

The team observed differences in the formation of the plaque-forming fibrils in samples containing only mice protein, samples with only the human protein and samples containing mixtures of the two.

The lead researcher, Dr Theodoros Karamanos, said: “These two versions of the proteins are almost exactly the same, with very slight differences in structure, but the outcomes are completely different. If I put a misfolding-prone protein in the human sample, I see the formation of fibrils in two days in the right conditions. If I do the same in the mouse sample, I can leave it for weeks and there are no fibrils.

Dr Karamanos added: “The exciting thing is that if you mix the proteins—with only one mouse protein for every five human proteins—you see a significant disruption of the formation of fibrils.”

The study used Nuclear Magnetic Resonance spectroscopy to look at a molecular level at the interactions of the different proteins and identified tiny differences in the physical and chemical properties of the surfaces that made a great difference to whether plaques are formed.

The results showed that the mouse protein binds to the human protein more tightly than the human protein binds to its misfolded form. Interestingly, subtle differences in the driving forces of binding (i.e. the balance of hydrophobic and charge-charge interactions) in the binding interface govern the outcome of assembly.

Dr Karamanos said: “We can’t just load up a syringe and inject mouse protein into patients. But if we know the properties of the interface between the two proteins that are responsible for the inhibition effect, we can ask the chemists to design small molecule drugs which mimic what the mouse protein does to the human protein. That may be a key insight into how to stop the plaque building process.”

Mitochondrial Digestion and the sorting of waste

The process of mitophagy, in which tiny digestive bubbles surround the mitochondria, serves to recycle waste for the cell. Damaged proteins can no longer carry out their function correctly and need to be broken down. Errors in the digestion of mitochondria appear in old age and in the case of neurodegenerative diseases like Parkinson’s and Alzheimer’s.

Up to now, it was unclear whether this cells sorted out defective proteins when they digest mitochondria. Dr. Jörn Dengjel from the Center for Biological Systems Analysis (ZBSA), Freiburg Institute for Advanced Studies (FRIAS), and the Cluster of Excellence BIOSS Centre for Biological Signalling Studies of the University of Freiburg has now discovered in collaboration with researchers from the Hebrew University in Jerusalem, Israel, that the proteins are sorted out during the constant fusion and fission of mitochondria. The team published their findings in the journal Nature Communications.

Hagai Abeliovich, Mostafa Zarei, Kristoffer T. G. Rigbolt, Richard J. Youle, Joern Dengjel. Involvement of mitochondrial dynamics in the segregation of mitochondrial matrix proteins during stationary phase mitophagy. Nature Communications, 2013; 4 DOI: 10.1038/ncomms3789

Yeast cells digest their mitochondria in long-time cultures. This process is called mitophagy. Proteins that are digested at a different speed are marked with a fluorescent dye. (Credit: © Joern Dengjel)

Molecular biology mystery unravelled

The nature of the machinery responsible for the entry of proteins into cell membranes has been unravelled by scientists, who hope the breakthrough could ultimately be exploited for the design of new anti-bacterial drugs.

Groups of researchers from the University of Bristol and the European Molecular Biology Laboratory (EMBL) used new genetic engineering technologies to reconstruct and isolate the cell’s protein trafficking machinery. Its analysis has shed new light on a process which had previously been a mystery for molecular biologists.

The findings, published this week in the Proceedings of the National Academy of Sciences (PNAS), could also have applications for synthetic biology - an emerging field of science and technology, for the development of novel membrane proteins with useful activities.

Proteins are the building blocks of all life and are essential for the growth of cells and tissue repair. The proteins in the membrane typically help the cell interact with its environment and conserve energy. 

Researchers were able to identify the ‘holo-translocon’ as the machinery which inserts proteins into the membrane. It is a large membrane protein complex and is uniquely capable of both protein-secretion and membrane-insertion.

Professor Ian Collinson, from the School of Biochemistry at Bristol University, said: “These findings are important as they address outstanding questions in one of the central pillars of biology, a process essential in every cell in every organism. Having unravelled how this vital holo-translocon works, we’re now in a position to look at its components to see if they can help in the design or screening for new anti-bacterial drugs.”

Scientists discover why newborns get sick so often

 A new research finding published in the November 2013 issue of the Journal of Leukocyte Biology sheds new light on why newborns appear to be so prone to getting sick with viruses—they are born without one of the key proteins needed to protect them. This protein, called “toll-like receptor 3” or “TLR3,” is involved in the recognition of different viruses and mediates the immune response to them. Without this protein, newborn immune cells are not equipped to recognize and react appropriately to certain viruses, in particular, the herpes simplex virus known as HSV.

"This study helps to understand the molecular basis for the immaturity of the immune system of newborns, which we believe will contribute to development of therapeutic interventions to protect this vulnerable population group," said Lucija Slavica, a researcher involved in the work from the Department of Rheumatology and Inflammation Research at the University of Gothenburg in Gothenburg, Sweden.

Lucija Slavica, Inger Nordström, Merja Nurkkala Karlsson, Hadi Valadi, Marian Kacerovsky, Bo Jacobsson, and Kristina Eriksson.
TLR3 impairment in human newborns. J Leukoc Biol. November 2013 94:1003-1011; doi:10.1189/jlb.1212617 ; http://www.jleukbio.org/content/94/5/1003.abstract

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