Category Archives: Journal Club

Cadmium: toxic to mammals, harmless to a bacterium, helpful to an alga

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Joe Magliocca

Joe MaglioccaI'm on ScienceSeeker-Microscope

Heavy metal poisoning is a major health concern across the world. Heavy metal ions frequently leak into the environment from industrial waste causing multiple health problems in humans, animals, and other organisms. While there is no universally accepted definition of what elements are heavy metals, the definition I find most useful includes the metal rubidium and all metals heavier than it.  These metals have large atomic masses, and aside from molybdenum (and possibly tungsten), have no essential biological function; they only interfere with other biological functions.

One heavy metal of significant concern is element 48, cadmium. This element is mostly found in nature as an impurity in zinc ore, but small amounts are scattered throughout soil, seawater, coal, and other mineral deposits. It first became known as an environmental and medical hazard when a disease known as “itai-itai” (literally “it hurts-it hurts”) appeared around the city of Toyama, Japan between the Russo-Japanese war and World War II (roughly 1905-1945). This city was a major center for zinc mining, and the cadmium waste from this process was found to be the cause of the disease.

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Novel industrial applications from salt loving extremophiles

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Bob Grinshpon

Graduate Student Bob GrinshponI'm on ScienceSeeker-Microscope

This blog will review two recent publications that explore environmentally friendly advances in biotechnology by exploiting halophilic organisms from the family Halobacteriaceae. Halophiles are found in all kingdoms of life. They employ two different survival mechanisms to cope with their typically inhospitable environment. The first strategy, ‘organic solutes in,’ excludes external salt from the cytoplasm, and synthesizes osmolytes to balance the turgor pressure with the
environment. The second survival mechanism, ‘high salt in,’ is less common, and requires that the entire proteome adapt to high salt conditions. Halobacteriaceae consist of members that strictly
use the second strategy. The similarity between the two papers ends there, but each approach is
interesting in its own right.

In the first paper (1), they characterize β-galactosidase (bga gene) from the recently discovered polyextremophile, Halorubrum lacusprofundi, and assess it for potential use as an extremozyme. β-galactosidase is involved in the breakdown of β-galactosides into monosaccharides. It is noted for its use in production of lactose free milk. However, it is assumed that lactose is not typically available in H. lacusprofundi’s environment, and the bga gene is found clustered with other genes that suggest their role is in the breakdown of plant polymers.

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Rubredoxin the Indestructible

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Annette Bodenheimer

Graduate student Annette BodenheimerI'm on ScienceSeeker-Microscope

Most biochemists have had the “pleasure” of working with proteins that require cool atmospheres and a comfy solvent to keep them temporarily happy (until they randomly decide to aggregate into protein snot). Rubredoxin from the organism Pyrococcus furiosus, on the other hand, is like an old Jeep that keeps on working despite repeated abuse and temperature fluctuations.

P. furiosus was initially discovered near a deep sea volcanic vent. This hyperthermophilic archae is an anaerobe that grows optimally around 370K (or 100 °C). Rubredoxin, as seen in Figure 1, is a small 53 amino acid protein and has a high spin state iron that is coordinated between four cysteine residues. It is responsible for electron transfer reactions, although the specific reactions it participates in is still unknown. Early research found that rubredoxin maintains its globular or tertiary structure up to 473K.

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The ever important role of thermophiles in biofuel production

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Laura Edwards NCSU Biochemistry graduate student

Laura EdwardsI'm on ScienceSeeker-Microscope

Well, it’s no secret that there are some major issues with our current dependency on fossil fuels. First of all, they don’t last forever, so at some point we’re going to run out (don’t worry, not any time soon). Second of all, when they are burned they emit greenhouse gases that are bad for the environment… not to mention the environmental damage done trying to get fossil fuels out of the ground. Lastly, the cost of gas for the American consumer has dramatically increased in the past years (it’s definitely hurting my wallet). These and other factors have prompted the research and development of alternative, renewable fuel sources such as biofuel (using organic matter for energy). Plants are a great source of energy, and the concept of using that energy for biofuel production has been around for decades. So why can’t we just stuff a stalk of corn in our gas tanks and call it day? Well, several reasons… plants are really good at converting solar energy and storing it as cell wall polymers, but the challenge comes from extracting out that energy and converting it into usable fuel, such as ethanol.

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Conan the Bacterium

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Bryan Rogers

Bryan Rogers I'm on ScienceSeeker-Microscope

We have all heard of these extremophiles that can thrive in extreme heat, cold, desiccation, acidity, or maybe even extreme radiation. However, the list of extremophiles grows thin as you add multiple life threatening conditions to the fray. Enter: the few, the proud, the Deinococcus radiodurans. Desiccate these guys in a Pyrex beaker under a zero humidity vacuum, toss the beaker in an 85 °C (185 °F) oven, and then flip the radiation switch on to 500,000 rad for 2 hours and the bacterium will survive – easily1 (1000 rad will kill a human in a week. 1 rad = 0.01 J/kg). Increasing the radiation to two million rad causes the molecular structure of the Pyrex glass to begin to break down and makes D. radiodurans… unhappy. Increase the radiation to three million rad and the bacterium somehow still manages to survive while the Pyrex beaker turns brown and becomes too brittle to touch. Named the World’s Toughest Bacterium by the Guinness Book of World Records, D. radiodurans has enormous potential in bioremediation of radioactive wastes. Check out this page for more on these possibilities.

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NCSU Biochemistry is going EXTREME!

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christie cade

Christie Cade I'm on ScienceSeeker-Microscope

In our Protein Journal Club this semester, we are studying proteins from extremophiles. As their name suggests, extremophiles are organisms that can survive under extreme conditions. These extreme conditions include acidic or basic environments, severe hot or cold environments, lack of oxygen, high salt concentrations, high sugar concentrations, high hydrostatic pressure, high levels of ionizing radiation, high concentrations of heavy metals, and extremely dry conditions such as those found in deserts.

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Order in the cell maintained by a disordered protein?

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Annette Bodenheimer

Graduate student Annette BodenheimerI'm on ScienceSeeker-Microscope

Normally proteins have a globular shape in order to be enzymatically or structurally relevant. Intrinsically disordered proteins (IDPs) broke the protein norms by maintaining their functional roles with little to no overall structure. Most proteins have regions of disorder, such as loops or linker regions (these are the bane of a crystallographer’s life). One of these IDPs appears to be a Swiss Army knife of proteins, CBP [CREB {cAMP (cyclic adenosine monophosphate) response element binding protein} Binding Protein].

CBP has a paralogue, an ancestral sibling, known as p300. These two proteins are key players in many diverse roles within the cell, such as DNA damage response, cell cycle regulation, cellular differentiation, proliferation, and apoptosis. In other words, it has been implicated in every stage of a cell’s life. p300 and CBP are both coactivators of transcription by relaxing chromatin through acetylation of histones and serving as a scaffold for transcriptional machinery.

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Cyclotides: A new ‘wave’ of discovery

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Bob Grinshpon

Graduate Student Bob GrinshponI'm on ScienceSeeker-Microscope

The cyclotide family is the the largest class of circular proteins with as many as 50,000 predicted members. They are currently only found in the Violaceae, Cucurbitaceae, Rubiaceae and recently (1) Fabaceae family of the plant kingdom (violets, gourds, coffee and legumes, respectively ). Cyclotides are a prime example of typical circular proteins; they are small (~30 residues), they maintain internal stabilizing covalent bonds between amino acid side chains, and they have a seamless topologically circular peptide backbone that is processed from mature mRNA transcripts to connect the free N- and C-terminal ends. The evolutionary origin of the mechanism of cyclization is subject to speculation, because peptide bond formation is thermodynamically unfavorable. Unfavorable reactions typically do not take place unless the expended energy results in an increased survival advantage. But how could the advantage be realized and passed on if the reaction theoretically shouldn’t take place?

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The perfect combination: wine, intrinsically disordered proteins and mass spectrometry

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Laura Edwards NCSU Biochemistry graduate student

Laura EdwardsI'm on ScienceSeeker-Microscope

After spending a great deal of time and energy on cancer research everyday, sometimes I like to go home and down a glass of red wine (or two, depending on the day). Then, I am left to ponder the simpler things in life like: Why am I left with a dry mouth sensation after drinking a glass of red wine? The correct term for this sensation is called astringency, and is considered one of the six primary tastes (it’s very similar to bitterness). Considering I’m a poor graduate student, my price limit for a bottle of wine these days is around $5… so obviously I’m no wine connoisseur, but to me astringency is not a pleasant sensation. And, you guys, SCIENCE is to blame for this. What’s happening is compounds found in red wine called tannins bind to salivary proteins in your mouth and precipitate these proteins. This is thought to reduce saliva’s ability to lubricate, causing dryness. Why would this happen? Many researchers believe this is our body’s “first line of defense” against the negative effects caused by ingesting tannins, including inhibition of digestive enzymes. On the other hand, tannins contribute to several positive effects of red wine, including its anti-oxidative properties, as well as its color and odor1. As with anything, there needs to be a balance between tannin-ful and tannin-less red wine. Many winemakers use a technique called fining, which minimizes tannins to reduce astringency. Another way to prevent ingesting too many tannins is to refrain from drinking a whole bottle or two of wine by yourself. This has several additional advantages to your well-being, including reduced hangover and liver damage. Okay, enough with the wine talk… let’s get back to science.

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The Bcl-2 family of proteins: A life or death situation

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christie cade

Christie Cade I'm on ScienceSeeker-Microscope

If you’ve taken a biochemistry class, you’ve probably heard the structure-function paradigm for proteins: amino acid sequence dictates how the protein will be folded, and the ordered 3D structure of the protein is necessary for function.(1) For example, proper formation of an active site is necessary for an enzyme to be able to carry out catalysis. You may have heard some of the models for how proteins fit with their binding partners. For example, the lock-and-key model assumes that the protein and its binding partner are rigid, and this rigid shape determines how well they interact. These models can be useful, but they tend to leave out an important group of proteins: those whose function depends on disorder. Based on sequence analysis, it is estimated that more than 30% of proteins in cells have disordered regions of greater than or equal to 50 consecutive residues.

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