JMS/sandbox7

spinqualitylabelsall models Structure of alpha-type carbonic anhydrase (dCAII) (PDB entry 1y7w) Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image

Contents 1 A comparative representation of the three forms of DNA 2 Where there is no man, be a bacteria 3 Extremophiles talk in thermodynamics terms 4 At the the Weizmann Institute, scientists discover enzymes in the Dead Sea 5 Thermophilic enzymes adapt by changing their Enthalpic and Entropic properties

A comparative representation of the three forms of DNA

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spinqualitylabelsall models A-DNA Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image

spinqualitylabelsall models B-DNA Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image

spinqualitylabelsall models Z-DNA Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image

Synchronize the three applets showing A-, B- and Z-DNA by clicking the checkbox

Where there is no man, be a bacteria

Where no man or plant could survive, bacteria have been eking out a living, and some even thriving. From the Dead Sea which has 10 times the concentration of salt in salt sea water to the hot springs heated by the molten center of the earth, that pour forth through vents deep under the sea - in all these hostile environments, life has found footing. To make the question stronger, realize that many things can go wrong, cells could burst or shrivel, DNA can become undone and tattered, protein can unfold into a jumbled mass of amino acids, and membranes made of fat molecules can rip and melt. Environment stress usually achieves all or many of these deadly process to organisms - yet some bacteria survive. To study how the extremophiles (extreme-loving bacteria) survive involves explaining how each of the above processes that should kill the bacteria, in fact do not occur. To understand all of these is a tall order, but to start, in this Proteopedia article, we'll tackle the protein survival under extreme stress problem.

Extremophiles talk in thermodynamics terms

All stresses must be interpreted into the language of thermodynamics, since that is the most faithful representation of the problems the environment brings to proteins, and the way the structures have solved this problem, and found a way to maintain their stability.

The principle equation is:

∆G = ∆H - T∆S..

Where ∆G is negative, the movement to products in the reaction is spontaneous. This means, for the case of going from unfolded protein to folded protein as the product, a negative ∆G wold correspond to a stable protein structure. The other three terms: ∆H, T, and ∆S correspond to the change in enthalpy, the temperature (in Kalvins), and the change in entropy. Where the product is more stable than the reactants, ∆H will be negative, and there the produce is more ordered than the reactant, ∆S will be negative. It can be seen from the equation that ∆G becomes more negative for a more negative ∆H or for a less negative ∆S.

At the the Weizmann Institute, scientists discover enzymes in the Dead Sea

Our first example comes from the algae Dunaliella salina, found growing on the shores of the dea sea by Prof. Volcani, working at the Experimental Research Station (now the Volcani Institute), and then housed on the campus of the Daniel Sieff Institute (now the Weizmann Institute). Appropriately, scientist from the Weizmann Institute, Prof Joel Sussman, Dr. Adi Zamir and collegues, crystallized the that hangs out of the membrane of D. salina. Now, living on the shore of the Dead Sea presents a special problem for the living. While the dead sea is a challenge with its enormous concentration of salt, living on its shores means one must cope with high salt concentrations, but also - normal salt concentrations. That is, the adaptations to high salt must leave open the possibility of living with normal salt concentrations, too. After comparing the enzyme found on shore dwelling bacteria - appropriately named halo-tolerant (able to withstand high and normal salt concentrations) with enzymes from normal bacteria and purely halophilic ones (some bacteria can even live inside a salt crystal!), they noticed a particular feature of a the protein's structure which was associated with halotolerance. There were less positively-charged amino acids - particularly Lysine - on its surface compared to the amount found in the normal enzymes. And unlike the halophilic enzymes, which also had more negatively-charged amino acids, the halotolerant enzyme had a normal number of negatively charged amino acids. Apparently, this intermediate structural property enables the halotolerant enzyme to walk the tightrope, balancing adaptation for high and for medium salt concentrations. Because the thermodynamic threat of salt is not well understood, and nor is the role of increasing the negative surface charge, I label the thermodynamic definition of the structural adaptation ambiguously by not specifying whether it is enthalpic or entropic:

∆G = .

In the next example, however, I specify the thermodynamic terms which a structural adaptation personifies. For that, we turn to a thermophilic enzyme, also solved by Weizmann Institute lab - Porfessor Yigal Burstein and his team of scientists.

Thermophilic enzymes adapt by changing their Enthalpic and Entropic properties

Studying , Pof Burstein noticed two special features that appear to explain this enzymes ability to maintain its structure in over 83℃! For comparison, you could fry an egg at 65℃, which mean all the protein in an egg - and mammals, plants.. denature at significantly less than 83℃. To demonstrate the special structural properties of the thermophilic enzyme underlies its thermophilic prowess, Prof Burstein selectively altered normal enzymes to have the two structural features, and indeed found that the normal enzymes had become thermophilic. The two properties relate to ∆H and to ∆S. Firstly, he found the thermophilic enzyme had a unique four amino acid binding-network that encompassed two monomers of the tetrameric enzyme, repeating between each monomer and its two partner monomers. This network apparently makes the oligomer more stable, or ∆H more negative. Secondly, the thermophilic enzyme was enriched for proline. Because proline's residue (side chain) has no, or minimal, possible degree of freedom, therefore proline's side chains, unlike other amino acids - is not restricted by folding. Therefore, ∆S is less negative. These two structural properties are labelled by the corresponding term in the thermodynamics equation:

∆G = - T.