Wednesday, April 27, 2016

Metallocenter Biosynthesis & Assembly #chempaperaday 268

It's generally accepted that about 30% of proteins are metalloproteins, and metal ions in these proteins have several different roles. I will not go into that. For a long time, I have been really interested in one thing in particular: how do these metal ions find their ways to these proteins? Cells have several different metal ions, what really brings a particular metal ion to a particular metalloprotein? Metal ions at different oxidation states have different radii, but some of these are very similar to each other. How come one is swapped by another? What regulates all these? In fact, I should call myself lucky because I asked some of these questions to Harry B. Gray in person. But, reading the literature and really learning is such a different thing.

Well all the questions above and many more can be answered by this amazing book chapter. It's a perfect introductory text for people interested in metals in biology. Here is the abstract :

Cells synthesize biological metallocenters by use of several recurring themes, often with multiple themes combined into a single pathway. In the simplest situation, binding of a metal ion to a biological ligand occurs by reversible thermodynamic control; however, the prevalence of metallocenters deeply buried within macromolecules, the exceedingly low concentrations of free metal ions within cells, and the sophisticated structures of many metal-containing active sites and cofactors provide evidence that alternative and more complex approaches must also exist. In some cases, metal binding is accompanied by posttranslational modification of the target protein, either before or after the metal binds. Many metallocenters contain additional components that are added along with the metal ion. In other cases, metallochaperones are used to deliver the metal of interest to an apoprotein. Another alternative is to incorporate the metal into a protein subunit that subsequently swaps for an apoprotein subunit in the native protein. In addition, electron-transfer reactions may be coupled with metal assembly. Other proteins require a preassembled metal-containing cofactor rather than just the free metal ions. The cofactor may bind reversibly or be delivered by a chaperone, and scaffolding proteins may be used to provide a framework for construction of such a cofactor. Covalent attachment of the cofactor occurs in some cases. Finally, molecular chaperones that directly or indirectly alter the conformation of the target apoprotein may be utilized. In many cases, the function of the molecular chaperone is coupled to nucleotide triphosphate hydrolysis. Examples are provided for each of these metallocenter biosynthetic mechanisms.

Friday, April 8, 2016

What is wrong with this periodic table?

Here is an interesting periodic table from the journal Cell. The title is definitely interesting and I really want to read the article. But, I can't help but staring at this periodic table.

First of all, the d-block has 11 groups instead of 10. A whole group (either 17 or 18, you pick one) is missing. Finally, the f-block has 15 groups. I am not sure but it looks like there are 118 elements in total which is fine. But, you don't see a periodic table like this often. I am wondering if any of the authors or an editor ever noticed anything wrong with this. I am also wondering where they got this periodic table from.

I think it's open access, so go ahead and look at it. 


Thursday, April 7, 2016

Genetic Optimization of Metalloenzymes: Enhancing Enzymes for Non-Natural Reactions #chempaperaday 267

Bioinorganic catalys is not that new but "artificial metalloenzymes" as it is called is a relatively new research area. But, I think it is one of the most amazing ones. Just think about it, you genetically modify an enzyme to do something else or to do something extra! How cool is that? For beginners, it is a nice review and starting point to dive into that world. Many examples of these enzymes and how single modifications can show dramatic effect on reactivity or selectivity.

It's open access!

The 4s and 3d subshells: Which one fills first in progressing through the periodic table and which one fills first in any particular atom? #chempaperaday 266

Electron configuration of transition metals sometimes get complicated due to some "irregularities". If you have NEVER noticed this, look them up in an inorganic textbook. This paper doesn't really give you anything new if you already know the underlying reason for those configurations. However, the authors did a computational experiment to show us which orbitals are more stable upon adding an electron. So, that's useful in terms of teaching.

The summary is that  "there is no scientific reason to write the electron configuration of transition elements as [Ar] 4s 3d and the correct form is [Ar] 3d 4s."