Breakthrough in industrial mining of Uranium from... a see water!

Do you know that see water contains heaps of Uranium (in form of UO2++ ion) with average concentration 13.7nM. Well, it looks not impressive but water in the ocean in total have 100o times more of uranium that our earth crust. Problem is that no one came up with an idea how efficiently extract this precious metal out of water. Also, remember that presence of a similar type metals such as Vanadium, Copper etc which are presented in a water at even higher concentration will be outcompeting Uranium. And just to make task even more daunting, carbonate complexate with uranyl ion what leaves only 10(-17)  Mollar of free ion. Thus someone need to design a molecule with at least femtomolar affinity 10(-15) in order to effectively extract Uranyl at this negligibly low free concentration.
Group of Professors Luhua Lai (Peking University) and Chuan He (Chikago University) engineered a protein with fM affinity for Uranyl ion! They just have published in recent Nature Chemistry issue. The collaborative workflow they have presented in the paper is tremendous!  Briefly, they computed around 13000 of PDB known scaffolds for mutants that possibly can bind Uranyl which 'ccordination' geometry is very well known. They came up with 5000 hits, after couple of rounds of refining the library they were able to pick around ten with only four proteins amenable for expression. The best candidate has an affinity 37nM wich is far from perfect, but good luck and some of computation tricks led them to find a mutant with 1000-higher affinity (fM!). They were able to extract up to 95% of Uranyl from synthetic see water leaving just 3 ppb (!) of Uranyl in the filtrate. Now they are thinking of cheap device that would be able to replenish itself with protein Uranyl-binder. The most simple would be to use bacterias who can express this protein on the surface. So just by simply growing these bacterias now one can extract uranium out of see water. Although a whole idea is very smart and environmentally friendly (simple filtration of ocean water), use of bacterias will require stringent stages of water purification after it's been in contact with biomass given the huge masses of water that will be passing though these 'filters'.

Raising genes from the Last Common Ancestor demonstrates its complexity

I do not why but papers about evolution always fascinate me (if they are not overwhelmed with population genetics and other hard core stats and math). This time I cam across a paper in JACS where authors used a computational technique called Ancestral sequence reconstruction (ASR) to rebuilt  ancient enzymes that nowadays form closely related bi-enzymatic complex. Basically, knowing the phylogeny (map of how species relates to each other) let you estimate the probability (maximum likelihood) that some mutation would occur back in its evolutionary history or vice versa: you can estimate the probability that current phylogeny would evolve given that ancestral protein sequence. Exactingly, you can go as back as you can (means - to the very Last Common organism Ancestor that we all evolved from, LUCA). In order to get that far the wider phylogeny tree you have the better: say from the most distant archaea to the bacterias. Authors asked a question whether LUCA back than 3.5 billion years ago had elaborate enzymatic networks. For that reason they rebuilt bieznyme complex (cyclase subunit HisF and the glutaminase subunit HisH) of imidazole glycerol phosphate synthase. Note that, without one another subunit would not work due to their close relationship in the synthesis reaction. They were able to show that the reconstructed proteins still retain almost the same specific activity and surprisingly able to tightly associate with each other. This work demonstrates that even LUCA had enzymes that were very closely associated and were able to perform such things as substrate tunneling (when product of one reaction is directly passed to another enzyme) or allosteric regulation (when product of one reaction regulates another enzyme). I wonder how would ribosome would look like given its high evolution conservativety.

The reason I decided to make a post about this paper is that ASR technique nowadays on the realm of very cheap gene synthesis let us 'play' with protein sequences such that we can go back in evolution and make probably more promiscuous enzyme that we can more easily 'teach' to perform reaction we want as these. Alternatively, we can improve folding properties of our protein by more targeted mutagenesis (since we have a good guess about its evolutionary history). Also, we might be able to produce an orthogonal protein/protein networks that still retains the specific activity while being not regulated by intracellular proteins. Any other ideas?

Building chemical nanoreactors out of proteins

Hi there! Today's short post is about usage of proteins as a generic scaffolds for designing chemical reactors.

Many good chemistries can not be simply accomplished in the tube because in order to proceed these reactions require very special conditions, such as presence of a metal in a certain oxidized state, or whole reaction should be shielded from the water solution since very unstable intermediate complex is formed during the reaction path. Thus having a nanoreactors with controllable conditions is a target of many chemists nowadays. There were numerous attempts to build such things out of complex organic molecules, however every single one needs a special approach and therefore lot's of effort. In contrast, mother nature successfully solved this problem (and keeps solving it) with proteins - the most generic chemical reactor. The reactions centers of many enzymes provide special conditions such as high hydrophobicity (lack of water molecules), or positioning of these water molecules in a reaction-favorable places. Upon finishing the reactions, active site of a protein will be freed from the product due to the special its characteristics. Thus some of the enzymes are able to perform reaction up to million times per second (turnover rate for carboanhydrase is half a million!) - much faster than chemistry in homogeneous environment would allow.

This time a group from University of Basel under the leadership of Professor Nico Bruns used a  protein that normally helps other proteins to fold (chaperonin) as a nanoreactor for polymerization. These sort of proteins form hydrophobic pores that are large enough to let macromolecules enter and leave it. Thus authors conjectured that this would be a perfect scaffold for assisting polymerization reaction. They simply modified chaperonin mutant cysteine residue with EDTA-like compound what let the catalytic Copper ion to be trapped inside the cavity, whereas monomers were allowed to enter the pore by diffusion. As a result they were able to obtain polymer with very low polydispercity index. 

Another example, probably less successful (that's why it is in 'Chembiochem', not in the 'Angewandte chemie' where previous paper appeared) but still interesting. Group of chemists under the supervison of Prof. Jared C. Lewis from University of Chicago introduced metal ions into protein scaffolds via unnatural aminoacids. Firstly they synthesized a protein containing clickable amino acid ( Azidophenylalanine) via reassigning the amber-codon (pEVOL system, developed by Prof. Peter G. Schultz). Then they coupled a number of BCN-linked organic ligands to the protein via Strain Promoted Azyde-Alkyne Cycloadition (SPAAC). Ligands in turn could form a complex with metals such as Rhodium, Manganese and Copper. Although authors could not reach anticipated velocities of some of the reactions they still were able to demonstrate the possibility to build such artificial metallo-enzymes. May be use of other protein scaffolds (such as mentioned above chaperonin) with  computational design aid (or probably directed evolution) could help us to get very active enzymes for biotech and pharma industry in future.