The never-born proteins

To look at the vast Sahara desert is challenging from the point of view of biochemical research. What do all these never-born proteins (NBP) look like Are they only trivial variations of the proteins we already know, or - since there is such an immensity of them out there - would it be possible that some of them possess unknown structure and properties Have they not been produced simply and solely because of lack of time and bad luck - or due to the concomitance of some unknown and more subtle reasons (Of course we have many still unknown proteins on our Earth, but clearly the question of the never-born proteins has a quite different flavor, as they were never selected). 

A simpler question related to structure concerns the folding. We know that our proteins display a biological function only when they assume a specific conformation. Let us assume to be able to make a large library of NBPs what would be the frequency of folding - namely which percentage of them would assume a stable tertiary conformation  

This question can be tackled with a concrete research project, which started recently in my group. The basic idea is to make a large number of NBPs 50 residues long. The maximum theoretical number of such chains is 20, and by using the well-known technique of phage display, gene libraries containing approximately 10 clones can be produced. 

In principle, it is not fair, or course, to approach a problem of prebiotic chemistry by using sophisticated techniques of present-day molecular biology, such as phage display. However in this case the particular research question was not the origin of life, but rather the question given a vast library of random polypeptide chains, what is the folding frequency The criterion utilized for determining whether a protein is folded or not was based on resistance to the hydrolytic power of proteases, with 

There is another general lesson that we can learn from these experiments. If our proteins are the product of contingency, most probably the pathway to their prebiotic synthesis cannot be reproduced in the laboratory. This is indeed the bottle neck in the bottom-up approach to the origin of life. 

---

The space outside our atom , or our grain of sand, is the space of the never-born proteins , the proteins that are not with us - either because they didn t have the chance to be formed, or because they came and were then obliterated. This arithmetic, although trivial, bears an important message in order to reproduce our proteins we would have to hit the target of that particular grain of sand in the whole Sahara. 

Figure 4.6 The phage display scheme for the production of never-born proteins. Proline-arginine-glycine (PRG), is a substrate for thrombin, and TAG is the antibody target. (Modified from Chiarabelli et al, in press.)...

The elongation step under a simulated environmental pressure is possible, as a never-born protein with 43 residues was obtained, although not by catalytic fragment condensation but by the Merrifield method (Chessari et al, unpublished data). 

---