Protein complexity evolution

Three pieces of evidence are cited in support of an RNA World. Firstly, some 17 RNA ribozyme catalysts have been discovered that produce a diverse array of organic molecules, including peptide bond formation. Second, the ability to form the peptide bond and build proteins may lead to a complex evolution favoured by the proximity of proto-proteins, producing enhanced reaction efficiency. Finally, RNA is the intermediate in the biosynthesis of DNA, suggesting that it must have preceded DNA in the evolutionary process. 

Gabaldon T, Rainey D, Huynen MA (2005) Tracing the evolution of a large protein complex in the eukaryotes, NADH ubiquinone oxidoreductase (complex I). J Mol Biol 348 857-870... 

Molecular evolution demands inherent self-reproductivity. RNA seems to fulfill this function best of all known macromolecules. On account of its complex structure RNA must first have appeared in nature long after proteins or protein-like structures. A protein can by chance fulfill a particular function, but this fulfilment is determined by purely structural and not at all by functional criteria. Adaptation to a particular function, however, demands an inherent mechanism of self-reproduction. The only logically justifiable way of exploiting the immense functional capacity of the proteins in evolution lies in an intermarriage between these two classes of macromolecules, that is, in the translation into protein of the information stored in the self-reproductive RNA structures. 

In ribosome display, the physical link between genotype and phenotype is accomplished by mRNA-ribosome—protein complexes, which are directly used for selection. If a library of different mRNA molecules is translated, a protein library results in which each protein is produced from its own mRNA and remains connected to it. Since these complexes of the proteins and their encoding mRNAs are stable for several days under the appropriate conditions, very stringent selections can be performed. As all steps of ribosome display are carried out in vitro, reaction conditions of the individual steps can be tailored to the requirements of the protein species investigated, as well as the objectives of the selection or evolution experiment. Application of ribosome display has produced scFv fragments of antibodies with affinities in the picomolar range from libraries prepared from immunized mice (Hanes et al., 1998) and more recently from a naive, completely synthetic library (Hanes et al., 2000), and has been used to evolve improved off-rates and stability (Jermutus et al., 2000). 

The chlorophyll-protein complexes are oriented in the lamellar membranes in such a way that the electron transfer steps at the reaction centers lead to an outward movement of electrons. For instance, the electron donated by Photosystem II moves from the lumen side to the stromal side of a thylakoid (see Figs. 1-10 and 5-19). The electron that is donated back to the trap chi (Pgg0) comes from H20, leading to the evolution of 02 by Photosystem II (Eq. 5.8). The 02 and the H+ from this reaction are released inside the thylakoid (Fig. 5-19). Because 02 is a small neutral molecule, it readily diffuses out across the lamellar membranes into the chloroplast stroma. However, the proton (H+) carries a charge and hence has a low partition coefficient (Chapter 1, Section 1.4A) for the membrane, so it does not readily move out of the thylakoid lumen. 

A still more ambitious goal would be the evolution of a multiprotein complex. This is a rather challenging task, due to the increased complexity of the space to be searched. The task can be made manageable by asking a rather general evolutionary question. One can seek to evolve, for example, a multiprotein complex that can serve as the coat protein complex for a virus. Since there are many proteins that may accomplish this task, this evolutionary task may not be as specific and difficult as it might seem at first. 

The protein problem, wliich lies at the intersection of many disciplines, is highly complex. Evolution complicates the situation even further. Human design allows for... 

---