Evolution finding sequences

An essential progress in this direction was achieved [69-71] with the following reformulation of the problem. Instead of trying to solve a very complex problem of real biological evolution, an attempt was made to find a way of preparing sequences ensuring certain properties of the synthesized heteropolymer. This problem is called polymer sequence design. Gen-... 

Staden, R. (1999). Finding protein coding regions in genomic sequences. In Doolittle, R. (ed.), Molecular Evolution Computer Analysis of Protein and Nucleic Acid Sequences, Methods in Enzymology. vol. 183. Academic Press, San Diego. 

Every NMR experiment must have a preparation sequence (inducing the nuclei to resonate) and detection capability (finding out what happened). Two-dimensional NMR spectroscopy adds two more domains between preparation and detection. These are an indirect evolution time, q, and a mixing sequence (see Figure 3.15). The two dimensions of two-dimensional NMR spectroscopy are those of time. In one time domain, FIDs containing frequency and intensity information about the observed nuclei is collected. The second time dimension refers to the time that elapses between some perturbation of the system and the onset of data collection in the time domain. The second time period is varied, and a series of FID responses are collected for each of the variations. 

This finding allows the development of an evolution reactor, in which optimally reproducing RNA sequences may be produced in a relatively short time. This in turn makes possible the development of a principle for the evolution of RNA structures with optimized translation products. Experiments in this direction are in progress. 

The constant refinement of techniques for directed protein evolution also involves the development of increasingly sophisticated in silico tools. This co-evolution of experimental and computational methods enriches our toolkit for finding the sequence that fits. It is this mutual impact which makes ProSa a valuable component in designing both experiments and proteins. 

Whereas the electron acceptors in the anaerobic organisms are the bacterial-type ferredoxins that contain [4Fe-S] clusters as the redox center, in the case of the halobacteria the electrons are transferred to [2Fe-S] ferredoxins. These ferredoxins were isolated from two different halobacteria and their amino acid sequences were determined (Hase et al., 1977, 1980) and shown to be highly homologous to the chloroplast (and cyanobacterial) ferredoxins. The implications of these perplexing findings for the question of the molecular evolution of the system is discussed in detail in Kerscher and Oesterhelt (1982). 

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