Evolution, protein

McCardiy, A. D., and Hardie, D. G., 1984. Fatty acid. syntha.se—An example of protein evolution by gene fn.sion. Trends in Biochemical Sciences 9 60-63. 

Yuan, L., Kurek, I., English, J. and Keenan, R. (2005) Laboratory-directed protein evolution. Microbiology and Molecular Biology Reviews, 69, 373-392. 

Geddie, M.L., Rowe, L.A., Alexander, O.B. and Matsumura, I. (2004) High throughput microplate screens for directed protein evolution. Methods in Enzymology, 388, 134-145. 

A sophisticated model of protein evolution was developed by Dayhoff et al. (1978) who measured the frequency with which each amino acid was replaced by every other in sets of closely related sequences. This was converted into a Markov model, which was used to generate the probability of any amino acid being substituted by any other or remaining unchanged after different amounts of evolution. The amount of evolution was measured in PAMs (point accepted mutations), which are mean numbers of substitutions per 100 residues. This is, of course, the same... 

To understand general principles of protein evolution it is instructive to focus on specific examples. Here, VWA and other domains are discussed as representative families that are present in archaea, bacteria, and eukarya. 

McDonald, J., and Kreitman, M. (1991). Adaptive protein evolution at adh locus in Drosophila. Nature 351, 652-654. 

Patthy, L. Protein Evolution. Blackwell Science. Inc, Malden, MA, 1999. 

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. 

A. L. Kurtzman, S. Govindarajan, K. Vahle, J. T. Jones, V. Heinrichs, and P. A. Patten, Advances in directed protein evolution by recursive genetic recombination applications to therapeutic proteins, Curr. Opin. Biotechnol. 2001, 32, 361-370. 

M. Zaccolo and E. Gherardi, The effect of high-frequency random mutagenesis on in vitro protein evolution a study on TEM-1 beta-lactamase, J. Mol. Biol. 1999, 285, 775-783. 

RATIONAL EVOLUTIONARY DESIGN THE THEORY OF In Vitro PROTEIN EVOLUTION... 

There is a wealth of theory on the process of evolution that is largely overlooked in the experimental literature. Part of the difficulty is the abundance of jargon that is specific to relatively small clusters of theoretical literature. Theoretical studies on protein evolution, RNA evolution, DNA evolution, and algorithms in computer science often have interchangeable results. For instance, motifs that have important implications for experiments with proteins emerge from RNA secondary structure studies. However, using the information requires a substantial translation of the language. 

In a similar study, protein evolution has been analyzed using the random energy model (Macken and Perelson, 1989). Macken and Perel-son calculate the probability of a random walk taking k steps to a local optimum as... 

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