Protein molecular evolution function

Maki M, Kitaura Y, Satoh H et al (2002) Structures, functions and molecular evolution of the penta-EF-hand Ca2+-binding proteins. Biochim Biophys Acta 1600 51-60... 

Nakamura K, Go N. 2005. Function and molecular evolution of multicopper blue proteins. Cellular Mol Life Sci 62 2050-2066. 

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. 

Mike Lassner (Verdia Inc.) presented examples of the usefulness of directed molecular evolution as an in vitro process that more easily achieves what was traditionally attempted via reproductive crossing and recurrent selection (plant breeding). Proteins may be engineered that have specific desirable characteristics via methods that "evolve" the basic underlying DNA. For example, the outcome can be enzymes with improved kinetic properties that result in enhanced primary production, or proteins that remain operational under extreme conditions. In addition, compositional proteins may be enhanced to provide functional performance that was not achievable via conventional methods. 

Any theoretical study of applied molecular evolution needs information on the fitnesses of the molecules in the search space, as it is not possible to characterize the performance of search algorithms without knowing properties of the landscape being searched [63], Since the ideals of sequence-to-structure or sequence-to-function models are not yet possible, it is necessary to use approximations to these relationships or make assumptions about their functional form. To this end, a large variety of models have been developed, ranging from randomly choosing affinities from a probability distribution to detailed biophysical descriptions of sequence-structure prediction. These models are often used to study protein folding, the immune system and molecular evolution (the study of macromolecule evolution and the reconstruction of evolutionary histories), but they can also be used to study applied molecular evolution [4,39,53,64-67], A number ofthese models are reviewed below. 

One of the problems with DNA is that it is essentially a linear code that stores information. The functional groups (nucleotides) only interact with each other and, while this can lead to the elegant double helix, it limits the ability of DNA to form different secondary and extensive tertiary structures. RNA is rather more amenable to forming other structural motifs, hence the RNA World theory of molecular evolution, but it appears that only proteins with their varied side chains are able to adopt truly complex structures. 

Directed evolution and antibody affinity maturation offer efficient routes to redesigning proteins for new functional characteristics. Adaptive mutations and well-defined selection pressures allow structural analysis of the evolved products to provide insights into the molecular basis of protein structure and function. It is interesting to note that the majority of mutations that were obtained in the present maturation and directed evolution experiments were located at positions away from the enzymatic active sites. Perhaps this is due to the inherent difficulty in retaining catalytic activity with most active site amino acid substitutions. 

SHELLEY D. COPLEY is a professor of molecular, cellular and developmental biology at the University of Colorado at Boulder. Her research interests center on the molecular evolution of enzymes and metabolic pathways and protein structure-function relationships. Dr. Copley is a member of the Council of Fellows of the University of Colorado s Cooperative Institute for Research in Environmental Sciences. Dr. Copley served on the NSF Molecular Biochemistry Panel (1999-2003), was co-chair for the Gordon Conference on Enzymes, Coenzymes, and Metabolic Pathways (2004), and currently serves on the National Institutes of Health Genetic Variation and Evolution Study Section. 

It is in the realm of very large combinatorial libraries that selection rather than screening gains crucial importance. As the focus shifts from randomizing an eight-residue peptide to a 100 amino acid protein (the typical size of a small functional domain, for example a chorismate mutase domain), the number of sequence permutations rises to an astronomical 20100. The ability to assay even a tiny fraction of this sequence space in directed molecular evolution experiments demands selection, even though initial development of an appropriate system may be considerably more involved than the setup of a screening procedure. 

RNA has three basic roles in the cell. First, it serves as the intermediate in the flow of information from DNA to protein, the primary functional molecules of the cell. The DNA is copied, or transcribed, into messenger RNA (mRNA), and the mRNA is translated into protein. Second, RNA molecules serve as adaptors that translate the information in the nucleic acid sequence of mRNA into information designating the sequence of constituents that make up a protein. Finally, RNA molecules are important functional components of the molecular machinery, called ribosomes, that carries out the translation process. As will be discussed in Chapter 2, the unique position of RNA between the storage of genetic information in DNA and the functional expression of this information as protein as well as its potential to combine genetic and catalytic capabilities are indications that RNA played an important role in the evolution of life. 

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