Modeling Protein Evolution - Computational Modeling of Biological Systems - page 322

5 Other Evolutionary Processes

It is clear that many other evolutionary processes involve proteins. Examples include
the evolution of biochemical and regulatory networks, the origin of pleiotropy
and epistasis, co-evolution between, for instance, hosts and pathogens, hybrid
incompatibility and speciation, phenotypic buffering, the existence and impact of
neutral networks on evolution, and the evolution of evolvability, modularity, and
robustness. There has been a history of exploring these processes with the aid
of simple models that tend to ignore the particular (evolved) characteristics of
the proteins that mediate these effects. With our growing ability to model protein
evolution, these topics will be increasingly amenable to the types of simulations
described in this chapter.

6 Conclusion

Our explorations of biological systems rest on our understanding of evolution. In
addition to its own importance as a biological process, evolution can provide us
with important insights into critical biological phenomena. We can develop our
comprehension of evolution by modeling interesting but tractable systems, such
as simplified models of proteins. Proteins provide us with a plausible mapping
of genotype to phenotype, allowing us to explore topics beyond the “toy model”
stage. Conversely, modeling the evolution of proteins also can provide insights
regarding the nature of these biomolecules, what properties they would be expected
to possess, how to interpret signatures encoded in their sequences, and how they
function in their biological context. The properties of proteins arise as a result of
the evolutionary process, while the evolutionary process is itself constrained by the
properties of the evolving proteins. This circle of causality, influence, and constraint
has proven to be a fruitful area for both those interested in proteins and those
concerned with evolution. As these evolutionary models become more and more
complex, they will have an increasing impact on a wide range of questions not just
in evolution and protein biophysics, but also in biochemistry, cell and organismal
biology, and ecology.

References

1. Dennett, D.C.: Darwin's Dangerous Idea. Simon and Schuster, New York (1996)
2. Nabakov, V.: Ada, or Ardor: A Family Chronicle. McGraw-Hill, New York (1969)
3. Samudrala, R., Levitt, M.: Decoys 'R' Us: a database of incorrect conformations to improve
protein structure prediction. Protein. Sci. 9 , (7):1399-1401 (2000).
4. Crippen, G.M.: Topology of globular proteins. J. Theor. Biol. 45 , (2):327-338 (1974).