Recent applications of evolutionary biophysics

In the mid-20th century, Linus Pauling and Emile Zuckerlandl published a series of articles that became hallmarks in the study of evolution at the molecular levels. However, evolution and biophysics became isolated for many decades, even in the physical sense with the departmental structure in most universities. It is very clear, though, that the collaboration between the two areas can have an exceptionally synergistic effect - molecular evolution studies can produce very interesting results when characters used for building phylogenies are understood as entities with specific physical-chemical characteristics that affect structure and function, while at the same time biophysicists and biochemists who characterize proteins can have a much better understanding on their studied subjects when understanding that they are not isolated entities but the result of mutations, selection or gene duplications followed by divergence.
Here, we describe two methods on evolutionary biophysics and recent applications from our laboratory: the detection of conservation and coevolution patterns in large sets of protein families and how they can be used to infer useful information from individual proteins, design or interpret site-directed mutagenesis experiments or help discover functions in novel proteins; and how to use ancestral sequence reconstruction to estimate the most likely sequences of proteins that existed in the past, which can then be produced heterologously after synthetic genes are transformed in expression systems and then characterized by standard experimental biophysical techniques.
Our examples include using conservation/coevolution analysis to study the previously uncharacterized protein Pb27 and to study the origin of new functions in Transthyretins.