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| Evolution of Protein Structure Function |
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The aim of our group is to reverse engineer the function of a protein through studying its evolution. We use bioinformatics to get the first inkling of the layout and mechanism of these biological nanomachines, and computer simulation to test, to the extent it currently allows, the reasonableness of our interpretation of bioinformatics data. Ultimately, the goal is to build a straightforward hypothesis which can then be tested experimentally. Therefore we invest serious effort into developing ways to present our findings in the most useful and compact way to our experimentalist colleagues.
In evolution, as in any statistical process, anything that can happen will happen. Compared, however, to the options open to a simple physical system, "can happen" is a somewhat more elaborate condition. While the physics of DNA stability may allow for a mutation, this mutation might severely degrade the stability of the protein it encodes, which in turn may kill the organism carrying the mutation. Another mutation might be irrelevant to the protein stability, but it may adversely impact its interaction with another protein, thus disrupting a pathway in the hapless organism. Keeping that scenario in mind, we can compare proteins performing the same function in living and thriving organisms, and look for regions in the protein in which mutations, or certain types of mutations, are conspicuously absent. Since we can reasonably assume that mutations do happen sporadically in those places, as they do in all underlying positions in the DNA, we may suspect that the carriers were eliminated from the gene pool because the mutation resulted in some disadvantage for the organism, be it on the translational, folding, or protein-protein interaction level. |
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The correlation between the degree of conservation of a protein region and the impact the mutation has on the organism is most readily observable in the case of enzymes, small chemical factories that are a very common type of protein. In the illustration in Figure 1 (from an enzyme, called HPPD, from the tyrosine degradation pathway), the most highly conserved regions (yellow) cannot be mutated without causing the organism's demise, while the slightly less conserved regions (red), if mutated, cause health problems of various degrees of severity. |
| Figure 1 |
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| When trying to understand the protein function, we may adopt a top-down (reverse engineering) approach and look for the functional regions among the most conserved ones. While detecting such "conserved" regions in a protein may not be a very challenging bioinformatics task, interpreting their meaning most certainly is. Thus, for example, in a study of a protein called Ku (from the large group of telomere-related proteins) the conservation map pointed to several regions (the largest two shown in red and blue in Figure 2) the conservation of which seemed quite mysterious. The results were turned straight away to our experimental colleagues who were able to establish, through site directed mutagenesis, that several pathways were critically affected, distinct pathways intriguingly assorting with distinct protein regions. |
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| Figure 2 |
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| The goal of our group is to push forward, through analogy and explicit computational simulation, the point at which the experiment needs to be invoked, thus both deepening our understanding of proteins and shortening the benchwork time. |
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