Grant: Discovery Grants Program - Individual

Proteins are one of the fundamental building blocks of the cells in our bodies. They are composed of long chains of 20 amino acids, and the sequence of the amino acids along the protein direct the shape and function of the protein. Subsets of the 20 amino acids are similar to each other, for example some amino acids are 'oily', and others are negatively charged. Amino acids of the same sub-type can partially replace each other if the replacement does not dramatically alter the overall shape of the protein. Thus, a protein with the same function can be constructed in many different ways. *One way that this replacement can occur is if two amino acids change in concert. Thus if amino acid position A is changed from small to large, a compensating change at amino acid position B from large to small could conserve the overall size or volume. Alternatively, if two positions interact because one has a negative and the other a positive charge, the sequence can be changed so that their charges are reversed. Over long periods of time, position pairs that compensate in these ways become correlated. There are many different ways to computationally determine covarying positions in protein sequences. However, until recently it was difficult and expensive to determine if those computational predictions were correct. My lab and others have generated a series of tools that find pairs of positions in the sequence that covary. Additionally, we have developed methods that allow us to test many different pairs of positions in different protein families at the same time to validate those predictions. Thus, we propose to make predictions with three independent computational methods, and to test those predictions in a high throughput way to determine how covarying positions affect the structure and function of proteins. Understanding how covariant positions arise and contribute to protein structure and function will allow investigators and industries to design better enzymes. Enzymes are widely used in industry; for example many home cleaning products contain enzymes to degrade proteins, cellulose and lipids. As another example, custom enzymes are also used in several steps that convert corn into high fructose corn syrup, or into industrial ethanol.*