Proteins are the workhorses of the cell. With different combinations of the 20 common amino acids (and some modifications of these amino acids), proteins have evolved with a staggering array of functions and capabilities including: the specific binding of ligands, catalysis of complex chemical reactions, functionality in extreme environments, transportation of valuable molecules, and the exhibition of diverse structural and material properties. Therefore, there has been a long and rich body of research aimed at the investigation of proteins and their abilities, which has been partially motivated due to their widespread participation in disease processes.
The main thrusts in the field of protein engineering can be loosely divided into two areas. Originally, protein engineering evolved as a powerful method for the investigation and verification of hypotheses during the study of protein functions. For example, theories that arose about the mechanisms of enzymatic catalysis could be proven or debunked through the mutation of key amino acid side chains. This approach has greatly enhanced our understanding and appreciation of a wide variety of protein structures and functions. Out of this academic pursuit, it was soon realized that these same techniques could also be used to engineer proteins for desired improvements. Proteins are generally optimized to function in their native environments. As enzymes are increasingly employed in new situations, such as in novel industrial and therapeutic applications, methods for the rapid and targeted improvements of proteins are required.
In order to make alterations to proteins, two main approaches have been developed and described: 1) rational mutagenesis, and 2) combinatorial methods. In rational mutagenesis, a "top-down" approach is taken, where a hypothesis is made about mutations at a specific location, which is often guided by 3-D structural information, and the hypothesis is tested through the mutation of specific amino acids and assays of the subsequent mutant proteins. This is in contrast to the combinatorial paradigms, where a "bottom-up" approach is taken. In this approach, a library of different mutant proteins is produced. A method is then developed to screen or select members of the library that have an improved trait, and then the mutations that caused the improvement are determined afterwards. Both of these methods have been extensively used for the successful engineering of a wide variety of important proteins.
In our research group, we use both rational and combinatorial protein engineering techniques to tackle important problems in bioengineering. We are especially interested in developing new screening and selection methods that can be used to broaden the application of combinatorial methods in protein engineering.