Recent advances in computational techniques have allowed researchers to select amino acid sequences that will fold into proteins with a desired three dimensional structure. Nevertheless, it remains a challenge to supply novel proteins with real function such as enzyme catalysis of signal transduction. The theoretical understanding of protein-ligand binding interactions is a very important yet difficult step towards the design of such molecules. Here, we propose to redesign a naturally existing receptor in order to alter its binding properties. For this purpose we have chosen calmodulin (CaM), a small ubiquitous Ca2+-binding protein that can bind very tightly to at least 30 functionally and structurally diverse targets. Optimization of the CaM binding interface will be done using a discrete set of amino acid rotamers and a very fast sequence selection algorithm based on the Dead-End Elimination theorem. First, we will test the performance of rotamers and a very fast sequence selection algorithm based on the Dead-End Elimination theorem. First, we will test the performance of our computational technique on CaM complexed with its natural target, smooth muscle myosin light chain kinase. Second, we will modify the CaM sequence to make it bind to peptides that show no appreciable binding to the wild-type CaM. Finally, we will supply CaM with more specific binding characteristics by introducing residues capable of forming specific hydrogen bonds with a particular target, while failing to interact favorably with all other targets. The calculation results will be verified by synthesizing the redesigned CaM molecule and determining its binding affinities for the targets. The calculation results will be verified by synthesizing the redesigned CaM molecule and determining its binding affinities for the targets. Experimental testing on the redesigned CaM will allow us to determine the calculation parameters appropriate for protein-ligand interactions. We anticipate that this work will improve our general understanding of the binding process which could greatly facilitate the development of new drugs and peptide vaccines.
