A Residual Dipolar Coupling analysis of methyl containing side chains in ubiquitin

The side chain moieties within a protein structure represent a valuable probe for investigating structural and dynamics properties relating to protein-protein interaction and stability. NMR methods, such as spin relaxation, have been applied for some time to study these properties. The application of Residual Dipolar Coupling (RDC) based methods to probe the carbon-carbon framework of methyl containing side chains can offer a complementary view of their conformation and dynamic properties. However, novel methods are needed in order to deconstruct fully the conformational complexity available from RDC data. With sufficient RDC data, models of motion can be applied to understand the conformational averaging to which RDCs are sensitive. The characterization of the conformation of methyl-containing side chains in ubiquitin inevitably allows corresponding insights into the structural and dynamic contributions to ubiquitin's unusually high stability. Here is presented a study of methyl-containing side chains using an RDC based multiple alignment approach for the protein ubiquitin.