Integrated structural biology approaches for the study of nucleic acid binding proteins

Abstract

Proteins are the ultimate effectors of biological mechanisms and are involved in every aspect of cellular life. The functional properties of proteins depend on their three-dimensional structure. Indeed, proteins are not rigid entities and internal motions, on a wide range of timescales and distances, are necessary to accomplish a specific function. While certain proteins adopt a compact conformation and undergo small-scale rearrangements, others are more flexible and withstand more dramatic movements. Proteins that exhibit a regulatory role function by binding multiple partners, such as small molecules, DNA, RNA, other proteins. Increased levels of flexibility favour this binding promiscuity. A long-standing goal in molecular biology has been the development of new methods to enable the determination of three-dimensional structures of proteins that exhibit a high level of dynamic complexity. In fact, it is becoming clearer every day that individual structural techniques have several limitations. An integrative structural biology approach provides the tools to decipher the dynamic configuration of proteins by combining information from multiple sources, including biochemical, bioinformatics and biophysical methods. In this thesis, an integrated approach is used to structurally characterize two extremely different nucleic acids binding proteins, the human Staufen1 protein and the archaeal Pyrococcus abyssi MCM complex. In this study, I show that an integrated structural biology approach is not only essential to determine the architecture of small, flexible proteins, which are traditionally difficult targets for conventional approaches, but it is also beneficial to understand the dynamic behavior of large, more compact macromolecular complexes.