The emergence of allostery: a multi-technique exploration of allosteric space at atomic resolution – AlloSpace

Proteins are best seen as a dynamic ensemble of conformations in continuous exchange. The multiple functions of proteins, e.g. as enzymes, receptors, channels intimately rely on this conformational diversity and flexibility. A particularly intriguing property of many proteins is their ability to modulate their activity at one site, by an event (e.g. ligand-binding) at a remote site. The phenomenon, known as “allostery”, has been discovered more than have a century ago, and intensely studied. It is clear now that conformational dynamics is central to it. Allostery is nowadays even exploited when designing new drugs, which do not target the active site of an enzyme or receptor of interest, but a distal site that is allosterically coupled to the active site; such drugs promise to be more specific than “classical” active-site binders.
The complex free-energy landscape of protein conformations, i.e. the protein dynamics, directly depends on the amino acid sequence; mutations change the conformational ensemble, and, therefore, the capability to act as an enzyme and its allosteric properties. AlloSpace will answer key unresolved questions. How did proteins acquire allostery? And what distinguish allosteric from non-allosteric proteins, particularly in terms of dynamics?
AlloSpace brings together several key “ingredients” to successfully answer to these long-standing fundamental questions: (i) we chose a large enzyme super-family that is central for metabolism, the lactate/malate dehydrogenases, for which many non-allosteric, pre-allosteric and allosteric proteins are known; in particular, we have identified recently a sub-group from which allostery emerged. (ii) We use state-of-the-art bioinformatics tools to resurrect ancestors. (iii) We employ a host of complementary experimental and in silico methods to decipher, at the atomic scale, the networks of interactions that allow or prevent signal propagation in a series of representative non-allosteric, allosteric and pre-allosteric enzymes. Our consortium is based on the complementarity and expertise of 7 laboratories, that aim to achieve the following goals
- Seeing the invisible : describe the conformation of transient structures that are representative of the molecular movements associated with function and regulation. This part, which is the heart of the project, relies on complementary biophysical methods.
- Understanding the history : indeed to understand a phenomenon is to place it in the evolutionary context. Here we continue our investigation in search of enzymes that inform us about the key events that allowed the selection of allosteric regulation.
- Exploring new drugs: we combine our conceptual knowledge and our technological capacities to participate in a process of development of therapeutic molecules that target allosteric sites.
- Improving our tools: we will use chemical synthesis for tailored isotope labeling to investigate protein dynamics more accurately and faster, such that we can study more proteins and draw broader conclusions about the dynamics – allostery link. Those tools will be useful well beyond AlloSpace.