AlloSpace. The emergence and mechanisms of allostery

Living cells use molecules from their environment, and use them to generate everything they need to build: they generate new molecules and energy to build up complex structures and processes. The catalysts that enable all these chemical reactions in the cell are called enzymes, a particular class of proteins. Enzymes use a certain small molecule and each enzyme has its specificity for only one or few such substrates and transforms it into something else. Because the cell contains such a complex network of different reactions it is important that the efficiency of these catalysts can be fine -tuned, depending on the state of the cell, such as its metabolic state, energy demand etc. Fine -tuning of catalysts can be done by simply making more or less of that catalyst, i.e. by regulating the production of enzyme in the cell. A more elegant and efficient way of fine-tuning, however, is if the same enzyme can be more or less active, depending on how much of a certain molecule is present in the cell; if a lot of it is present, then there is no urge to produce that particular molecule, and then it may actually be beneficial to process this molecule into something else. This capacity of an enzyme to be regulated by its own substrate or by another molecule has enabled cells to react so smoothly to changes in environmental conditions. Generally, this fine -tuning is achieved by a molecule that binds to an enzyme, and this binding changes the activity of the enzyme at a distant site. This capacity of regulating an active site of an enzyme over distance is called allostery. Over the billions of years of evolution since the emergence of the bacterial world allostery has emerged many times but not all enzymes are allosteric. What makes an enzyme allosteric while another one is not allosteric? And how did allostery emerge by evolution? What is the exact mechanism by which an allosteric signal such as the binding of a molecule somewhere on the enzyme is transmitted to the active site, to change the activity of the enzyme? AlloSpace wants to address exactly these questions. We investigate a large family of enzymes in an important metabolic pathway, using proteins from all kingdoms of life (bacteria, archaea, eukaryotes). We use bioinformatic approaches to see the differences of the amino acid sequences of these proteins. We study a selected set of these proteins then experimentally: analysing the enzymatic properties we decipher which ones are allosteric. We determine 3D structures, and investigate the ir dynamics experimentally and by simulation, in order to understand what makes some allosteric while others are not. Finally, we will use this knowledge to design rationally the allosteric behavior of these enzymes. Overall, we want to understand the molecular mechanisms of allosteric enzymes, and also how allostery has emerged in evolution, with broader implications in understanding how the complexity of protein properties has developed.