Structural Studies of Binding Proteins: Investigations of Flexibility, Specificity and Stability

Abstract: Binding proteins are present both in gram-negative and gram-positive bacteria. They are the recognition components of the ABC transport systems that transport different nutrients into the cell, and are in some cases also involved in chemotaxis. In gram-negative bacteria, they are present in the periplasm between the inner and the porous outer membrane. Here, these highly specific proteins can bind to a certain ligand such as ions, sugars and amino acids. The protein-ligand complex can then interact with permeases bound to the inner membrane that transport the nutrient into the cell. Gram-positive bacteria lack an outer membrane and the binding protein must therefore be anchored to the cell membrane.In this thesis different aspects of three members of the super-family of the periplasmic binding proteins have been studied. In the case of the allose-binding protein (ALBP) from E. coli we focused on the movement of the protein when ligand is bound and released. This protein was also compared with the ribose-binding protein (RBP) which belongs to the same structural cluster and from which both open and closed structures are available. The leucine-binding protein (LBP) from E. coli was studied with regards to the structural basis of its specificity for different ligands as well as its conformational changes. The leucine-isoleucine-valine protein has 80% sequence identity with LBP but still exhibits a different preference for ligands. The structure of the maltose-binding protein (MBP) was obtained from a gram-positive thermoacidophile, A. acidocaldarius. Here, our goal was to study acid-stability of proteins. Since little is known about this and structures of the mesophilic counterpart in E. coli are available, as well as structures from two hyperthermophiles, we had an opportunity to study differences in their structural properties that could explain their differing stabilities.