| Abstract |
The structures of nineteen bacterial, periplasmic binding proteins are investigated in all their known conformations and comparisons have take place between them. All proteins consist of one single polypeptide chain and they mature following the digestion of the signal peptide. With respect to their size, the proteins can be divided in three classes. The proteins are bilobal; each lobe represents one domain, which in the case of ArgT, DppA, MalE and OppA can be also characterized as a rigid body. The two lobes can come closer or get further apart to capture or release the ligand; the two corresponding forms of the protein are called closed and open. Both domains of the small and medium proteins and the second domain of the large proteins share the α/β/α sandwich architecture. In the first domain of the large proteins, the α/β/α sandwich is still present but there is an addition of another β-sheet and a layer of helixes. Between the proteins ArgT, GlnH, HisJ, DppA and OppA, there are extended topological equivalences, especially in the main β-sheet of the domains and also significant similarities in the connections of the secondary structure elements. These similarities reveal probably evulutionary relationships between the proteins. The structure of the domains for those proteins which have both forms determined, is slightly different in each form. In the case of proteins with more than one closed forms known (each of these with different ligand), the structural differences between these forms are negligible. The relative locations of the Cα atoms of the residues of each domain, that form the interdomain contact surface are almost unvaried. Even more conserved are the relative locations of the Cα atoms of the residues of the binding site. In the binding proteins, where the closed form is determined, the ligand contacts mainly hydrophilic residues and forms many hydrogen bonds. Nearly the same residues are involved in the binding of all the different ligands that the protein binds. The domains of these proteins are connected with two or three parts of the polypeptide chain. Two of them are short (two to five residues long) and are arranged close to each other and almost parallel. Usually they have the β-strand conformation and they frequently represent extensions of the β-strands of the domains. The third connective chain is usually longer and independent of the two others. In the majority of the cases examined, glycine residues are present either inside the connective chains or immediately next to them and are expected to allow the bending of the connective chains and the domain movement.
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Συγκριτική Μελέτη τής Δομής των Βακτηριακών, Εξωπλασματικών Πρωτεϊνών Δέσμευσης Ουσιών
